Sample records for bounded diffusion models
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Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...
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NASA Astrophysics Data System (ADS)
Stefferson, Michael W.; Norris, Samantha L.; Vernerey, Franck J.; Betterton, Meredith D.; E Hough, Loren
2017-08-01
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Examples include membrane proteins or lipids with some entry and diffusion within lipid domains and proteins that can enter into membraneless organelles or compartments such as the nucleolus. Using a lattice model, we studied the diffusive movement of tracer particles which bind to soft obstacles, allowing tracers and obstacles to occupy the same lattice site. For sticky obstacles, bound tracer particles are immobile, while for slippery obstacles, bound tracers can hop without penalty to adjacent obstacles. In both models, binding significantly alters tracer motion. The type and degree of motion while bound is a key determinant of the tracer mobility: slippery obstacles can allow nearly unhindered diffusion, even at high obstacle filling fraction. To mimic compartmentalization in a cell, we examined how obstacle size and a range of bound diffusion coefficients affect tracer dynamics. The behavior of the model is similar in two and three spatial dimensions. Our work has implications for protein movement and interactions within cells.
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Bound Pool Fractions Complement Diffusion Measures to Describe White Matter Micro and Macrostructure
Stikov, Nikola; Perry, Lee M.; Mezer, Aviv; Rykhlevskaia, Elena; Wandell, Brian A.; Pauly, John M.; Dougherty, Robert F.
2010-01-01
Diffusion imaging and bound pool fraction (BPF) mapping are two quantitative magnetic resonance imaging techniques that measure microstructural features of the white matter of the brain. Diffusion imaging provides a quantitative measure of the diffusivity of water in tissue. BPF mapping is a quantitative magnetization transfer (qMT) technique that estimates the proportion of exchanging protons bound to macromolecules, such as those found in myelin, and is thus a more direct measure of myelin content than diffusion. In this work, we combine BPF estimates of macromolecular content with measurements of diffusivity within human white matter tracts. Within the white matter, the correlation between BPFs and diffusivity measures such as fractional anisotropy and radial diffusivity was modest, suggesting that diffusion tensor imaging and bound pool fractions are complementary techniques. We found that several major tracts have high BPF, suggesting a higher density of myelin in these tracts. We interpret these results in the context of a quantitative tissue model. PMID:20828622
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Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA.
Vestergaard, Christian L; Blainey, Paul C; Flyvbjerg, Henrik
2018-03-16
We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1's (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.
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NASA Astrophysics Data System (ADS)
Hartman, Thomas; Hartnoll, Sean A.; Mahajan, Raghu
2017-10-01
The linear growth of operators in local quantum systems leads to an effective light cone even if the system is nonrelativistic. We show that the consistency of diffusive transport with this light cone places an upper bound on the diffusivity: D ≲v2τeq. The operator growth velocity v defines the light cone, and τeq is the local equilibration time scale, beyond which the dynamics of conserved densities is diffusive. We verify that the bound is obeyed in various weakly and strongly interacting theories. In holographic models, this bound establishes a relation between the hydrodynamic and leading nonhydrodynamic quasinormal modes of planar black holes. Our bound relates transport data—including the electrical resistivity and the shear viscosity—to the local equilibration time, even in the absence of a quasiparticle description. In this way, the bound sheds light on the observed T -linear resistivity of many unconventional metals, the shear viscosity of the quark-gluon plasma, and the spin transport of unitary fermions.
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The effects of bound state motion on macromolecular diffusion
NASA Astrophysics Data System (ADS)
Hough, Loren; Stefferson, Michael; Norris, Samantha; Maguire, Laura; Vernerey, Franck; Betterton, Meredith
The diffusion of macromolecules is modified in crowded environments by both inert obstacles and interaction sites. Molecules are generally slowed in their movement inducing transient anomalous subdiffusion. Obstacles also modify the kinetics and equilibrium behavior of interaction between mobile proteins. In some biophysical contexts, bound molecules can still experience mobility, for example transcription factors sliding along DNA, membrane proteins with some entry and diffusion within lipid domains, or proteins that can enter into non-membrane bound compartments such as the nucleolus. We used lattice and continuum models to study the diffusive behavior of tracer particles which bind to obstacles and can diffuse within them. We show that binding significantly alters the motion of tracers. The type and degree of motion while bound is a key determinant of the tracer mobility. Our work has implications for protein-protein movement and interactions within living cells, including those involving intrinsically disordered proteins.
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Bounded fractional diffusion in geological media: Definition and Lagrangian approximation
NASA Astrophysics Data System (ADS)
Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang
2016-11-01
Spatiotemporal fractional-derivative models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and nonzero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing nonzero-value spatial-nonlocal boundary conditions with directional superdiffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eulerian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the nonlocal and nonsymmetric fractional diffusion. For a nonzero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite domains to those with any size and boundary conditions.
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Bounded diffusion impedance characterization of battery electrodes using fractional modeling
NASA Astrophysics Data System (ADS)
Gabano, Jean-Denis; Poinot, Thierry; Huard, Benoît
2017-06-01
This article deals with the ability of fractional modeling to describe the bounded diffusion behavior encountered in modern thin film and nanoparticles lithium battery electrodes. Indeed, the diffusion impedance of such batteries behaves as a half order integrator characterized by the Warburg impedance at high frequencies and becomes a classical integrator described by a capacitor at low frequencies. The transition between these two behaviors depends on the particles geometry. Three of them will be considered in this paper: planar, cylindrical and spherical ones. The fractional representation proposed is a gray box model able to perfectly fit the low and high frequency diffusive impedance behaviors while optimizing the frequency response transition. Identification results are provided using frequential simulation data considering the three electrochemical diffusion models based on the particles geometry. Furthermore, knowing this geometry allows to estimate the diffusion ionic resistance and time constant using the relationships linking these physical parameters to the structural fractional model parameters. Finally, other simulations using Randles impedance models including the charge transfer impedance and the external resistance demonstrate the interest of fractional modeling in order to identify properly not only the charge transfer impedance but also the diffusion physical parameters whatever the particles geometry.
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Bounded fractional diffusion in geological media: Definition and Lagrangian approximation
Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang
2016-01-01
Spatiotemporal Fractional-Derivative Models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and non-zero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing non-zero-value spatial-nonlocal boundary conditions with directional super-diffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eularian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the non-local and non-symmetric fractional diffusion. For a non-zero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite do mains to those with any size and boundary conditions.
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On Large Time Behavior and Selection Principle for a Diffusive Carr-Penrose Model
NASA Astrophysics Data System (ADS)
Conlon, Joseph G.; Dabkowski, Michael; Wu, Jingchen
2016-04-01
This paper is concerned with the study of a diffusive perturbation of the linear LSW model introduced by Carr and Penrose. A main subject of interest is to understand how the presence of diffusion acts as a selection principle, which singles out a particular self-similar solution of the linear LSW model as determining the large time behavior of the diffusive model. A selection principle is rigorously proven for a model which is a semiclassical approximation to the diffusive model. Upper bounds on the rate of coarsening are also obtained for the full diffusive model.
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Turbulent patterns in wall-bounded flows: A Turing instability?
NASA Astrophysics Data System (ADS)
Manneville, Paul
2012-06-01
In their way to/from turbulence, plane wall-bounded flows display an interesting transitional regime where laminar and turbulent oblique bands alternate, the origin of which is still mysterious. In line with Barkley's recent work about the pipe flow transition involving reaction-diffusion concepts, we consider plane Couette flow in the same perspective and transform Waleffe's classical four-variable model of self-sustaining process into a reaction-diffusion model. We show that, upon fulfillment of a condition on the relative diffusivities of its variables, the featureless turbulent regime becomes unstable against patterning as the result of a Turing instability. A reduced two-variable model helps us to delineate the appropriate region of parameter space. An intrinsic status is therefore given to the pattern's wavelength for the first time. Virtues and limitations of the model are discussed, calling for a microscopic support of the phenomenological approach.
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NASA Astrophysics Data System (ADS)
McMillen, Laura M.; Vavylonis, Dimitrios
2016-12-01
Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex. The slowly diffusing proteins appear as extended ‘clouds’ while proteins bound to the actin filament network appear as speckles that undergo retrograde flow. Speckle appearance and disappearance events correspond to assembly and dissociation from the actin filament network and speckle lifetimes correspond to the dissociation rate. The slowly diffusing capping protein could represent severed capped actin filament fragments or membrane-bound capping protein. Prior evidence suggests that slowly diffusing Apr2/3 complex associates with the membrane. We use the measured rates and estimates of diffusion coefficients of capping protein and Arp2/3 complex in a Monte Carlo simulation that includes particles in association with a filament network and diffuse in the cytoplasm. We consider two separate pools of diffuse proteins, representing fast and slowly diffusing species. We find a steady state with concentration gradients involving a balance of diffusive flow of fast and slow species with retrograde flow. We show that simulations of FRAP are consistent with prior experiments performed on different cell types. We provide estimates for the ratio of bound to diffuse complexes and calculate conditions where Arp2/3 complex recycling by diffusion may become limiting. We discuss the implications of slowly diffusing populations and suggest experiments to distinguish among mechanisms that influence long range transport.
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Effective matrix diffusion in kilometer‐scale transport in fractured crystalline rock
Shapiro, Allen M.
2001-01-01
Concentrations of tritium (3H) and dichlorodifluoromethane (CFC‐12) in water samples taken from glacial drift and fractured crystalline rock over 4 km2 in central New Hampshire are interpreted to identify a conceptual model of matrix diffusion and the magnitude of the diffusion coefficient. Dispersion and mass transfer to and from fractures has affected the 3H concentration to the extent that the peak 3H concentration of the 1960s is no longer distinguishable. Because of heterogeneity in the bedrock the sparsely distributed chemical data do not warrant a three‐dimensional transport model. Instead, a one‐dimensional model of CFC‐12 and 3H migration along flow lines in the glacial drift and bedrock is used to place bounds on the processes affecting kilometer‐scale transport, arid model parameters are varied to reproduce the measured relation between 3H and CFC‐12, rather than their spatial distributions. A model of mass exchange to and from fractures that is dependent on the time‐varying concentration gradient at fracture surfaces qualitatively reproduces the measured relation between 3H and CFC‐12 with an upper bound for the fracture dispersivity approximately equal to 250 m and a lower bound for the effective matrix diffusion coefficient equal to 1 m2 yr−1. The diffusion coefficient at the kilometer scale is at least 3 orders of magnitude greater than laboratory estimates of diffusion in crystalline rock. The large diffusion coefficient indicates that diffusion into an immobile fluid phase (rock matrix) is masked at the kilometer scale by advective mass exchange between fractures with large contrasts in trarismissivity. The measured transmissivity of fractures in the study area varies over more than 6 orders of magnitude. Advective mass exchange from high‐permeability fractures to low‐permeability fractures results in short migration distances of a chemical constituent in low‐permeability fractures over an extended period of time before reentering high‐permeability fractures; viewed at the kilometer scale, this process is analogous to the chemical constituent diffusing into and out of an immobile fluid phase.
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Fractional diffusion on bounded domains
Defterli, Ozlem; D'Elia, Marta; Du, Qiang; ...
2015-03-13
We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.
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Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.
2015-01-01
This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figuremore » 1 is the evolution of the diffusion profiles of a containment granuloma over time.« less
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Theoretical and experimental models of the diffuse radar backscatter from Mars
NASA Technical Reports Server (NTRS)
England, A. W.
1995-01-01
The general objective for this work was to develop a theoretically and experimentally consistent explanation for the diffuse component of radar backscatter from Mars. The strength, variability, and wavelength independence of Mars' diffuse backscatter are unique among our Moon and the terrestrial planets. This diffuse backscatter is generally attributed to wavelength-scale surface roughness and to rock clasts within the Martian regolith. Through the combination of theory and experiment, the authors attempted to bound the range of surface characteristics that could produce the observed diffuse backscatter. Through these bounds they gained a limited capability for data inversion. Within this umbrella, specific objectives were: (1) To better define the statistical roughness parameters of Mars' surface so that they are consistent with observed radar backscatter data, and with the physical and chemical characteristics of Mars' surface as inferred from Mariner 9, the Viking probes, and Earth-based spectroscopy; (2) To better understand the partitioning between surface and volume scattering in the Mars regolith; (3) To develop computational models of Mars' radio emission that incorporate frequency dependent, surface and volume scattering.
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NASA Astrophysics Data System (ADS)
Wen, Zijuan; Fu, Shengmao
2009-08-01
In this paper, an n-species strongly coupled cooperating diffusive system is considered in a bounded smooth domain, subject to homogeneous Neumann boundary conditions. Employing the method of energy estimates, we obtain some conditions on the diffusion matrix and inter-specific cooperatives to ensure the global existence and uniform boundedness of a nonnegative solution. The globally asymptotical stability of the constant positive steady state is also discussed. As a consequence, all the results hold true for multi-species Lotka-Volterra type competition model and prey-predator model.
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Hindered Diffusion in Polymeric Solutions Studied by Fluorescence Correlation Spectroscopy
Zustiak, Silviya P.; Nossal, Ralph; Sackett, Dan L.
2011-01-01
Diffusion of molecules in the crowded and charged interior of the cell has long been of interest for understanding cellular processes. Here, we introduce a model system of hindered diffusion that includes both crowding and binding. In particular, we obtained the diffusivity of the positively charged protein, ribonuclease A (RNase), in solutions of dextrans of various charges (binding) and concentrations (crowding), as well as combinations of both, in a buffer of physiological ionic strength. Using fluorescence correlation spectroscopy, we observed that the diffusivity of RNase was unaffected by the presence of positively charged or neutral dextrans in the dilute regime but was affected by crowding at higher polymer concentrations. Conversely, protein diffusivity was significantly reduced by negatively charged dextrans, even at 0.4 μM (0.02% w/v) dextran. The diffusivity of RNase decreased with increasing concentrations of negative dextran, and the amount of bound RNase increased until it reached a plateau of ∼80% bound RNase. High salt concentrations were used to establish the electrostatic nature of the binding. Binding of RNase to the negatively charged dextrans was further confirmed by ultrafiltration. PMID:21723836
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Forward and back diffusion through argillaceous formations
NASA Astrophysics Data System (ADS)
Yang, Minjune; Annable, Michael D.; Jawitz, James W.
2017-05-01
The exchange of solutes between aquifers and lower-permeability argillaceous formations is of considerable interest for solute and contaminant fate and transport. We present a synthesis of analytical solutions for solute diffusion between aquifers and single aquitard systems, validated in well-controlled experiments, and applied to several data sets from laboratory and field-scale problems with diffusion time and length scales ranging from 10-2 to 108 years and 10-2 to 102 m. One-dimensional diffusion models were applied using the method of images to consider the general cases of a finite aquitard bounded by two aquifers at the top and bottom, or a semiinfinite aquitard bounded by an aquifer. The simpler semiinfinite equations are appropriate for all domains with dimensionless relative diffusion length, ZD < 0.7. At dimensionless length scales above this threshold, application of semiinfinite equations to aquitards of finite thickness leads to increasing errors and solutions based on the method of images are required. Measured resident solute concentration profiles in aquitards and flux-averaged solute concentrations in surrounding aquifers were accurately modeled by appropriately accounting for generalized dynamic aquifer-aquitard boundary conditions, including concentration gradient reversals. Dimensionless diffusion length scales were used to illustrate the transferability of these relatively simple models to physical systems with dimensions that spanned 10 orders of magnitude. The results of this study offer guidance on the application of a simplified analytical approach to environmentally important layered problems with one or two diffusion interfaces.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Guo, D.; Akis, R.; Brinkman, D.
An improved model of copper p-type doping in CdTe absorbers is proposed that accounts for the mechanisms related to tightly bound Cu(i)-Cu(Cd) and Cd(i)-Cu(Cd) complexes that both limit diffusion and cause self-compensation of Cu species. The new model explains apparent discrepancy between DFT-calculated and fitted diffusion parameters of Cu reported in our previous work, and allows for better understanding of performance and metastabilities in CdTe PV devices.
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A critical examination of the validity of simplified models for radiant heat transfer analysis.
NASA Technical Reports Server (NTRS)
Toor, J. S.; Viskanta, R.
1972-01-01
Examination of the directional effects of the simplified models by comparing the experimental data with the predictions based on simple and more detailed models for the radiation characteristics of surfaces. Analytical results indicate that the constant property diffuse and specular models do not yield the upper and lower bounds on local radiant heat flux. In general, the constant property specular analysis yields higher values of irradiation than the constant property diffuse analysis. A diffuse surface in the enclosure appears to destroy the effect of specularity of the other surfaces. Semigray and gray analyses predict the irradiation reasonably well provided that the directional properties and the specularity of the surfaces are taken into account. The uniform and nonuniform radiosity diffuse models are in satisfactory agreement with each other.
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Song, Yoon S; Koontz, John L; Juskelis, Rima O; Zhao, Yang
2013-01-01
The migration of low molecular weight organic compounds through polyethylene terephthalate (PET) films was determined by using a custom permeation cell assembly. Fatty food simulant (Miglyol 812) was added to the receptor chamber, while the donor chamber was filled with 1% and 10% (v/v) migrant compounds spiked in simulant. The permeation cell was maintained at 40°C, 66°C, 100°C or 121°C for up to 25 days of polymer film exposure time. Migrants in Miglyol were directly quantified without a liquid-liquid extraction step by headspace-GC-MS analysis. Experimental diffusion coefficients (DP) of toluene, benzyl alcohol, ethyl butyrate and methyl salicylate through PET film were determined. Results from Limm's diffusion model showed that the predicted DP values for PET were all greater than the experimental values. DP values predicted by Piringer's diffusion model were also greater than those determined experimentally at 66°C, 100°C and 121°C. However, Piringer's model led to the underestimation of benzyl alcohol (Áp = 3.7) and methyl salicylate (Áp = 4.0) diffusion at 40°C with its revised "upper-bound" Áp value of 3.1 at temperatures below the glass transition temperature (Tg) of PET (<70°C). This implies that input parameters of Piringer's model may need to be revised to ensure a margin of safety for consumers. On the other hand, at temperatures greater than the Tg, both models appear too conservative and unrealistic. The highest estimated Áp value from Piringer's model was 2.6 for methyl salicylate, which was much lower than the "upper-bound" Áp value of 6.4 for PET. Therefore, it may be necessary further to refine "upper-bound" Áp values for PET such that Piringer's model does not significantly underestimate or overestimate the migration of organic compounds dependent upon the temperature condition of the food contact material.
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NASA Astrophysics Data System (ADS)
Magdziarz, M.; Mista, P.; Weron, A.
2007-05-01
We introduce an approximation of the risk processes by anomalous diffusion. In the paper we consider the case, where the waiting times between successive occurrences of the claims belong to the domain of attraction of alpha -stable distribution. The relationship between the obtained approximation and the celebrated fractional diffusion equation is emphasised. We also establish upper bounds for the ruin probability in the considered model and give some numerical examples.
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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'.
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Spreading-vanishing dichotomy in a diffusive logistic model with a free boundary, II
NASA Astrophysics Data System (ADS)
Du, Yihong; Guo, Zongming
We study the diffusive logistic equation with a free boundary in higher space dimensions and heterogeneous environment. Such a model may be used to describe the spreading of a new or invasive species, with the free boundary representing the expanding front. For simplicity, we assume that the environment and the solution are radially symmetric. In the special case of one space dimension and homogeneous environment, this free boundary problem was investigated in Du and Lin (2010) [10]. We prove that the spreading-vanishing dichotomy established in Du and Lin (2010) [10] still holds in the more general and ecologically realistic setting considered here. Moreover, when spreading occurs, we obtain best possible upper and lower bounds for the spreading speed of the expanding front. When the environment is asymptotically homogeneous at infinity, these two bounds coincide. Our results indicate that the asymptotic spreading speed determined by this model does not depend on the spatial dimension.
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Geomorphic control of radionuclide diffusion in desert soils
Pelletier, J.D.; Harrington, C.D.; Whitney, J.W.; Cline, M.; DeLong, S.B.; Keating, G.; Ebert, T.K.
2005-01-01
Diffusion is a standard model for the vertical migration of radionuclides in soil profiles. Here we show that diffusivity values inferred from fallout 137CS profiles in soils on the Fortymile Wash alluvial fan, Nye County, Nevada, have a strong inverse correlation with the age of the geomorphic surface. This result suggests that radionuclide-bound particles are predominantly transported by infiltration rather than by bulk-mixing processes such as wetting/ drying, freeze/thaw, and bioturbation. Our results provide a preliminary basis for using soil-geomorphic mapping, point-based calibration data, and the diffusion model to predict radionuclide trans desert soils within a pedotransfer-function approach. Copyright 2005 by the American Geophysical Union.
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Probing the Interplay between Dendritic Spine Morphology and Membrane-Bound Diffusion.
Adrian, Max; Kusters, Remy; Storm, Cornelis; Hoogenraad, Casper C; Kapitein, Lukas C
2017-11-21
Dendritic spines are protrusions along neuronal dendrites that harbor the majority of excitatory postsynapses. Their distinct morphology, often featuring a bulbous head and small neck that connects to the dendritic shaft, has been shown to facilitate compartmentalization of electrical and cytoplasmic signaling stimuli elicited at the synapse. The extent to which spine morphology also forms a barrier for membrane-bound diffusion has remained unclear. Recent simulations suggested that especially the diameter of the spine neck plays a limiting role in this process. Here, we examine the connection between spine morphology and membrane-bound diffusion through a combination of photoconversion, live-cell superresolution experiments, and numerical simulations. Local photoconversion was used to obtain the timescale of diffusive equilibration in spines and followed by global sparse photoconversion to determine spine morphologies with nanoscopic resolution. These morphologies were subsequently used to assess the role of morphology on the diffusive equilibration. From the simulations, we could determine a robust relation between the equilibration timescale and a generalized shape factor calculated using both spine neck width and neck length, as well as spine head size. Experimentally, we found that diffusive equilibration was often slower, but rarely faster than predicted from the simulations, indicating that other biological confounders further reduce membrane-bound diffusion in these spines. This shape-dependent membrane-bound diffusion in mature spines may contribute to spine-specific compartmentalization of neurotransmitter receptors and signaling molecules and thereby support long-term plasticity of synaptic contacts. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Joint estimation of phase and phase diffusion for quantum metrology.
Vidrighin, Mihai D; Donati, Gaia; Genoni, Marco G; Jin, Xian-Min; Kolthammer, W Steven; Kim, M S; Datta, Animesh; Barbieri, Marco; Walmsley, Ian A
2014-04-14
Phase estimation, at the heart of many quantum metrology and communication schemes, can be strongly affected by noise, whose amplitude may not be known, or might be subject to drift. Here we investigate the joint estimation of a phase shift and the amplitude of phase diffusion at the quantum limit. For several relevant instances, this multiparameter estimation problem can be effectively reshaped as a two-dimensional Hilbert space model, encompassing the description of an interferometer phase probed with relevant quantum states--split single-photons, coherent states or N00N states. For these cases, we obtain a trade-off bound on the statistical variances for the joint estimation of phase and phase diffusion, as well as optimum measurement schemes. We use this bound to quantify the effectiveness of an actual experimental set-up for joint parameter estimation for polarimetry. We conclude by discussing the form of the trade-off relations for more general states and measurements.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Andersson, Anders David Ragnar; Pastore, Giovanni; Liu, Xiang-Yang
2014-11-07
This report summarizes the development of new fission gas diffusion models from lower length scale simulations and assessment of these models in terms of annealing experiments and fission gas release simulations using the BISON fuel performance code. Based on the mechanisms established from density functional theory (DFT) and empirical potential calculations, continuum models for diffusion of xenon (Xe) in UO 2 were derived for both intrinsic conditions and under irradiation. The importance of the large X eU3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequencemore » of its high mobility and stability. These models were implemented in the MARMOT phase field code, which is used to calculate effective Xe diffusivities for various irradiation conditions. The effective diffusivities were used in BISON to calculate fission gas release for a number of test cases. The results are assessed against experimental data and future directions for research are outlined based on the conclusions.« less
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NASA Astrophysics Data System (ADS)
Coronel-Escamilla, A.; Gómez-Aguilar, J. F.; Torres, L.; Escobar-Jiménez, R. F.
2018-02-01
A reaction-diffusion system can be represented by the Gray-Scott model. The reaction-diffusion dynamic is described by a pair of time and space dependent Partial Differential Equations (PDEs). In this paper, a generalization of the Gray-Scott model by using variable-order fractional differential equations is proposed. The variable-orders were set as smooth functions bounded in (0 , 1 ] and, specifically, the Liouville-Caputo and the Atangana-Baleanu-Caputo fractional derivatives were used to express the time differentiation. In order to find a numerical solution of the proposed model, the finite difference method together with the Adams method were applied. The simulations results showed the chaotic behavior of the proposed model when different variable-orders are applied.
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Vuong, A.-T.; Rauch, A. D.
2017-01-01
We present a computational model for the interaction of surface- and volume-bound scalar transport and reaction processes with a deformable porous medium. The application in mind is pericellular proteolysis, i.e. the dissolution of the solid phase of the extracellular matrix (ECM) as a response to the activation of certain chemical species at the cell membrane and in the vicinity of the cell. A poroelastic medium model represents the extra cellular scaffold and the interstitial fluid flow, while a surface-bound transport model accounts for the diffusion and reaction of membrane-bound chemical species. By further modelling the volume-bound transport, we consider the advection, diffusion and reaction of sequestered chemical species within the extracellular scaffold. The chemo-mechanical coupling is established by introducing a continuum formulation for the interplay of reaction rates and the mechanical state of the ECM. It is based on known experimental insights and theoretical work on the thermodynamics of porous media and degradation kinetics of collagen fibres on the one hand and a damage-like effect of the fibre dissolution on the mechanical integrity of the ECM on the other hand. The resulting system of partial differential equations is solved via the finite-element method. To the best of our knowledge, it is the first computational model including contemporaneously the coupling between (i) advection–diffusion–reaction processes, (ii) interstitial flow and deformation of a porous medium, and (iii) the chemo-mechanical interaction impelled by the dissolution of the ECM. Our numerical examples show good agreement with experimental data. Furthermore, we outline the capability of the methodology to extend existing numerical approaches towards a more comprehensive model for cellular biochemo-mechanics. PMID:28413347
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Force Generation by Membrane-Associated Myosin-I
Pyrpassopoulos, Serapion; Arpağ, Göker; Feeser, Elizabeth A.; Shuman, Henry; Tüzel, Erkan; Ostap, E. Michael
2016-01-01
Vertebrate myosin-IC (Myo1c) is a type-1 myosin that links cell membranes to the cytoskeleton via its actin-binding motor domain and its phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding tail domain. While it is known that Myo1c bound to PtdIns(4,5)P2 in fluid-lipid bilayers can propel actin filaments in an unloaded motility assay, its ability to develop forces against external load on actin while bound to fluid bilayers has not been explored. Using optical tweezers, we measured the diffusion coefficient of single membrane-bound Myo1c molecules by force-relaxation experiments, and the ability of ensembles of membrane-bound Myo1c molecules to develop and sustain forces. To interpret our results, we developed a computational model that recapitulates the basic features of our experimental ensemble data and suggests that Myo1c ensembles can generate forces parallel to lipid bilayers, with larger forces achieved when the myosin works away from the plane of the membrane or when anchored to slowly diffusing regions. PMID:27156719
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Density Bounded H II Regions: Ionization of the Diffuse Interstellar and Intergalactic Media
NASA Astrophysics Data System (ADS)
Zurita, A.; Rozas, M.; Beckman, J. E.
2000-05-01
We present a study of the diffuse ionized gas (DIG) for a sample of nearby spiral galaxies using Hα images, after constructing their H II region catalogues. The integrated Hα emission of the DIG accounts for between 25% to 60% of the total Hα of the galaxy and a high ionizing photon flux is necessary to keep this gas ionized. We suggest that Lyman photons leaking from the most luminous H II regions are the prime source of the ionization of the DIG; they are more than enough to ionize the measured DIG in the model in which H II regions with luminosity in Hα greater than LStr=1038.6 erg sme are density bounded. We go on to show that this model can quantify the ionization observed in the skins of the high velocity clouds well above the plane of our Galaxy and predicts the ionization of the intergalactic medium.
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Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity
Yamamoto, Eiji; Akimoto, Takuma; Kalli, Antreas C.; Yasuoka, Kenji; Sansom, Mark S. P.
2017-01-01
Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:28116358
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Strong solutions for an incompressible Navier-Stokes/Allen-Cahn system with different densities
NASA Astrophysics Data System (ADS)
Li, Yinghua; Huang, Mingxia
2018-06-01
In this paper, we investigate a coupled Navier-Stokes/Allen-Cahn system describing a diffuse interface model for two-phase flow of viscous incompressible fluids with different densities in a bounded domain Ω \\subset R^N(N=2,3). We prove the existence and uniqueness of local strong solutions to the initial boundary value problem when the initial density function ρ _0 has a positive lower bound.
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NASA Astrophysics Data System (ADS)
Nickelsen, Daniel
2017-07-01
The statistics of velocity increments in homogeneous and isotropic turbulence exhibit universal features in the limit of infinite Reynolds numbers. After Kolmogorov’s scaling law from 1941, many turbulence models aim for capturing these universal features, some are known to have an equivalent formulation in terms of Markov processes. We derive the Markov process equivalent to the particularly successful scaling law postulated by She and Leveque. The Markov process is a jump process for velocity increments u(r) in scale r in which the jumps occur randomly but with deterministic width in u. From its master equation we establish a prescription to simulate the She-Leveque process and compare it with Kolmogorov scaling. To put the She-Leveque process into the context of other established turbulence models on the Markov level, we derive a diffusion process for u(r) using two properties of the Navier-Stokes equation. This diffusion process already includes Kolmogorov scaling, extended self-similarity and a class of random cascade models. The fluctuation theorem of this Markov process implies a ‘second law’ that puts a loose bound on the multipliers of the random cascade models. This bound explicitly allows for instances of inverse cascades, which are necessary to satisfy the fluctuation theorem. By adding a jump process to the diffusion process, we go beyond Kolmogorov scaling and formulate the most general scaling law for the class of Markov processes having both diffusion and jump parts. This Markov scaling law includes She-Leveque scaling and a scaling law derived by Yakhot.
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New insights into silica-based NMR “chromatography”
NASA Astrophysics Data System (ADS)
Pemberton, Chava; Hoffman, Roy; Aserin, Abraham; Garti, Nissim
2011-02-01
Silica is used as an important component for NMR “chromatography”. In this study the effect of the binding strength to silica of a variety of compounds on their diffusion rate is measured for the first time. Over two orders of magnitude of diffusion difference enhancement was obtained in the presence of silica for some compounds. An explanation of the enhancement is given that also allows one to predict the “chromatographic” behavior of new compounds or mixtures. The binding strength is divided into categories of weakly bound, singly bound and multiply bound. Carboxylates, sulfonates, and diols are found to be particularly strongly bound and to diffuse up to 2½ orders of magnitude more slowly in the presence of silica.
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Imaging of Formaldehyde Adsorption and Diffusion on TiO2(110)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Zhenrong; Tang, Miru; Wang, Zhitao
2015-03-01
Surface reactions of formaldehyde with reduced TiO2(110) surfaces have been studied using variable-temperature scanning tunneling microscopy (STM) and density functional theory (DFT). STM results show that formaldehyde preferably adsorbs on the bridging bonded oxygen (Ob) vacancy (VO) defect site. Bias-dependent STM images show that both the Ti-bound CH2O and the VO-bound CH2O are positioned between the Ob row and the Ti row. The VO-bound formaldehyde rotates at 95 K. It starts to diffuse along the Ob row as –CH2– at ~170 K and starts to diffuse along the Ti row as a molecule at ~215 K. However, the stabilities andmore » the configurations of the Ti-bound and the VO-bound formaldehyde calculated using DFT are not in line with the experimental results. The values of diffusion barriers determined experimentally and theoretically are also different. The discrepancy between the experiment and theory indicates the presence of a complex charge distribution related to the defects.« less
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Active and passive transport of cargo in a corrugated channel: A lattice model study
NASA Astrophysics Data System (ADS)
Dey, Supravat; Ching, Kevin; Das, Moumita
2018-04-01
Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.
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Effect of measurement on the ballistic-diffusive transition in turbid media.
Glasser, Ziv; Yaroshevsky, Andre; Barak, Bavat; Granot, Er'el; Sternklar, Shmuel
2013-10-01
The dependence of the transition between the ballistic and the diffusive regimes of turbid media on the experimental solid angle of the detection system is analyzed theoretically and experimentally. A simple model is developed which shows the significance of experimental conditions on the location of the ballistic-diffusive transition. It is demonstrated that decreasing the solid angle expands the ballistic regime; however, this benefit is bounded by the initial Gaussian beam diffraction. In addition, choosing the appropriate wavelength according to the model's principles provides another means of expanding the ballistic regime. Consequently, by optimizing the experimental conditions, it should be possible to extract the ballistic image of a tissue with a thickness of 1 cm.
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Analysis on a diffusive SIS epidemic model with logistic source
NASA Astrophysics Data System (ADS)
Li, Bo; Li, Huicong; Tong, Yachun
2017-08-01
In this paper, we are concerned with an SIS epidemic reaction-diffusion model with logistic source in spatially heterogeneous environment. We first discuss some basic properties of the parabolic system, including the uniform upper bound of solutions and global stability of the endemic equilibrium when spatial environment is homogeneous. Our primary focus is to determine the asymptotic profile of endemic equilibria (when exist) if the diffusion (migration) rate of the susceptible or infected population is small or large. Combined with the results of Li et al. (J Differ Equ 262:885-913, 2017) where the case of linear source is studied, our analysis suggests that varying total population enhances persistence of infectious disease.
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Remediation of soil-bound polynuclear aromatic hydrocarbons using nonionic surfactants
DOE Office of Scientific and Technical Information (OSTI.GOV)
Yeom, IckTae; Ghosh, Mriganka; Cox, C.
1996-12-31
The solubilization and biodegradation of soil-bound PAHs from a manufactured gas plant (MGP) site soil was investigated using surfactants. Three nonionic polyoxyethylene (POE) surfactants, Triton X-100, Tween 80, and Brij 35, were used. The fate of four PAHs, phenanthrene, anthracene, pyrene, and benzo(a)pyrene were monitored during the remediation process. The measured concentrations of solubilized PAHs agreed well with those estimated using micelle-water partitioning coefficient, K{sub m}, and Raoult`s law. The solubilization of soil-bound PAHs by surfactants is a slow, nonequilibrium process. Diffusion of PAH molecules within the weathered soil-tar matrix is proposed as the rate-limiting step in solubilizing PAHs frommore » such soils. A radial diffusion model is used to describe solubilization of PAHs by surfactant washing. The model predicts experimental results fairly well at low surfactant dosages while at high dosages it somewhat overestimates the extent of solubilization. Biodegradation studies were performed using a natural consortium of microorganisms enriched from PAH-contaminated soils. Surfactants enhanced biodegradation of PAHs except for Tween 80. However, biodegradation of surfactants themselves appear to attenuate the beneficial effects of surfactant-mediated bioremediation.« less
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Radiosity diffusion model in 3D
NASA Astrophysics Data System (ADS)
Riley, Jason D.; Arridge, Simon R.; Chrysanthou, Yiorgos; Dehghani, Hamid; Hillman, Elizabeth M. C.; Schweiger, Martin
2001-11-01
We present the Radiosity-Diffusion model in three dimensions(3D), as an extension to previous work in 2D. It is a method for handling non-scattering spaces in optically participating media. We present the extension of the model to 3D including an extension to the model to cope with increased complexity of the 3D domain. We show that in 3D more careful consideration must be given to the issues of meshing and visibility to model the transport of light within reasonable computational bounds. We demonstrate the model to be comparable to Monte-Carlo simulations for selected geometries, and show preliminary results of comparisons to measured time-resolved data acquired on resin phantoms.
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A double medium model for diffusion in fluid-bearing rock
NASA Astrophysics Data System (ADS)
Wang, H. F.
1993-09-01
The concept of a double porosity medium to model fluid flow in fractured rock has been applied to model diffusion in rock containing a small amount of a continuous fluid phase that surrounds small volume elements of the solid matrix. The model quantifies the relative role of diffusion in the fluid and solid phases of the rock. The fluid is the fast diffusion path, but the solid contains the volumetrically significant amount of the diffusing species. The double medium model consists of two coupled differential equations. One equation is the diffusion equation for the fluid concentration; it contains a source term for change in the average concentration of the diffusing species in the solid matrix. The second equation represents the assumption that the change in average concentration in a solid element is proportional to the difference between the average concentration in the solid and the concentration in the fluid times the solid-fluid partition coefficient. The double medium model is shown to apply to laboratory data on iron diffusion in fluid-bearing dunite and to measured oxygen isotope ratios at marble-metagranite contacts. In both examples, concentration profiles are calculated for diffusion taking place at constant temperature, where a boundary value changes suddenly and is subsequently held constant. Knowledge of solid diffusivities can set a lower bound to the length of time over which diffusion occurs, but only the product of effective fluid diffusivity and time is constrained for times longer than the characteristic solid diffusion time. The double medium results approach a local, grain-scale equilibrium model for times that are large relative to the time constant for solid diffusion.
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Zhang, Changzhe; Bu, Yuxiang
2016-09-14
Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.
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Li, Bo; Zhao, Yanxiang
2013-01-01
Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation.
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The impact of physiological crowding on the diffusivity of membrane bound proteins.
Houser, Justin R; Busch, David J; Bell, David R; Li, Brian; Ren, Pengyu; Stachowiak, Jeanne C
2016-02-21
Diffusion of transmembrane and peripheral membrane-bound proteins within the crowded cellular membrane environment is essential to diverse biological processes including cellular signaling, endocytosis, and motility. Nonetheless we presently lack a detailed understanding of the influence of physiological levels of crowding on membrane protein diffusion. Utilizing quantitative in vitro measurements, here we demonstrate that the diffusivities of membrane bound proteins follow a single linearly decreasing trend with increasing membrane coverage by proteins. This trend holds for homogenous protein populations across a range of protein sizes and for heterogeneous mixtures of proteins of different sizes, such that protein diffusivity is controlled by the total coverage of the surrounding membrane. These results demonstrate that steric exclusion within the crowded membrane environment can fundamentally limit the diffusive rate of proteins, regardless of their size. In cells this "speed limit" could be modulated by changes in local membrane coverage, providing a mechanism for tuning the rate of molecular interaction and assembly.
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NASA Astrophysics Data System (ADS)
Bai, M.; Miskowiec, A.; Wang, S.-K.; Taub, H.; Jenkins, T.; Tyagi, M.; Neumann, D. A.; Hansen, F. Y.
2010-03-01
Bilayer lipid membranes supported on a solid surface are attractive model systems for understanding the structure and dynamics of more complex biological membranes that form the outer boundary of living cells. We have recently demonstrated the feasibility of using quasielastic neutron scattering to study on a ˜1 ns time scale the diffusion of water bound to single-supported bilayer lipid membranes. Two different membrane samples characterized by AFM were investigated: protonated DMPC + D2O and tail-deuterated DMPC + H2O. Both fully hydrated membranes were deposited onto SiO2-coated Si(100) substrates. Measurements of elastic neutron intensity as a function of temperature on the High Flux Backscattering Spectrometer at NIST reveal features in the diffusive motion of water that have not been observed previously using multilayer membrane stacks. On slow cooling, the elastic intensity shows sharp step-like increases in the temperature range 265 to 272 K that we tentatively interpret as successive mobile-to-immobile transitions of water bound to the membrane.
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Resolvent-based modeling of passive scalar dynamics in wall-bounded turbulence
NASA Astrophysics Data System (ADS)
Dawson, Scott; Saxton-Fox, Theresa; McKeon, Beverley
2017-11-01
The resolvent formulation of the Navier-Stokes equations expresses the system state as the output of a linear (resolvent) operator acting upon a nonlinear forcing. Previous studies have demonstrated that a low-rank approximation of this linear operator predicts many known features of incompressible wall-bounded turbulence. In this work, this resolvent model for wall-bounded turbulence is extended to include a passive scalar field. This formulation allows for a number of additional simplifications that reduce model complexity. Firstly, it is shown that the effect of changing scalar diffusivity can be approximated through a transformation of spatial wavenumbers and temporal frequencies. Secondly, passive scalar dynamics may be studied through the low-rank approximation of a passive scalar resolvent operator, which is decoupled from velocity response modes. Thirdly, this passive scalar resolvent operator is amenable to approximation by semi-analytic methods. We investigate the extent to which this resulting hierarchy of models can describe and predict passive scalar dynamics and statistics in wall-bounded turbulence. The support of AFOSR under Grant Numbers FA9550-16-1-0232 and FA9550-16-1-0361 is gratefully acknowledged.
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NASA Astrophysics Data System (ADS)
Phillips, Philip W.; Setty, Chandan; Zhang, Shuyi
2018-05-01
Motivated by recent bounds for charge diffusion in critical matter, we investigate the following question: What sets the scale for the velocity for diffusing degrees of freedom in a scale-invariant system? To make our statements precise, we analyze the diffusion pole in an exactly solvable model for a Mott transition in the presence of a long-range interaction term. To achieve scale invariance, we limit our discussion to the flat-band regime. We find in this limit that the diffusion pole, which would normally obtain at finite energy, is pushed to zero energy, resulting in a vanishing of the diffusion constant. This occurs even in the presence of interactions in certain limits, indicating the robustness of this result to the inclusion of a scale in the problem. Consequently, scale invariance precludes any reasonable definition of the diffusion constant. Nonetheless, we do find that a scale can be defined, albeit irrelevant to diffusion, which is the product of the squared band velocity and the density of states.
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Perceptual decision making: drift-diffusion model is equivalent to a Bayesian model
Bitzer, Sebastian; Park, Hame; Blankenburg, Felix; Kiebel, Stefan J.
2014-01-01
Behavioral data obtained with perceptual decision making experiments are typically analyzed with the drift-diffusion model. This parsimonious model accumulates noisy pieces of evidence toward a decision bound to explain the accuracy and reaction times of subjects. Recently, Bayesian models have been proposed to explain how the brain extracts information from noisy input as typically presented in perceptual decision making tasks. It has long been known that the drift-diffusion model is tightly linked with such functional Bayesian models but the precise relationship of the two mechanisms was never made explicit. Using a Bayesian model, we derived the equations which relate parameter values between these models. In practice we show that this equivalence is useful when fitting multi-subject data. We further show that the Bayesian model suggests different decision variables which all predict equal responses and discuss how these may be discriminated based on neural correlates of accumulated evidence. In addition, we discuss extensions to the Bayesian model which would be difficult to derive for the drift-diffusion model. We suggest that these and other extensions may be highly useful for deriving new experiments which test novel hypotheses. PMID:24616689
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Critical conditions for the buoyancy-driven detachment of a wall-bound pendant drop
NASA Astrophysics Data System (ADS)
Lamorgese, A.; Mauri, R.
2016-03-01
We investigate numerically the critical conditions for detachment of an isolated, wall-bound emulsion droplet acted upon by surface tension and wall-normal buoyancy forces alone. To that end, we present a simple extension of a diffuse-interface model for partially miscible binary mixtures that was previously employed for simulating several two-phase flow phenomena far and near the critical point [A. G. Lamorgese et al. "Phase-field approach to multiphase flow modeling," Milan J. Math. 79(2), 597-642 (2011)] to allow for static contact angles other than 90°. We use the same formulation of the Cahn boundary condition as first proposed by Jacqmin ["Contact-line dynamics of a diffuse fluid interface," J. Fluid Mech. 402, 57-88 (2000)], which accommodates a cubic (Hermite) interpolation of surface tensions between the wall and each phase at equilibrium. We show that this model can be successfully employed for simulating three-phase contact line problems in stable emulsions with nearly immiscible components. We also show a numerical determination of critical Bond numbers as a function of static contact angle by phase-field simulation.
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Analysis of diffusion in curved surfaces and its application to tubular membranes
Klaus, Colin James Stockdale; Raghunathan, Krishnan; DiBenedetto, Emmanuele; Kenworthy, Anne K.
2016-01-01
Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick’s law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry. PMID:27733625
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The exit-time problem for a Markov jump process
NASA Astrophysics Data System (ADS)
Burch, N.; D'Elia, M.; Lehoucq, R. B.
2014-12-01
The purpose of this paper is to consider the exit-time problem for a finite-range Markov jump process, i.e, the distance the particle can jump is bounded independent of its location. Such jump diffusions are expedient models for anomalous transport exhibiting super-diffusion or nonstandard normal diffusion. We refer to the associated deterministic equation as a volume-constrained nonlocal diffusion equation. The volume constraint is the nonlocal analogue of a boundary condition necessary to demonstrate that the nonlocal diffusion equation is well-posed and is consistent with the jump process. A critical aspect of the analysis is a variational formulation and a recently developed nonlocal vector calculus. This calculus allows us to pose nonlocal backward and forward Kolmogorov equations, the former equation granting the various moments of the exit-time distribution.
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Resistivity bound for hydrodynamic bad metals
Lucas, Andrew; Hartnoll, Sean A.
2017-01-01
We obtain a rigorous upper bound on the resistivity ρ of an electron fluid whose electronic mean free path is short compared with the scale of spatial inhomogeneities. When such a hydrodynamic electron fluid supports a nonthermal diffusion process—such as an imbalance mode between different bands—we show that the resistivity bound becomes ρ≲AΓ. The coefficient A is independent of temperature and inhomogeneity lengthscale, and Γ is a microscopic momentum-preserving scattering rate. In this way, we obtain a unified mechanism—without umklapp—for ρ∼T2 in a Fermi liquid and the crossover to ρ∼T in quantum critical regimes. This behavior is widely observed in transition metal oxides, organic metals, pnictides, and heavy fermion compounds and has presented a long-standing challenge to transport theory. Our hydrodynamic bound allows phonon contributions to diffusion constants, including thermal diffusion, to directly affect the electrical resistivity. PMID:29073054
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Greenbaum, Gili
2015-09-07
Evaluation of the time scale of the fixation of neutral mutations is crucial to the theoretical understanding of the role of neutral mutations in evolution. Diffusion approximations of the Wright-Fisher model are most often used to derive analytic formulations of genetic drift, as well as for the time scales of the fixation of neutral mutations. These approximations require a set of assumptions, most notably that genetic drift is a stochastic process in a continuous allele-frequency space, an assumption appropriate for large populations. Here equivalent approximations are derived using a coalescent theory approach which relies on a different set of assumptions than the diffusion approach, and adopts a discrete allele-frequency space. Solutions for the mean and variance of the time to fixation of a neutral mutation derived from the two approaches converge for large populations but slightly differ for small populations. A Markov chain analysis of the Wright-Fisher model for small populations is used to evaluate the solutions obtained, showing that both the mean and the variance are better approximated by the coalescent approach. The coalescence approximation represents a tighter upper-bound for the mean time to fixation than the diffusion approximation, while the diffusion approximation and coalescence approximation form an upper and lower bound, respectively, for the variance. The converging solutions and the small deviations of the two approaches strongly validate the use of diffusion approximations, but suggest that coalescent theory can provide more accurate approximations for small populations. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Turbulent vertical diffusivity in the sub-tropical stratosphere
NASA Astrophysics Data System (ADS)
Pisso, I.; Legras, B.
2008-02-01
Vertical (cross-isentropic) mixing is produced by small-scale turbulent processes which are still poorly understood and paramaterized in numerical models. In this work we provide estimates of local equivalent diffusion in the lower stratosphere by comparing balloon borne high-resolution measurements of chemical tracers with reconstructed mixing ratio from large ensembles of random Lagrangian backward trajectories using European Centre for Medium-range Weather Forecasts analysed winds and a chemistry-transport model (REPROBUS). We focus on a case study in subtropical latitudes using data from HIBISCUS campaign. An upper bound on the vertical diffusivity is found in this case study to be of the order of 0.5 m2 s-1 in the subtropical region, which is larger than the estimates at higher latitudes. The relation between diffusion and dispersion is studied by estimating Lyapunov exponents and studying their variation according to the presence of active dynamical structures.
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Data assimilation experiments using the diffusive back and forth nudging for the NEMO ocean model
NASA Astrophysics Data System (ADS)
Ruggiero, G. A.; Ourmières, Y.; Cosme, E.; Blum, J.; Auroux, D.; Verron, J.
2014-07-01
The Diffusive Back and Forth Nudging (DBFN) is an easy-to-implement iterative data assimilation method based on the well-known Nudging method. It consists in a sequence of forward and backward model integrations, within a given time window, both of them using a feedback term to the observations. Therefore in the DBFN, the Nudging asymptotic behavior is translated into an infinite number of iterations within a bounded time domain. In this method, the backward integration is carried out thanks to what is called backward model, which is basically the forward model with reversed time step sign. To maintain numeral stability the diffusion terms also have their sign reversed, giving a diffusive character to the algorithm. In this article the DBFN performance to control a primitive equation ocean model is investigated. In this kind of model non-resolved scales are modeled by diffusion operators which dissipate energy that cascade from large to small scales. Thus, in this article the DBFN approximations and their consequences on the data assimilation system set-up are analyzed. Our main result is that the DBFN may provide results which are comparable to those produced by a 4Dvar implementation with a much simpler implementation and a shorter CPU time for convergence.
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NASA Astrophysics Data System (ADS)
Yan, Fuhan; Li, Zhaofeng; Jiang, Yichuan
2016-05-01
The issues of modeling and analyzing diffusion in social networks have been extensively studied in the last few decades. Recently, many studies focus on uncertain diffusion process. The uncertainty of diffusion process means that the diffusion probability is unpredicted because of some complex factors. For instance, the variety of individuals' opinions is an important factor that can cause uncertainty of diffusion probability. In detail, the difference between opinions can influence the diffusion probability, and then the evolution of opinions will cause the uncertainty of diffusion probability. It is known that controlling the diffusion process is important in the context of viral marketing and political propaganda. However, previous methods are hardly feasible to control the uncertain diffusion process of individual opinion. In this paper, we present suitable strategy to control this diffusion process based on the approximate estimation of the uncertain factors. We formulate a model in which the diffusion probability is influenced by the distance between opinions, and briefly discuss the properties of the diffusion model. Then, we present an optimization problem at the background of voting to show how to control this uncertain diffusion process. In detail, it is assumed that each individual can choose one of the two candidates or abstention based on his/her opinion. Then, we present strategy to set suitable initiators and their opinions so that the advantage of one candidate will be maximized at the end of diffusion. The results show that traditional influence maximization algorithms are not applicable to this problem, and our algorithm can achieve expected performance.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Komornicka, Dorota; Wolcyrz, Marek, E-mail: m.wolcyrz@int.pan.wroc.pl; Pietraszko, Adam
2012-08-15
Local structure of dirubidium tetralithium tris(selenate(VI)) dihydrate - Rb{sub 2}Li{sub 4}(SeO{sub 4}){sub 3}{center_dot} 2H{sub 2}O has been determined basing on the modeling of X-ray diffuse scattering. The origin of observed structured diffuse streaks is SeO{sub 4} tetrahedra switching between two alternative positions in two quasi-planar layers existing in each unit cell and formation of domains with specific SeO{sub 4} tetrahedra configuration locally fulfilling condition for C-centering in the 2a Multiplication-Sign 2b Multiplication-Sign c superstructure cell. The local structure solution is characterized by a uniform distribution of rather large domains (ca. thousand of unit cells) in two layers, but also monodomainsmore » can be taken into account. Inside a single domain SeO{sub 4} tetrahedra are ordered along ab-diagonal forming two-string ribbons. Inside the ribbons SeO{sub 4} and LiO{sub 4} tetrahedra share the oxygen corners, whereas ribbons are bound to each other by a net of hydrogen bonds and fastened by corner sharing SeO{sub 4} tetrahedra of the neighboring layers. - Graphical abstract: Experimental sections of the reciprocal space showing diffraction effects observed for RLSO. Bragg spots are visible on sections with integer indices (1 kl section - on the left), streaks - on sections with fractional ones (1.5 kl section - on the right). At the center: resulting local structure of the A package modeled as a microdomain: two-string ribbons of ordered oxygen-corners-sharing SeO{sub 4} and LiO{sub 4} terahedra extended along ab-diagonal are seen; ribbons are bound by hydrogen bonds (shown in pink); the multiplied 2a Multiplication-Sign 2b unit cell is shown. Highlights: Black-Right-Pointing-Pointer X-ray diffuse scattering in RLSO was registered and modeled. Black-Right-Pointing-Pointer The origin of diffuse streaks is SeO{sub 4} tetrahedra switching in two structure layers. Black-Right-Pointing-Pointer The local structure is characterized by a uniform distribution of microdomains. Black-Right-Pointing-Pointer Inside a single domain SeO{sub 4} tetrahedra are ordered along ab-diagonal forming ribbons. Black-Right-Pointing-Pointer The ribbons are bound to each other by a net of hydrogen bonds.« less
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NASA Astrophysics Data System (ADS)
Pilli, Siva P.
Moisture plays a significant role in influencing the mechanical behavior and long-term durability of composites. The objective of this dissertation was to understand the basic concepts of moisture transport in polymeric composites. Humidity test chambers were used in combination with D2O water to characterize the diffusion of D2O using Nuclear Reaction Analysis (NRA). Moisture content was measured as a function of through-thickness depth using NRA. In this study a novel method to measure the orthotropic diffusivities of polymer matrix composites has been demonstrated. This was achieved by soaking the samples in D2O vapor and subsequently characterizing the diffusion of D2O at all edges of the coupon using NRA. The diffusivity through the surface was 3½ times higher than the diffusivity through the edges. A direct comparison of experimental data with models using orthotropic diffusivities was in relatively good agreement. Surface moisture content was also measured as a function of time using NRA. It was shown that the surface concentration reaches an intermediate value of 79% Mm very rapidly and is followed by a slow linear increase to the saturation level (Mm). This research also interrogates the effect of pressure on diffusion. Test chambers were built to maintain a constant relative humidity of 80% at 60°C at three different pressures (0.101 MPa, 0.517 MPa and 1.034 MPa) including a liquid water immersion test chamber at 60°C. In this study it was observed that the time to saturation increased with increasing chamber pressure. This was primarily due to the increased maximum moisture content at higher pressures. Liquid immersion of the test samples provided the upper bound for maximum moisture content and a lower bound for time to saturation. The effects of material systems and layups on humidity measurements were also studied using two different polymer composite material systems, Cycom and Toray. Diffusivity results were identical for different layups whereas differences were observed for different material systems. Finally three-dimensional numeric models were developed, using ANSYS, to compare with the measured moisture content. Models incorporating the time-dependent and 3-D diffusion have shown an improved correlation with experiments.
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On the effects of nonlinear boundary conditions in diffusive logistic equations on bounded domains
NASA Astrophysics Data System (ADS)
Cantrell, Robert Stephen; Cosner, Chris
We study a diffusive logistic equation with nonlinear boundary conditions. The equation arises as a model for a population that grows logistically inside a patch and crosses the patch boundary at a rate that depends on the population density. Specifically, the rate at which the population crosses the boundary is assumed to decrease as the density of the population increases. The model is motivated by empirical work on the Glanville fritillary butterfly. We derive local and global bifurcation results which show that the model can have multiple equilibria and in some parameter ranges can support Allee effects. The analysis leads to eigenvalue problems with nonstandard boundary conditions.
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The electron diffusion coefficient in Jupiter's magnetosphere
NASA Technical Reports Server (NTRS)
Birmingham, T.; Northrop, T.; Baxter, R.; Hess, W.; Lojko, M.
1974-01-01
A steady-state model of Jupiter's electron radiation belt is developed. The model includes injection from the solar wind, radial diffusion, energy degradation by synchrotron radiation, and absorption at Jupiter's surface. A diffusion coefficient of the form D sub RR/R sub J squared = k times R to the m-th power is assumed, and then observed data on synchrotron radiation are used to fit the model. The free parameters determined from this fit are m = 1.95 plus or minus 0.5, k = 1.7 plus or minus 0.5 x 10 to the 9th power per sec, and the magnetic moment of injected particles equals 770 plus or minus 300 MeV/G. The value of m shows quite clearly that the diffusion is not caused by magnetic pumping by a variable solar wind or by a fluctuating convection electric field. The process might be field line exchange driven by atmospheric-ionospheric winds; our diffusion coefficient has roughly the same radial dependence but is considerably smaller in magnitude than the upper bound diffusion coefficients recently suggested for this process by Brice and McDonough (1973) and Jacques and Davis (1972).
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Gold Nanorods as Plasmonic Sensors for Particle Diffusion.
Wulf, Verena; Knoch, Fabian; Speck, Thomas; Sönnichsen, Carsten
2016-12-01
Plasmonic gold nanoparticles are normally used as sensor to detect analytes permanently bound to their surface. If the interaction between the analyte and the nanosensor surface is negligible, it only diffuses through the sensor's sensing volume, causing a small temporal shift of the plasmon resonance position. By using a very sensitive and fast detection scheme, we are able to detect these small fluctuations in the plasmon resonance. With the help of a theoretical model consistent with our detection geometry, we determine the analyte's diffusion coefficient. The method is verified by observing the trends upon changing diffusor size and medium viscosity, and the diffusion coefficients obtained were found to reflect reduced diffusion close to a solid interface. Our method, which we refer to as NanoPCS (for nanoscale plasmon correlation spectroscopy), is of practical importance for any application involving the diffusion of analytes close to nanoparticles.
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Arora, Neha; Syed, Aleem; Sander, Suzanne; Smith, Emily A
2014-10-07
A combination of sterol modulation with cyclodextrins plus fluorescence microscopy revealed a biophysical mechanism behind cholesterol's influence on the diffusion of a ubiquitous class of receptors called integrins. The heterogeneous diffusion of integrins bound to ligand-coated quantum dots was measured using single particle tracking (SPT), and the ensemble changes in integrin diffusion were measured by fluorescence recovery after photobleaching (FRAP). A 25 ± 1% reduction of membrane cholesterol resulted in three significant changes to the diffusion of ligand-bound αPS2CβPS integrins as measured by SPT. There was a 23% increase in ligand-bound mobile integrins; there was a statistically significant increase in the average diffusion coefficient inside zones of confined diffusion, and histograms of confined integrin trajectories showed an increased frequency in the range of 0.1-1 μm(2) s(-1) and a decreased frequency in the 0.001-0.1 μm(2) s(-1) range. No statistical change was measured in the duration of confinement nor the size of confined zones. Restoring the cholesterol-depleted cells with exogenous cholesterol or exogenous epicholesterol resulted in similar diffusion properties. Epicholesterol differs from cholesterol in the orientation of a single hydroxyl group. The ability of epicholesterol to substitute for cholesterol suggests a biophysical mechanism for cholesterol's effect on integrin diffusion. Influences of bilayer thickness, viscosity and organization are discussed as possible explanations for the measured changes in integrin diffusion when the membrane cholesterol concentration is reduced.
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Bulk diffusion in a kinetically constrained lattice gas
NASA Astrophysics Data System (ADS)
Arita, Chikashi; Krapivsky, P. L.; Mallick, Kirone
2018-03-01
In the hydrodynamic regime, the evolution of a stochastic lattice gas with symmetric hopping rules is described by a diffusion equation with density-dependent diffusion coefficient encapsulating all microscopic details of the dynamics. This diffusion coefficient is, in principle, determined by a Green-Kubo formula. In practice, even when the equilibrium properties of a lattice gas are analytically known, the diffusion coefficient cannot be computed except when a lattice gas additionally satisfies the gradient condition. We develop a procedure to systematically obtain analytical approximations for the diffusion coefficient for non-gradient lattice gases with known equilibrium. The method relies on a variational formula found by Varadhan and Spohn which is a version of the Green-Kubo formula particularly suitable for diffusive lattice gases. Restricting the variational formula to finite-dimensional sub-spaces allows one to perform the minimization and gives upper bounds for the diffusion coefficient. We apply this approach to a kinetically constrained non-gradient lattice gas in two dimensions, viz. to the Kob-Andersen model on the square lattice.
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The exit-time problem for a Markov jump process
DOE Office of Scientific and Technical Information (OSTI.GOV)
Burch, N.; D'Elia, Marta; Lehoucq, Richard B.
2014-12-15
The purpose of our paper is to consider the exit-time problem for a finite-range Markov jump process, i.e, the distance the particle can jump is bounded independent of its location. Such jump diffusions are expedient models for anomalous transport exhibiting super-diffusion or nonstandard normal diffusion. We refer to the associated deterministic equation as a volume-constrained nonlocal diffusion equation. The volume constraint is the nonlocal analogue of a boundary condition necessary to demonstrate that the nonlocal diffusion equation is well-posed and is consistent with the jump process. A critical aspect of the analysis is a variational formulation and a recently developedmore » nonlocal vector calculus. Furthermore, this calculus allows us to pose nonlocal backward and forward Kolmogorov equations, the former equation granting the various moments of the exit-time distribution.« less
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Fluoride-induced enhancement of diffusion in streptococcal model plaque biofilms.
Rose, R K; Turner, S J
1998-01-01
It has been demonstrated that fluoride decreases the calcium-binding affinity of Streptococcus mutans and approximately doubles the calcium-binding capacity. To investigate the effect of this mechanism on calcium mobility in plaque, 45Ca flux was measured from a condensed films of S. mutans into tracer-free solution. Bacteria were suspended in pH 7.0 or 5.0 buffer including 0, 5, 10, 15 or 20 mmol/l Ca2+ carrier, with or without 5 mmol/l F- and with 45Ca and 3H-inulin. The appearance of 45Ca and 3H-inulin in carrier-containing but initially tracer-free buffer was measured and extracellular fraction (Ve) and bound calcium were calculated. As the ratio (R) of bound to free Ca2+ approached zero at high [Ca2+], the measured diffusion coefficient (rDe) approached the effective diffusion coefficient (De), such that: rDe = De/(1+R). Fluoride increased the rate of calcium diffusion by a reduction in the binding affinity. This work demonstrates that fluoride significantly increases mobility in plaque; this may increase the rate at which calcium is transported between plaque and an underlying lesion and so promote remineralization. This mechanism could also increase the penetration of bacteriocides and suggests a novel method for biofilm treatment.
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NASA Astrophysics Data System (ADS)
Rutenberg, Andrew D.; Brown, Aidan I.; Kreplak, Laurent
2016-08-01
Collagen fibril cross-sectional radii show no systematic variation between the interior and the periphery of fibril bundles, indicating an effectively constant rate of collagen incorporation into fibrils throughout the bundle. Such spatially homogeneous incorporation constrains the extracellular diffusion of collagen precursors from sources at the bundle boundary to sinks at the growing fibrils. With a coarse-grained diffusion equation we determine stringent bounds, using parameters extracted from published experimental measurements of tendon development. From the lack of new fibril formation after birth, we further require that the concentration of diffusing precursors stays below the critical concentration for fibril nucleation. We find that the combination of the diffusive bound, which requires larger concentrations to ensure homogeneous fibril radii, and lack of nucleation, which requires lower concentrations, is only marginally consistent with fully processed collagen using conservative bounds. More realistic bounds may leave no consistent concentrations. Therefore, we propose that unprocessed pC-collagen diffuses from the bundle periphery followed by local C-proteinase activity and subsequent collagen incorporation at each fibril. We suggest that C-proteinase is localized within bundles, at fibril surfaces, during radial fibrillar growth. The much greater critical concentration of pC-collagen, as compared to fully processed collagen, then provides broad consistency between homogeneous fibril radii and the lack of fibril nucleation during fibril growth.
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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.
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NASA Astrophysics Data System (ADS)
Plante, Ianik; Cucinotta, Francis A.
2011-11-01
Cell communication is a key mechanism in tissue responses to radiation. Several molecules are implicated in radiation-induced signaling between cells, but their contributions to radiation risk are poorly understood. Meanwhile, Green's functions for diffusion-influenced reactions have appeared in the literature, which are applied to describe the diffusion of molecules near a plane membrane comprising bound receptors with the possibility of reversible binding of a ligand and activation of signal transduction proteins by the ligand-receptor complex. We have developed Brownian dynamics algorithms to simulate particle histories in this system which can accurately reproduce the theoretical distribution of distances of a ligand from the membrane, the number of reversibly bound particles, and the number of receptor complexes activating signaling proteins as a function of time, regardless of the number of time steps used for the simulation. These simulations will be of great importance to model interactions at low doses where stochastic effects induced by a small number of molecules or interactions come into play.
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Tania, Nessy; Prosk, Erin; Condeelis, John; Edelstein-Keshet, Leah
2011-01-01
Cofilin is an important regulator of actin polymerization, cell migration, and chemotaxis. Recent experimental data on mammary carcinoma cells reveal that stimulation by epidermal growth factor (EGF) generates a pool of active cofilin that results in a peak of actin filament barbed ends on the timescale of 1 min. Here, we present results of a mathematical model for the dynamics of cofilin and its transition between several pools in response to EGF stimulation. We describe the interactions of phospholipase C, membrane lipids (PIP2), and cofilin bound to PIP2 and to F-actin, as well as diffusible cofilin in active G-actin-monomer-bound or phosphorylated states. We consider a simplified representation in which the thin cell edge (lamellipod) and the cell interior are represented by two compartments that are linked by diffusion. We demonstrate that a high basal level of active cofilin stored by binding to PIP2, as well as the highly enriched local milieu of F-actin at the cell edge, is essential to capture the EGF-induced barbed-end amplification observed experimentally. PMID:21504724
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Abbou, Jeremy; Anne, Agnès; Demaille, Christophe
2006-11-16
The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.
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Hock, Sabrina; Hasenauer, Jan; Theis, Fabian J
2013-01-01
Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed in-vitro and in-vivo using microscopy based imaging techniques. The resulting time-series of two dimensional, high-resolutions images in combination with mechanistic models enable the quantitative analysis of the underlying mechanisms. However, such a model-based analysis is still challenging due to measurement noise and sparse observations, which result in uncertainties of the model parameters. We introduce a likelihood function for image-based measurements with log-normal distributed noise. Based upon this likelihood function we formulate the maximum likelihood estimation problem, which is solved using PDE-constrained optimization methods. To assess the uncertainty and practical identifiability of the parameters we introduce profile likelihoods for diffusion processes. As proof of concept, we model certain aspects of the guidance of dendritic cells towards lymphatic vessels, an example for haptotaxis. Using a realistic set of artificial measurement data, we estimate the five kinetic parameters of this model and compute profile likelihoods. Our novel approach for the estimation of model parameters from image data as well as the proposed identifiability analysis approach is widely applicable to diffusion processes. The profile likelihood based method provides more rigorous uncertainty bounds in contrast to local approximation methods.
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Terry, Alan J.; Sturrock, Marc; Dale, J. Kim; Maroto, Miguel; Chaplain, Mark A. J.
2011-01-01
In the vertebrate embryo, tissue blocks called somites are laid down in head-to-tail succession, a process known as somitogenesis. Research into somitogenesis has been both experimental and mathematical. For zebrafish, there is experimental evidence for oscillatory gene expression in cells in the presomitic mesoderm (PSM) as well as evidence that Notch signalling synchronises the oscillations in neighbouring PSM cells. A biological mechanism has previously been proposed to explain these phenomena. Here we have converted this mechanism into a mathematical model of partial differential equations in which the nuclear and cytoplasmic diffusion of protein and mRNA molecules is explictly considered. By performing simulations, we have found ranges of values for the model parameters (such as diffusion and degradation rates) that yield oscillatory dynamics within PSM cells and that enable Notch signalling to synchronise the oscillations in two touching cells. Our model contains a Hill coefficient that measures the co-operativity between two proteins (Her1, Her7) and three genes (her1, her7, deltaC) which they inhibit. This coefficient appears to be bounded below by the requirement for oscillations in individual cells and bounded above by the requirement for synchronisation. Consistent with experimental data and a previous spatially non-explicit mathematical model, we have found that signalling can increase the average level of Her1 protein. Biological pattern formation would be impossible without a certain robustness to variety in cell shape and size; our results possess such robustness. Our spatially-explicit modelling approach, together with new imaging technologies that can measure intracellular protein diffusion rates, is likely to yield significant new insight into somitogenesis and other biological processes. PMID:21386903
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Terry, Alan J; Sturrock, Marc; Dale, J Kim; Maroto, Miguel; Chaplain, Mark A J
2011-02-28
In the vertebrate embryo, tissue blocks called somites are laid down in head-to-tail succession, a process known as somitogenesis. Research into somitogenesis has been both experimental and mathematical. For zebrafish, there is experimental evidence for oscillatory gene expression in cells in the presomitic mesoderm (PSM) as well as evidence that Notch signalling synchronises the oscillations in neighbouring PSM cells. A biological mechanism has previously been proposed to explain these phenomena. Here we have converted this mechanism into a mathematical model of partial differential equations in which the nuclear and cytoplasmic diffusion of protein and mRNA molecules is explicitly considered. By performing simulations, we have found ranges of values for the model parameters (such as diffusion and degradation rates) that yield oscillatory dynamics within PSM cells and that enable Notch signalling to synchronise the oscillations in two touching cells. Our model contains a Hill coefficient that measures the co-operativity between two proteins (Her1, Her7) and three genes (her1, her7, deltaC) which they inhibit. This coefficient appears to be bounded below by the requirement for oscillations in individual cells and bounded above by the requirement for synchronisation. Consistent with experimental data and a previous spatially non-explicit mathematical model, we have found that signalling can increase the average level of Her1 protein. Biological pattern formation would be impossible without a certain robustness to variety in cell shape and size; our results possess such robustness. Our spatially-explicit modelling approach, together with new imaging technologies that can measure intracellular protein diffusion rates, is likely to yield significant new insight into somitogenesis and other biological processes.
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NASA Technical Reports Server (NTRS)
Takahashi, Fumiaki; Katta, Viswanath R.
2003-01-01
Diffusion flame stabilization is of essential importance in both Earth-bound combustion systems and spacecraft fire safety. Local extinction, re-ignition, and propagation processes may occur as a result of interactions between the flame zone and vortices or fire-extinguishing agents. By using a computational fluid dynamics code with a detailed chemistry model for methane combustion, the authors have revealed the chemical kinetic structure of the stabilizing region of both jet and flat-plate diffusion flames, predicted the flame stability limit, and proposed diffusion flame attachment and detachment mechanisms in normal and microgravity. Because of the unique geometry of the edge of diffusion flames, radical back-diffusion against the oxygen-rich entrainment dramatically enhanced chain reactions, thus forming a peak reactivity spot, i.e., reaction kernel, responsible for flame holding. The new results have been obtained for the edge diffusion flame propagation and attached flame structure using various C1-C3 hydrocarbons.
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Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.
Werner, Tomás
2015-07-01
Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings.
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Diffusion-limited mixing by incompressible flows
NASA Astrophysics Data System (ADS)
Miles, Christopher J.; Doering, Charles R.
2018-05-01
Incompressible flows can be effective mixers by appropriately advecting a passive tracer to produce small filamentation length scales. In addition, diffusion is generally perceived as beneficial to mixing due to its ability to homogenize a passive tracer. However we provide numerical evidence that, in cases where advection and diffusion are both actively present, diffusion may produce negative effects by limiting the mixing effectiveness of incompressible optimal flows. This limitation appears to be due to the presence of a limiting length scale given by a generalised Batchelor length (Batchelor 1959 J. Fluid Mech. 5 113–33). This length scale limitation may in turn affect long-term mixing rates. More specifically, we consider local-in-time flow optimisation under energy and enstrophy flow constraints with the objective of maximising the mixing rate. We observe that, for enstrophy-bounded optimal flows, the strength of diffusion may not impact the long-term mixing rate. For energy-constrained optimal flows, however, an increase in the strength of diffusion can decrease the mixing rate. We provide analytical lower bounds on mixing rates and length scales achievable under related constraints (point-wise bounded speed and rate-of-strain) by extending the work of Lin et al (2011 J. Fluid Mech. 675 465–76) and Poon (1996 Commun. PDE 21 521–39).
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The effect of reactions on the formation and readout of the gradient of Bicoid
NASA Astrophysics Data System (ADS)
Perez Ipiña, Emiliano; Ponce Dawson, Silvina
2017-02-01
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. In this work we analyze an SDID model that includes the Interaction of Bcd with binding sites. We simulate numerically the resulting full reaction-diffusion system in a cylindrical domain using previously determined biophysical parameters and a simplified version of the Bcd source. In this way we obtain solutions that depend on the spatial location approximately as observed experimentally and that reach such dependence at a time that is also compatible with the experimental observations. Analyzing the differences between the free and bound Bcd distributions we observe that the latter spans over a longer lengthscale. We conclude that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the Hill coefficient that relates the concentrations of Bcd and of the protein, Hunchback, whose production is regulated by Bcd.
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Analytical performance bounds for multi-tensor diffusion-MRI.
Ahmed Sid, Farid; Abed-Meraim, Karim; Harba, Rachid; Oulebsir-Boumghar, Fatima
2017-02-01
To examine the effects of MR acquisition parameters on brain white matter fiber orientation estimation and parameter of clinical interest in crossing fiber areas based on the Multi-Tensor Model (MTM). We compute the Cramér-Rao Bound (CRB) for the MTM and the parameter of clinical interest such as the Fractional Anisotropy (FA) and the dominant fiber orientations, assuming that the diffusion MRI data are recorded by a multi-coil, multi-shell acquisition system. Considering the sum-of-squares method for the reconstructed magnitude image, we introduce an approximate closed-form formula for Fisher Information Matrix that has the simplicity and easy interpretation advantages. In addition, we propose to generalize the FA and the mean diffusivity to the multi-tensor model. We show the application of the CRB to reduce the scan time while preserving a good estimation precision. We provide results showing how the increase of the number of acquisition coils compensates the decrease of the number of diffusion gradient directions. We analyze the impact of the b-value and the Signal-to-Noise Ratio (SNR). The analysis shows that the estimation error variance decreases with a quadratic rate with the SNR, and that the optimum b-values are not unique but depend on the target parameter, the context, and eventually the target cost function. In this study we highlight the importance of choosing the appropriate acquisition parameters especially when dealing with crossing fiber areas. We also provide a methodology for the optimal tuning of these parameters using the CRB. Copyright © 2016 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Bai, M.; Miskowiec, A.; Hansen, F. Y.; Taub, H.; Jenkins, T.; Tyagi, M.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.; Wang, S.-K.
2012-05-01
High-energy-resolution quasielastic neutron scattering has been used to elucidate the diffusion of water molecules in proximity to single bilayer lipid membranes supported on a silicon substrate. By varying sample temperature, level of hydration, and deuteration, we identify three different types of diffusive water motion: bulk-like, confined, and bound. The motion of bulk-like and confined water molecules is fast compared to those bound to the lipid head groups (7-10 H2O molecules per lipid), which move on the same nanosecond time scale as H atoms within the lipid molecules.
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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.
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Ziemba, Brian P.; Falke, Joseph J.
2013-01-01
Peripheral membrane proteins bound to lipids on bilayer surfaces play central roles in a wide array of cellular processes, including many signaling pathways. These proteins diffuse in the plane of the bilayer and often undergo complex reactions involving the binding of regulatory and substrate lipids and proteins they encounter during their 2-D diffusion. Some peripheral proteins, for example pleckstrin homology (PH) domains, dock to the bilayer in a relatively shallow position with little penetration into the bilayer. Other peripheral proteins exhibit more complex bilayer contacts, for example classical protein kinase C isoforms (PKCs) bind as many as six lipids in stepwise fashion, resulting in the penetration of three PKC domains (C1A, C1B, C2) into the bilayer headgroup and hydrocarbon regions. A molecular understanding of the molecular features that control the diffusion speeds of proteins bound to supported bilayers would enable key molecular information to be extracted from experimental diffusion constants, revealing protein-lipid and protein-bilayer interactions difficult to study by other methods. The present study investigates a range of 11 different peripheral protein constructs comprised by 1 to 3 distinct domains (PH, C1A, C1B, C2, anti-lipid antibody). By combining these constructs with various combinations of target lipids, the study measures 2-D diffusion constants on supported bilayers for 17 different protein-lipid complexes. The resulting experimental diffusion constants, together with the known membrane interaction parameters of each complex, are used to analyze the molecular features correlated with diffusional slowing and bilayer friction. The findings show that both 1) individual bound lipids and 2) individual protein domains that penetrate into the hydrocarbon core make additive contributions to the friction against the bilayer, thereby defining the 2-D diffusion constant. An empirical formula is developed that accurately estimates the diffusion constant and bilayer friction of a peripheral protein in terms of its number of bound lipids and its geometry of penetration into the bilayer hydrocarbon core, yielding an excellent global best fit (R2 of 0.97) to the experimental diffusion constants. Finally, the observed additivity of the frictional contributions suggests that further development of current theory describing bilayer dynamics may be needed. The present findings provide constraints that will be useful in such theory development. PMID:23701821
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Ziemba, Brian P; Falke, Joseph J
2013-01-01
Peripheral membrane proteins bound to lipids on bilayer surfaces play central roles in a wide array of cellular processes, including many signaling pathways. These proteins diffuse in the plane of the bilayer and often undergo complex reactions involving the binding of regulatory and substrate lipids and proteins they encounter during their 2D diffusion. Some peripheral proteins, for example pleckstrin homology (PH) domains, dock to the bilayer in a relatively shallow position with little penetration into the bilayer. Other peripheral proteins exhibit more complex bilayer contacts, for example classical protein kinase C isoforms (PKCs) bind as many as six lipids in stepwise fashion, resulting in the penetration of three PKC domains (C1A, C1B, C2) into the bilayer headgroup and hydrocarbon regions. A molecular understanding of the molecular features that control the diffusion speeds of proteins bound to supported bilayers would enable key molecular information to be extracted from experimental diffusion constants, revealing protein-lipid and protein-bilayer interactions difficult to study by other methods. The present study investigates a range of 11 different peripheral protein constructs comprised by 1-3 distinct domains (PH, C1A, C1B, C2, anti-lipid antibody). By combining these constructs with various combinations of target lipids, the study measures 2D diffusion constants on supported bilayers for 17 different protein-lipid complexes. The resulting experimental diffusion constants, together with the known membrane interaction parameters of each complex, are used to analyze the molecular features correlated with diffusional slowing and bilayer friction. The findings show that both (1) individual bound lipids and (2) individual protein domains that penetrate into the hydrocarbon core make additive contributions to the friction against the bilayer, thereby defining the 2D diffusion constant. An empirical formula is developed that accurately estimates the diffusion constant and bilayer friction of a peripheral protein in terms of its number of bound lipids and its geometry of penetration into the bilayer hydrocarbon core, yielding an excellent global best fit (R(2) of 0.97) to the experimental diffusion constants. Finally, the observed additivity of the frictional contributions suggests that further development of current theory describing bilayer dynamics may be needed. The present findings provide constraints that will be useful in such theory development. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.
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Existence and uniqueness of steady state solutions of a nonlocal diffusive logistic equation
NASA Astrophysics Data System (ADS)
Sun, Linan; Shi, Junping; Wang, Yuwen
2013-08-01
In this paper, we consider a dynamical model of population biology which is of the classical Fisher type, but the competition interaction between individuals is nonlocal. The existence, uniqueness, and stability of the steady state solution of the nonlocal problem on a bounded interval with homogeneous Dirichlet boundary conditions are studied.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wu, Hong-Ming; Ho, Hao-I; Tsai, Shi-Jane
2016-03-21
We report on the Ge auto-doping and out-diffusion in InGaP epilayer with Cu-Pt ordering grown on 4-in. Ge substrate. Ge profiles determined from secondary ion mass spectrometry indicate that the Ge out-diffusion depth is within 100 nm. However, the edge of the wafer suffers from stronger Ge gas-phase auto-doping than the center, leading to ordering deterioration in the InGaP epilayer. In the edge, we observed a residual Cu-Pt ordering layer left beneath the surface, suggesting that the ordering deterioration takes place after the deposition rather than during the deposition and In/Ga inter-diffusion enhanced by Ge vapor-phase auto-doping is responsible for themore » deterioration. We thus propose a di-vacancy diffusion model, in which the amphoteric Ge increases the di-vacancy density, resulting in a Ge density dependent diffusion. In the model, the In/Ga inter-diffusion and Ge out-diffusion are realized by the random hopping of In/Ga host atoms and Ge atoms to di-vacancies, respectively. Simulation based on this model well fits the Ge out-diffusion profiles, suggesting its validity. By comparing the Ge diffusion coefficient obtained from the fitting and the characteristic time constant of ordering deterioration estimated from the residual ordering layer, we found that the hopping rates of Ge and the host atoms are in the same order of magnitude, indicating that di-vacancies are bound in the vicinity of Ge atoms.« less
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Nucleation of rotating crystals by Thiovulum majus bacteria
NASA Astrophysics Data System (ADS)
Petroff, A. P.; Libchaber, A.
2018-01-01
Thiovulum majus self-organize on glass surfaces into active two-dimensional crystals of rotating cells. Unlike classical crystals, these bacterial crystallites continuously rotate and reorganize as the power of rotating cells is dissipated by the surrounding flow. In this article, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. This process occurs in three steps. First a free-swimming cell collides with the wall and becomes hydrodynamically bound to the two-dimensional surface. We present a simple model to understand how viscous forces localize cells near the chamber walls. Next, the cell diffuses over the surface for an average of 63+/- 6 s before escaping to the bulk fluid. The diffusion coefficient {D}{{eff}}=7.98 +/- 0.1 μ {{{m}}}2 {{{s}}}-1 of these 8.5 μ {{m}} diameter cells corresponds to a temperature of (4.16+/- 0.05)× {10}4 K, and thus cannot be explained by equilibrium fluctuations. Finally, two cells coalesce into a rotating dimer when the convergent flow created by each cell overwhelms their active Brownian motion. This occurs when cells diffuse to within a distance of 13.3 ± 0.2 μm of each other.
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Diffusion theory of decision making in continuous report.
Smith, Philip L
2016-07-01
I present a diffusion model for decision making in continuous report tasks, in which a continuous, circularly distributed, stimulus attribute in working memory is matched to a representation of the attribute in the stimulus display. Memory retrieval is modeled as a 2-dimensional diffusion process with vector-valued drift on a disk, whose bounding circle represents the decision criterion. The direction and magnitude of the drift vector describe the identity of the stimulus and the quality of its representation in memory, respectively. The point at which the diffusion exits the disk determines the reported value of the attribute and the time to exit the disk determines the decision time. Expressions for the joint distribution of decision times and report outcomes are obtained by means of the Girsanov change-of-measure theorem, which allows the properties of the nonzero-drift diffusion process to be characterized as a function of a Euclidian-distance Bessel process. Predicted report precision is equal to the product of the decision criterion and the drift magnitude and follows a von Mises distribution, in agreement with the treatment of precision in the working memory literature. Trial-to-trial variability in criterion and drift rate leads, respectively, to direct and inverse relationships between report accuracy and decision times, in agreement with, and generalizing, the standard diffusion model of 2-choice decisions. The 2-dimensional model provides a process account of working memory precision and its relationship with the diffusion model, and a new way to investigate the properties of working memory, via the distributions of decision times. (PsycINFO Database Record (c) 2016 APA, all rights reserved).
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Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models
NASA Astrophysics Data System (ADS)
Giese, Wolfgang; Eigel, Martin; Westerheide, Sebastian; Engwer, Christian; Klipp, Edda
2015-12-01
In silico experiments bear the potential for further understanding of biological transport processes by allowing a systematic modification of any spatial property and providing immediate simulation results. Cell polarization and spatial reorganization of membrane proteins are fundamental for cell division, chemotaxis and morphogenesis. We chose the yeast Saccharomyces cerevisiae as an exemplary model system which entails the shuttling of small Rho GTPases such as Cdc42 and Rho, between an active membrane-bound form and an inactive cytosolic form. We used partial differential equations to describe the membrane-cytosol shuttling of proteins. In this study, a consistent extension of a class of 1D reaction-diffusion systems into higher space dimensions is suggested. The membrane is modeled as a thin layer to allow for lateral diffusion and the cytosol is modeled as an enclosed volume. Two well-known polarization mechanisms were considered. One shows the classical Turing-instability patterns, the other exhibits wave-pinning dynamics. For both models, we investigated how cell shape and diffusion barriers like septin structures or bud scars influence the formation of signaling molecule clusters and subsequent polarization. An extensive set of in silico experiments with different modeling hypotheses illustrated the dependence of cell polarization models on local membrane curvature, cell size and inhomogeneities on the membrane and in the cytosol. In particular, the results of our computer simulations suggested that for both mechanisms, local diffusion barriers on the membrane facilitate Rho GTPase aggregation, while diffusion barriers in the cytosol and cell protrusions limit spontaneous molecule aggregations of active Rho GTPase locally.
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Data assimilation experiments using diffusive back-and-forth nudging for the NEMO ocean model
NASA Astrophysics Data System (ADS)
Ruggiero, G. A.; Ourmières, Y.; Cosme, E.; Blum, J.; Auroux, D.; Verron, J.
2015-04-01
The diffusive back-and-forth nudging (DBFN) is an easy-to-implement iterative data assimilation method based on the well-known nudging method. It consists of a sequence of forward and backward model integrations, within a given time window, both of them using a feedback term to the observations. Therefore, in the DBFN, the nudging asymptotic behaviour is translated into an infinite number of iterations within a bounded time domain. In this method, the backward integration is carried out thanks to what is called backward model, which is basically the forward model with reversed time step sign. To maintain numeral stability, the diffusion terms also have their sign reversed, giving a diffusive character to the algorithm. In this article the DBFN performance to control a primitive equation ocean model is investigated. In this kind of model non-resolved scales are modelled by diffusion operators which dissipate energy that cascade from large to small scales. Thus, in this article, the DBFN approximations and their consequences for the data assimilation system set-up are analysed. Our main result is that the DBFN may provide results which are comparable to those produced by a 4Dvar implementation with a much simpler implementation and a shorter CPU time for convergence. The conducted sensitivity tests show that the 4Dvar profits of long assimilation windows to propagate surface information downwards, and that for the DBFN, it is worth using short assimilation windows to reduce the impact of diffusion-induced errors. Moreover, the DBFN is less sensitive to the first guess than the 4Dvar.
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Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species
NASA Astrophysics Data System (ADS)
Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar
2018-02-01
The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.
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Chakraverty, S; Sahoo, B K; Rao, T D; Karunakar, P; Sapra, B K
2018-02-01
Modelling radon transport in the earth crust is a useful tool to investigate the changes in the geo-physical processes prior to earthquake event. Radon transport is modeled generally through the deterministic advection-diffusion equation. However, in order to determine the magnitudes of parameters governing these processes from experimental measurements, it is necessary to investigate the role of uncertainties in these parameters. Present paper investigates this aspect by combining the concept of interval uncertainties in transport parameters such as soil diffusivity, advection velocity etc, occurring in the radon transport equation as applied to soil matrix. The predictions made with interval arithmetic have been compared and discussed with the results of classical deterministic model. The practical applicability of the model is demonstrated through a case study involving radon flux measurements at the soil surface with an accumulator deployed in steady-state mode. It is possible to detect the presence of very low levels of advection processes by applying uncertainty bounds on the variations in the observed concentration data in the accumulator. The results are further discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Marangoni-driven chemotaxis, chemotactic collapse, and the Keller-Segel equation
NASA Astrophysics Data System (ADS)
Shelley, Michael; Masoud, Hassan
2013-11-01
Almost by definition, chemotaxis involves the biased motion of motile particles along gradients of a chemical concentration field. Perhaps the most famous model for collective chemotaxis in mathematical biology is the Keller-Segel model, conceived to describe collective aggregation of slime mold colonies in response to an intrinsically produced, and diffusing, chemo-attractant. Heavily studied, particularly in 2D where the system is ``super-critical'', it has been proved that the KS model can develop finite-time singularities - so-called chemotactic collapse - of delta-function type. Here, we study the collective dynamics of immotile particles bound to a 2D interface above a 3D fluid. These particles are chemically active and produce a diffusing field that creates surface-tension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. Remarkably, we show that this system involving 3D diffusion and fluid dynamics, exactly yields the 2D Keller-Segel model for the surface-flow of active particles. We discuss the consequences of collapse on the 3D fluid dynamics, and generalizations of the fluid-dynamical model.
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NASA Technical Reports Server (NTRS)
Susko, M.
1977-01-01
Electrets used to detect the chemical composition of rocket exhaust effluents were investigated. The effectiveness of electrets was assessed while comparisons were made with hydrogen chloride measuring devices from chamber and field tests, and computed results from a multilayer diffusion model. The experimental data used were obtained from 18 static test firings, chamber tests, and the Viking 1 launch to Mars. Results show that electrets have multipollutant measuring capabilities, simplicity of deployment, and speed of assessment. The electrets compared favorably with other hydrogen chloride measuring devices. The summary of the measured data from the electrets and the hydrogen chloride detectors was within the upper and lower bounds of the computed hydrogen chloride concentrations from the multilayer diffusion model.
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Baij, Lambert; Hermans, Joen J; Keune, Katrien; Iedema, Piet
2018-06-18
The formation of metal soaps (metal complexes of saturated fatty acids) is a serious problem affecting the appearance and structural integrity of many oil paintings. Tailored model systems for aged oil paint and time-dependent attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to study the diffusion of palmitic acid and subsequent metal soap crystallization. The simultaneous presence of free saturated fatty acids and polymer-bound metal carboxylates leads to rapid metal soap crystallization, following a complex mechanism that involves both acid and metal diffusion. Solvent flow, water, and pigments all enhance metal soap crystallization in the model systems. These results contribute to the development of paint cleaning strategies, a better understanding of oil paint degradation, and highlight the potential of time-dependent ATR-FTIR spectroscopy for studying dynamic processes in polymer films. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
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2013-01-01
Background The coexistence of macromolecular replicators and thus the stability of presumed prebiotic replicator communities have been shown to critically depend on spatially constrained catalytic cooperation among RNA-like modular replicators. The necessary spatial constraints might have been supplied by mineral surfaces initially, preceding the more effective compartmentalization in membrane vesicles which must have been a later development of chemical evolution. Results Using our surface-bound RNA world model – the Metabolic Replicator Model (MRM) platform – we show that the mobilities on the mineral substrate surface of both the macromolecular replicators and the small molecules of metabolites they produce catalytically are the key factors determining the stable persistence of an evolvable metabolic replicator community. Conclusion The effects of replicator mobility and metabolite diffusion on different aspects of replicator coexistence in MRM are determined, including the maximum attainable size of the metabolic replicator system and its resistance to the invasion of parasitic replicators. We suggest a chemically plausible hypothetical scenario for the evolution of the first protocell starting from the surface-bound MRM system. PMID:24053177
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Thermal diffusivity and butterfly velocity in anisotropic Q-lattice models
NASA Astrophysics Data System (ADS)
Jeong, Hyun-Sik; Ahn, Yongjun; Ahn, Dujin; Niu, Chao; Li, Wei-Jia; Kim, Keun-Young
2018-01-01
We study a relation between the thermal diffusivity ( D T ) and two quantum chaotic properties, Lyapunov time (τ L ) and butterfly velocity ( v B ) in strongly correlated systems by using a holographic method. Recently, it was shown that E_i:={D}_{T,i}/({v}{^{B,i}}^2{τ}_L)(i=x,y) is universal in the sense that it is determined only by some scaling exponents of the IR metric in the low temperature limit regardless of the matter fields and ultraviolet data. Inspired by this observation, by analyzing the anisotropic IR scaling geometry carefully, we find the concrete expressions for E_i in terms of the critical dynamical exponents z i in each direction, E_i={z}_i/2({z}_i-1) . Furthermore, we find the lower bound of E_i is always 1 /2, which is not affected by anisotropy, contrary to the η/s case. However, there may be an upper bound determined by given fixed anisotropy.
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MESOSCOPIC MODELING OF STOCHASTIC REACTION-DIFFUSION KINETICS IN THE SUBDIFFUSIVE REGIME
BLANC, EMILIE; ENGBLOM, STEFAN; HELLANDER, ANDREAS; LÖTSTEDT, PER
2017-01-01
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model of subdiffusion into an accurate and consistent reaction-subdiffusion computational framework. Two different possible models of chemical reaction are revealed and some basic dynamic properties are derived. In certain cases those mesoscopic models have a direct interpretation at the macroscopic level as fractional partial differential equations in a bounded time interval. Through analysis and numerical experiments we estimate the macroscopic effects of reactions under subdiffusive mixing. The models display properties observed also in experiments: for a short time interval the behavior of the diffusion and the reaction is ordinary, in an intermediate interval the behavior is anomalous, and at long times the behavior is ordinary again. PMID:29046618
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Conceptual model for transport processes in the Culebra Dolomite Member, Rustler Formation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Holt, R.M.
1997-08-01
The Culebra Dolomite Member of the Rustler Formation represents a possible pathway for contaminants from the Waste Isolation Pilot Plant underground repository to the accessible environment. The geologic character of the Culebra is consistent with a double-porosity, multiple-rate model for transport in which the medium is conceptualized as consisting of advective porosity, where solutes are carried by the groundwater flow, and fracture-bounded zones of diffusive porosity, where solutes move through slow advection or diffusion. As the advective travel length or travel time increases, the nature of transport within a double-porosity medium changes. This behavior is important for chemical sorption, becausemore » the specific surface area per unit mass of the diffusive porosity is much greater than in the advective porosity. Culebra transport experiments conducted at two different length scales show behavior consistent with a multiple-rate, double-porosity conceptual model for Culebra transport. Tracer tests conducted on intact core samples from the Culebra show no evidence of significant diffusion, suggesting that at the core scale the Culebra can be modeled as a single-porosity medium where only the advective porosity participates in transport. Field tracer tests conducted in the Culebra show strong double-porosity behavior that is best explained using a multiple-rate model.« less
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Mason, R P; Chester, D W
1989-01-01
A "membrane bilayer pathway" model, involving ligand partition into the bilayer, lateral diffusion, and receptor binding has been invoked to describe the 1,4-dihydropyridine (DHP) calcium channel antagonist receptor binding mechanism. In an earlier study (Chester et al. 1987. Biophys. J. 52:1021-1030), the diffusional component of this model was examined using an active fluorescence labeled DHP calcium channel antagonist, nisoldipine-lissamine rhodamine B (Ns-R), in purified cardiac sarcolemmal (CSL) lipid multibilayers. Diffusion coefficient measurements on membrane-bound drug and phospholipid at maximum bilayer hydration yielded similar values (3.8 x 10(-8) cm2/s). However, decreases in bilayer hydration resulted in dramatically reduced diffusion coefficient values for both probes with substantially greater impact on Ns-R diffusion. These data suggested that hydration dependent diffusional differences could be a function of relative probe location along the bilayer normal. In this communication, we have addressed the relative effect of the rhodamine substituent on Ns-R diffusion complex by examining the diffusional dynamics of free rhodamine B under the same conditions used to evaluate Ns-R complex and phospholipid diffusion. X-ray diffraction studies were performed to determine the Ns-R location in the membrane and model the CSL lipid bilayer profile structure to give a rationale for the differences in probe diffusional dynamics as a function of interbilayer water space. PMID:2611332
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Tania, Nessy; Prosk, Erin; Condeelis, John; Edelstein-Keshet, Leah
2011-04-20
Cofilin is an important regulator of actin polymerization, cell migration, and chemotaxis. Recent experimental data on mammary carcinoma cells reveal that stimulation by epidermal growth factor (EGF) generates a pool of active cofilin that results in a peak of actin filament barbed ends on the timescale of 1 min. Here, we present results of a mathematical model for the dynamics of cofilin and its transition between several pools in response to EGF stimulation. We describe the interactions of phospholipase C, membrane lipids (PIP(2)), and cofilin bound to PIP(2) and to F-actin, as well as diffusible cofilin in active G-actin-monomer-bound or phosphorylated states. We consider a simplified representation in which the thin cell edge (lamellipod) and the cell interior are represented by two compartments that are linked by diffusion. We demonstrate that a high basal level of active cofilin stored by binding to PIP(2), as well as the highly enriched local milieu of F-actin at the cell edge, is essential to capture the EGF-induced barbed-end amplification observed experimentally. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Kinetics of Surface-Mediated Fibrillization of Amyloid-β (12-28) Peptides.
Lin, Yi-Chih; Li, Chen; Fakhraai, Zahra
2018-04-17
Surfaces or interfaces are considered to be key factors in facilitating the formation of amyloid fibrils under physiological conditions. In this report, we study the kinetics of the surface-mediated fibrillization (SMF) of an amyloid-β fragment (Aβ 12-28 ) on mica. We employ a spin-coating-based drying procedure to control the exposure time of the substrate to a low-concentration peptide solution and then monitor the fibril growth as a function of time via atomic force microscopy (AFM). The evolution of surface-mediated fibril growth is quantitatively characterized in terms of the length histogram of imaged fibrils and their surface concentration. A two-dimensional (2D) kinetic model is proposed to numerically simulate the length evolution of surface-mediated fibrils by assuming a diffusion-limited aggregation (DLA) process along with size-dependent rate constants. We find that both monomer and fibril diffusion on the surface are required to obtain length histograms as a function of time that resemble those observed in experiments. The best-fit simulated data can accurately describe the key features of experimental length histograms and suggests that the mobility of loosely bound amyloid species is crucial in regulating the kinetics of SMF. We determine that the mobility exponent for the size dependence of the DLA rate constants is α = 0.55 ± 0.05, which suggests that the diffusion of loosely bound surface fibrils roughly depends on the inverse of the square root of their size. These studies elucidate the influence of deposition rate and surface diffusion on the formation of amyloid fibrils through SMF. The method used here can be broadly adopted to study the diffusion and aggregation of peptides or proteins on various surfaces to investigate the role of chemical interactions in two-dimensional fibril formation and diffusion.
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Hill, Reghan J.; Wang, Chih-Ying
2014-01-01
A variety of observations—sometimes controversial—have been made in recent decades when attempting to elucidate the roles of interfacial slip on tracer diffusion in phospholipid membranes. Evans–Sackmann theory (1988) has furnished membrane viscosities and lubrication-film thicknesses for supported membranes from experimentally measured lateral diffusion coefficients. Similar to the Saffman and Delbrück model, which is the well-known counterpart for freely supported membranes, the bilayer is modelled as a single two-dimensional fluid. However, the Evans–Sackman model cannot interpret the mobilities of monotopic tracers, such as individual lipids or rigidly bound lipid assemblies; neither does it account for tracer–leaflet and inter-leaflet slip. To address these limitations, we solve the model of Wang and Hill, in which two leaflets of a bilayer membrane, a circular tracer and supports are coupled by interfacial friction, using phenomenological friction/slip coefficients. This furnishes an exact solution that can be readily adopted to interpret the mobilities of a variety of mosaic elements—including lipids, integral monotopic and polytopic proteins, and lipid rafts—in supported bilayer membranes. PMID:25002822
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Diffusion Influenced Adsorption Kinetics.
Miura, Toshiaki; Seki, Kazuhiko
2015-08-27
When the kinetics of adsorption is influenced by the diffusive flow of solutes, the solute concentration at the surface is influenced by the surface coverage of solutes, which is given by the Langmuir-Hinshelwood adsorption equation. The diffusion equation with the boundary condition given by the Langmuir-Hinshelwood adsorption equation leads to the nonlinear integro-differential equation for the surface coverage. In this paper, we solved the nonlinear integro-differential equation using the Grünwald-Letnikov formula developed to solve fractional kinetics. Guided by the numerical results, analytical expressions for the upper and lower bounds of the exact numerical results were obtained. The upper and lower bounds were close to the exact numerical results in the diffusion- and reaction-controlled limits, respectively. We examined the validity of the two simple analytical expressions obtained in the diffusion-controlled limit. The results were generalized to include the effect of dispersive diffusion. We also investigated the effect of molecular rearrangement of anisotropic molecules on surface coverage.
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Tam, Zhi Yang; Cai, Yi Hui; Gunawan, Rudiyanto
2010-11-17
Mitochondrial regulation of apoptosis depends on the programmed release of proapoptotic proteins such as cytochrome c (Cyt c) through the outer mitochondrial membrane (OMM). Although a few key processes involved in this release have been identified, including the liberation of inner membrane-bound Cyt c and formation of diffusible pores on the OMM, other details like the transport of Cyt c within complex mitochondrial compartments, e.g., the cristae and crista junctions, are not yet fully understood (to our knowledge). In particular, a remodeling of the inner mitochondrial membrane accompanying apoptosis seen in a few studies, in which crista junctions widen, has been hypothesized to be a necessary step in the Cyt c release. Using a three-dimensional spatial modeling of mitochondrial crista and the crista junction, model simulations and analysis illustrated how the interplay among solubilization of Cyt c, fast diffusion of Cyt c, and OMM permeabilization gives rise to the observed experimental release profile. Importantly, the widening of the crista junction was found to have a negligible effect on the transport of free Cyt c from cristae. Finally, model simulations showed that increasing the fraction of free/loosely-bound Cyt c can sensitize the cell to apoptotic stimuli in a threshold manner, which may explain increased sensitivity to cell death associated with aging. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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1982-01-01
The surface distribution of concanavalin A (Con A) bound to cell membrane receptors varies dramatically as a function of mitotic phase. The lectin is distributed diffusely on cells labeled and observed between mid-prophase and early anaphase, whereas cells observed in late anaphase or telophase demonstrate a marked accumulation of Con A- receptor complexes over the developing cleavage furrow (Berlin, Oliver, and Walter. 1978. Cell. 15:327-341). In this report, we first use a system based on video intensification fluorescence microscopy to describe the simultaneous changes in cell shape and in lectin-receptor complex topography during progression of single cells through the mitotic cycle. The video analysis establishes that fluorescein succinyl Con A (F-S Con A)-receptor complex redistribution begins coincident with the first appearance of the cleavage furrow and is essentially complete within 2-3 min. This remarkable redistribution of surface fluorescence occurs during only a modest change in cell shape from a sphere to a belted cylinder. It reflects the translocation of complexes and not the accumulation of excess labeled membrane in the cleavage furrow: first, bound fluorescent cholera toxin which faithfully outlines the plasma membrane is not accumulated in the cleavage furrow, and, second, electron microscopy of peroxidase-Con A labeled cells undergoing cleavage shows that there is a high linear density of lectin within the furrow while Con A is virtually eliminated from the poles. The rate of surface movement of F-S Con A was quantitated by photon counting during a repetitive series of laser-excited fluorescence scans across dividing cells. Results were analyzed in terms of two alternative models of movement: a flow model in which complexes moved unidirectionally at constant velocity, and a diffusion model in which complexes could diffuse freely but were trapped at the cleavage furrow. According to these models, the observed rates of accumulation were attainable at either an effective flow velocity of approximately 1 micron/min, or an effective diffusion coefficient of approximately 10(- 9) cm2/s. However, in separate experiments the lectin-receptor diffusion rate measured directly by the method of fluorescence recovery after photobleaching (FRAP) on metaphase cells was only approximately 10(-10) cm2/s. Most importantly, photobleaching experiments during the actual period of F-S Con A accumulation showed that lectin-receptor movement during cleavage occurs unidirectionally. These results rule out diffusion and make a process of oriented flow of ligand-receptor complexes the most likely mechanism for ligand-receptor accumulation in the cleavage furrow. PMID:7119007
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Ando, Tadashi; Skolnick, Jeffrey
2014-12-01
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.
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Coupling between diffusion and orientation of pentacene molecules on an organic surface.
Rotter, Paul; Lechner, Barbara A J; Morherr, Antonia; Chisnall, David M; Ward, David J; Jardine, Andrew P; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor
2016-04-01
The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems.
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Analysis of diffusion in curved surfaces and its application to tubular membranes.
Klaus, Colin James Stockdale; Raghunathan, Krishnan; DiBenedetto, Emmanuele; Kenworthy, Anne K
2016-12-01
Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick's law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry. © 2016 Klaus, Raghunathan, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
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The effect of a realistic thermal diffusivity on numerical model of a subducting slab
NASA Astrophysics Data System (ADS)
Maierova, P.; Steinle-Neumann, G.; Cadek, O.
2010-12-01
A number of numerical studies of subducting slab assume simplified (constant or only depth-dependent) models of thermal conductivity. The available mineral physics data indicate, however, that thermal diffusivity is strongly temperature- and pressure-dependent and may also vary among different mantle materials. In the present study, we examine the influence of realistic thermal properties of mantle materials on the thermal state of the upper mantle and the dynamics of subducting slabs. On the basis of the data published in mineral physics literature we compile analytical relationships that approximate the pressure and temperature dependence of thermal diffusivity for major mineral phases of the mantle (olivine, wadsleyite, ringwoodite, garnet, clinopyroxenes, stishovite and perovskite). We propose a simplified composition of mineral assemblages predominating in the subducting slab and the surrounding mantle (pyrolite, mid-ocean ridge basalt, harzburgite) and we estimate their thermal diffusivity using the Hashin-Shtrikman bounds. The resulting complex formula for the diffusivity of each aggregate is then approximated by a simpler analytical relationship that is used in our numerical model as an input parameter. For the numerical modeling we use the Elmer software (open source finite element software for multiphysical problems, see http://www.csc.fi/english/pages/elmer). We set up a 2D Cartesian thermo-mechanical steady-state model of a subducting slab. The model is partly kinematic as the flow is driven by a boundary condition on velocity that is prescribed on the top of the subducting lithospheric plate. Reology of the material is non-linear and is coupled with the thermal equation. Using the realistic relationship for thermal diffusivity of mantle materials, we compute the thermal and flow fields for different input velocity and age of the subducting plate and we compare the results against the models assuming a constant thermal diffusivity. The importance of the realistic description of thermal properties in models of subducted slabs is discussed.
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Generation and mobility of radon in soil
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rose, A.W.; Jester, W.A.; Ciolkosz, E.J.
This study has confirmed large seasonal and daily variations of Rn in soil gas, developed models for the effects of temperature and moisture on air-water Rn partition, inhibited Rn diffusion from wet soil into sparse large air-filled pores and effects of diffusion into bedrock, demonstrated that organic matter is a major host for 226Ra in soils and that organic-bound Ra largely determines the proportion of 222Rn emanated to pore space, shown that in contrast 220Rn is emanated mainly from 224Ra in Fe-oxides, detected significant disequilibrium between 226Ra and 238U in organic matter and in some recent glacial soils, demonstrated bymore » computer models that air convection driven by temperature differences is expected in moderately permeable soils on hillsides.« less
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Generation and mobility of radon in soil. Technical report
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rose, A.W.; Jester, W.A.; Ciolkosz, E.J.
This study has confirmed large seasonal and daily variations of Rn in soil gas, developed models for the effects of temperature and moisture on air-water Rn partition, inhibited Rn diffusion from wet soil into sparse large air-filled pores and effects of diffusion into bedrock, demonstrated that organic matter is a major host for 226Ra in soils and that organic-bound Ra largely determines the proportion of 222Rn emanated to pore space, shown that in contrast 220Rn is emanated mainly from 224Ra in Fe-oxides, detected significant disequilibrium between 226Ra and 238U in organic matter and in some recent glacial soils, demonstrated bymore » computer models that air convection driven by temperature differences is expected in moderately permeable soils on hillsides.« less
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Tsetsos, Konstantinos; Gao, Juan; McClelland, James L.; Usher, Marius
2012-01-01
When people make decisions, do they give equal weight to evidence arriving at different times? A recent study (Kiani et al., 2008) using brief motion pulses (superimposed on a random moving dot display) reported a primacy effect: pulses presented early in a motion observation period had a stronger impact than pulses presented later. This observation was interpreted as supporting the bounded diffusion (BD) model and ruling out models in which evidence accumulation is subject to leakage or decay of early-arriving information. We use motion pulses and other manipulations of the timing of the perceptual evidence in new experiments and simulations that support the leaky competing accumulator (LCA) model as an alternative to the BD model. While the LCA does include leakage, we show that it can exhibit primacy as a result of competition between alternatives (implemented via mutual inhibition), when the inhibition is strong relative to the leak. Our experiments replicate the primacy effect when participants must be prepared to respond quickly at the end of a motion observation period. With less time pressure, however, the primacy effect is much weaker. For 2 (out of 10) participants, a primacy bias observed in trials where the motion observation period is short becomes weaker or reverses (becoming a recency effect) as the observation period lengthens. Our simulation studies show that primacy is equally consistent with the LCA or with BD. The transition from primacy-to-recency can also be captured by the LCA but not by BD. Individual differences and relations between the LCA and other models are discussed. PMID:22701399
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Lebedev, Konstantin; Mafé, Salvador; Stroeve, Pieter
2006-04-15
We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.
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Modeling uptake of hydrophobic organic contaminants into polyethylene passive samplers.
Thompson, Jay M; Hsieh, Ching-Hong; Luthy, Richard G
2015-02-17
Single-phase passive samplers are gaining acceptance as a method to measure hydrophobic organic contaminant (HOC) concentration in water. Although the relationship between the HOC concentration in water and passive sampler is linear at equilibrium, mass transfer models are needed for nonequilibrium conditions. We report measurements of organochlorine pesticide diffusion and partition coefficients with respect to polyethylene (PE), and present a Fickian approach to modeling HOC uptake by PE in aqueous systems. The model is an analytic solution to Fick's second law applied through an aqueous diffusive boundary layer and a polyethylene layer. Comparisons of the model with existing methods indicate agreement at appropriate boundary conditions. Laboratory release experiments on the organochlorine pesticides DDT, DDE, DDD, and chlordane in well-mixed slurries support the model's applicability to aqueous systems. In general, the advantage of the model is its application in the cases of well-agitated systems, low values of polyethylene-water partioning coefficients, thick polyethylene relative to the boundary layer thickness, and/or short exposure times. Another significant advantage is the ability to estimate, or at least bound, the needed exposure time to reach a desired CPE without empirical model inputs. A further finding of this work is that polyethylene diffusivity does not vary by transport direction through the sampler thickness.
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NASA Astrophysics Data System (ADS)
Menzel, Andreas M.
2015-11-01
Diffusion of colloidal particles in a complex environment such as polymer networks or biological cells is a topic of high complexity with significant biological and medical relevance. In such situations, the interaction between the surroundings and the particle motion has to be taken into account. We analyze a simplified diffusion model that includes some aspects of a complex environment in the framework of a nonlinear friction process: at low particle speeds, friction grows linearly with the particle velocity as for regular viscous friction; it grows more than linearly at higher particle speeds; finally, at a maximum of the possible particle speed, the friction diverges. In addition to bare diffusion, we study the influence of a constant drift force acting on the diffusing particle. While the corresponding stationary velocity distributions can be derived analytically, the displacement statistics generally must be determined numerically. However, as a benefit of our model, analytical progress can be made in one case of a special maximum particle speed. The effect of a drift force in this case is analytically determined by perturbation theory. It will be interesting in the future to compare our results to real experimental systems. One realization could be magnetic colloidal particles diffusing through a shear-thickening environment such as starch suspensions, possibly exposed to an external magnetic field gradient.
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The magnetic field at the core-mantle boundary
NASA Technical Reports Server (NTRS)
Bloxham, J.; Gubbins, D.
1985-01-01
Models of the geomagnetic field are, in general, produced from a least-squares fit of the coefficients in a truncated spherical harmonic expansion to the available data. Downward continuation of such models to the core-mantle boundary (CMB) is an unstable process: the results are found to be critically dependent on the choice of truncation level. Modern techniques allow this fundamental difficulty to be circumvented. The method of stochastic inversion is applied to modeling the geomagnetic field. Prior information is introduced by requiring that the spectrum of spherical harmonic coefficients to fall-off in a particular manner which is consistent with the Ohmic heating in the core having a finite lower bound. This results in models with finite errors in the radial field at the CMB. Curves of zero radial field can then be determined and integrals of the radial field over patches on the CMB bounded by these null-flux curves calculated. With the assumption of negligible magnetic diffusion in the core; frozen-flux hypothesis, these integrals are time-invariant.
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Lateral Membrane Diffusion Modulated by a Minimal Actin Cortex
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
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NASA Astrophysics Data System (ADS)
Sumi, Tomonari; Okumoto, Atsushi; Goto, Hitoshi; Sekino, Hideo
2017-10-01
A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.
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How to Detect the Location and Time of a Covert Chemical Attack: A Bayesian Approach
2009-12-01
Inverse Problems, Design and Optimization Symposium 2004. Rio de Janeiro , Brazil. Chan, R., and Yee, E. (1997). A simple model for the probability...sensor interpretation applications and has been successfully applied, for example, to estimate the source strength of pollutant releases in multi...coagulation, and second-order pollutant diffusion in sorption- desorption, are not linear. Furthermore, wide uncertainty bounds exist for several of
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Persistent random walk of cells involving anomalous effects and random death
NASA Astrophysics Data System (ADS)
Fedotov, Sergei; Tan, Abby; Zubarev, Andrey
2015-04-01
The purpose of this paper is to implement a random death process into a persistent random walk model which produces sub-ballistic superdiffusion (Lévy walk). We develop a stochastic two-velocity jump model of cell motility for which the switching rate depends upon the time which the cell has spent moving in one direction. It is assumed that the switching rate is a decreasing function of residence (running) time. This assumption leads to the power law for the velocity switching time distribution. This describes the anomalous persistence of cell motility: the longer the cell moves in one direction, the smaller the switching probability to another direction becomes. We derive master equations for the cell densities with the generalized switching terms involving the tempered fractional material derivatives. We show that the random death of cells has an important implication for the transport process through tempering of the superdiffusive process. In the long-time limit we write stationary master equations in terms of exponentially truncated fractional derivatives in which the rate of death plays the role of tempering of a Lévy jump distribution. We find the upper and lower bounds for the stationary profiles corresponding to the ballistic transport and diffusion with the death-rate-dependent diffusion coefficient. Monte Carlo simulations confirm these bounds.
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E. coli chemotaxis and super-diffusion
NASA Astrophysics Data System (ADS)
Dobnikar, Jure; Matthäus, Franziska; Jagodic, Marko
2010-03-01
The bacteria E. coli actively propel by switching between clockwise and anti-clockwise rotation of the flagella attached to their cell membranes. This results in two modes of motion: tumbling and swimming. The switching between the two modes is coupled to the ligand sensing through the chemotactic signalling pathway inside the cell. We modelled the signalling pathway and performed numerical simulations of the chemotactic motion of a large number of E. coli bacteria under various external conditions. We have shown that under certain conditions the thermal noise in the level of receptor-bound CheR (an enzyme responsible for methylation of the receptor sites) leads to super-diffusive behaviour (L'evy walk) which is advantageous for the bacterial populations in environments with scarce food. Exerting external pressure we might observe evolution of the wild-type to the super-diffusive populations.
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Diffusion-Based Model for Synaptic Molecular Communication Channel.
Khan, Tooba; Bilgin, Bilgesu A; Akan, Ozgur B
2017-06-01
Computational methods have been extensively used to understand the underlying dynamics of molecular communication methods employed by nature. One very effective and popular approach is to utilize a Monte Carlo simulation. Although it is very reliable, this method can have a very high computational cost, which in some cases renders the simulation impractical. Therefore, in this paper, for the special case of an excitatory synaptic molecular communication channel, we present a novel mathematical model for the diffusion and binding of neurotransmitters that takes into account the effects of synaptic geometry in 3-D space and re-absorption of neurotransmitters by the transmitting neuron. Based on this model we develop a fast deterministic algorithm, which calculates expected value of the output of this channel, namely, the amplitude of excitatory postsynaptic potential (EPSP), for given synaptic parameters. We validate our algorithm by a Monte Carlo simulation, which shows total agreement between the results of the two methods. Finally, we utilize our model to quantify the effects of variation in synaptic parameters, such as position of release site, receptor density, size of postsynaptic density, diffusion coefficient, uptake probability, and number of neurotransmitters in a vesicle, on maximum number of bound receptors that directly affect the peak amplitude of EPSP.
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STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.
Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik
2012-05-10
Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/
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STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies
2012-01-01
Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/ PMID:22574658
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Information accumulation system by inheritance and diffusion
NASA Astrophysics Data System (ADS)
Shin, J. K.
2009-09-01
This paper suggests a new model, called as the IAS (Information Accumulation System), for the description of the dynamic process that people use to accumulate their information (knowledge or opinion) for specific issues. Using the concept of information, both the internal and the external mechanism of the opinion dynamics are treated on a unified frame. The information is quantified as a real number with fixed bounds. New concepts, such as inheritance and differential absorption, are incorporated in IAS in addition to the conventional diffusive interaction between people. Thus, the dynamics of the IAS are governed by following three factors: inheritance rate, diffusivity and absorption rate. The original set of equations was solved with an agent based modeling technique. In addition, the individual equations for each of the agents were assembled and transformed into a set of equations for the ensemble averages, which are greatly reduced in number and can be solved analytically. The example simulations showed interesting results such as the critical behavior with respect to diffusivity, the information polarization out of zero-sum news and the dependence of the solutions on the initial conditions alone. The results were speculated in relation to today’s modern society where the diffusivity of information has been greatly increased through the internet and mobile phones.
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Extremal equilibria for reaction-diffusion equations in bounded domains and applications
NASA Astrophysics Data System (ADS)
Rodríguez-Bernal, Aníbal; Vidal-López, Alejandro
We show the existence of two special equilibria, the extremal ones, for a wide class of reaction-diffusion equations in bounded domains with several boundary conditions, including non-linear ones. They give bounds for the asymptotic dynamics and so for the attractor. Some results on the existence and/or uniqueness of positive solutions are also obtained. As a consequence, several well-known results on the existence and/or uniqueness of solutions for elliptic equations are revisited in a unified way obtaining, in addition, information on the dynamics of the associated parabolic problem. Finally, we ilustrate the use of the general results by applying them to the case of logistic equations. In fact, we obtain a detailed picture of the positive dynamics depending on the parameters appearing in the equation.
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Influence of the bound polymer layer on nanoparticle diffusion in polymer melts
Griffin, Philip J.; Bocharova, Vera; Middleton, L. Robert; ...
2016-09-23
We measure the center-of-mass diffusion of silica nanoparticles (NPs) in entangled poly(2-vinylpyridine) (P2VP) melts using Rutherford backscattering spectrometry. While these NPs are well within the size regime where enhanced, nonhydrodynamic NP transport is theoretically predicted and has been observed experimentally (2R NP/d tube ≈ 3, where 2R NP is the NP diameter and d tube is the tube diameter), we find that the diffusion of these NPs in P2VP is in fact well-described by the hydrodynamic Stokes–Einstein relation. The effective NP diameter 2R eff is significantly larger than 2R NP and strongly dependent on P2VP molecular weight, consistent with themore » presence of a bound polymer layer on the NP surface with thickness h eff ≈ 1.1R g. Our results show that the bound polymer layer significantly augments the NP hydrodynamic size in polymer melts with attractive polymer–NP interactions and effectively transitions the mechanism of NP diffusion from the nonhydrodynamic to hydrodynamic regime, particularly at high molecular weights where NP transport is expected to be notably enhanced. Lastly, these results provide the first experimental demonstration that hydrodynamic NP transport in polymer melts requires particles of size ≳5d tube, consistent with recent theoretical predictions.« less
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Mok, Wilson; Stylianopoulos, Triantafyllos; Boucher, Yves; Jain, Rakesh K.
2010-01-01
Purpose Although oncolytic viral vectors show promise for the treatment of various cancers, ineffective initial distribution and propagation throughout the tumor mass often limit the therapeutic response. A mathematical model is developed to describe the spread of herpes simplex virus from the initial injection site. Experimental Design The tumor is modeled as a sphere of radius R. The model incorporates reversible binding, interstitial diffusion, viral degradation, and internalization and physiologic parameters. Three species are considered as follows: free interstitial virus, virus bound to cell surfaces, and internalized virus. Results This analysis reveals that both rapid binding and internalization as well as hindered diffusion contain the virus to the initial injection volume, with negligible spread to the surrounding tissue. Unfortunately, increasing the dose to saturate receptors and promote diffusion throughout the tumor is not a viable option: the concentration necessary would likely compromise safety. However, targeted modifications to the virus that decrease the binding affinity have the potential to increase the number of infected cells by 1.5-fold or more. An increase in the effective diffusion coefficient can result in similar gains. Conclusions This analysis suggests criteria by which the potential response of a tumor to oncolytic herpes simplex virus therapy can be assessed. Furthermore, it reveals the potential of modifications to the vector delivery method, physicochemical properties of the virus, and tumor extracellular matrix composition to enhance efficacy. PMID:19318482
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Basconi, Joseph E; Carta, Giorgio; Shirts, Michael R
2015-04-14
Multiscale simulation is used to study the adsorption of lysozyme onto ion exchangers obtained by grafting charged polymers into a porous matrix, in systems with various polymer properties and strengths of electrostatic interaction. Molecular dynamics simulations show that protein partitioning into the polymer-filled pore space increases with the overall charge content of the polymers, while the diffusivity in the pore space decreases. However, the combination of greatly increased partitioning and modestly decreased diffusion results in macroscopic transport rates that increase as a function of charge content, as the large concentration driving force due to enhanced pore space partitioning outweighs the reduction in the pore space diffusivity. Matrices having greater charge associated with the grafted polymers also exhibit more diffuse intraparticle concentration profiles during transient adsorption. In systems with a high charge content per polymer and a low protein loading, the polymers preferentially partition toward the surface due to favorable interactions with the surface-bound protein. These results demonstrate the potential of multiscale modeling to illuminate qualitative trends between molecular properties and the adsorption equilibria and kinetic properties observable on macroscopic scales.
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Direct observation of transcription activator-like effector (TALE) protein dynamics
NASA Astrophysics Data System (ADS)
Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M.
2014-03-01
In this work, we describe a single molecule assay to probe the site-search dynamics of transcription activator-like effector (TALE) proteins along DNA. In modern genetics, the ability to selectively edit the human genome is an unprecedented development, driven by recent advances in targeted nuclease proteins. Specific gene editing can be accomplished using TALE proteins, which are programmable DNA-binding proteins that can be fused to a nuclease domain. In this way, TALENs are a leading technology that has shown great success in the genomic editing of pluripotent stem cells. A major hurdle facing clinical implementation, however, is the potential for deleterious off-target binding events. For these reasons, a molecular-level understanding of TALE binding and target sequence search on DNA is essential. To this end, we developed a single-molecule fluorescence imaging assay that provides a first-of-its-kind view of the 1-D diffusion of TALE proteins along stretched DNA. Taken together with co-crystal structures of DNA-bound TALEs, our results suggest a rotationally-coupled, major groove tracking model for diffusion. We further report diffusion constants for TALE proteins as a function of salt concentration, consistent with previously described models of 1-D protein diffusion.
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Bounds on the conductivity of a suspension of random impenetrable spheres
NASA Astrophysics Data System (ADS)
Beasley, J. D.; Torquato, S.
1986-11-01
We compare the general Beran bounds on the effective electrical conductivity of a two-phase composite to the bounds derived by Torquato for the specific model of spheres distributed throughout a matrix phase. For the case of impenetrable spheres, these bounds are shown to be identical and to depend on the microstructure through the sphere volume fraction φ2 and a three-point parameter ζ2, which is an integral over a three-point correlation function. We evaluate ζ2 exactly through third order in φ2 for distributions of impenetrable spheres. This expansion is compared to the analogous results of Felderhof and of Torquato and Lado, all of whom employed the superposition approximation for the three-particle distribution function involved in ζ2. The results indicate that the exact ζ2 will be greater than the value calculated under the superposition approximation. For reasons of mathematical analogy, the results obtained here apply as well to the determination of the thermal conductivity, dielectric constant, and magnetic permeability of composite media and the diffusion coefficient of porous media.
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Formation of the long range Dpp morphogen gradient.
Schwank, Gerald; Dalessi, Sascha; Yang, Schu-Fee; Yagi, Ryohei; de Lachapelle, Aitana Morton; Affolter, Markus; Bergmann, Sven; Basler, Konrad
2011-07-01
The TGF-β homolog Decapentaplegic (Dpp) acts as a secreted morphogen in the Drosophila wing disc, and spreads through the target tissue in order to form a long range concentration gradient. Despite extensive studies, the mechanism by which the Dpp gradient is formed remains controversial. Two opposing mechanisms have been proposed: receptor-mediated transcytosis (RMT) and restricted extracellular diffusion (RED). In these scenarios the receptor for Dpp plays different roles. In the RMT model it is essential for endocytosis, re-secretion, and thus transport of Dpp, whereas in the RED model it merely modulates Dpp distribution by binding it at the cell surface for internalization and subsequent degradation. Here we analyzed the effect of receptor mutant clones on the Dpp profile in quantitative mathematical models representing transport by either RMT or RED. We then, using novel genetic tools, experimentally monitored the actual Dpp gradient in wing discs containing receptor gain-of-function and loss-of-function clones. Gain-of-function clones reveal that Dpp binds in vivo strongly to the type I receptor Thick veins, but not to the type II receptor Punt. Importantly, results with the loss-of-function clones then refute the RMT model for Dpp gradient formation, while supporting the RED model in which the majority of Dpp is not bound to Thick veins. Together our results show that receptor-mediated transcytosis cannot account for Dpp gradient formation, and support restricted extracellular diffusion as the main mechanism for Dpp dispersal. The properties of this mechanism, in which only a minority of Dpp is receptor-bound, may facilitate long-range distribution.
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Moens, Pierre D.J.; Digman, Michelle A.; Gratton, Enrico
2015-01-01
The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. PMID:25809257
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Moens, Pierre D J; Digman, Michelle A; Gratton, Enrico
2015-03-24
The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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A refined reaction-diffusion model of tau-microtubule dynamics and its application in FDAP analysis.
Igaev, Maxim; Janning, Dennis; Sündermann, Frederik; Niewidok, Benedikt; Brandt, Roland; Junge, Wolfgang
2014-12-02
Fluorescence decay after photoactivation (FDAP) and fluorescence recovery after photobleaching (FRAP) are well established approaches for studying the interaction of the microtubule (MT)-associated protein tau with MTs in neuronal cells. Previous interpretations of FDAP/FRAP data have revealed dwell times of tau on MTs in the range of several seconds. However, this is difficult to reconcile with a dwell time recently measured by single-molecule analysis in neuronal processes that was shorter by two orders of magnitude. Questioning the validity of previously used phenomenological interpretations of FDAP/FRAP data, we have generalized the standard two-state reaction-diffusion equations by 1), accounting for the parallel and discrete arrangement of MTs in cell processes (i.e., homogeneous versus heterogeneous distribution of tau-binding sites); and 2), explicitly considering both active (diffusion upon MTs) and passive (piggybacking upon MTs at rates of slow axonal transport) motion of bound tau. For some idealized cases, analytical solutions were derived. By comparing them with the full numerical solution and Monte Carlo simulations, the respective validity domains were mapped. Interpretation of our FDAP data (from processes of neuronally differentiated PC12 cells) in light of the heterogeneous formalism yielded independent estimates for the association (∼2 ms) and dwell (∼100 ms) times of tau to/on a single MT rather than in an MT array. The dwell time was shorter by orders of magnitude than that in a previous report where a homogeneous topology of MTs was assumed. We found that the diffusion of bound tau was negligible in vivo, in contrast to an earlier report that tau diffuses along the MT lattice in vitro. Methodologically, our results demonstrate that the heterogeneity of binding sites cannot be ignored when dealing with reaction-diffusion of cytoskeleton-associated proteins. Physiologically, the results reveal the behavior of tau in cellular processes, which is noticeably different from that in vitro. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Star Formation and the Hall Effect
NASA Astrophysics Data System (ADS)
Braiding, Catherine
2011-10-01
Magnetic fields play an important role in star formation by regulating the removal of angular momentum from collapsing molecular cloud cores. Hall diffusion is known to be important to the magnetic field behaviour at many of the intermediate densities and field strengths encountered during the gravitational collapse of molecular cloud cores into protostars, and yet its role in the star formation process is not well-studied. This thesis describes a semianalytic self-similar model of the collapse of rotating isothermal molecular cloud cores with both Hall and ambipolar diffusion, presenting similarity solutions that demonstrate that the Hall effect has a profound influence on the dynamics of collapse. ... Hall diffusion also determines the strength of the magnetic diffusion and centrifugal shocks that bound the pseudo and rotationally-supported discs, and can introduce subshocks that further slow accretion onto the protostar. In cores that are not initially rotating Hall diffusion can even induce rotation, which could give rise to disc formation and resolve the magnetic braking catastrophe. The Hall effect clearly influences the dynamics of gravitational collapse and its role in controlling the magnetic braking and radial diffusion of the field would be worth exploring in future numerical simulations of star formation.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nogues, Gilles, E-mail: gilles.nogues@neel.cnrs.fr; Den Hertog, Martien; Inst. NEEL, CNRS, F-38042 Grenoble
We perform correlated studies of individual GaN nanowires in scanning electron microscopy combined to low temperature cathodoluminescence, microphotoluminescence, and scanning transmission electron microscopy. We show that some nanowires exhibit well localized regions emitting light at the energy of a stacking fault bound exciton (3.42 eV) and are able to observe the presence of a single stacking fault in these regions. Precise measurements of the cathodoluminescence signal in the vicinity of the stacking fault give access to the exciton diffusion length near this location.
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Resolvent positive linear operators exhibit the reduction phenomenon
Altenberg, Lee
2012-01-01
The spectral bound, s(αA + βV), of a combination of a resolvent positive linear operator A and an operator of multiplication V, was shown by Kato to be convex in . Kato's result is shown here to imply, through an elementary “dual convexity” lemma, that s(αA + βV) is also convex in α > 0, and notably, ∂s(αA + βV)/∂α ≤ s(A). Diffusions typically have s(A) ≤ 0, so that for diffusions with spatially heterogeneous growth or decay rates, greater mixing reduces growth. Models of the evolution of dispersal in particular have found this result when A is a Laplacian or second-order elliptic operator, or a nonlocal diffusion operator, implying selection for reduced dispersal. These cases are shown here to be part of a single, broadly general, “reduction” phenomenon. PMID:22357763
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Springer, Andreas; Hagen, Volker; Cherepanov, Dmitry A.; Antonenko, Yuri N.; Pohl, Peter
2011-01-01
Proton diffusion along membrane surfaces is thought to be essential for many cellular processes such as energy transduction. Commonly, it is treated as a succession of jumps between membrane-anchored proton-binding sites. Our experiments provide evidence for an alternative model. We released membrane-bound caged protons by UV flashes and monitored their arrival at distant sites by fluorescence measurements. The kinetics of the arrival is probed as a function of distance for different membranes and for different water isotopes. We found that proton diffusion along the membrane is fast even in the absence of ionizable groups in the membrane, and it decreases strongly in D2O as compared to H2O. We conclude that the fast proton transport along the membrane is dominated by diffusion via interfacial water, and not via ionizable lipid moieties. PMID:21859952
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NASA Astrophysics Data System (ADS)
Yi, Zhou; Deng, Pei-Na; Zhang, Li-Li; Li, Hua
2016-10-01
The dynamic behaviors of water contained in calcium-silicate-hydrate (C-S-H) gel with different water content values from 10% to 30% (by weight), are studied by using an empirical diffusion model (EDM) to analyze the experimental data of quasi-elastic neutron scattering (QENS) spectra at measured temperatures ranging from 230 K to 280 K. In the study, the experimental QENS spectra with the whole Q-range are considered. Several important parameters including the bound/immobile water elastic coefficient A, the bound water index BWI, the Lorentzian with a half-width at half-maximum (HWHM) Γ 1(Q) and Γ 2(Q), the self-diffusion coefficients D t1 and D t2 of water molecules, the average residence times τ 01 and τ 02, and the proton mean squared displacement (MSD) are obtained. The results show that the QENS spectra can be fitted very well not only for small Q (≤ 1 Å-1) but also for large Q. The bound/immobile water fraction in a C-S-H gel sample can be shown by the fitted BWI. The distinction between bound/immobile and mobile water, which includes confined water and ultra-confined water, can be seen by the fitted MSD. All the MSD tend to be the smallest value below 0.25 Å2 (the MSD of bound/immobile water) as the Q increases to 1.9 Å-1, no matter what the temperature and water content are. Furthermore, by the abrupt changes of the fitted values of D t1, τ 01, and Γ 1(Q), a crossover temperature at 250 K, namely the liquid-to-crystal-like transition temperature, can be identified for confined water in large gel pores (LGPs) and/or small gel pores (SGPs) contained in the C-S-H gel sample with 30% water content.
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NASA Astrophysics Data System (ADS)
You, K.; Flemings, P. B.
2016-12-01
We developed two 2-D numerical models to simulate hydrate formation by long range methane gas transport and short-range methane diffusion. We interpret that methane hydrates in thick sands are most likely formed by long range gas transport where methane gas is transported upward into the hydrate stability zone (HSZ) under buoyancy and locally forms hydrate to its stability limit. In short-range methane diffusion, methane is generated locally by biodegradation of organic matter in mud and diffused into bounding sands where it forms hydrate. We could not simulate enough methane transport by diffusion to account for its observed concentration in thick sands. In our models, we include the capillary effect on dissolved methane solubility and on the hydrate phase boundary, sedimentation and different compaction in sand and mud, fracture generation as well as the fully coupled multiphase flow and multicomponent transport. We apply our models to a 12 meter-thick hydrate-bearing sand layer at Walker Ridge 313, Northern Gulf of Mexico. With the long-range gas transport, hydrate saturation is greater than 90% and salinity is increased from seawater to about 8 wt.% through the entire sand. With short-range diffusion, hydrate saturation is more than 90% at the sand base and is less than 10% in the overlying section; salinity is close to seawater when sand is deposited to 800 meter below seafloor by short-range methane diffusion. With short-range diffusion, the amount of hydrate formed is much less than that interpreted from the well log data. Two transient gas layers separated by a hydrate layer are formed from short-range diffusion caused by capillary effect. This could be interpreted as a double bottom simulating reflector. This study provides further insights into different hydrate formation mechanisms, and could serve as a base to confirm the hydrate formation mechanism in fields.
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Non-universal tracer diffusion in crowded media of non-inert obstacles.
Ghosh, Surya K; Cherstvy, Andrey G; Metzler, Ralf
2015-01-21
We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.
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Rapid innovation diffusion in social networks.
Kreindler, Gabriel E; Young, H Peyton
2014-07-22
Social and technological innovations often spread through social networks as people respond to what their neighbors are doing. Previous research has identified specific network structures, such as local clustering, that promote rapid diffusion. Here we derive bounds that are independent of network structure and size, such that diffusion is fast whenever the payoff gain from the innovation is sufficiently high and the agents' responses are sufficiently noisy. We also provide a simple method for computing an upper bound on the expected time it takes for the innovation to become established in any finite network. For example, if agents choose log-linear responses to what their neighbors are doing, it takes on average less than 80 revision periods for the innovation to diffuse widely in any network, provided that the error rate is at least 5% and the payoff gain (relative to the status quo) is at least 150%. Qualitatively similar results hold for other smoothed best-response functions and populations that experience heterogeneous payoff shocks.
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Rapid innovation diffusion in social networks
Kreindler, Gabriel E.; Young, H. Peyton
2014-01-01
Social and technological innovations often spread through social networks as people respond to what their neighbors are doing. Previous research has identified specific network structures, such as local clustering, that promote rapid diffusion. Here we derive bounds that are independent of network structure and size, such that diffusion is fast whenever the payoff gain from the innovation is sufficiently high and the agents’ responses are sufficiently noisy. We also provide a simple method for computing an upper bound on the expected time it takes for the innovation to become established in any finite network. For example, if agents choose log-linear responses to what their neighbors are doing, it takes on average less than 80 revision periods for the innovation to diffuse widely in any network, provided that the error rate is at least 5% and the payoff gain (relative to the status quo) is at least 150%. Qualitatively similar results hold for other smoothed best-response functions and populations that experience heterogeneous payoff shocks. PMID:25024191
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Transversely bounded DFB lasers. [bounded distributed-feedback lasers
NASA Technical Reports Server (NTRS)
Elachi, C.; Evans, G.; Yeh, C.
1975-01-01
Bounded distributed-feedback (DFB) lasers are studied in detail. Threshold gain and field distribution for a number of configurations are derived and analyzed. More specifically, the thin-film guide, fiber, diffusion guide, and hollow channel with inhomogeneous-cladding DFB lasers are considered. Optimum points exist and must be used in DFB laser design. Different-modes feedback and the effects of the transverse boundaries are included. A number of applications are also discussed.
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Fisher information and Cramér-Rao lower bound for experimental design in parallel imaging.
Bouhrara, Mustapha; Spencer, Richard G
2018-06-01
The Cramér-Rao lower bound (CRLB) is widely used in the design of magnetic resonance (MR) experiments for parameter estimation. Previous work has considered only Gaussian or Rician noise distributions in this calculation. However, the noise distribution for multi-coil acquisitions, such as in parallel imaging, obeys the noncentral χ-distribution under many circumstances. The purpose of this paper is to present the CRLB calculation for parameter estimation from multi-coil acquisitions. We perform explicit calculations of Fisher matrix elements and the associated CRLB for noise distributions following the noncentral χ-distribution. The special case of diffusion kurtosis is examined as an important example. For comparison with analytic results, Monte Carlo (MC) simulations were conducted to evaluate experimental minimum standard deviations (SDs) in the estimation of diffusion kurtosis model parameters. Results were obtained for a range of signal-to-noise ratios (SNRs), and for both the conventional case of Gaussian noise distribution and noncentral χ-distribution with different numbers of coils, m. At low-to-moderate SNR, the noncentral χ-distribution deviates substantially from the Gaussian distribution. Our results indicate that this departure is more pronounced for larger values of m. As expected, the minimum SDs (i.e., CRLB) in derived diffusion kurtosis model parameters assuming a noncentral χ-distribution provided a closer match to the MC simulations as compared to the Gaussian results. Estimates of minimum variance for parameter estimation and experimental design provided by the CRLB must account for the noncentral χ-distribution of noise in multi-coil acquisitions, especially in the low-to-moderate SNR regime. Magn Reson Med 79:3249-3255, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.
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Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V
2007-04-01
During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.
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Minimal wave speed for a class of non-cooperative reaction-diffusion systems of three equations
NASA Astrophysics Data System (ADS)
Zhang, Tianran
2017-05-01
In this paper, we study the traveling wave solutions and minimal wave speed for a class of non-cooperative reaction-diffusion systems consisting of three equations. Based on the eigenvalues, a pair of upper-lower solutions connecting only the invasion-free equilibrium are constructed and the Schauder's fixed-point theorem is applied to show the existence of traveling semi-fronts for an auxiliary system. Then the existence of traveling semi-fronts of original system is obtained by limit arguments. The traveling semi-fronts are proved to connect another equilibrium if natural birth and death rates are not considered and to be persistent if these rates are incorporated. Then non-existence of bounded traveling semi-fronts is obtained by two-sided Laplace transform. Then the above results are applied to some disease-transmission models and a predator-prey model.
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Eulerian Dynamics with a Commutator Forcing
2017-01-09
SIAM Review 56(4) (2014) 577–621. [Pes2015] J. Peszek. Discrete Cucker-Smale flocking model with a weakly singular weight. SIAM J. Math . Anal., to...viscosities in bounded domains. J. Math . Pures Appl. (9), 87(2):227– 235, 2007. [CV2010] L. Caffarelli, A. Vasseur, Drift diffusion equations with...Further time regularity for fully non-linear parabolic equations. Math . Res. Lett., 22(6):1749–1766, 2015. [CCTT2016] José A. Carrillo, Young-Pil
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Mathematical Modeling of Cancer Invasion: The Role of Membrane-Bound Matrix Metalloproteinases
Deakin, Niall E.; Chaplain, Mark A. J.
2013-01-01
One of the hallmarks of cancer growth and metastatic spread is the process of local invasion of the surrounding tissue. Cancer cells achieve protease-dependent invasion by the secretion of enzymes involved in proteolysis. These overly expressed proteolytic enzymes then proceed to degrade the host tissue allowing the cancer cells to disseminate throughout the microenvironment by active migration and interaction with components of the extracellular matrix (ECM) such as collagen. In this paper we develop a mathematical model of cancer invasion which consider the role of matrix metalloproteinases (MMPs). Specifically our model will focus on two distinct types of MMP, i.e., soluble, diffusible MMPs (e.g., MMP-2) and membrane-bound MMPs (e.g., MT1-MMP), and the roles each of these plays in cancer invasion. The implications of MMP-2 activation by MMP-14 and the tissue inhibitor of metalloproteinases-2 are considered alongside the effect the architecture of the matrix may have when applied to a model of cancer invasion. Elements of the ECM architecture investigated include pore size of the matrix, since in some highly dense collagen structures such as breast tissue, the cancer cells are unable to physically fit through a porous region, and the crosslinking of collagen fibers. In this scenario, cancer cells rely on membrane-bound MMPs to forge a path through which degradation by other MMPs and movement of cancer cells becomes possible. PMID:23565505
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Azunre, P.
Here in this paper, two novel techniques for bounding the solutions of parametric weakly coupled second-order semilinear parabolic partial differential equations are developed. The first provides a theorem to construct interval bounds, while the second provides a theorem to construct lower bounds convex and upper bounds concave in the parameter. The convex/concave bounds can be significantly tighter than the interval bounds because of the wrapping effect suffered by interval analysis in dynamical systems. Both types of bounds are computationally cheap to construct, requiring solving auxiliary systems twice and four times larger than the original system, respectively. An illustrative numerical examplemore » of bound construction and use for deterministic global optimization within a simple serial branch-and-bound algorithm, implemented numerically using interval arithmetic and a generalization of McCormick's relaxation technique, is presented. Finally, problems within the important class of reaction-diffusion systems may be optimized with these tools.« less
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Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results
Anil Kumar, V.S.; Marathe, Madhav V.; Ravi, S.S.; Rosenkrantz, Daniel J.
2014-01-01
We consider the problem of inhibiting undesirable contagions (e.g. rumors, spread of mob behavior) in social networks. Much of the work in this context has been carried out under the 1-threshold model, where diffusion occurs when a node has just one neighbor with the contagion. We study the problem of inhibiting more complex contagions in social networks where nodes may have thresholds larger than 1. The goal is to minimize the propagation of the contagion by removing a small number of nodes (called critical nodes) from the network. We study several versions of this problem and prove that, in general, they cannot even be efficiently approximated to within any factor ρ ≥ 1, unless P = NP. We develop efficient and practical heuristics for these problems and carry out an experimental study of their performance on three well known social networks, namely epinions, wikipedia and slashdot. Our results show that these heuristics perform significantly better than five other known methods. We also establish an efficiently computable upper bound on the number of nodes to which a contagion can spread and evaluate this bound on many real and synthetic networks. PMID:25750583
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NASA Astrophysics Data System (ADS)
Benguria, Rafael D.; Depassier, M. Cristina; Loss, Michael
2012-12-01
We study the effect of a cutoff on the speed of pulled fronts of the one-dimensional reaction diffusion equation. To accomplish this, we first use variational techniques to prove the existence of a heteroclinic orbit in phase space for traveling wave solutions of the corresponding reaction diffusion equation under conditions that include discontinuous reaction profiles. This existence result allows us to prove rigorous upper and lower bounds on the minimal speed of monotonic fronts in terms of the cut-off parameter ɛ. From these bounds we estimate the range of validity of the Brunet-Derrida formula for a general class of reaction terms.
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Diffuse reflection from a stochastically bounded, semi-infinite medium
NASA Technical Reports Server (NTRS)
Lumme, K.; Peltoniemi, J. I.; Irvine, W. M.
1990-01-01
In order to determine the diffuse reflection from a medium bounded by a rough surface, the problem of radiative transfer in a boundary layer characterized by a statistical distribution of heights is considered. For the case that the surface is defined by a multivariate normal probability density, the propagation probability for rays traversing the boundary layer is derived and, from that probability, a corresponding radiative transfer equation. A solution of the Eddington (two stream) type is found explicitly, and examples are given. The results should be applicable to reflection from the regoliths of solar system bodies, as well as from a rough ocean surface.
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Counterion effects in protein nanoparticle electrostatic binding: a theoretical study.
Ghosh, Goutam
2015-04-01
Effects of counterions on the folding conformation of proteins, bound electrostatically on the surface of charge-ligand functionalized nanoparticles, have been investigated based on the protein folding energy calculation. The folding energy of a protein has been taken as a sum of the short range interaction energies, like, the van der Waals attraction and the hydrogen bond energies, and the long range coulomb interaction energy. On electrostatic binding, counterions associated with surface ligands of nanoparticles diffuse into bound proteins through the medium of dispersion. As a result, bound proteins partially unfold, as observed in circular dichroism experiments, which has been realized using the "charge-dipole" and the "charge-induced dipole" interactions of counterions with polar and non-polar residues, respectively. The effect of counterions solvation in the dispersing medium, e.g., water, which causes water molecules to polarize around the counterions, has also been considered. The folding energy of bound proteins has been seen to decrease proportionally with the increasing number of diffusion of counterions and their polarizability. Copyright © 2015 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Mirbagheri, Seyed Amir; Fu, Henry Chien
2016-05-01
Helicobacter pylori swims through mucus gel by generating ammonia that locally neutralizes the acidic gastric environment, turning nearby gel into a fluid pocket. The size of the fluid zone is important for determining the physics of the motility: in a large zone swimming occurs as in a fluid through hydrodynamic principles, while in a very small zone the motility could be strongly influenced by nonhydrodynamic cell-mucus interactions including chemistry and adhesion. Here, we calculate the size of the fluid pocket. We model how swimming depends on the de-gelation range using a Taylor sheet swimming through a layer of Newtonian fluid bounded by a Brinkman fluid. Then, we model how the de-gelation range depends on the swimming speed by considering the advection-diffusion of ammonia exuded from a translating sphere. Self-consistency between both models determines the values of the swimming speed and the de-gelation range. We find that H. pylori swims through mucus as if unconfined, in a large pocket of Newtonian fluid.
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A CTRW-based model of time-resolved fluorescence lifetime imaging in a turbid medium
NASA Astrophysics Data System (ADS)
Chernomordik, Victor; Gandjbakhche, Amir H.; Hassan, Moinuddin; Pajevic, Sinisa; Weiss, George H.
2010-12-01
We develop an analytic model of time-resolved fluorescent imaging of photons migrating through a semi-infinite turbid medium bounded by an infinite plane in the presence of a single stationary point fluorophore embedded in the medium. In contrast to earlier models of fluorescent imaging in which photon motion is assumed to be some form of continuous diffusion process, the present analysis is based on a continuous-time random walk (CTRW) on a simple cubic lattice, the objective being to estimate the position and lifetime of the fluorophore. This can provide information related to local variations in pH and temperature with potential medical significance. Aspects of the theory were tested using time-resolved measurements of the fluorescence from small inclusions inside tissue-like phantoms. The experimental results were found to be in good agreement with theoretical predictions provided that the fluorophore was not located too close to the planar boundary, a common problem in many diffusive systems.
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Cornelisse, C J; Hermens, W T; Joe, M T; Duijndam, W A; van Duijn, P
1976-11-01
A numerical method was developed for computing the steady-state concentration gradient of a diffusible enzyme reaction product in a membrane-limited compartment of a simplified theoretical cell model. In cytochemical enzyme reactions proceeding according to the metal-capture principle, the local concentration of the primary reaction product is an important factor in the onset of the precipitation process and in the distribution of the final reaction product. The following variables were incorporated into the model: enzyme activity, substrate concentration, Km, diffusion coefficient of substrate and product, particle radius and cell radius. The method was applied to lysosomal acid phosphatase. Numerical values for the variables were estimated from experimental data in the literature. The results show that the calculated phosphate concentrations inside lysosomes are several orders of magnitude lower than the critical concentrations for efficient phosphate capture found in a previous experimental model study. Reasons for this apparent discrepancy are discussed.
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Xu, Jianqiao; Huang, Shuyao; Jiang, Ruifen; Cui, Shufen; Luan, Tiangang; Chen, Guosheng; Qiu, Junlang; Cao, Chenyang; Zhu, Fang; Ouyang, Gangfeng
2016-04-21
Elucidating the availability of the bound analytes for the mass transfer through the diffusion boundary layers (DBLs) adjacent to passive samplers is important for understanding the passive sampling kinetics in complex samples, in which the lability factor of the bound analyte in the DBL is an important parameter. In this study, the mathematical expression of lability factor was deduced by assuming a pseudo-steady state during passive sampling, and the equation indicated that the lability factor was equal to the ratio of normalized concentration gradients between the bound and free analytes. Through the introduction of the mathematical expression of lability factor, the modified effective average diffusion coefficient was proven to be more suitable for describing the passive sampling kinetics in the presence of mobile binding matrixes. Thereafter, the lability factors of the bound polycyclic aromatic hydrocarbons (PAHs) with sodium dodecylsulphate (SDS) micelles as the binding matrixes were figured out according to the improved theory. The lability factors were observed to decrease with larger binding ratios and smaller micelle sizes, and were successfully used to predict the mass transfer efficiencies of PAHs through DBLs. This study would promote the understanding of the availability of bound analytes for passive sampling based on the theoretical improvements and experimental assessments. Copyright © 2016 Elsevier B.V. All rights reserved.
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White, Paul B; Wang, Tuo; Park, Yong Bum; Cosgrove, Daniel J; Hong, Mei
2014-07-23
Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water (1)H polarization to polysaccharides through distance- and mobility-dependent (1)H-(1)H dipolar couplings and detecting it through polysaccharide (13)C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water-pectin polarization transfer is much faster than water-cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water-polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water-pectin spin diffusion precedes water-cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.
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Arabidopsis thalianafrom Polarization Transfer Solid-State NMR
DOE Office of Scientific and Technical Information (OSTI.GOV)
White, Paul B; Wang, Tuo; Park, Yong Bum
2014-07-23
Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water 1H polarization to polysaccharides through distance- and mobility-dependent 1H–1H dipolar couplings and detecting it through polysaccharide 13C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water–pectin polarizationmore » transfer is much faster than water–cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water–polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water–pectin spin diffusion precedes water–cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.« less
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Using a model comparison approach to describe the assembly pathway for histone H1
Contreras, Carlos; Villasana, Minaya; Hendzel, Michael J.
2018-01-01
Histones H1 or linker histones are highly dynamic proteins that diffuse throughout the cell nucleus and associate with chromatin (DNA and associated proteins). This binding interaction of histone H1 with the chromatin is thought to regulate chromatin organization and DNA accessibility to transcription factors and has been proven to involve a kinetic process characterized by a population that associates weakly with chromatin and rapidly dissociates and another population that resides at a binding site for up to several minutes before dissociating. When considering differences between these two classes of interactions in a mathematical model for the purpose of describing and quantifying the dynamics of histone H1, it becomes apparent that there could be several assembly pathways that explain the kinetic data obtained in living cells. In this work, we model these different pathways using systems of reaction-diffusion equations and carry out a model comparison analysis using FRAP (fluorescence recovery after photobleaching) experimental data from different histone H1 variants to determine the most feasible mechanism to explain histone H1 binding to chromatin. The analysis favors four different chromatin assembly pathways for histone H1 which share common features and provide meaningful biological information on histone H1 dynamics. We show, using perturbation analysis, that the explicit consideration of high- and low-affinity associations of histone H1 with chromatin in the favored assembly pathways improves the interpretation of histone H1 experimental FRAP data. To illustrate the results, we use one of the favored models to assess the kinetic changes of histone H1 after core histone hyperacetylation, and conclude that this post-transcriptional modification does not affect significantly the transition of histone H1 from a weakly bound state to a tightly bound state. PMID:29352283
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Strange, Richard W; Hough, Michael A; Antonyuk, Svetlana V; Hasnain, S Samar
2012-01-01
Copper-zinc superoxide dismutase (SOD) is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O(2) and H(2)O(2). SOD also reacts with H(2)O(2), leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO(2)) and H(2)O(2), this peroxidase activity is enhanced and produces the carbonate radical. This freely diffusible reactive oxygen species is proposed as the agent for oxidation of large substrates that are too bulky to enter the active site. Here, we provide direct structural evidence, from a 2.15 Å resolution crystal structure, of (bi)carbonate captured at the active site of reduced SOD, consistent with the view that a bound carbonate intermediate could be formed, producing a diffusible carbonate radical upon reoxidation of copper. The bound carbonate blocks direct access of substrates to Cu(I), suggesting that an adjunct to the accepted mechanism of SOD catalysed dismutation of superoxide operates, with Cu(I) oxidation by superoxide being driven via a proton-coupled electron transfer mechanism involving the bound carbonate rather than the solvent. Carbonate is captured in a different site when SOD is oxidised, being located in the active site channel adjacent to the catalytically important Arg143. This is the probable route of diffusion from the active site following reoxidation of the copper. In this position, the carbonate is poised for re-entry into the active site and binding to the reduced copper.
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Strange, Richard W.; Hough, Michael A.; Antonyuk, Svetlana V.; Hasnain, S. Samar
2012-01-01
Copper-zinc superoxide dismutase (SOD) is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O2 and H2O2. SOD also reacts with H2O2, leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO2) and H2O2, this peroxidase activity is enhanced and produces the carbonate radical. This freely diffusible reactive oxygen species is proposed as the agent for oxidation of large substrates that are too bulky to enter the active site. Here, we provide direct structural evidence, from a 2.15 Å resolution crystal structure, of (bi)carbonate captured at the active site of reduced SOD, consistent with the view that a bound carbonate intermediate could be formed, producing a diffusible carbonate radical upon reoxidation of copper. The bound carbonate blocks direct access of substrates to Cu(I), suggesting that an adjunct to the accepted mechanism of SOD catalysed dismutation of superoxide operates, with Cu(I) oxidation by superoxide being driven via a proton-coupled electron transfer mechanism involving the bound carbonate rather than the solvent. Carbonate is captured in a different site when SOD is oxidised, being located in the active site channel adjacent to the catalytically important Arg143. This is the probable route of diffusion from the active site following reoxidation of the copper. In this position, the carbonate is poised for re-entry into the active site and binding to the reduced copper. PMID:22984565
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Cs-137 immobilization in C-S-H gel nanopores.
Duque-Redondo, Eduardo; Kazuo, Yamada; López-Arbeloa, Iñigo; Manzano, Hegoi
2018-04-04
Cementation is a widespread technique to immobilize nuclear waste due to the low leachability of cementitious materials. The capacity of calcium silicate hydrate (C-S-H), the main component of cement, to retain radionuclide Cs has been empirically studied at the macroscale, yet the specific molecular scale mechanisms that govern the retention have not been determined. In this work, we employed molecular dynamics simulations to investigate the adsorption and diffusivity of Cs into a C-S-H gel nanopore. From the simulations, it was possible to distinguish three types of Cs adsorption configurations on the C-S-H: an inner-sphere surface site where Cs is strongly bound, an outer-sphere surface site where Cs is loosely bound, and Cs free in the nanopore. For each configuration, we determined the sorption energy, and the diffusion coefficients, up to two orders of magnitude lower than in bulk water due to the effect of nanoconfinement in the worst case scenario. It has also proved that Cs cannot displace the intrinsic Ca from the C-S-H surface, and we calculated the binding strength and the residence time of the cations in the surface adsorption sites. Finally, we quantified the average number of adsorption sites per nm2 of the C-S-H surface. All these results are the first insights into Cs retention in cement at the molecular scale and will be useful to build macroscopic diffusion models and devise cement formulations to improve radionuclide Cs retention from spent nuclear fuel.
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Conditions for supersonic bent Marshak waves
DOE Office of Scientific and Technical Information (OSTI.GOV)
Xu, Qiang, E-mail: xuqiangxu@pku.edu.cn; Ren, Xiao-dong; Li, Jing
Supersonic radiation diffusion approximation is an useful method to study the radiation transportation. Considering the 2-d Marshak theory, and an invariable source temperature, conditions for supersonic radiation diffusion are proved to be coincident with that for radiant flux domination in the early time when √(ε)x{sub f}/L≪1. However, they are even tighter than conditions for radiant flux domination in the late time when √(ε)x{sub f}/L≫1, and can be expressed as M>4(1+ε/3)/3 and τ>1. A large Mach number requires the high temperature, while the large optical depth requires the low temperature. Only when the source temperature is in a proper region themore » supersonic diffusion conditions can be satisfied. Assuming a power-low (in temperature and density) opacity and internal energy, for a given density, the supersonic diffusion regions are given theoretically. The 2-d Marshak theory is proved to be able to bound the supersonic diffusion conditions in both high and low temperature regions, however, the 1-d theory only bounds it in low temperature region. Taking SiO{sub 2} and the Au, for example, these supersonic regions are shown numerically.« less
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A nonlocal spatial model for Lyme disease
NASA Astrophysics Data System (ADS)
Yu, Xiao; Zhao, Xiao-Qiang
2016-07-01
This paper is devoted to the study of a nonlocal and time-delayed reaction-diffusion model for Lyme disease with a spatially heterogeneous structure. In the case of a bounded domain, we first prove the existence of the positive steady state and a threshold type result for the disease-free system, and then establish the global dynamics for the model system in terms of the basic reproduction number. In the case of an unbound domain, we obtain the existence of the disease spreading speed and its coincidence with the minimal wave speed. At last, we use numerical simulations to verify our analytic results and investigate the influence of model parameters and spatial heterogeneity on the disease infection risk.
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Correction of spin diffusion during iterative automated NOE assignment
NASA Astrophysics Data System (ADS)
Linge, Jens P.; Habeck, Michael; Rieping, Wolfgang; Nilges, Michael
2004-04-01
Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus β-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.
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A simple model for closure temperature of a trace element in cooling bi-mineralic systems
NASA Astrophysics Data System (ADS)
Liang, Yan
2015-09-01
Closure temperature is defined as the lower temperature limit at which the element of interest effectively ceases diffusive exchange with its surrounding medium during cooling. Here we generalize the classic equation of Dodson (1973) for cooling mono-mineralic systems to cooling bi-mineralic aggregates by considering diffusive exchange of a trace element between the two minerals in a closed system. We present a simple analytical model that includes key parameters affecting the closure temperature of a trace element in cooling bi-mineralic systems: cooling rate, temperature-dependent diffusion coefficients for the trace element in the two minerals, temperature-dependent partition coefficient of the trace element between the two minerals, effective grain sizes of the two minerals, and volume proportions of the minerals in the system. We show that closure temperatures of a trace element in cooling bi-mineralic systems are bounded by the closure temperatures of the trace element in the two mono-mineralic systems and that our generalized model reduces to Dodson's equation when one of the mineral serves as "an effective infinite" reservoir to the other mineral. Application to closure temperatures of REE in orthopyroxene and clinopyroxene bi-mineralic systems highlights the importance of REE diffusion and partitioning in the pyroxenes as well as clinopyroxene modal abundance and grain size in the systems. Closure temperatures for REE in two-pyroxene bearing equigranular rocks are controlled primarily by diffusion in orthopyroxene unless the modal abundance of clinopyroxene is very small. This has important bearings on the interpretation of temperatures derived from the REE-in-two-pyroxene thermometer.
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Greathouse, Jeffery A.; Hart, David; Bowers, Geoffrey M.; ...
2015-07-20
In geologic settings relevant to a number of extraction and potential sequestration processes, nanopores bounded by clay mineral surfaces play a critical role in the transport of aqueous species. Solution structure and dynamics at clay–water interfaces are quite different from their bulk values, and the spatial extent of this disruption remains a topic of current interest. We have used molecular dynamics simulations to investigate the structure and diffusion of aqueous solutions in clay nanopores approximately 6 nm thick, comparing the effect of clay composition with model Na-hectorite and Na-montmorillonite surfaces. In addition to structural properties at the interface, water andmore » ion diffusion coefficients were calculated within each aqueous layer at the interface, as well as in the central bulk-like region of the nanopore. The results show similar solution structure and diffusion properties at each surface, with subtle differences in sodium adsorption complexes and water structure in the first adsorbed layer due to different arrangements of layer hydroxyl groups in the two clay models. Interestingly, the extent of surface disruption on bulk-like solution structure and diffusion extends to only a few water layers. Additionally, a comparison of sodium ion residence times confirms similar behavior of inner-sphere and outer-sphere surface complexes at each clay surface, but ~1% of sodium ions adsorb in ditrigonal cavities on the hectorite surface. Thus, the presence of these anhydrous ions is consistent with highly immobile anhydrous ions seen in previous nuclear magnetic resonance spectroscopic measurements of hectorite pastes.« less
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A potential-energy surface study of the 2A1 and low-lying dissociative states of the methoxy radical
NASA Technical Reports Server (NTRS)
Jackels, C. F.
1985-01-01
Accurate, ab initio quantum chemical techniques are applied in the present study of low lying bound and dissociative states of the methoxy radical at C3nu conformations, using a double zeta quality basis set that is augmented with polarization and diffuse functions. Excitation energy estimates are obtained for vertical excitation, vertical deexcitation, and system origin. The rate of methoxy photolysis is estimated to be too small to warrant its inclusion in atmospheric models.
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Azunre, P.
2016-09-21
Here in this paper, two novel techniques for bounding the solutions of parametric weakly coupled second-order semilinear parabolic partial differential equations are developed. The first provides a theorem to construct interval bounds, while the second provides a theorem to construct lower bounds convex and upper bounds concave in the parameter. The convex/concave bounds can be significantly tighter than the interval bounds because of the wrapping effect suffered by interval analysis in dynamical systems. Both types of bounds are computationally cheap to construct, requiring solving auxiliary systems twice and four times larger than the original system, respectively. An illustrative numerical examplemore » of bound construction and use for deterministic global optimization within a simple serial branch-and-bound algorithm, implemented numerically using interval arithmetic and a generalization of McCormick's relaxation technique, is presented. Finally, problems within the important class of reaction-diffusion systems may be optimized with these tools.« less
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Semistable extremal ground states for nonlinear evolution equations in unbounded domains
NASA Astrophysics Data System (ADS)
Rodríguez-Bernal, Aníbal; Vidal-López, Alejandro
2008-02-01
In this paper we show that dissipative reaction-diffusion equations in unbounded domains posses extremal semistable ground states equilibria, which bound asymptotically the global dynamics. Uniqueness of such positive ground state and their approximation by extremal equilibria in bounded domains is also studied. The results are then applied to the important case of logistic equations.
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NASA Technical Reports Server (NTRS)
Beckman, J. E.; Rozas, M.; Zurita, A.; Watson, R. A.; Knapen, J. H.
2000-01-01
In this paper we present evidence that the H II regions of high luminosity in disk galaxies may be density bounded, so that a significant fraction of the ionizing photons emitted by their exciting OB stars escape from the regions. The key piece of evidence is the presence, in the Ha luminosity functions (LFs) of the populations of H iI regions, of glitches, local sharp peaks at an apparently invariant luminosity, defined as the Stromgren luminosity Lstr), LH(sub alpha) = Lstr = 10(sup 38.6) (+/- 10(sup 0.1)) erg/ s (no other peaks are found in any of the LFs) accompanying a steepening of slope for LH(sub alpha) greater than Lstr This behavior is readily explicable via a physical model whose basic premises are: (a) the transition at LH(sub alpha) = Lstr marks a change from essentially ionization bounding at low luminosities to density bounding at higher values, (b) for this to occur the law relating stellar mass in massive star-forming clouds to the mass of the placental cloud must be such that the ionizing photon flux produced within the cloud is a function which rises more steeply than the mass of the cloud. Supporting evidence for the hypothesis of this transition is also presented: measurements of the central surface brightnesses of H II regions for LH(sub alpha) less than Lstr are proportional to L(sup 1/3, sub H(sub alpha)), expected for ionization bounding, but show a sharp trend to a steeper dependence for LH(sub alpha) greater than Lstr, and the observed relation between the internal turbulence velocity parameter, sigma, and the luminosity, L, at high luminosities, can be well explained if these regions are density bounded. If confirmed, the density-bounding hypothesis would have a number of interesting implications. It would imply that the density-bounded regions were the main sources of the photons which ionize the diffuse gas in disk galaxies. Our estimates, based on the hypothesis, indicate that these regions emit sufficient Lyman continuum not only to ionize the diffuse medium, but to cause a typical spiral to emit significant ionizing flux into the intergalactic medium. The low scatter observed in Lstr, less than 0.1 mag rms in the still quite small sample measured to date, is an invitation to widen the data base, and to calibrate against primary standards, with the aim of obtaining a precise, approx. 10(exp 5) solar luminosity widely distributed standard candle.
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NASA Astrophysics Data System (ADS)
Adolph, A. C.; Albert, M. R.
2014-02-01
The physical structure of polar firn plays a key role in the mechanisms by which glaciers and ice sheets preserve a natural archive of past atmospheric composition. This study presents the first measurements of gas diffusivity and permeability along with microstructural information measured from the near-surface firn through the firn column to pore close-off. Both fine- and coarse-grained firn from Summit, Greenland are included in this study to investigate the variability in firn caused by seasonal and storm-event layering. Our measurements reveal that the porosity of firn (derived from density) is insufficient to describe the full profiles of diffusivity and permeability, particularly at porosity values above 0.5. Thus, even a model that could perfectly predict the density profile would be insufficient for application to issues involving gas transport. The measured diffusivity profile presented here is compared to two diffusivity profiles modeled from firn air measurements from Summit. Because of differences in scale and in firn processes between the true field situation, firn modeling, and laboratory measurements, the results follow a similar overall pattern but do not align; our results constitute a lower bound on diffusive transport. In comparing our measurements of both diffusivity and permeability to previous parameterizations from numerical 3-D lattice-Boltzmann modeling, it is evident that the previous relationships to porosity are likely site-specific. We present parameterizations relating diffusivity and permeability to porosity as a possible tool, though use of direct measurements would be far more accurate when feasible. The relationships between gas transport properties and microstructural properties are characterized and compared to existing relationships for general porous media, specifically the Katz-Thompson (KT), Kozeny-Carman (KC), and Archie's law approximations. While those approximations can capture the general trend of gas transport relationships, they result in high errors for individual samples and fail to fully describe firn variability, particularly the differences between coarse- and fine-grained firn. We present a direct power law relationship between permeability and gas diffusivity based on our co-located measurements; further research will indicate if this type of relationship is site-specific. This set of measurements and relationships contributes a unique starting point for future investigations in developing more physically based models of firn gas transport.
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NASA Astrophysics Data System (ADS)
Sobol, Emil N.; Kitai, Moishe S.; Jones, Nicholas; Sviridov, Alexander P.; Milner, Thomas E.; Wong, Brian
1998-05-01
We develop a theoretical model to calculate the temperature field and the size of modified structure area in cartilaginous tissue. The model incorporates both thermal and mass transfer in a tissue regarding bulk absorption of laser radiation, water evaporation from a surface and temperature dependence of diffusion coefficient. It is proposed that due to bound- to free-phase transition of water in cartilage heated to about 70 degrees Celsius, some parts of cartilage matrix (proteoglycan units) became more mobile. The movement of these units takes place only when temperature exceed 70 degrees Celsius and results in alteration of tissue structure (denaturation). It is shown that (1) the maximal temperature is reached not on the surface irradiated at some distance from the surface; (2) surface temperature reaches a plateau quicker that the maximal temperature; (3) the depth of denatured area strongly depends on laser fluence and wavelength, exposure time and thickness of cartilage. The model allows to predict and control temperature and depth of structure alterations in the course of laser reshaping and treatment of cartilage.
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NASA Astrophysics Data System (ADS)
Macías-Díaz, J. E.
In the present manuscript, we introduce a finite-difference scheme to approximate solutions of the two-dimensional version of Fisher's equation from population dynamics, which is a model for which the existence of traveling-wave fronts bounded within (0,1) is a well-known fact. The method presented here is a nonstandard technique which, in the linear regime, approximates the solutions of the original model with a consistency of second order in space and first order in time. The theory of M-matrices is employed here in order to elucidate conditions under which the method is able to preserve the positivity and the boundedness of solutions. In fact, our main result establishes relatively flexible conditions under which the preservation of the positivity and the boundedness of new approximations is guaranteed. Some simulations of the propagation of a traveling-wave solution confirm the analytical results derived in this work; moreover, the experiments evince a good agreement between the numerical result and the analytical solutions.
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Methane mobility in carbon nanotubes
NASA Astrophysics Data System (ADS)
Bienfait, M.; Asmussen, B.; Johnson, M.; Zeppenfeld, P.
2000-07-01
Quasi-elastic neutron scattering has been used to characterize the diffusivity of CH 4 molecules condensed in single-wall carbon nanotubes. It is shown that the two sites of adsorption, previously observed by adsorption volumetry and calorimetry measurements, correspond to a solid-like phase for the more strongly bound site at T<120 K and to a liquid-like component for the more weakly bound site at 70< T<120 K. The diffusion coefficients of the mobile molecules range between 3×10 -7 to 15×10 -7 cm 2 s -1. The fraction of this viscous liquid diminishes as the temperature is decreased; the adsorbate is fully solidified at 50 K and below.
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A General Model for Estimating Macroevolutionary Landscapes.
Boucher, Florian C; Démery, Vincent; Conti, Elena; Harmon, Luke J; Uyeda, Josef
2018-03-01
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].
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NASA Astrophysics Data System (ADS)
Schorghofer, Norbert
2015-05-01
On the Moon, water molecules and other volatiles are thought to migrate along ballistic trajectories. Here, this migration process is described in terms of a two-dimensional partial differential equation for the surface concentration, based on the probability distribution of thermal ballistic hops. A random-walk model, a corresponding diffusion coefficient, and a continuum description are provided. In other words, a surface-bounded exosphere is described purely in terms of quantities on the surface, which can provide computational and conceptual advantages. The derived continuum equation can be used to calculate the steady-state distribution of the surface concentration of volatile water molecules. An analytic steady-state solution is obtained for an equatorial ring; it reveals the width and mass of the pileup of molecules at the morning terminator.
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A computer program for the simulation of heat and moisture flow in soils
NASA Technical Reports Server (NTRS)
Camillo, P.; Schmugge, T. J.
1981-01-01
A computer program that simulates the flow of heat and moisture in soils is described. The space-time dependence of temperature and moisture content is described by a set of diffusion-type partial differential equations. The simulator uses a predictor/corrector to numerically integrate them, giving wetness and temperature profiles as a function of time. The simulator was used to generate solutions to diffusion-type partial differential equations for which analytical solutions are known. These equations include both constant and variable diffusivities, and both flux and constant concentration boundary conditions. In all cases, the simulated and analytic solutions agreed to within the error bounds which were imposed on the integrator. Simulations of heat and moisture flow under actual field conditions were also performed. Ground truth data were used for the boundary conditions and soil transport properties. The qualitative agreement between simulated and measured profiles is an indication that the model equations are reasonably accurate representations of the physical processes involved.
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New Models for Velocity/Pressure-Gradient Correlations in Turbulent Boundary Layers
NASA Astrophysics Data System (ADS)
Poroseva, Svetlana; Murman, Scott
2014-11-01
To improve the performance of Reynolds-Averaged Navier-Stokes (RANS) turbulence models, one has to improve the accuracy of models for three physical processes: turbulent diffusion, interaction of turbulent pressure and velocity fluctuation fields, and dissipative processes. The accuracy of modeling the turbulent diffusion depends on the order of a statistical closure chosen as a basis for a RANS model. When the Gram-Charlier series expansions for the velocity correlations are used to close the set of RANS equations, no assumption on Gaussian turbulence is invoked and no unknown model coefficients are introduced into the modeled equations. In such a way, this closure procedure reduces the modeling uncertainty of fourth-order RANS (FORANS) closures. Experimental and direct numerical simulation data confirmed the validity of using the Gram-Charlier series expansions in various flows including boundary layers. We will address modeling the velocity/pressure-gradient correlations. New linear models will be introduced for the second- and higher-order correlations applicable to two-dimensional incompressible wall-bounded flows. Results of models' validation with DNS data in a channel flow and in a zero-pressure gradient boundary layer over a flat plate will be demonstrated. A part of the material is based upon work supported by NASA under award NNX12AJ61A.
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Ono, Jun; Takahashi, Daisuke; Guo, Xinyu; Takahashi, Shin; Takeoka, Hidetaka
2012-10-01
A three-dimensional/high-resolution transport model for persistent organic pollutants (POPs) has been developed for the East China Sea (ECS). The POPs model has four compartments (gaseous, dissolved, phytoplankton-bound, and detritus-bound phases) and includes processes for diffusive air-water exchange, phytoplankton uptake/depuration to POPs, decomposition of dissolved phase, vertical sinking of phytoplankton, detritus production by phytoplankton mortality, and vertical sinking and decomposition of detritus. The POPs model is coupled with an ocean circulation model that can reproduce the seasonal variation in physical variables to represent the advection and diffusion of POPs. We applied the POPs model to the polychlorinated biphenyl congener 153 (PCB 153) from the atmosphere and examined the behavior of PCB 153 in the ocean. The model showed a remarkable seasonal variability of PCB 153. Concentrations in the dissolved and particulate phases are high in winter (January-March) and low in summer (July-September). In coastal regions, where chlorophyll a concentration is high, horizontal and vertical distributions in the dissolved and particulate PCB 153 concentrations are strongly affected by phytoplankton uptake. The sensitivity experiments on the dynamics of PCB 153 suggested that a change of Henry's law constant associated with water temperature is the major factor controlling the seasonal variability of PCB 153. The model-based yearly mass balance of PCB 153 in the ECS indicated that most of the atmospheric input (35.5 kg year(-1)) is removed by the horizontal advection outside the ECS (19.0 kg year(-1)) and accumulates to the sea bottom by vertical sinking (15.7 kg year(-1)). For comparison with PCB 153, we also conducted simulations for PCB 52, 101, and 180. The seasonal variations are similar to that of PCB 153. The mass balance of PCB 52 that has short half-life time and less hydrophobic property shows the different results compared with PCB 101, 153, and 180. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Akan, Ozgur B.
2018-01-01
We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics. PMID:29415019
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Kuscu, Murat; Akan, Ozgur B
2018-01-01
We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.
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Marcello, Marco
2016-01-01
The range of biological outcomes generated by many signalling proteins in development and homeostasis is increased by their interactions with glycosaminoglycans, particularly heparan sulfate (HS). This interaction controls the localization and movement of these signalling proteins, but whether such control depends on the specificity of the interactions is not known. We used five fibroblast growth factors with an N-terminal HaloTag (Halo-FGFs) for fluorescent labelling, with well-characterized and distinct HS-binding properties, and measured their binding and diffusion in pericellular matrix of fixed rat mammary 27 fibroblasts. Halo-FGF1, Halo-FGF2 and Halo-FGF6 bound to HS, whereas Halo-FGF10 also interacted with chondroitin sulfate/dermatan sulfate, and FGF20 did not bind detectably. The distribution of bound FGFs in the pericellular matrix was not homogeneous, and for FGF10 exhibited striking clusters. Fluorescence recovery after photobleaching showed that FGF2 and FGF6 diffused faster, whereas FGF1 diffused more slowly, and FGF10 was immobile. The results demonstrate that the specificity of the interactions of proteins with glycosaminoglycans controls their binding and diffusion. Moreover, cells regulate the spatial distribution of different protein-binding sites in glycosaminoglycans independently of each other, implying that the extracellular matrix has long-range structure. PMID:27009190
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Dynamics of embedded curves by doubly-nonlocal reaction-diffusion systems
NASA Astrophysics Data System (ADS)
von Brecht, James H.; Blair, Ryan
2017-11-01
We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically motivated energetic models in terms of more classical, combinatorial measures of complexity for embedded curves. This line of investigation culminates in a family of complexity bounds that relate a rather broad class of models to a generalized, or weighted, variant of the crossing number. Our dynamic results include global well-posedness of the associated partial differential equations, regularity of equilibria for these flows as well as a more detailed investigation of dynamics near such equilibria. Finally, we explore a few global dynamical properties of these models numerically.
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A Role for the Juxtamembrane Cytoplasm in the Molecular Dynamics of Focal Adhesions
Wolfenson, Haguy; Lubelski, Ariel; Regev, Tamar; Klafter, Joseph; Henis, Yoav I.; Geiger, Benjamin
2009-01-01
Focal adhesions (FAs) are specialized membrane-associated multi-protein complexes that link the cell to the extracellular matrix and play crucial roles in cell-matrix sensing. Considerable information is available on the complex molecular composition of these sites, yet the regulation of FA dynamics is largely unknown. Based on a combination of FRAP studies in live cells, with in silico simulations and mathematical modeling, we show that the FA plaque proteins paxillin and vinculin exist in four dynamic states: an immobile FA-bound fraction, an FA-associated fraction undergoing exchange, a juxtamembrane fraction experiencing attenuated diffusion, and a fast-diffusing cytoplasmic pool. The juxtamembrane region surrounding FAs displays a gradient of FA plaque proteins with respect to both concentration and dynamics. Based on these findings, we propose a new model for the regulation of FA dynamics in which this juxtamembrane domain acts as an intermediary layer, enabling an efficient regulation of FA formation and reorganization. PMID:19172999
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NASA Astrophysics Data System (ADS)
Fu, Henry; Mirbagheri, Seyed Amir
2016-11-01
Helicobacter pylori swims through mucus gel by generating ammonia that locally neutralizes the acidic gastric environment, turning nearby gel into a fluid pocket. The size of the fluid zone is important for determining the physics of the motility: in a large zone swimming occurs as in a fluid through hydrodynamic principles, while in a very small zone the motility could be strongly influenced by nonhydrodynamic cell-mucus interactions including chemistry and adhesion. We calculate the size of the fluid pocket. We model how swimming depends on the de-gelation range using a Taylor sheet swimming through a layer of Newtonian fluid bounded by a Brinkman fluid. Then, we model how the de-gelation range depends on the swimming speed by considering the advection-diffusion of ammonia exuded from a translating sphere. Self-consistency between both models determines the values of the swimming speed and the de-gelation range. We find that H. pylori swims through mucus as if unconfined, in a large pocket of Newtonian fluid. Funded by National Science Foundation award CBET-1252182.
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Andrews, Steven S
2017-03-01
Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface. Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org . steven.s.andrews@gmail.com. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
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Butyrophenone on O-TiO2(110): one-dimensional motion in a weakly confined potential well.
Jensen, Stephen C; Shank, Alex; Madix, Robert J; Friend, Cynthia M
2012-04-24
We demonstrate the one-dimensional confinement of weakly bound butyrophenone molecules between strongly bound complexes formed via reaction with oxygen on TiO(2)(110). Butyrophenone weakly bound to Ti rows through the carbonyl oxygen diffuses freely in one dimension along the rows even at 55 K, persisting for many minutes before hopping out of the 1-D well. Quantitative analysis yields an estimate of the migration barrier of 0.11 eV and a frequency factor of 6.5 × 10(9) Hz. These studies demonstrate that weakly bound organic molecules can be confined on a surface by creating molecular barriers, potentially altering their assembly.
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Comparison of Turbulent Thermal Diffusivity and Scalar Variance Models
NASA Technical Reports Server (NTRS)
Yoder, Dennis A.
2016-01-01
In this study, several variable turbulent Prandtl number formulations are examined for boundary layers, pipe flow, and axisymmetric jets. The model formulations include simple algebraic relations between the thermal diffusivity and turbulent viscosity as well as more complex models that solve transport equations for the thermal variance and its dissipation rate. Results are compared with available data for wall heat transfer and profile measurements of mean temperature, the root-mean-square (RMS) fluctuating temperature, turbulent heat flux and turbulent Prandtl number. For wall-bounded problems, the algebraic models are found to best predict the rise in turbulent Prandtl number near the wall as well as the log-layer temperature profile, while the thermal variance models provide a good representation of the RMS temperature fluctuations. In jet flows, the algebraic models provide no benefit over a constant turbulent Prandtl number approach. Application of the thermal variance models finds that some significantly overpredict the temperature variance in the plume and most underpredict the thermal growth rate of the jet. The models yield very similar fluctuating temperature intensities in jets from straight pipes and smooth contraction nozzles, in contrast to data that indicate the latter should have noticeably higher values. For the particular low subsonic heated jet cases examined, changes in the turbulent Prandtl number had no effect on the centerline velocity decay.
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Numerical Solution of Time-Dependent Problems with a Fractional-Power Elliptic Operator
NASA Astrophysics Data System (ADS)
Vabishchevich, P. N.
2018-03-01
A time-dependent problem in a bounded domain for a fractional diffusion equation is considered. The first-order evolution equation involves a fractional-power second-order elliptic operator with Robin boundary conditions. A finite-element spatial approximation with an additive approximation of the operator of the problem is used. The time approximation is based on a vector scheme. The transition to a new time level is ensured by solving a sequence of standard elliptic boundary value problems. Numerical results obtained for a two-dimensional model problem are presented.
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Flow of chemically reactive magneto Cross nanoliquid with temperature-dependent conductivity
NASA Astrophysics Data System (ADS)
Hayat, Tasawar; Ullah, Ikram; Waqas, Muhammad; Alsaedi, Ahmed
2018-05-01
Influence of temperature-dependent thermal conductivity on MHD flow of Cross nanoliquid bounded by a stretched sheet is explored. The combined feature of Brownian motion and thermophoresis in nanoliquid modeling is retained. In addition, the attributes of zero mass flux at sheet are imposed. First-order chemical reaction is retained. The resulting problems are numerically computed. Plots and tabulated values are presented and examined. It is figured out that larger thermophoretic diffusion and thermal conductivity significantly rise the thermal field, whereas opposite situation is seen for heat transfer rate.
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A stochastic diffusion process for Lochner's generalized Dirichlet distribution
Bakosi, J.; Ristorcelli, J. R.
2013-10-01
The method of potential solutions of Fokker-Planck equations is used to develop a transport equation for the joint probability of N stochastic variables with Lochner’s generalized Dirichlet distribution as its asymptotic solution. Individual samples of a discrete ensemble, obtained from the system of stochastic differential equations, equivalent to the Fokker-Planck equation developed here, satisfy a unit-sum constraint at all times and ensure a bounded sample space, similarly to the process developed in for the Dirichlet distribution. Consequently, the generalized Dirichlet diffusion process may be used to represent realizations of a fluctuating ensemble of N variables subject to a conservation principle.more » Compared to the Dirichlet distribution and process, the additional parameters of the generalized Dirichlet distribution allow a more general class of physical processes to be modeled with a more general covariance matrix.« less
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Reaction rates for a generalized reaction-diffusion master equation
Hellander, Stefan; Petzold, Linda
2016-01-19
It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show inmore » two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules.« less
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Reaction rates for a generalized reaction-diffusion master equation
Hellander, Stefan; Petzold, Linda
2016-01-01
It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show in two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules. PMID:26871190
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Transient response in granular bounded heap flows
NASA Astrophysics Data System (ADS)
Xiao, Hongyi; Ottino, Julio M.; Lueptow, Richard M.; Umbanhowar, Paul B.
2017-11-01
Heap formation, a canonical granular flow, is common in industry and is also found in nature. Here, we study the transition between steady flow states in quasi-2D bounded heaps by suddenly changing the feed rate from one fixed value to another. During the transition, in both experiments and discrete element method simulations, an additional wedge of flowing particles propagates over the rising free surface. The downstream edge of the wedge - the wedge front - moves downstream with velocity inversely proportional to the square root of time. An additional longer duration transient process continues after the wedge front reaches the downstream wall. The transient flux profile during the entire transition is well modeled by a diffusion-like equation derived from local mass balance and a local linear relation between the flux and the surface slope. Scalings for the transient kinematics during the flow transitions are developed based on the flux profiles. Funded by NSF Grant CBET-1511450.
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Method of phase space beam dilution utilizing bounded chaos generated by rf phase modulation
Pham, Alfonse N.; Lee, S. Y.; Ng, K. Y.
2015-12-10
This paper explores the physics of chaos in a localized phase-space region produced by rf phase modulation applied to a double rf system. The study can be exploited to produce rapid particle bunch broadening exhibiting longitudinal particle distribution uniformity. Hamiltonian models and particle-tracking simulations are introduced to understand the mechanism and applicability of controlled particle diffusion. When phase modulation is applied to the double rf system, regions of localized chaos are produced through the disruption and overlapping of parametric resonant islands and configured to be bounded by well-behaved invariant tori to prevent particle loss. The condition of chaoticity and themore » degree of particle dilution can be controlled by the rf parameters. As a result, the method has applications in alleviating adverse space-charge effects in high-intensity beams, particle bunch distribution uniformization, and industrial radiation-effects experiments.« less
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Anomalous diffusion of single metal atoms on a graphene oxide support
Furnival, Tom; Leary, Rowan K.; Tyo, Eric C.; ...
2017-04-21
Recent studies of single-atom catalysts open up the prospect of designing exceptionally active and environmentally efficient chemical processes. The stability and durability of such catalysts is governed by the strength with which the atoms are bound to their support and their diffusive behaviour. Here we use aberration-corrected STEM to image the diffusion of single copper adatoms on graphene oxide. As a result, we discover that individual atoms exhibit anomalous diffusion as a result of spatial and energetic disorder inherent in the support, and interpret the origins of this behaviour to develop a physical picture for the surface diffusion of singlemore » metal atoms.« less
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NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2018-03-01
To predict the response of a biochemical system, knowledge of the intrinsic and effective rate constants of proteins is crucial. The experimentally accessible effective rate constant for association can be decomposed in a diffusion-limited rate at which proteins come into contact and an intrinsic association rate at which the proteins in contact truly bind. Reversely, when dissociating, bound proteins first separate into a contact pair with an intrinsic dissociation rate, before moving away by diffusion. While microscopic expressions exist that enable the calculation of the intrinsic and effective rate constants by conducting a single rare event simulation of the protein dissociation reaction, these expressions are only valid when the substrate has just one binding site. If the substrate has multiple binding sites, a bound enzyme can, besides dissociating into the bulk, also hop to another binding site. Calculating transition rate constants between multiple states with forward flux sampling requires a generalized rate expression. We present this expression here and use it to derive explicit expressions for all intrinsic and effective rate constants involving binding to multiple states, including rebinding. We illustrate our approach by computing the intrinsic and effective association, dissociation, and hopping rate constants for a system in which a patchy particle model enzyme binds to a substrate with two binding sites. We find that these rate constants increase as a function of the rotational diffusion constant of the particles. The hopping rate constant decreases as a function of the distance between the binding sites. Finally, we find that blocking one of the binding sites enhances both association and dissociation rate constants. Our approach and results are important for understanding and modeling association reactions in enzyme-substrate systems and other patchy particle systems and open the way for large multiscale simulations of such systems.
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Yogurtcu, Osman N.; Johnson, Margaret E.
2015-01-01
The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute to dense systems. PMID:26328828
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Numerical modelling of transient heat and moisture transport in protective clothing
NASA Astrophysics Data System (ADS)
Łapka, P.; Furmański, P.; Wisniewski, T. S.
2016-01-01
The paper presents a complex model of heat and mass transfer in a multi-layer protective clothing exposed to a flash fire and interacting with the human skin. The clothing was made of porous fabric layers separated by air gaps. The fabrics contained bound water in the fibres and moist air in the pores. The moist air was also present in the gaps between fabric layers or internal fabric layer and the skin. Three skin sublayers were considered. The model accounted for coupled heat transfer by conduction, thermal radiation and associated with diffusion of water vapour in the clothing layers and air gaps. Heat exchange due to phase transition of the bound water were also included in the model. Complex thermal and mass transfer conditions at internal or external boundaries between fabric layers and air gaps as well as air gap and skin were assumed. Special attention was paid to modelling of thermal radiation which was coming from the fire, penetrated through protective clothing and absorbed by the skin. For the first time non-grey properties as well as optical phenomena at internal or external boundaries between fabric layers and air gaps as well as air gap and skin were accounted for. A series of numerical simulations were carried out and the risk of heat injures was estimated.
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Thermodynamic approach to oxygen delivery in vivo by natural and artificial oxygen carriers.
Bucci, Enrico
2009-06-01
Oxygen is a toxic gas, still indispensable to aerobic life. This paper explores how normal physiology uses the physico-chemical and thermodynamic characteristics of oxygen for transforming a toxic gas into a non toxic indispensable metabolite. Plasma oxygen concentration is in the range of 10(-5) M, insufficient to sustain metabolism. Oxygen carriers, present in blood, release oxygen into plasma, thereby replacing consumed oxygen and buffering PO(2) near their P(50). They are the natural cell-bound carriers, like hemoglobin inside red cells, myoglobin inside myocytes, and artificial cell-free hemoglobin-based oxygen carriers (HBOC) dissolved in plasma. Metabolic oxygen replacement can be defined as cell-bound and cell-free delivery. Cell-bound delivery is retarded by the slow diffusion of oxygen in plasma and interstitial fluids. The 40% hematocrit of normal blood compensates for the delay, coping with the fast oxygen consumption by mitochondria. Facilitated oxygen diffusion by HBOCs corrects for the slow diffusion, making cell-free delivery relatively independent from P(50). At all oxygen affinities, HBOCs produce hyperoxygenations that are compensated by vasoconstrictions. There is a strict direct correlation between the rate of oxygen replacement and hemoglobin content of blood. The free energy loss of the gradient adds a relevant regulation of tissues oxygenation. Oxygen is retained intravascularly by the limited permeability to gases of vessel walls.
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Diffusion rate limitations in actin-based propulsion of hard and deformable particles.
Dickinson, Richard B; Purich, Daniel L
2006-08-15
The mechanism by which actin polymerization propels intracellular vesicles and invasive microorganisms remains an open question. Several recent quantitative studies have examined propulsion of biomimetic particles such as polystyrene microspheres, phospholipid vesicles, and oil droplets. In addition to allowing quantitative measurement of parameters such as the dependence of particle speed on its size, these systems have also revealed characteristic behaviors such a saltatory motion of hard particles and oscillatory deformation of soft particles. Such measurements and observations provide tests for proposed mechanisms of actin-based motility. In the actoclampin filament end-tracking motor model, particle-surface-bound filament end-tracking proteins are involved in load-insensitive processive insertion of actin subunits onto elongating filament plus-ends that are persistently tethered to the surface. In contrast, the tethered-ratchet model assumes working filaments are untethered and the free-ended filaments grow as thermal ratchets in a load-sensitive manner. This article presents a model for the diffusion and consumption of actin monomers during actin-based particle propulsion to predict the monomer concentration field around motile particles. The results suggest that the various behaviors of biomimetic particles, including dynamic saltatory motion of hard particles and oscillatory vesicle deformations, can be quantitatively and self-consistently explained by load-insensitive, diffusion-limited elongation of (+)-end-tethered actin filaments, consistent with predictions of the actoclampin filament-end tracking mechanism.
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Quantum Hamilton equations of motion for bound states of one-dimensional quantum systems
NASA Astrophysics Data System (ADS)
Köppe, J.; Patzold, M.; Grecksch, W.; Paul, W.
2018-06-01
On the basis of Nelson's stochastic mechanics derivation of the Schrödinger equation, a formal mathematical structure of non-relativistic quantum mechanics equivalent to the one in classical analytical mechanics has been established in the literature. We recently were able to augment this structure by deriving quantum Hamilton equations of motion by finding the Nash equilibrium of a stochastic optimal control problem, which is the generalization of Hamilton's principle of classical mechanics to quantum systems. We showed that these equations allow a description and numerical determination of the ground state of quantum problems without using the Schrödinger equation. We extend this approach here to deliver the complete discrete energy spectrum and related eigenfunctions for bound states of one-dimensional stationary quantum systems. We exemplify this analytically for the one-dimensional harmonic oscillator and numerically by analyzing a quartic double-well potential, a model of broad importance in many areas of physics. We furthermore point out a relation between the tunnel splitting of such models and mean first passage time concepts applied to Nelson's diffusion paths in the ground state.
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NASA Astrophysics Data System (ADS)
Kȩdzierski, Marcin; Wajnryb, Eligiusz
2011-10-01
Self-diffusion of colloidal particles confined to a cylindrical microchannel is considered theoretically and numerically. Virial expansion of the self-diffusion coefficient is performed. Two-body and three-body hydrodynamic interactions are evaluated with high precision using the multipole method. The multipole expansion algorithm is also used to perform numerical simulations of the self-diffusion coefficient, valid for all possible particle packing fractions. Comparison with earlier results shows that the widely used method of reflections is insufficient for calculations of hydrodynamic interactions even for small packing fractions and small particles radii, contrary to the prevalent opinion.
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Multiple-scattering coefficients and absorption controlled diffusive processes
NASA Astrophysics Data System (ADS)
Godoy, Salvador; García-Colín, L. S.; Micenmacher, Victor
1999-11-01
Multiple-scattering transmission and reflection coefficients (T,R) are introduced in addition to the diffusion coefficient D for the description of ballistic diffusion in the presence of absorption. For 1D (one-dimensional) systems, the measurement of only one between T and D imposes restrictions on the possible values of the other. If D is measured, then T is bounded between the Landauer and Lambert-Beer equations. Measurements of both (T,D) imply the theoretical knowledge of the microscopic absorption Σa and scattering rΣs cross sections.
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Short-Path Statistics and the Diffusion Approximation
NASA Astrophysics Data System (ADS)
Blanco, Stéphane; Fournier, Richard
2006-12-01
In the field of first return time statistics in bounded domains, short paths may be defined as those paths for which the diffusion approximation is inappropriate. This is at the origin of numerous open questions concerning the characterization of residence time distributions. We show here how general integral constraints can be derived that make it possible to address short-path statistics indirectly by application of the diffusion approximation to long paths. Application to the moments of the distribution at the low-Knudsen limit leads to simple practical results and novel physical pictures.
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Computational investigation of cholesterol binding sites on mitochondrial VDAC.
Weiser, Brian P; Salari, Reza; Eckenhoff, Roderic G; Brannigan, Grace
2014-08-21
The mitochondrial voltage-dependent anion channel (VDAC) allows passage of ions and metabolites across the mitochondrial outer membrane. Cholesterol binds mammalian VDAC, and we investigated the effects of binding to human VDAC1 with atomistic molecular dynamics simulations that totaled 1.4 μs. We docked cholesterol to specific sites on VDAC that were previously identified with NMR, and we tested the reliability of multiple docking results in each site with simulations. The most favorable binding modes were used to build a VDAC model with cholesterol occupying five unique sites, and during multiple 100 ns simulations, cholesterol stably and reproducibly remained bound to the protein. For comparison, VDAC was simulated in systems with identical components but with cholesterol initially unbound. The dynamics of loops that connect adjacent β-strands were most affected by bound cholesterol, with the averaged root-mean-square fluctuation (RMSF) of multiple residues altered by 20-30%. Cholesterol binding also stabilized charged residues inside the channel and localized the surrounding electrostatic potentials. Despite this, ion diffusion through the channel was not significantly affected by bound cholesterol, as evidenced by multi-ion potential of mean force measurements. Although we observed modest effects of cholesterol on the open channel, our model will be particularly useful in experiments that investigate how cholesterol affects VDAC function under applied electrochemical forces and also how other ligands and proteins interact with the channel.
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Computational Investigation of Cholesterol Binding Sites on Mitochondrial VDAC
2015-01-01
The mitochondrial voltage-dependent anion channel (VDAC) allows passage of ions and metabolites across the mitochondrial outer membrane. Cholesterol binds mammalian VDAC, and we investigated the effects of binding to human VDAC1 with atomistic molecular dynamics simulations that totaled 1.4 μs. We docked cholesterol to specific sites on VDAC that were previously identified with NMR, and we tested the reliability of multiple docking results in each site with simulations. The most favorable binding modes were used to build a VDAC model with cholesterol occupying five unique sites, and during multiple 100 ns simulations, cholesterol stably and reproducibly remained bound to the protein. For comparison, VDAC was simulated in systems with identical components but with cholesterol initially unbound. The dynamics of loops that connect adjacent β-strands were most affected by bound cholesterol, with the averaged root-mean-square fluctuation (RMSF) of multiple residues altered by 20–30%. Cholesterol binding also stabilized charged residues inside the channel and localized the surrounding electrostatic potentials. Despite this, ion diffusion through the channel was not significantly affected by bound cholesterol, as evidenced by multi-ion potential of mean force measurements. Although we observed modest effects of cholesterol on the open channel, our model will be particularly useful in experiments that investigate how cholesterol affects VDAC function under applied electrochemical forces and also how other ligands and proteins interact with the channel. PMID:25080204
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NASA Astrophysics Data System (ADS)
Fang, Tilden T.; Fang, Wingra T. C.; Griffin, Peter B.; Plummer, James D.
1996-02-01
Investigation of boron diffusion in strained silicon germanium buried layers reveals a fractional interstitial component of boron diffusion (fBI) in Se0.8Ge0.2 approximately equal to the fBI value in silicon. In conjunction with computer-simulated boron profiles, the results yield an absolute lower-bound of fBI in Si0.8Ge0.2 of ˜0.8. In addition, the experimental methodology provides a unique vehicle for measuring the segregation coefficient; oxidation-enhanced diffusion is used instead of an extended, inert anneal to rapidly diffuse the dopant to equilibrium levels across the interface, allowing the segregation coefficient to be measured more quickly.
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Peak-locking error reduction by birefringent optical diffusers
NASA Astrophysics Data System (ADS)
Kislaya, Ankur; Sciacchitano, Andrea
2018-02-01
The use of optical diffusers for the reduction of peak-locking errors in particle image velocimetry is investigated. The working principle of the optical diffusers is based on the concept of birefringence, where the incoming rays are subject to different deflections depending on the light direction and polarization. The performances of the diffusers are assessed via wind tunnel measurements in uniform flow and wall-bounded turbulence. Comparison with best-practice image defocusing is also conducted. It is found that the optical diffusers yield an increase of the particle image diameter up to 10 µm in the sensor plane. Comparison with reference measurements showed a reduction of both random and systematic errors by a factor of 3, even at low imaging signal-to-noise ratio.
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Brain tumor modeling: glioma growth and interaction with chemotherapy
NASA Astrophysics Data System (ADS)
Banaem, Hossein Y.; Ahmadian, Alireza; Saberi, Hooshangh; Daneshmehr, Alireza; Khodadad, Davood
2011-10-01
In last decade increasingly mathematical models of tumor growths have been studied, particularly on solid tumors which growth mainly caused by cellular proliferation. In this paper we propose a modified model to simulate the growth of gliomas in different stages. Glioma growth is modeled by a reaction-advection-diffusion. We begin with a model of untreated gliomas and continue with models of polyclonal glioma following chemotherapy. From relatively simple assumptions involving homogeneous brain tissue bounded by a few gross anatomical landmarks (ventricles and skull) the models have been expanded to include heterogeneous brain tissue with different motilities of glioma cells in grey and white matter. Tumor growth is characterized by a dangerous change in the control mechanisms, which normally maintain a balance between the rate of proliferation and the rate of apoptosis (controlled cell death). Result shows that this model closes to clinical finding and can simulate brain tumor behavior properly.
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Coarse-grained molecular dynamics simulation of activated penetrant transport in glassy polymers.
Zhang, Kai; Meng, Dong; Müller-Plathe, Florian; Kumar, Sanat K
2018-01-17
Membrane separations of gas mixtures strive to maximize the permeability of a desired species while keeping out undesired ones. Permeability vs. selectivity data from many polymer membranes for a given gas pair with diameters d A and d B are typically collected in a "Robeson plot"', and are bound from above by a line with a slope λ = (d B /d A ) 2 - 1. A microscopic understanding of this relationship, especially λ, is still missing. We perform molecular dynamics simulations of penetrant diffusion using three different coarse-grained polymer models over a wide range of penetrant sizes, temperatures, and monomer densities. The empirically relevant λ = (d B /d A ) 2 - 1 is only found for polymers that are either supercooled liquids with caged segmental dynamics or glasses and when the penetrant size is approximately half the Kuhn length of the chains, for which the penetrant diffusion is an activated process.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, W., E-mail: we.liu@epfl.ch, E-mail: gwenole.jacopin@epfl.ch; Carlin, J.-F.; Grandjean, N.
2016-07-25
We investigate the dynamics of donor bound excitons (D°X{sub A}) at T = 10 K around an isolated single edge dislocation in homoepitaxial GaN, using a picosecond time-resolved cathodoluminescence (TR-CL) setup with high temporal and spatial resolutions. An ∼ 1.3 meV dipole-like energy shift of D°X{sub A} is observed around the dislocation, induced by the local strain fields. By simultaneously recording the variations of both the exciton lifetime and the CL intensity across the dislocation, we directly assess the dynamics of excitons around the defect. Our observations are well reproduced by a diffusion model. It allows us to deduce an exciton diffusion length ofmore » ∼24 nm as well as an effective area of the dislocation with a radius of ∼95 nm, where the recombination can be regarded as entirely non-radiative.« less
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Zhang, Yun; Liu, Fang; Nie, Jinfang; Jiang, Fuyang; Zhou, Caibin; Yang, Jiani; Fan, Jinlong; Li, Jianping
2014-05-07
In this paper, we report for the first time an electrochemical biosensor for single-step, reagentless, and picomolar detection of a sequence-specific DNA-binding protein using a double-stranded, electrode-bound DNA probe terminally modified with a redox active label close to the electrode surface. This new methodology is based upon local repression of electrolyte diffusion associated with protein-DNA binding that leads to reduction of the electrochemical response of the label. In the proof-of-concept study, the resulting electrochemical biosensor was quantitatively sensitive to the concentrations of the TATA binding protein (TBP, a model analyte) ranging from 40 pM to 25.4 nM with an estimated detection limit of ∼10.6 pM (∼80 to 400-fold improvement on the detection limit over previous electrochemical analytical systems).
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nole, Michael; Daigle, Hugh; Mohanty, Kishore
We have developed a 3D methane hydrate reservoir simulator to model marine methane hydrate systems. Our simulator couples highly nonlinear heat and mass transport equations and includes heterogeneous sedimentation, in-situ microbial methanogenesis, the influence of pore size contrast on solubility gradients, and the impact of salt exclusion from the hydrate phase on dissolved methane equilibrium in pore water. Using environmental parameters from Walker Ridge in the Gulf of Mexico, we first simulate hydrate formation in and around a thin, dipping, planar sand stratum surrounded by clay lithology as it is buried to 295mbsf. We find that with sufficient methane beingmore » supplied by organic methanogenesis in the clays, a 200x pore size contrast between clays and sands allows for a strong enough concentration gradient to significantly drop the concentration of methane hydrate in clays immediately surrounding a thin sand layer, a phenomenon that is observed in well log data. Building upon previous work, our simulations account for the increase in sand-clay solubility contrast with depth from about 1.6% near the top of the sediment column to 8.6% at depth, which leads to a progressive strengthening of the diffusive flux of methane with time. By including an exponentially decaying organic methanogenesis input to the clay lithology with depth, we see a decrease in the aqueous methane supplied to the clays surrounding the sand layer with time, which works to further enhance the contrast in hydrate saturation between the sand and surrounding clays. Significant diffusive methane transport is observed in a clay interval of about 11m above the sand layer and about 4m below it, which matches well log observations. The clay-sand pore size contrast alone is not enough to completely eliminate hydrate (as observed in logs), because the diffusive flux of aqueous methane due to a contrast in pore size occurs slower than the rate at which methane is supplied via organic methanogenesis. Therefore, it is likely that additional mechanisms are at play, notably bound water activity reduction in clays. Three-dimensionality allows for inclusion of lithologic heterogeneities, which focus fluid flow and subsequently allow for heterogeneity in the methane migration mechanisms that dominate in marine sediments at a local scale. Incorporating recently acquired 3D seismic data from Walker Ridge to inform the lithologic structure of our modeled reservoir, we show that even with deep adjective sourcing of methane along highly permeable pathways, local hydrate accumulations can be sourced either by diffusive or advective methane flux; advectively-sourced hydrates accumulate evenly in highly permeable strata, while diffusively-sourced hydrates are characterized by thin strata-bound intervals with high clay-sand pore size contrasts.« less
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On The Molecular Mechanism Of Positive Novolac Resists
NASA Astrophysics Data System (ADS)
Huang, Jian-Ping; Kwei, T. K.; Reiser, Arnost
1989-08-01
A molecular mechanism for the dissolution of novolac is proposed, based on the idea of a critical degree of deprotonation as being the condition for the transfer of polymer into solution. The rate at which the critical deprotonation condition is achieved is controlled by the supply of developer into a thin penetration zone, and depends in particular on the rate of diffusion of the base cations which are the developer component with the lowest mobility. The penetration zone contains phenolate ions and ion-bound water, but it retains the structure of a rigid polymer membrane, as evidenced by the diffusion coefficient of cations in the pene;tration zone which is several orders of magnitude slower than in an open gel of the same material. When the critical degree of deprotonation is reached, the membrane structure unravels and all subsequent events, chain rearrangement and transfer into solution, occur rapidly. The supralinear dependence of dissolution rate on base concentration and the effect of the size of the base cation are plausibly interpreted by the model. The diffusion of developer components is assumed to occur preferentially via hydrophilic sites in the polymer matrix. These sites define a diffusion path which acts like a hydrophilic diffusion channel. Suitably designed hydrophobic molecules can block some of the channels and in this way alter the dissolution rate. They reduce in effect the diffusion crossect ion of the material. Hydrophilic additives, on the other hand, introduce additional channels into the system and promote dissolution. The concept of diffusion channels appears to provide a unified interpretation for a number of common observations.
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NASA Astrophysics Data System (ADS)
Li, Huicong; Wang, Xuefeng; Wu, Yanxia
2014-11-01
We consider the logistic diffusion equation on a bounded domain, which has two components with a thin coating surrounding a body. The diffusion tensor is isotropic on the body, and anisotropic on the coating. The size of the diffusion tensor on these components may be very different; within the coating, the diffusion rates in the normal and tangent directions may be in different scales. We find effective boundary conditions (EBCs) that are approximately satisfied by the solution of the diffusion equation on the boundary of the body. We also prove that the lifespan of each EBC, which measures how long the EBC remains effective, is infinite. The EBCs enable us to see clearly the effect of the coating and ease the difficult task of solving the PDE in a thin region with a small diffusion tensor. The motivation of the mathematics includes a nature reserve surrounded by a buffer zone.
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Half-collision analysis of far-wing diffuse structure in Cs-Xe
NASA Technical Reports Server (NTRS)
Exton, R. J.; Hillard, M. E.; Lempert, W. R.
1987-01-01
Laser excitation in the far red wing of the second principal series doublet of Cs mixed with Xe revealed a diffuse structure associated with the 2P(3/2) component. The structure is thought to originate from a reflection type of spectrum between the weakly bound E 2Sigma(1/2) excited state and the X 2Sigma(1/2) repulsive ground state of CsXe.
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Atomic Gas in Blue Ultra Diffuse Galaxies around Hickson Compact Groups
NASA Astrophysics Data System (ADS)
Spekkens, Kristine; Karunakaran, Ananthan
2018-03-01
We have found the atomic gas (H I) reservoirs of the blue ultra diffuse galaxy (UDG) candidates identified by Róman and Trujillo in images near Hickson Compact Groups (HCGs). We confirm that all of the objects are indeed UDGs with effective radii {R}e> 1.5 kpc. Three of them are likely to be gravitationally bound to the HCG near which they project, one is plausibly gravitationally bound to the nearest HCG, and one is in the background. We measure H I masses and velocity widths for each object directly from the spectra, and use the widths together with the UDG effective radii to estimate dynamical masses and halo spin parameters. The location of the blue UDGs in the H I mass–stellar mass plane is consistent with that of the broader gas-rich galaxy population, and both their H I masses and gas richnesses are correlated with their effective radii. The blue UDGs appear to be low-mass objects with high-spin halos, although their properties are not as extreme as those of the faintest diffuse objects found in H I searches. The data presented here highlight the potential of single-dish radio observations for measuring the physical properties of blue diffuse objects detected in the optical.
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Concentration profiles of actin-binding molecules in lamellipodia
NASA Astrophysics Data System (ADS)
Falcke, Martin
2016-04-01
Motile cells form lamellipodia in the direction of motion, which are flat membrane protrusions containing an actin filament network. The network flows rearward relative to the leading edge of the lamellipodium due to actin polymerization at the front. Thus, actin binding molecules are subject to transport towards the rear of the cell in the bound state and diffuse freely in the unbound state. We analyze this reaction-diffusion-advection process with respect to the concentration profiles of these species and provide an analytic approximation for them. Network flow may cause a depletion zone of actin binding molecules close to the leading edge. The existence of such zone depends on the free molecule concentration in the cell body, on the ratio of the diffusion length to the distance bound molecules travel rearward with the flow before dissociating, and the ratio of the diffusion length to the width of the region with network flow and actin binding. Our calculations suggest the existence of depletion zones for the F-actin cross-linkers filamin and α-actinin in fish keratocytes (and other cell types), which is in line with the small elastic moduli of the F-actin network close to the leading edge found in measurements of the force motile cells are able to exert.
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Variational bounds on the temperature distribution
NASA Astrophysics Data System (ADS)
Kalikstein, Kalman; Spruch, Larry; Baider, Alberto
1984-02-01
Upper and lower stationary or variational bounds are obtained for functions which satisfy parabolic linear differential equations. (The error in the bound, that is, the difference between the bound on the function and the function itself, is of second order in the error in the input function, and the error is of known sign.) The method is applicable to a range of functions associated with equalization processes, including heat conduction, mass diffusion, electric conduction, fluid friction, the slowing down of neutrons, and certain limiting forms of the random walk problem, under conditions which are not unduly restrictive: in heat conduction, for example, we do not allow the thermal coefficients or the boundary conditions to depend upon the temperature, but the thermal coefficients can be functions of space and time and the geometry is unrestricted. The variational bounds follow from a maximum principle obeyed by the solutions of these equations.
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Effects of Transition-Metal Mixing on Na Ordering and Kinetics in Layered P 2 Oxides
NASA Astrophysics Data System (ADS)
Zheng, Chen; Radhakrishnan, Balachandran; Chu, Iek-Heng; Wang, Zhenbin; Ong, Shyue Ping
2017-06-01
Layered P 2 oxides are promising cathode materials for rechargeable sodium-ion batteries. In this work, we systematically investigate the effects of transition-metal (TM) mixing on Na ordering and kinetics in the NaxCo1 -yMnyO2 model system using density-functional-theory (DFT) calculations. The DFT-predicted 0-K stability diagrams indicate that Co-Mn mixing reduces the energetic differences between Na orderings, which may account for the reduction of the number of phase transformations observed during the cycling of mixed-TM P 2 layered oxides compared to a single TM. Using ab initio molecular-dynamics simulations and nudged elastic-band calculations, we show that the TM composition at the Na(1) (face-sharing) site has a strong influence on the Na site energies, which in turn impacts the kinetics of Na diffusion towards the end of the charge. By employing a site-percolation model, we establish theoretical upper and lower bounds for TM concentrations based on their effect on Na(1) site energies, providing a framework to rationally tune mixed-TM compositions for optimal Na diffusion.
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NASA Astrophysics Data System (ADS)
Langa, José A.; Rodríguez-Bernal, Aníbal; Suárez, Antonio
In this paper we study in detail the geometrical structure of global pullback and forwards attractors associated to non-autonomous Lotka-Volterra systems in all the three cases of competition, symbiosis or prey-predator. In particular, under some conditions on the parameters, we prove the existence of a unique nondegenerate global solution for these models, which attracts any other complete bounded trajectory. Thus, we generalize the existence of a unique strictly positive stable (stationary) solution from the autonomous case and we extend to Lotka-Volterra systems the result for scalar logistic equations. To this end we present the sub-supertrajectory tool as a generalization of the now classical sub-supersolution method. In particular, we also conclude pullback and forwards permanence for the above models.
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Mechanically triggered solute uptake in soft contact lenses.
Tavazzi, Silvia; Ferraro, Lorenzo; Fagnola, Matteo; Cozza, Federica; Farris, Stefano; Bonetti, Simone; Simonutti, Roberto; Borghesi, Alessandro
2015-06-01
Molecular arrangement plays a role in the diffusion of water and solutes across soft contact lenses. In particular, the uptake of solutes in hydrated contact lenses can occur as long as free water is available for diffusion. In this work, we investigated the effect of mechanical vibrations of low frequency (200 Hz) on the solute uptake. Hyaluronan, a polysaccharide of ophthalmic use, was taken as example of solute of interest. For a specific water-hydrated hydrogel material, differential scanning calorimetry experiments showed that a large fraction of the hydration water accounted for loosely-bound water, both before and after one week of daily-wear of the lenses. The size (of the order of magnitude of few hundreds of nanometers) of hyaluronan in aqueous solution was found to be less than the size of the pores of the lens observed by scanning electron microscopy. However, solute uptake in already-hydrated lenses was negligible by simple immersion, while a significant increase occurred under mechanical vibrations of 200 Hz, thus providing experimental evidence of mechanically triggered enhanced solute uptake, which is attributed to the release of interfacial loosely-bound water. Also other materials were taken into consideration. However, the effectiveness of mechanical vibrations for hyaluronan uptake is restricted to lenses containing interfacial loosely-bound water. Indeed, loosely-bound water is expected to be bound to the polymer with bonding energies of the order of magnitude of 10-100 J/g, which are compatible with the energy input supplied by the vibrations. Copyright © 2015 Elsevier B.V. All rights reserved.
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Universal bounds on current fluctuations.
Pietzonka, Patrick; Barato, Andre C; Seifert, Udo
2016-05-01
For current fluctuations in nonequilibrium steady states of Markovian processes, we derive four different universal bounds valid beyond the Gaussian regime. Different variants of these bounds apply to either the entropy change or any individual current, e.g., the rate of substrate consumption in a chemical reaction or the electron current in an electronic device. The bounds vary with respect to their degree of universality and tightness. A universal parabolic bound on the generating function of an arbitrary current depends solely on the average entropy production. A second, stronger bound requires knowledge both of the thermodynamic forces that drive the system and of the topology of the network of states. These two bounds are conjectures based on extensive numerics. An exponential bound that depends only on the average entropy production and the average number of transitions per time is rigorously proved. This bound has no obvious relation to the parabolic bound but it is typically tighter further away from equilibrium. An asymptotic bound that depends on the specific transition rates and becomes tight for large fluctuations is also derived. This bound allows for the prediction of the asymptotic growth of the generating function. Even though our results are restricted to networks with a finite number of states, we show that the parabolic bound is also valid for three paradigmatic examples of driven diffusive systems for which the generating function can be calculated using the additivity principle. Our bounds provide a general class of constraints for nonequilibrium systems.
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Park, Jong-Hwan; Wang, Jim J; Xiao, Ran; Pensky, Scott M; Kongchum, Manoch; DeLaune, Ronald D; Seo, Dong-Cheol
2018-03-01
Mercury adsorption characteristics of Mississippi River deltaic plain (MRDP) freshwater marsh soil in the Louisiana Gulf coast were evaluated under various conditions. Mercury adsorption was well described by pseudo-second order and Langmuir isotherm models with maximum adsorption capacity of 39.8 mg g -1 . Additional fitting of intraparticle model showed that mercury in the MRDP freshwater marsh soil was controlled by both external surface adsorption and intraparticle diffusion. The partition of adsorbed mercury (mg g -1 ) revealed that mercury was primarily adsorbed into organic-bond fraction (12.09) and soluble/exchangeable fraction (10.85), which accounted for 63.5% of the total adsorption, followed by manganese oxide-bound (7.50), easily mobilizable carbonate-bound (4.53), amorphous iron oxide-bound (0.55), crystalline Fe oxide-bound (0.41), and residual fraction (0.16). Mercury adsorption capacity was generally elevated along with increasing solution pH even though dominant species of mercury were non-ionic HgCl 2 , HgClOH and Hg(OH) 2 at between pH 3 and 9. In addition, increasing background NaCl concentration and the presence of humic acid decreased mercury adsorption, whereas the presence of phosphate, sulfate and nitrate enhanced mercury adsorption. Mercury adsorption in the MRDP freshwater marsh soil was reduced by the presence of Pb, Cu, Cd and Zn with Pb showing the greatest competitive adsorption. Overall the adsorption capacity of mercury in the MRDP freshwater marsh soil was found to be significantly influenced by potential environmental changes, and such factors should be considered in order to manage the risks associated with mercury in this MRDP wetland for responding to future climate change scenarios. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Doan, Phuong T K; Watson, Sue B; Markovic, Stefan; Liang, Anqi; Guo, Jay; Mugalingam, Shan; Stokes, Jonathan; Morley, Andrew; Zhang, Weitao; Arhonditsis, George B; Dittrich, Maria
2018-04-24
Internal phosphorus (P) loading significantly contributes to hysteresis in ecosystem response to nutrient remediation, but the dynamics of sediment P transformations are often poorly characterized. Here, we applied a reaction-transport diagenetic model to investigate sediment P dynamics in the Bay of Quinte, a polymictic, spatially complex embayment of Lake Ontario, (Canada). We quantified spatial and temporal variability of sediment P binding forms and estimated P diffusive fluxes and sediment P retention in different parts of the bay. Our model supports the notion that diagenetic recycling of redox sensitive and organic bound P forms drive sediment P release. In the recent years, summer sediment P diffusive fluxes varied in the range of 3.2-3.6 mg P m -2 d -1 in the upper bay compared to 1.5 mg P m -2 d -1 in the middle-lower bay. Meanwhile sediment P retention ranged between 71% and 75% in the upper and middle-lower bay, respectively. The reconstruction of temporal trends of internal P loading in the past century, suggests that against the backdrop of reduced external P inputs, sediment P exerts growing control over the lake nutrient budget. Higher sediment P diffusive fluxes since mid-20th century with particular increase in the past 20 years in the shallower upper basins, emphasize limited sediment P retention potential and suggest prolonged ecosystem recovery, highlighting the importance of ongoing P control measures. Copyright © 2018 Elsevier B.V. All rights reserved.
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Collective behavior of minus-ended motors in mitotic microtubule asters gliding toward DNA
NASA Astrophysics Data System (ADS)
Athale, Chaitanya A.; Dinarina, Ana; Nedelec, Francois; Karsenti, Eric
2014-02-01
Microtubules (MTs) nucleated by centrosomes form star-shaped structures referred to as asters. Aster motility and dynamics is vital for genome stability, cell division, polarization and differentiation. Asters move either toward the cell center or away from it. Here, we focus on the centering mechanism in a membrane independent system of Xenopus cytoplasmic egg extracts. Using live microscopy and single particle tracking, we find that asters move toward chromatinized DNA structures. The velocity and directionality profiles suggest a random-walk with drift directed toward DNA. We have developed a theoretical model that can explain this movement as a result of a gradient of MT length dynamics and MT gliding on immobilized dynein motors. In simulations, the antagonistic action of the motor species on the radial array of MTs leads to a tug-of-war purely due to geometric considerations and aster motility resembles a directed random-walk. Additionally, our model predicts that aster velocities do not change greatly with varying initial distance from DNA. The movement of asymmetric asters becomes increasingly super-diffusive with increasing motor density, but for symmetric asters it becomes less super-diffusive. The transition of symmetric asters from superdiffusive to diffusive mobility is the result of number fluctuations in bound motors in the tug-of-war. Overall, our model is in good agreement with experimental data in Xenopus cytoplasmic extracts and predicts novel features of the collective effects of motor-MT interactions.
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Kumar, B V N Phani; Priyadharsini, S Umayal; Prameela, G K S; Mandal, Asit Baran
2011-08-01
The present work was undertaken with a view to understand the influence of a model non-ionic tri-block copolymer PEO-PPO-PEO (poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)) with molecular weight 5800 i.e., P123 [(EO)(20)-(PO)(70)-(EO)(20)] on the self-aggregation characteristics of the anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D(2)O) using NMR chemical shift, self-diffusion and nuclear spin-relaxation as suitable experimental probes. In addition, polymer diffusion has been monitored as a function of SDS concentration. The concentration-dependent chemical shift, diffusion data and relaxation data indicated the significant interaction of polymeric micelles with SDS monomers and micelles at lower and intermediate concentrations of SDS, whereas the weak interaction of the polymer with SDS micelles at higher concentrations of SDS. It has been observed that SDS starts aggregating on the polymer at a lower concentration i.e., critical aggregation concentration (cac=1.94 mM) compared to polymer-free situation, and the onset of secondary micelle concentration (C(2)=27.16 mM) points out the saturation of the 0.2 wt% polymer or free SDS monomers/micelles at higher concentrations of SDS. It has also been observed that the parameter cac is almost independent in the polymer concentrations of study. The TMS (tetramethylsilane) has been used as a solubilizate to measure the bound diffusion coefficient of SDS-polymer mixed system. The self-diffusion data were analyzed using two-site exchange model and the obtained information on aggregation dynamics was commensurate with that inferred from chemical shift and relaxation data. The information on slow motions of polymer-SDS system was also extracted using spin-spin and spin-lattice relaxation rate measurements. The relaxation data points out the disintegration of polymer network at higher concentrations of SDS. The present NMR investigations have been well corroborated by surface tension and conductivity measurements. Copyright © 2011 Elsevier Inc. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Duncan, Andrew, E-mail: a.duncan@imperial.ac.uk; Erban, Radek, E-mail: erban@maths.ox.ac.uk; Zygalakis, Konstantinos, E-mail: k.zygalakis@ed.ac.uk
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when onemore » or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.« less
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Diffusion in randomly perturbed dissipative dynamics
NASA Astrophysics Data System (ADS)
Rodrigues, Christian S.; Chechkin, Aleksei V.; de Moura, Alessandro P. S.; Grebogi, Celso; Klages, Rainer
2014-11-01
Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no longer invariant and there is the possibility of transport among them. Here we introduce a basic theoretical setting which enables us to study this hopping process from the perspective of anomalous transport using the concept of a random dynamical system with holes. We apply it to a simple model by investigating the role of hyperbolicity for the transport among basins. We show numerically that our system exhibits non-Gaussian position distributions, power-law escape times, and subdiffusion. Our simulation results are reproduced consistently from stochastic continuous time random walk theory.
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Optimal control of anthracnose using mixed strategies.
Fotsa Mbogne, David Jaures; Thron, Christopher
2015-11-01
In this paper we propose and study a spatial diffusion model for the control of anthracnose disease in a bounded domain. The model is a generalization of the one previously developed in [15]. We use the model to simulate two different types of control strategies against anthracnose disease. Strategies that employ chemical fungicides are modeled using a continuous control function; while strategies that rely on cultivational practices (such as pruning and removal of mummified fruits) are modeled with a control function which is discrete in time (though not in space). For comparative purposes, we perform our analyses for a spatially-averaged model as well as the space-dependent diffusion model. Under weak smoothness conditions on parameters we demonstrate the well-posedness of both models by verifying existence and uniqueness of the solution for the growth inhibition rate for given initial conditions. We also show that the set [0, 1] is positively invariant. We first study control by impulsive strategies, then analyze the simultaneous use of mixed continuous and pulse strategies. In each case we specify a cost functional to be minimized, and we demonstrate the existence of optimal control strategies. In the case of pulse-only strategies, we provide explicit algorithms for finding the optimal control strategies for both the spatially-averaged model and the space-dependent model. We verify the algorithms for both models via simulation, and discuss properties of the optimal solutions. Copyright © 2015 Elsevier Inc. All rights reserved.
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Dynamical properties of the hydration shell of fully deuterated myoglobin
DOE Office of Scientific and Technical Information (OSTI.GOV)
Achterhold, Klaus; Parak, Fritz G.; Ostermann, Andreas
2011-10-15
Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 {sup 1}H{sub 2}O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 A{sup -1} and a temperature range from 4 to 297 K. We used neutrons with a wavelength of {lambda}{alpha}E 6 A and an energy resolution of about 65 {mu}eV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra causedmore » by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjoelander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time {tau}{sub 0} in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time {tau}{sub 1} in a nonbound state followed again by the oscillatory motions for {tau}{sub 0} and so forth. We used the general formulation with no simplifications as {tau}{sub 0}>>{tau}{sub 1} or {tau}{sub 1}>>{tau}{sub 0}. At room temperature, we obtained {tau}{sub 0} {alpha}E 104 ps and {tau}{sub 1} {alpha}E 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.« less
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Detecting and Correcting Melt Inclusion Modification
NASA Astrophysics Data System (ADS)
Cottrell, E.; Kelley, K. A.
2008-12-01
Post entrapment diffusive modification of melt inclusions may mute or erase primary signatures. Corrections for post-entrapment crystallization (PEC) and Fe-loss are routinely applied and, because recent experimental studies suggest rapid diffusion of trace components into and out of olivine-hosted inclusions, the ability to discriminate between primary and secondary signatures is now even more critical. Two tools may assist in this endeavor. XANES measurements of Fe3+/ΣFe ratios in undegassed ol-hosted basaltic melt inclusions from global arcs are 16-36% (n=16), significantly higher than the 7-10% commonly assumed, and higher than in MORB or BABB lavas (Kelley and Cottrell, this mtg). The Fe3+/ΣFe ratios indicate melt-host equilibrium, with significantly less PEC or Fe-loss than would have been otherwise assumed. We conclude that Fe2+ diffusion has been minimal; therefore the residence time of these primitive inclusions in an evolved magma must have been short. Fe3+/ΣFe correlates positively with water concentration, but not with CO2 and S concentrations or Mg#. The oxidized nature of arc lavas and melt inclusions may therefore indicate an oxidized source rather than late-stage degassing or fractionation. Trace element concentrations evolve with time if an inclusion is out of equilibrium with its host. The numerical model of Cottrell et al., 2002, makes specific predictions about how suites of melt inclusions evolve, creating a tool to detect post-entrapment modification. Recent laboratory measurements of REE diffusion in olivine greatly diverge (at 1300°C, 1015 vs 1019m2/s). If REE diffusivity is extremely fast, melt inclusion HREE diversity shouldn't survive more than a few years in a magma chamber; but if slow, HREE variance could be preserved for >104 yrs. Model analysis of published suites of ol-hosted inclusions indicates that either REE diffusion is quite slow, or the residence time of melt inclusions at high temperature is very short. Loss of variance in suites of pl-hosted inclusions is consistent with long (>103 yrs) residence times. Suites of ol- and pl-hosted inclusions from the same magmatic system can therefore bracket residence times if diffusivities are known, or put reasonable bounds on diffusion rates.
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Steurer, Barbara; Janssens, Roel C; Geverts, Bart; Geijer, Marit E; Wienholz, Franziska; Theil, Arjan F; Chang, Jiang; Dealy, Shannon; Pothof, Joris; van Cappellen, Wiggert A; Houtsmuller, Adriaan B; Marteijn, Jurgen A
2018-05-08
Initiation and promoter-proximal pausing are key regulatory steps of RNA Polymerase II (Pol II) transcription. To study the in vivo dynamics of endogenous Pol II during these steps, we generated fully functional GFP-RPB1 knockin cells. GFP-RPB1 photobleaching combined with computational modeling revealed four kinetically distinct Pol II fractions and showed that on average 7% of Pol II are freely diffusing, while 10% are chromatin-bound for 2.4 seconds during initiation, and 23% are promoter-paused for only 42 seconds. This unexpectedly high turnover of Pol II at promoters is most likely caused by premature termination of initiating and promoter-paused Pol II and is in sharp contrast to the 23 minutes that elongating Pol II resides on chromatin. Our live-cell-imaging approach provides insights into Pol II dynamics and suggests that the continuous release and reinitiation of promoter-bound Pol II is an important component of transcriptional regulation. Copyright © 2018 the Author(s). Published by PNAS.
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Properties of branching exponential flights in bounded domains
NASA Astrophysics Data System (ADS)
Zoia, A.; Dumonteil, E.; Mazzolo, A.
2012-11-01
In a series of recent works, important results have been reported concerning the statistical properties of exponential flights evolving in bounded domains, a widely adopted model for finite-speed transport phenomena (Blanco S. and Fournier R., Europhys. Lett., 61 (2003) 168; Mazzolo A., Europhys. Lett., 68 (2004) 350; Bénichou O. et al., Europhys. Lett., 70 (2005) 42). Motivated by physical and biological systems where random spatial displacements are coupled with Galton-Watson birth-death mechanisms, such as neutron multiplication, diffusion of reproducing bacteria or spread of epidemics, in this letter we extend those results in two directions, via a Feynman-Kac formalism. First, we characterize the occupation statistics of exponential flights in the presence of absorption and branching, and give explicit moment formulas for the total length travelled by the walker and the number of performed collisions in a given domain. Then, we show that the survival and escape probability can be derived as well by resorting to a similar approach.
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NASA Astrophysics Data System (ADS)
Bhattacharya, P.; Viesca, R. C.
2017-12-01
In the absence of in situ field-scale observations of quantities such as fault slip, shear stress and pore pressure, observational constraints on models of fault slip have mostly been limited to laboratory and/or remote observations. Recent controlled fluid-injection experiments on well-instrumented faults fill this gap by simultaneously monitoring fault slip and pore pressure evolution in situ [Gugleilmi et al., 2015]. Such experiments can reveal interesting fault behavior, e.g., Gugleilmi et al. report fluid-activated aseismic slip followed only subsequently by the onset of micro-seismicity. We show that the Gugleilmi et al. dataset can be used to constrain the hydro-mechanical model parameters of a fluid-activated expanding shear rupture within a Bayesian framework. We assume that (1) pore-pressure diffuses radially outward (from the injection well) within a permeable pathway along the fault bounded by a narrow damage zone about the principal slip surface; (2) pore-pressure increase ativates slip on a pre-stressed planar fault due to reduction in frictional strength (expressed as a constant friction coefficient times the effective normal stress). Owing to efficient, parallel, numerical solutions to the axisymmetric fluid-diffusion and crack problems (under the imposed history of injection), we are able to jointly fit the observed history of pore-pressure and slip using an adaptive Monte Carlo technique. Our hydrological model provides an excellent fit to the pore-pressure data without requiring any statistically significant permeability enhancement due to the onset of slip. Further, for realistic elastic properties of the fault, the crack model fits both the onset of slip and its early time evolution reasonably well. However, our model requires unrealistic fault properties to fit the marked acceleration of slip observed later in the experiment (coinciding with the triggering of microseismicity). Therefore, besides producing meaningful and internally consistent bounds on in-situ fault properties like permeability, storage coefficient, resolved stresses, friction and the shear modulus, our results also show that fitting the complete observed time history of slip requires alternative model considerations, such as variations in fault mechanical properties or friction coefficient with slip.
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NASA Astrophysics Data System (ADS)
Oldenburg, C. M.; Zhou, Q.; Birkholzer, J. T.
2017-12-01
The injection of supercritical CO2 (scCO2) in fractured reservoirs has been conducted at several storage sites. However, no site-specific dual-continuum modeling for fractured reservoirs has been reported and modeling studies have generally underestimated the fracture-matrix interactions. We developed a conceptual model for enhanced CO2 storage to take into account global scCO2 migration in the fracture continuum, local storage of scCO2 and dissolved CO2 (dsCO2) in the matrix continuum, and driving forces for scCO2 invasion and dsCO2 diffusion from fractures. High-resolution discrete fracture-matrix models were developed for a column of idealized matrix blocks bounded by vertical and horizontal fractures and for a km-scale fractured reservoir. The column-scale simulation results show that equilibrium storage efficiency strongly depends on matrix entry capillary pressure and matrix-matrix connectivity while the time scale to reach equilibrium is sensitive to fracture spacing and matrix flow properties. The reservoir-scale modeling results shows that the preferential migration of scCO2 through fractures is coupled with bulk storage in the rock matrix that in turn retards the fracture scCO2 plume. We also developed unified-form diffusive flux equations to account for dsCO2 storage in brine-filled matrix blocks and found solubility trapping is significant in fractured reservoirs with low-permeability matrix.
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Static electricity of polymers reduced by treatment with iodine
NASA Technical Reports Server (NTRS)
Hermann, A. M.; Landel, R. F.; Rembaum, A.
1967-01-01
Treating organic polymers with iodine improves the electrical conductivity. Diffusion enables products of desired properties to be custom formulated. This eliminates a buildup of static electricity and the need for fillers or bound metal salts.
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The control gain region for synchronization in non-diffusively coupled complex networks
NASA Astrophysics Data System (ADS)
Gequn, Liu; Wenhui, Li; Huijie, Yang; Knowles, Gareth
2014-07-01
The control gain region for synchronization of non-diffusively coupled networks was studied with respect to three conditions: synchronization, synchronization in finite time, and synchronization in the minimum time. Based on cancellation control methodology and master stability function formalism, we found that a complete feasible control gain region may be bounded, unbounded, empty or a union of several bounded and unbounded regions, with a similar shape to the synchronized region. An interesting possibility emerged that a network could be synchronized by both negative and positive feedback control simultaneously. By bridging synchronizability and synchronizing response speeds with a settling time index, we have developed timed synchronized region (TSR) as a substitute for the classical synchronized region to study finite time synchronization. As for the last condition, a graphical method was developed to estimate control gain with the minimum synchronization time (CGMST). Each condition has examples provided for illustration and verification.
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A surface-bound molecule that undergoes optically biased Brownian rotation.
Hutchison, James A; Uji-i, Hiroshi; Deres, Ania; Vosch, Tom; Rocha, Susana; Müller, Sibylle; Bastian, Andreas A; Enderlein, Jörg; Nourouzi, Hassan; Li, Chen; Herrmann, Andreas; Müllen, Klaus; De Schryver, Frans; Hofkens, Johan
2014-02-01
Developing molecular systems with functions analogous to those of macroscopic machine components, such as rotors, gyroscopes and valves, is a long-standing goal of nanotechnology. However, macroscopic analogies go only so far in predicting function in nanoscale environments, where friction dominates over inertia. In some instances, ratchet mechanisms have been used to bias the ever-present random, thermally driven (Brownian) motion and drive molecular diffusion in desired directions. Here, we visualize the motions of surface-bound molecular rotors using defocused fluorescence imaging, and observe the transition from hindered to free Brownian rotation by tuning medium viscosity. We show that the otherwise random rotations can be biased by the polarization of the excitation light field, even though the associated optical torque is insufficient to overcome thermal fluctuations. The biased rotation is attributed instead to a fluctuating-friction mechanism in which photoexcitation of the rotor strongly inhibits its diffusion rate.
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Weimar, T; Harris, S L; Pitner, J B; Bock, K; Pinto, B M
1995-10-17
Transferred nuclear Overhauser enhancement (TRNOE) experiments have been performed to investigate the bound conformation of the trisaccharide repeating unit of the Streptococcus Group A cell-wall polysaccharide. Thus, the conformations of propyl 3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyran osyl)- alpha-L-rhamnopyranoside [C(A')B] (1) as a free ligand and when complexed to the monoclonal antibody Strep 9 were examined. Improved insights about the conformational preferences of the glycosidic linkages of the trisaccharide ligand showed that the free ligand populates various conformations in aqueous solution, thus displaying relatively flexible behavior. The NOE HNAc-H2A', which was not detected in previous work, accounts for a conformation at the beta-(1-->3) linkage with a phi angle of approximately 180 degrees. Observed TRNOEs for the complex are weak, and their analysis was further complicated by spin diffusion. With the use of transferred rotating-frame Overhauser enhancement (TRROE) experiments, the amount of spin diffusion was assessed experimentally, proving that all of the observed long-range TRNOEs arose through spin diffusion. Four interglycosidic distances, derived from the remaining TRNOEs and TRROEs, together with repulsive constraints, derived from the absence of TRROE effects, were used as input parameters in simulated annealing and molecular mechanics calculations to determine the bound conformation of the trisaccharide. Complexation by the antibody results in the selection of one defined conformation of the carbohydrate hapten. This bound conformation, which is a local energy minimum on the energy maps calculated for the trisaccharide ligand, shows only a change from a +gauche to a -gauche orientation at the psi angle of the alpha-(1-->2) linkage when compared to the global minimum conformation. The results infer that the bound conformation of the Streptococcus Group A cell-wall polysaccharide is different from its previously proposed solution structure (Kreis et al., 1995).
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Determination of krypton diffusion coefficients in uranium dioxide using atomic scale calculations
Vathonne, Emerson; Andersson, David Ragnar Anders; Freyss, Michel; ...
2016-12-16
We present a study of the diffusion of krypton in UO 2 using atomic scale calculations combined with diffusion models adapted to the system studied. The migration barriers of the elementary mechanisms for interstitial or vacancy assisted migration are calculated in the DFT + U framework using the nudged elastic band method. The attempt frequencies are obtained from the phonon modes of the defect at the initial and saddle points using empirical potential methods. The diffusion coefficients of Kr in UO 2 are then calculated by combining this data with diffusion models accounting for the concentration of vacancies and themore » interaction of vacancies with Kr atoms. We determined the preferred mechanism for Kr migration and the corresponding diffusion coefficient as a function of the oxygen chemical potential μ O or nonstoichiometry. For very hypostoichiometric (or U-rich) conditions, the most favorable mechanism is interstitial migration. For hypostoichiometric UO 2, migration is assisted by the bound Schottky defect and the charged uranium vacancy, V U 4–. Around stoichiometry, migration assisted by the charged uranium–oxygen divacancy (V UO 2–) and V U 4– is the favored mechanism. Finally, for hyperstoichiometric or O-rich conditions, the migration assisted by two V U 4– dominates. Kr migration is enhanced at higher μ O, and in this regime, the activation energy will be between 4.09 and 0.73 eV depending on nonstoichiometry. The experimental values available are in the latter interval. Since it is very probable that these values were obtained for at least slightly hyperstoichiometric samples, our activation energies are consistent with the experimental data, even if further experiments with precisely controlled stoichiometry are needed to confirm these results. Finally, the mechanisms and trends with nonstoichiometry established for Kr are similar to those found in previous studies of Xe.« less
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On the progressive enrichment of the oxygen isotopic composition of water along a leaf.
Farquhar, G. D.; Gan, K. S.
2003-06-01
A model has been derived for the enrichment of heavy isotopes of water in leaves, including progressive enrichment along the leaf. In the model, lighter water is preferentially transpired leaving heavier water to diffuse back into the xylem and be carried further along the leaf. For this pattern to be pronounced, the ratio of advection to diffusion (Péclet number) has to be large in the longitudinal direction, and small in the radial direction. The progressive enrichment along the xylem is less than that occurring at the sites of evaporation in the mesophyll, depending on the isolation afforded by the radial Péclet number. There is an upper bound on enrichment, and effects of ground tissue associated with major veins are included. When transpiration rate is spatially nonuniform, averaging of enrichment occurs more naturally with transpiration weighting than with area-based weighting. This gives zero average enrichment of transpired water, the modified Craig-Gordon equation for average enrichment at the sites of evaporation and the Farquhar and Lloyd (In Stable Isotopes and Plant Carbon-Water Relations, pp. 47-70. Academic Press, New York, USA, 1993) prediction for mesophyll water. Earlier results on the isotopic composition of evolved oxygen and of retro-diffused carbon dioxide are preserved if these processes vary in parallel with transpiration rate. Parallel variation should be indicated approximately by uniform carbon isotope discrimination across the leaf.
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Fogelson, Aaron L; Tania, Nessy
2005-01-01
A mathematical model of intravascular coagulation is presented; it encompasses the biochemistry of the tissue factor pathway, platelet activation and deposition on the subendothelium, and flow- and diffusion-mediated transport of coagulation proteins and platelets. Simulation experiments carried out with the model indicate the predominant role played by the physical processes of platelet deposition and flow-mediated removal of enzymes in inhibiting coagulation in the vicinity of vascular injury. Sufficiently rapid production of factors IXa and Xa by the TF:VIIa complex can overcome this inhibition and lead to formation of significant amounts of the tenase complex on the surface of activated platelets and, as a consequence, to substantial thrombin production. Chemical inhibitors are seen to play almost no (TFPI) or little (AT-III and APC) role in determining whether substantial thrombin production will occur. The role of APC is limited by the necessity for diffusion of thrombin from the site of injury to nearby endothelial cells to form the thrombomodulin-thrombin complex and for diffusion in the reverse direction of the APC made by this complex. TFPI plays an insignificant part in inhibiting the TF:VIIa complex under the conditions studied whether its action involves sequential binding of TFPI to Xa and then TFPI:Xa to TF:VIIa, or direct binding of TFPI to Xa already bound to the TF:VIIa complex. Copyright 2005 S. Karger AG, Basel.
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Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F(1)-ATPase.
Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko
2015-06-19
The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F(1), which is a component of F(o)F(1) adenosine triphosphate synthase. We discuss the energetic properties of F(1) and identify a high energy barrier of the rotary potential to be 20k(B)T, with the condition that the adenosine diphosphates are tightly bound to the F(1) catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.
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Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F1-ATPase
NASA Astrophysics Data System (ADS)
Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko
2015-06-01
The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F1 , which is a component of Fo F1 adenosine triphosphate synthase. We discuss the energetic properties of F1 and identify a high energy barrier of the rotary potential to be 20 kBT , with the condition that the adenosine diphosphates are tightly bound to the F1 catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.
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Solution of a cauchy problem for a diffusion equation in a Hilbert space by a Feynman formula
NASA Astrophysics Data System (ADS)
Remizov, I. D.
2012-07-01
The Cauchy problem for a class of diffusion equations in a Hilbert space is studied. It is proved that the Cauchy problem in well posed in the class of uniform limits of infinitely smooth bounded cylindrical functions on the Hilbert space, and the solution is presented in the form of the so-called Feynman formula, i.e., a limit of multiple integrals against a gaussian measure as the multiplicity tends to infinity. It is also proved that the solution of the Cauchy problem depends continuously on the diffusion coefficient. A process reducing an approximate solution of an infinite-dimensional diffusion equation to finding a multiple integral of a real function of finitely many real variables is indicated.
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NASA Astrophysics Data System (ADS)
Liu, Bingchen; Dong, Mengzhen; Li, Fengjie
2018-04-01
This paper deals with a reaction-diffusion problem with coupled nonlinear inner sources and nonlocal boundary flux. Firstly, we propose the critical exponents on nonsimultaneous blow-up under some conditions on the initial data. Secondly, we combine the scaling technique and the Green's identity method to determine four kinds of simultaneous blow-up rates. Thirdly, the lower and the upper bounds of blow-up time are derived by using Sobolev-type differential inequalities.
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Velocity Resolved---Scalar Modeled Simulations of High Schmidt Number Turbulent Transport
NASA Astrophysics Data System (ADS)
Verma, Siddhartha
The objective of this thesis is to develop a framework to conduct velocity resolved - scalar modeled (VR-SM) simulations, which will enable accurate simulations at higher Reynolds and Schmidt (Sc) numbers than are currently feasible. The framework established will serve as a first step to enable future simulation studies for practical applications. To achieve this goal, in-depth analyses of the physical, numerical, and modeling aspects related to Sc " 1 are presented, specifically when modeling in the viscous-convective subrange. Transport characteristics are scrutinized by examining scalar-velocity Fourier mode interactions in Direct Numerical Simulation (DNS) datasets and suggest that scalar modes in the viscous-convective subrange do not directly affect large-scale transport for high Sc . Further observations confirm that discretization errors inherent in numerical schemes can be sufficiently large to wipe out any meaningful contribution from subfilter models. This provides strong incentive to develop more effective numerical schemes to support high Sc simulations. To lower numerical dissipation while maintaining physically and mathematically appropriate scalar bounds during the convection step, a novel method of enforcing bounds is formulated, specifically for use with cubic Hermite polynomials. Boundedness of the scalar being transported is effected by applying derivative limiting techniques, and physically plausible single sub-cell extrema are allowed to exist to help minimize numerical dissipation. The proposed bounding algorithm results in significant performance gain in DNS of turbulent mixing layers and of homogeneous isotropic turbulence. Next, the combined physical/mathematical behavior of the subfilter scalar-flux vector is analyzed in homogeneous isotropic turbulence, by examining vector orientation in the strain-rate eigenframe. The results indicate no discernible dependence on the modeled scalar field, and lead to the identification of the tensor-diffusivity model as a good representation of the subfilter flux. Velocity resolved - scalar modeled simulations of homogeneous isotropic turbulence are conducted to confirm the behavior theorized in these a priori analyses, and suggest that the tensor-diffusivity model is ideal for use in the viscous-convective subrange. Simulations of a turbulent mixing layer are also discussed, with the partial objective of analyzing Schmidt number dependence of a variety of scalar statistics. Large-scale statistics are confirmed to be relatively independent of the Schmidt number for Sc " 1, which is explained by the dominance of subfilter dissipation over resolved molecular dissipation in the simulations. Overall, the VR-SM framework presented is quite effective in predicting large-scale transport characteristics of high Schmidt number scalars, however, it is determined that prediction of subfilter quantities would entail additional modeling intended specifically for this purpose. The VR-SM simulations presented in this thesis provide us with the opportunity to overlap with experimental studies, while at the same time creating an assortment of baseline datasets for future validation of LES models, thereby satisfying the objectives outlined for this work.
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Emotion shapes the diffusion of moralized content in social networks
Wills, Julian A.; Jost, John T.; Tucker, Joshua A.; Van Bavel, Jay J.
2017-01-01
Political debate concerning moralized issues is increasingly common in online social networks. However, moral psychology has yet to incorporate the study of social networks to investigate processes by which some moral ideas spread more rapidly or broadly than others. Here, we show that the expression of moral emotion is key for the spread of moral and political ideas in online social networks, a process we call “moral contagion.” Using a large sample of social media communications about three polarizing moral/political issues (n = 563,312), we observed that the presence of moral-emotional words in messages increased their diffusion by a factor of 20% for each additional word. Furthermore, we found that moral contagion was bounded by group membership; moral-emotional language increased diffusion more strongly within liberal and conservative networks, and less between them. Our results highlight the importance of emotion in the social transmission of moral ideas and also demonstrate the utility of social network methods for studying morality. These findings offer insights into how people are exposed to moral and political ideas through social networks, thus expanding models of social influence and group polarization as people become increasingly immersed in social media networks. PMID:28652356
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Emotion shapes the diffusion of moralized content in social networks.
Brady, William J; Wills, Julian A; Jost, John T; Tucker, Joshua A; Van Bavel, Jay J
2017-07-11
Political debate concerning moralized issues is increasingly common in online social networks. However, moral psychology has yet to incorporate the study of social networks to investigate processes by which some moral ideas spread more rapidly or broadly than others. Here, we show that the expression of moral emotion is key for the spread of moral and political ideas in online social networks, a process we call "moral contagion." Using a large sample of social media communications about three polarizing moral/political issues ( n = 563,312), we observed that the presence of moral-emotional words in messages increased their diffusion by a factor of 20% for each additional word. Furthermore, we found that moral contagion was bounded by group membership; moral-emotional language increased diffusion more strongly within liberal and conservative networks, and less between them. Our results highlight the importance of emotion in the social transmission of moral ideas and also demonstrate the utility of social network methods for studying morality. These findings offer insights into how people are exposed to moral and political ideas through social networks, thus expanding models of social influence and group polarization as people become increasingly immersed in social media networks.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Myoung-Jae; Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr; Department of Applied Physics and Department of Bionanotechnology, Hanyang University, Ansan, Kyunggi-Do 15588
The dispersion relation and the dissipation process of the space-charge wave propagating in a bounded plasma such as a cylindrical waveguide are investigated by employing the longitudinal dielectric permittivity that contains the diffusivity based on the Dupree theory of turbulent plasma. We derived the dispersion relation for space-charge wave in terms of the radius of cylindrical waveguide and the roots of the Bessel function of the first kind which appears as the boundary condition. We find that the wave frequency for a lower-order root of the Bessel function is higher than that of a higher-order root. We also find thatmore » the dissipation is greatest for the lowest-order root, but it is suppressed significantly as the order of the root increases. The wave frequency and the dissipation process are enhanced as the radius of cylindrical waveguide increases. However, they are always smaller than the case of bulk plasma. We find that the diffusivity of turbulent plasma would enhance the damping of space-charge waves, especially, in the range of small wave number. For a large wave number, the diffusivity has little effect on the damping.« less
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Fluidized-bed reactor modeling for production of silicon by silane pyrolysis
NASA Technical Reports Server (NTRS)
Dudukovic, M. P.; Ramachandran, P. A.; Lai, S.
1986-01-01
An ideal backmixed reactor model (CSTR) and a fluidized bed bubbling reactor model (FBBR) were developed for silane pyrolysis. Silane decomposition is assumed to occur via two pathways: homogeneous decomposition and heterogeneous chemical vapor deposition (CVD). Both models account for homogeneous and heterogeneous silane decomposition, homogeneous nucleation, coagulation and growth by diffusion of fines, scavenging of fines by large particles, elutriation of fines and CVD growth of large seed particles. At present the models do not account for attrition. The preliminary comparison of the model predictions with experimental results shows reasonable agreement. The CSTR model with no adjustable parameter yields a lower bound on fines formed and upper estimate on production rates. The FBBR model overpredicts the formation of fines but could be matched to experimental data by adjusting the unkown jet emulsion exchange efficients. The models clearly indicate that in order to suppress the formation of fines (smoke) good gas-solid contacting in the grid region must be achieved and the formation of the bubbles suppressed.
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Isotopic fractionation of gases during its migration: experiments and 2D numerical simulation
NASA Astrophysics Data System (ADS)
Kara, S.; Prinzhofer, A.
2003-04-01
Several works have been developed in the last decade on the experimental isotope fractionation of gases during migration (Prinzhofer et al., 1997 and Zhang &Krooss, 2001 among others). We add to these results new experiments on diffusion of CO_2, which becomes currently a crucial subject for environmental purpose. Our experiments showed that transport by diffusion of CO_2 through a water saturated shale induces a significant and systematic carbon isotopic fractionation with heavier (13C enriched) CO_2 migrating first. In all experiments, significant isotope fractionation was found but still remains without quantitative interpretation. To interpret these data, we developed a 2D numerical model at the pore scale. The general principle of this model is the study of transport by water solubilization/diffusion of gas in a capillary saturated with water with two different media : a mobile zone representing free water and a immobile zone representing bounded water. The model takes also into account solubilization coefficients of gas in water, as well as the migration distance and the volume of upstream and downstream reservoirs. Using our numerical model, we could reproduce the evolution of isotopic fractionations and the velocity of CO_2 migration versus the production factor F (proportion of diffused gas). We determined some physical parameters of the porous medium (bentonite) which are not directly measurable at the present time. Furthermore, we used these parameters to reproduce the curves of isotopic fractionation obtained by Pernaton (1998) on methane migration with the same porous rock. We used also a modified version of this model with infinite reservoirs to reproduce the curves of isotopic fractionation of Zhang &Krooss (2001). Application of this model to geological scale is under progress, in order to implement it into sedimentary basins modelling. REFERENCES: Zhang T. and Krooss M. (2001). Geochim. Cosmochim. Acta, Vol. 65, No.16, pp. 2723-2742. Pernaton E. (1998) PhD. Thesis, Université de Paris VII, 272 pp. Prinzhofer A. and Pernaton E. (1997) Chem. Geol., vol. 142, 193-200.
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NASA Astrophysics Data System (ADS)
He, Ying; Puckett, Elbridge Gerry; Billen, Magali I.
2017-02-01
Mineral composition has a strong effect on the properties of rocks and is an essentially non-diffusive property in the context of large-scale mantle convection. Due to the non-diffusive nature and the origin of compositionally distinct regions in the Earth the boundaries between distinct regions can be nearly discontinuous. While there are different methods for tracking rock composition in numerical simulations of mantle convection, one must consider trade-offs between computational cost, accuracy or ease of implementation when choosing an appropriate method. Existing methods can be computationally expensive, cause over-/undershoots, smear sharp boundaries, or are not easily adapted to tracking multiple compositional fields. Here we present a Discontinuous Galerkin method with a bound preserving limiter (abbreviated as DG-BP) using a second order Runge-Kutta, strong stability-preserving time discretization method for the advection of non-diffusive fields. First, we show that the method is bound-preserving for a point-wise divergence free flow (e.g., a prescribed circular flow in a box). However, using standard adaptive mesh refinement (AMR) there is an over-shoot error (2%) because the cell average is not preserved during mesh coarsening. The effectiveness of the algorithm for convection-dominated flows is demonstrated using the falling box problem. We find that the DG-BP method maintains sharper compositional boundaries (3-5 elements) as compared to an artificial entropy-viscosity method (6-15 elements), although the over-/undershoot errors are similar. When used with AMR the DG-BP method results in fewer degrees of freedom due to smaller regions of mesh refinement in the neighborhood of the discontinuity. However, using Taylor-Hood elements and a uniform mesh there is an over-/undershoot error on the order of 0.0001%, but this error increases to 0.01-0.10% when using AMR. Therefore, for research problems in which a continuous field method is desired the DG-BP method can provide improved tracking of sharp compositional boundaries. For applications in which strict bound-preserving behavior is desired, use of an element that provides a divergence-free condition on the weak formulation (e.g., Raviart-Thomas) and an improved mesh coarsening scheme for the AMR are required.
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Cournane, S; León Vintró, L; Mitchell, P I
2010-11-01
A microcosm laboratory experiment was conducted to determine the impact of biological reworking by the ragworm Nereis diversicolor on the redistribution of particle-bound radionuclides deposited at the sediment-water interface. Over the course of the 40-day experiment, as much as 35% of a (137)Cs-labelled particulate tracer deposited on the sediment surface was redistributed to depths of up to 11 cm by the polychaete. Three different reworking models were employed to model the profiles and quantify the biodiffusion and biotransport coefficients: a gallery-diffuser model, a continuous sub-surface egestion model and a biodiffusion model. Although the biodiffusion coefficients obtained for each model were quite similar, the continuous sub-surface egestion model provided the best fit to the data. The average biodiffusion coefficient, at 1.8 +/- 0.9 cm(2) y(-1), is in good agreement with the values quoted by other workers on the bioturbation effects of this polychaete species. The corresponding value for the biotransport coefficient was found to be 0.9 +/- 0.4 cm y(-1). The effects of non-local mixing were incorporated in a model to describe the temporal evolution of measured (99)Tc and (60)Co radionuclide sediment profiles in the eastern Irish Sea, influenced by radioactive waste discharged from the Sellafield reprocessing plant. Reworking conditions in the sediment column were simulated by considering an upper mixed layer, an exponentially decreasing diffusion coefficient, and appropriate biotransport coefficients to account for non-local mixing. The diffusion coefficients calculated from the (99)Tc and (60)Co cores were in the range 2-14 cm(2) y(-1), which are consistent with the values found by other workers in the same marine area, while the biotransport coefficients were similar to those obtained for a variety of macrobenthic organisms in controlled laboratories and field studies.
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A physics-based model for maintenance of the pH gradient in the gastric mucus layer.
Lewis, Owen L; Keener, James P; Fogelson, Aaron L
2017-12-01
It is generally accepted that the gastric mucus layer provides a protective barrier between the lumen and the mucosa, shielding the mucosa from acid and digestive enzymes and preventing autodigestion of the stomach epithelium. However, the precise mechanisms that contribute to this protective function are still up for debate. In particular, it is not clear what physical processes are responsible for transporting hydrogen protons, secreted within the gastric pits, across the mucus layer to the lumen without acidifying the environment adjacent to the epithelium. One hypothesis is that hydrogen may be bound to the mucin polymers themselves as they are convected away from the mucosal surface and eventually degraded in the stomach lumen. It is also not clear what mechanisms prevent hydrogen from diffusing back toward the mucosal surface, thereby lowering the local pH. In this work we investigate a physics-based model of ion transport within the mucosal layer based on a Nernst-Planck-like equation. Analysis of this model shows that the mechanism of transporting protons bound to the mucus gel is capable of reproducing the trans-mucus pH gradients reported in the literature. Furthermore, when coupled with ion exchange at the epithelial surface, our analysis shows that bicarbonate secretion alone is capable of neutralizing the epithelial pH, even in the face of enormous diffusive gradients of hydrogen. Maintenance of the pH gradient is found to be robust to a wide array of perturbations in both physiological and phenomenological model parameters, suggesting a robust physiological control mechanism. NEW & NOTEWORTHY This work combines modeling techniques based on physical principles, as well as novel numerical simulations to test the plausibility of one hypothesized mechanism for proton transport across the gastric mucus layer. Results show that this mechanism is able to maintain the extreme pH gradient seen in in vivo experiments and suggests a highly robust regulation mechanism to maintain this gradient in the face of dynamic lumen composition. Copyright © 2017 the American Physiological Society.
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Diffusive retention of atmospheric gases in chert
NASA Astrophysics Data System (ADS)
Pettitt, E.; Cherniak, D. J.; Watson, E. B.; Schaller, M. F.
2016-12-01
Throughout Earth's history, the volatile contents (N2, CO2, Ar) of both deep and shallow terrestrial reservoirs has been dynamic. Volatiles are important chemical constituents because they play a significant role in regulating Earth's climate, mediating the evolution of complex life, and controlling the properties of minerals and rocks. Estimating levels of atmospheric volatiles in the deep geological past requires interrogation of materials that have acquired and retained a chemical memory from that time. Cherts have the potential to trap atmospheric components during formation and later release those gases for analysis in the laboratory. However, cherts have been underexploited in this regard, partly because their ability to retain a record of volatile components has not been adequately evaluated. Before cherts can be reliably used as indicators of past levels of major atmospheric gases, it is crucial that we understand the diffusive retentiveness of these cryptocrystalline silica phases. As the first step toward quantifying the diffusivity and solubility of carbon dioxide and nitrogen in chert, we have performed 1-atmosphere diffusive-uptake experiments at temperatures up to 450°C. Depth profiles of in-diffusing gases are measured by nuclear reaction analysis (NRA) to help us understand the molecular-scale transport of volatiles and thus the validity of using chert-bound volatiles to record information about Earth history. Data collected to date suggest that at least some cherts are ideal storage containers and can retain volatiles for a geologically long time. In addition to these diffusion experiments, preliminary online-crush fast-scan measurements using a quadrupole mass spectrometer indicate that atmospheric volatiles are released upon crushing various chert samples. By coupling such volatile-release measurements made by mass spectrometry with diffusion experiments, we are uniquely able to address the storage and fidelity of volatiles bound in crustal materials; an important step toward understanding atmospheric evolution over geologic history.
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Quantitative Characterization of the Microstructure and Transport Properties of Biopolymer Networks
Jiao, Yang; Torquato, Salvatore
2012-01-01
Biopolymer networks are of fundamental importance to many biological processes in normal and tumorous tissues. In this paper, we employ the panoply of theoretical and simulation techniques developed for characterizing heterogeneous materials to quantify the microstructure and effective diffusive transport properties (diffusion coefficient De and mean survival time τ) of collagen type I networks at various collagen concentrations. In particular, we compute the pore-size probability density function P(δ) for the networks and present a variety of analytical estimates of the effective diffusion coefficient De for finite-sized diffusing particles, including the low-density approximation, the Ogston approximation, and the Torquato approximation. The Hashin-Strikman upper bound on the effective diffusion coefficient De and the pore-size lower bound on the mean survival time τ are used as benchmarks to test our analytical approximations and numerical results. Moreover, we generalize the efficient first-passage-time techniques for Brownian-motion simulations in suspensions of spheres to the case of fiber networks and compute the associated effective diffusion coefficient De as well as the mean survival time τ, which is related to nuclear magnetic resonance (NMR) relaxation times. Our numerical results for De are in excellent agreement with analytical results for simple network microstructures, such as periodic arrays of parallel cylinders. Specifically, the Torquato approximation provides the most accurate estimates of De for all collagen concentrations among all of the analytical approximations we consider. We formulate a universal curve for τ for the networks at different collagen concentrations, extending the work of Yeong and Torquato [J. Chem. Phys. 106, 8814 (1997)]. We apply rigorous cross-property relations to estimate the effective bulk modulus of collagen networks from a knowledge of the effective diffusion coefficient computed here. The use of cross-property relations to link other physical properties to the transport properties of collagen networks is also discussed. PMID:22683739
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Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks
Ringbauer, Harald; Coop, Graham
2017-01-01
Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These identity-by-descent (IBD) blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulas for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite-likelihood approach to fit these formulas. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block-sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the Population Reference Sample data set. We show that ancestry diffusing with a rate of σ≈50−−100 km/gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance. PMID:28108588
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A hyperbolastic type-I diffusion process: Parameter estimation by means of the firefly algorithm.
Barrera, Antonio; Román-Román, Patricia; Torres-Ruiz, Francisco
2018-01-01
A stochastic diffusion process, whose mean function is a hyperbolastic curve of type I, is presented. The main characteristics of the process are studied and the problem of maximum likelihood estimation for the parameters of the process is considered. To this end, the firefly metaheuristic optimization algorithm is applied after bounding the parametric space by a stagewise procedure. Some examples based on simulated sample paths and real data illustrate this development. Copyright © 2017 Elsevier B.V. All rights reserved.
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Multi-Dimensional Asymptotically Stable 4th Order Accurate Schemes for the Diffusion Equation
NASA Technical Reports Server (NTRS)
Abarbanel, Saul; Ditkowski, Adi
1996-01-01
An algorithm is presented which solves the multi-dimensional diffusion equation on co mplex shapes to 4th-order accuracy and is asymptotically stable in time. This bounded-error result is achieved by constructing, on a rectangular grid, a differentiation matrix whose symmetric part is negative definite. The differentiation matrix accounts for the Dirichlet boundary condition by imposing penalty like terms. Numerical examples in 2-D show that the method is effective even where standard schemes, stable by traditional definitions fail.
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Diffuse X-ray emission from Abell clusters 401 and 399 - A gravitationally bound system
NASA Technical Reports Server (NTRS)
Ulmer, M. P.; Kinzer, R.; Cruddace, R. G.; Wood, K.; Evans, W.; Byram, E. T.; Chubb, T. A.; Friedman, H.
1979-01-01
The X-ray emission from the Abell 401-399 region has been studied using data obtained by the A-1 proportional counter aboard HEAO 1 in two different ways. The first involved routine scanning of the region during the all-sky survey, and the second was an observation in which the instrument was pointed at A401 during a lunar occultation. The emission is shown to be unusually extended and to be centered on a point lying between A401 and A399. The best fit of a uniform disk model to the data yielded a radius of 25.5 + or -4.4 arcmin for the lunar occultation and 42 + or - 17 arcmin for the scans. A possible explanation of the results is that A401 and A399 are both diffuse cluster X-ray sources. Alternatively, the emission may come from a large gas cloud of at least 10 to the 15th solar masses enveloping both clusters.
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Localization of lung fields in HRCT images using a deep convolution neural network
NASA Astrophysics Data System (ADS)
Kumar, Abhishek; Agarwala, Sunita; Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Nandi, Debashis; Garg, Mandeep; Khandelwal, Niranjan; Kalra, Naveen
2018-02-01
Lung field segmentation is a prerequisite step for the development of a computer-aided diagnosis system for interstitial lung diseases observed in chest HRCT images. Conventional methods of lung field segmentation rely on a large gray value contrast between lung fields and surrounding tissues. These methods fail on lung HRCT images with dense and diffused pathology. An efficient prepro- cessing could improve the accuracy of segmentation of pathological lung field in HRCT images. In this paper, a convolution neural network is used for localization of lung fields in HRCT images. The proposed method provides an optimal bounding box enclosing the lung fields irrespective of the presence of diffuse pathology. The performance of the proposed algorithm is validated on 330 lung HRCT images obtained from MedGift database on ZF and VGG networks. The model achieves a mean average precision of 0.94 with ZF net and a slightly better performance giving a mean average precision of 0.95 in case of VGG net.
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Discrete ordinates solutions of nongray radiative transfer with diffusely reflecting walls
NASA Technical Reports Server (NTRS)
Menart, J. A.; Lee, Haeok S.; Kim, Tae-Kuk
1993-01-01
Nongray gas radiation in a plane parallel slab bounded by gray, diffusely reflecting walls is studied using the discrete ordinates method. The spectral equation of transfer is averaged over a narrow wavenumber interval preserving the spectral correlation effect. The governing equations are derived by considering the history of multiple reflections between two reflecting wails. A closure approximation is applied so that only a finite number of reflections have to be explicitly included. The closure solutions express the physics of the problem to a very high degree and show relatively little error. Numerical solutions are obtained by applying a statistical narrow-band model for gas properties and a discrete ordinates code. The net radiative wail heat fluxes and the radiative source distributions are obtained for different temperature profiles. A zeroth-degree formulation, where no wall reflection is handled explicitly, is sufficient to predict the radiative transfer accurately for most cases considered, when compared with increasingly accurate solutions based on explicitly tracing a larger number of wail reflections without any closure approximation applied.
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Topological quantum error correction in the Kitaev honeycomb model
NASA Astrophysics Data System (ADS)
Lee, Yi-Chan; Brell, Courtney G.; Flammia, Steven T.
2017-08-01
The Kitaev honeycomb model is an approximate topological quantum error correcting code in the same phase as the toric code, but requiring only a 2-body Hamiltonian. As a frustrated spin model, it is well outside the commuting models of topological quantum codes that are typically studied, but its exact solubility makes it more amenable to analysis of effects arising in this noncommutative setting than a generic topologically ordered Hamiltonian. Here we study quantum error correction in the honeycomb model using both analytic and numerical techniques. We first prove explicit exponential bounds on the approximate degeneracy, local indistinguishability, and correctability of the code space. These bounds are tighter than can be achieved using known general properties of topological phases. Our proofs are specialized to the honeycomb model, but some of the methods may nonetheless be of broader interest. Following this, we numerically study noise caused by thermalization processes in the perturbative regime close to the toric code renormalization group fixed point. The appearance of non-topological excitations in this setting has no significant effect on the error correction properties of the honeycomb model in the regimes we study. Although the behavior of this model is found to be qualitatively similar to that of the standard toric code in most regimes, we find numerical evidence of an interesting effect in the low-temperature, finite-size regime where a preferred lattice direction emerges and anyon diffusion is geometrically constrained. We expect this effect to yield an improvement in the scaling of the lifetime with system size as compared to the standard toric code.
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Scaling oxygen microprofiles at the sediment interface of deep stratified waters
NASA Astrophysics Data System (ADS)
Schwefel, Robert; Hondzo, Miki; Wüest, Alfred; Bouffard, Damien
2017-02-01
Dissolved oxygen microprofiles at the sediment-water interface of Lake Geneva were measured concurrently with velocities 0.25 to 2 m above the sediment. The measurements and scaling analyses indicate dissolved oxygen fluctuations and turbulent fluxes in exceedance of molecular diffusion in the proximity of the sediment-water interface. The measurements allowed the parameterization of the turbulent diffusion as a function of the dimensionless height above the sediment and the turbulence above the sediment-water interface. Turbulent diffusion depended strongly on the friction velocity and differed from formulations reported in the literature that are based on concepts of turbulent and developed wall-bounded flows. The dissolved oxygen microprofiles and proposed parameterization of turbulent diffusion enable a foundation for the similarity scaling of oxygen microprofiles in proximity to the sediment. The proposed scaling allows the estimation of diffusive boundary layer thickness, oxygen flux, and oxygen microprofile distribution in the near-sediment boundary layer.
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Vertical Eddy Diffusivity as a Control Parameter in the Tropical Pacific Ocean
NASA Astrophysics Data System (ADS)
Martinez Avellaneda, N.; Cornuelle, B.; Mazloff, M. R.; Stammer, D.
2012-12-01
Ocean models suffer from errors in the treatment of turbulent sub-grid scale motions causing mixing and energy dissipation. Unrealistic small-scale features in models can have large-scale consequences, such as biases in the upper ocean temperature, a symptom of poorly-simulated upwelling, currents and air-sea interactions. This is of special importance in the tropical Pacific Ocean, which is home to energetic air-sea interactions that affect global climate. It has been shown in a number of studies that the simulated ENSO variability is highly dependent on the state of the ocean (e.g.: background mixing). Moreover, the magnitude of the vertical numerical diffusion is of primary importance in properly reproducing the Pacific equatorial thermocline. Yet, it is a common practice to use spatially uniform mixing parameters in ocean simulations. This work is part of a NASA-funded project to estimate the space-varying ocean mixing coefficients in an eddy-permitting model of the tropical Pacific. The usefulness of assimilation techniques in estimating mixing parameters has been previously explored (e.g.: Stammer, 2005, Ferreira et al., 2005). The authors also demonstrated that the spatial structure of the Equatorial Undercurrent (EUC) could be improved by adjusting wind-stress and surface buoyancy flux within their error bounds. In our work, we address the important question of whether adjusting mixing parameterizations can bring about similar improvements. To that end, an eddy-permitting state estimate for the tropical Pacific is developed using the MIT general circulation model and its adjoint where the vertical diffusivity is set as a control parameter. Complementary adjoint-based sensitivity results show strong sensitivities of the Tropical Pacific thermocline (thickness and location) and the EUC transport to the vertical diffusivity in the tropics. Argo, CTD, XBT and mooring in-situ data, as well as TMI SST and altimetry observations are assimilated in order to reduce the misfit between the model simulations and the ocean observations. Model domain topography of 1/3dgr of spatial resolution interpolated from ETOPO 2. The first and the last color levels represent regions shallower than 100m and deeper than 5000m, respectively
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Hyde, M W; Schmidt, J D; Havrilla, M J
2009-11-23
A polarimetric bidirectional reflectance distribution function (pBRDF), based on geometrical optics, is presented. The pBRDF incorporates a visibility (shadowing/masking) function and a Lambertian (diffuse) component which distinguishes it from other geometrical optics pBRDFs in literature. It is shown that these additions keep the pBRDF bounded (and thus a more realistic physical model) as the angle of incidence or observation approaches grazing and better able to model the behavior of light scattered from rough, reflective surfaces. In this paper, the theoretical development of the pBRDF is shown and discussed. Simulation results of a rough, perfect reflecting surface obtained using an exact, electromagnetic solution and experimental Mueller matrix results of two, rough metallic samples are presented to validate the pBRDF.
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The Hall effect in star formation
NASA Astrophysics Data System (ADS)
Braiding, C. R.; Wardle, M.
2012-05-01
Magnetic fields play an important role in star formation by regulating the removal of angular momentum from collapsing molecular cloud cores. Hall diffusion is known to be important to the magnetic field behaviour at many of the intermediate densities and field strengths encountered during the gravitational collapse of molecular cloud cores into protostars, and yet its role in the star formation process is not well studied. We present a semianalytic self-similar model of the collapse of rotating isothermal molecular cloud cores with both Hall and ambipolar diffusion, and similarity solutions that demonstrate the profound influence of the Hall effect on the dynamics of collapse. The solutions show that the size and sign of the Hall parameter can change the size of the protostellar disc by up to an order of magnitude and the protostellar accretion rate by 50 per cent when the ratio of the Hall to ambipolar diffusivities is varied between -0.5 ≤ηH/ηA≤ 0.2. These changes depend upon the orientation of the magnetic field with respect to the axis of rotation and create a preferred handedness to the solutions that could be observed in protostellar cores using next-generation instruments such as ALMA. Hall diffusion also determines the strength and position of the shocks that bound the pseudo and rotationally supported discs, and can introduce subshocks that further slow accretion on to the protostar. In cores that are not initially rotating (not examined here), Hall diffusion can even induce rotation, which could give rise to disc formation and resolve the magnetic braking catastrophe. The Hall effect clearly influences the dynamics of gravitational collapse and its role in controlling the magnetic braking and radial diffusion of the field merits further exploration in numerical simulations of star formation.
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Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
Miao, Yinglong; Baudry, Jerome
2011-01-01
Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site. PMID:21943431
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The effect of ligand affinity on integrins' lateral diffusion in cultured cells.
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.
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Phosphorus-defect interactions during thermal annealing of ion implanted silicon
NASA Astrophysics Data System (ADS)
Keys, Patrick Henry
Ion implantation of dopant atoms into silicon generates nonequilibrium levels of crystal defects that can lead to the detrimental effects of transient enhanced diffusion (TED), incomplete dopant activation, and p-n junction leakage. In order to control these effects, it is vital to have a clear understanding of dopant-defect interactions and develop models that account for these interactions. This research focuses on experimentally investigating and modeling the clustering of phosphorus dopant atoms with silicon interstitials. Damage recovery of 40keV Si+ implants in phosphorus doped wells is experimentally analyzed. The effects of background phosphorus concentration, self implant dose, and anneal temperature are investigated. Phosphorus concentrations ranging from 2.0 x 1017 to 4.0 x 1019 cm-3 and Si+ doses ranging from 5.0 x 1013 cm-2 to 2.0 x 1014 cm-2 are studied during 650-800°C anneals. A dramatic reduction in the number of interstitials bound in {311} defects with increasing phosphorus background concentration is observed. It is suggested that the reduction of interstitials in {311} defects at high phosphorus concentrations is due to the formation of phosphorus-interstitial clusters (PICs). The critical concentration for clustering (approximately 1.0 x 1019 cm-3 at 750°C) is strongly temperature dependent and in close agreement with the kink concentration of phosphorus diffusion. Information gained from these "well experiments" is applied to the study of direct phosphorus implantation. An experimental study is conducted on 40keV phosphorus implanted to a dose of 1.0 x 1014 cm-2 during 650-800°C anneals. Electrically inactive PICs are shown to form at concentrations below the solid solubility limit due to high interstitial supersaturations. Data useful for developing a model to accurately predict phosphorus diffusion under nonequilibrium conditions are extracted from the experimental results. A cluster-mediated diffusion model is developed using the Florida Object Oriented Process Simulator (FLOOPS). The nucleation of defects is controlled by the diffusion-limited competition for excess interstitials between PICs and {311} clusters. The release of interstitials is driven by cluster dissolution. Modeling results show a strong correlation to those experimentally observed over a wide temporal and thermal domain using a single set of parameters. Improvements in process simulator accuracy are demonstrated with respect to dopant activation, TED, and dose loss.
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Application of solid state NMR for the study of surface bound species and fossil fuels
DOE Office of Scientific and Technical Information (OSTI.GOV)
Althaus, Stacey
2014-01-01
In this study, stimulated echo with pulsed field gradients was used to measure the diffusion of two different solvents, water and hexane, in AP-MSN-2.7 and AP-MSN-3.7. The resulting data were then fit using two different methods. Based on these fits, the diffusion of hexane in AP-MSN-2.7 was shown to be slower than in the larger pores. This agrees well with our studies of catalytic activity, which show an increase in the reaction rate with the increase in pore size. Thus, both substrate inhibition and diffusion played a role in the decreased efficiency of the APMSN with small pore sizes.
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Edge Diffusion Flame Propagation and Stabilization Studied
NASA Technical Reports Server (NTRS)
Takahashi, Fumiaki; Katta, Viswanath R.
2004-01-01
In most practical combustion systems or fires, fuel and air are initially unmixed, thus forming diffusion flames. As a result of flame-surface interactions, the diffusion flame often forms an edge, which may attach to burner walls, spread over condensed fuel surfaces, jump to another location through the fuel-air mixture formed, or extinguish by destabilization (blowoff). Flame holding in combustors is necessary to achieve design performance and safe operation of the system. Fires aboard spacecraft behave differently from those on Earth because of the absence of buoyancy in microgravity. This ongoing in-house flame-stability research at the NASA Glenn Research Center is important in spacecraft fire safety and Earth-bound combustion systems.
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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.
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The formation of low-ionization emission in the halo of NGC 891
NASA Technical Reports Server (NTRS)
Sokolowski, James; Bland-Hawthorn, Jonathan
1993-01-01
Imaging and Spectroscopic study first revealed the presence of a diffuse ionized medium (DIM), having unusual excitation, pervading the lower halo of the edge-on spiral galaxy NGC 891. Emission from this DIM is strongest northeast of the nucleus, at radii between 2 and 8 kpc (hereafter region 1). The (N2)(lambda)6583/H(alpha) and (S2)(lambda) (lambda)6716,6731/H(alpha) ratios increase dramatically with z in region 1, from 0.6 and 0.5 respectively at z is approximately equal to 500 pc to 1.1 and 1.0 at z is approximately equal to 1 kpc, while nondetections of (O1)(lambda)6300 and (O3)(lambda)5007 emission yield upper limits of (O1)(lambda)6300/H(alpha) less than or equal to 0.05 and (O3)(lambda)5007/H(alpha) less than or equal to 0.15 for z less than 1 kpc. Previous photoionization models, using the radiation field from disk O and B stars, have been successful in reproducing the elevated (N2)(lambda)6583/H(alpha) and (S2)(lambda)(lambda)6716.6731/H(alpha) ratios observed. However, these radiation bounded models also produce significant (O3)(lambda)5007 emission, in conflict with the observed upper limit. Here, we report the results of new, matter bounded models for the photoionization of the DIM in region 1 of NGC 891.
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12. SW corner of 2nd floor of Tender Frame Shop ...
12. SW corner of 2nd floor of Tender Frame Shop showing heating duct and diffuser. - Central of Georgia Railway, Savannah Repair Shops & Terminal Facilities, Tender Frame Shop, Bounded by West Broad, Jones, West Boundary & Hull Streets, Savannah, Chatham County, GA
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Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space
Blainey, Paul C.; Graziano, Vito; Pérez-Berná, Ana J.; McGrath, William J.; Flint, S. Jane; San Martín, Carmen; Xie, X. Sunney; Mangel, Walter F.
2013-01-01
Precursor proteins used in the assembly of adenovirus virions must be processed by the virally encoded adenovirus proteinase (AVP) before the virus particle becomes infectious. An activated adenovirus proteinase, the AVP-pVIc complex, was shown to slide along viral DNA with an extremely fast one-dimensional diffusion constant, 21.0 ± 1.9 × 106 bp2/s. In principle, one-dimensional diffusion can provide a means for DNA-bound proteinases to locate and process DNA-bound substrates. Here, we show that this is correct. In vitro, AVP-pVIc complexes processed a purified virion precursor protein in a DNA-dependent reaction; in a quasi in vivo environment, heat-disrupted ts-1 virions, AVP-pVIc complexes processed five different precursor proteins in DNA-dependent reactions. Sliding of AVP-pVIc complexes along DNA illustrates a new biochemical mechanism by which a proteinase can locate its substrates, represents a new paradigm for virion maturation, and reveals a new way of exploiting the surface of DNA. PMID:23043138
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Strong diffusion formulation of Markov chain ensembles and its optimal weaker reductions
NASA Astrophysics Data System (ADS)
Güler, Marifi
2017-10-01
Two self-contained diffusion formulations, in the form of coupled stochastic differential equations, are developed for the temporal evolution of state densities over an ensemble of Markov chains evolving independently under a common transition rate matrix. Our first formulation derives from Kurtz's strong approximation theorem of density-dependent Markov jump processes [Stoch. Process. Their Appl. 6, 223 (1978), 10.1016/0304-4149(78)90020-0] and, therefore, strongly converges with an error bound of the order of lnN /N for ensemble size N . The second formulation eliminates some fluctuation variables, and correspondingly some noise terms, within the governing equations of the strong formulation, with the objective of achieving a simpler analytic formulation and a faster computation algorithm when the transition rates are constant or slowly varying. There, the reduction of the structural complexity is optimal in the sense that the elimination of any given set of variables takes place with the lowest attainable increase in the error bound. The resultant formulations are supported by numerical simulations.
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Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.
Zhang, Jichuan; Zhou, Ruobo; Inoue, Jin; Mikawa, Tsutomu; Ha, Taekjip
2014-04-01
Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20-500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.
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Apparatus and method for suppressing sound in a gas turbine engine powerplant
NASA Technical Reports Server (NTRS)
Wynosky, Thomas A. (Inventor); Mischke, Robert J. (Inventor)
1992-01-01
A method and apparatus for suppressing jet noise in a gas turbine engine powerplant 10 is disclosed. Various construction details are developed for providing sound suppression at sea level take-off operative conditions and not providing sound suppression at cruise operative conditions. In one embodiment, the powerplant 10 has a lobed mixer 152 between a primary flowpath 44 and a second flowpath 46, a diffusion region downstream of the lobed mixer region (first mixing region 76), and a deployable ejector/mixer 176 in the diffusion region which forms a second mixing region 78 having a diffusion flowpath 72 downstream of the ejector/mixer and sound absorbing structure 18 bounding the flowpath throughout the diffusion region. The method includes deploying the ejector/mixer 176 at take-off and stowing the ejector/mixer at cruise.
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NASA Astrophysics Data System (ADS)
Zheng, Jiashan
2017-05-01
This paper deals with a quasilinear chemotaxis-haptotaxis system with generalized logistic source {ut=∇ṡ(ϕ(u)∇u)-∇ṡ(u∇v)-∇ṡ(u∇w)+u(1-ur-1-w),vt=Δv-v+u,wt=-vw, under homogeneous Neumann boundary conditions in a smooth bounded domain {{{R}}N}(N≥slant 3) , with parameter r > 1, where the given function φ (u) is the nonlinear diffusion. Besides appropriate smoothness assumptions, in this paper it is only required that φ (u)≥slant {{C}φ}(u+1){{}m-1} for all u≥slant 0 with some {{C}φ}>0 and some m{>2-2N if 1
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Harnessing surface-bound enzymatic reactions to organize microcapsules in solution
Shklyaev, Oleg E.; Shum, Henry; Sen, Ayusman; Balazs, Anna C.
2016-01-01
By developing new computational models, we examine how enzymatic reactions on an underlying surface can be harnessed to direct the motion and organization of reagent-laden microcapsules in a fluid-filled microchannel. In the presence of appropriate reagents, surface-bound enzymes can act as pumps, which drive large-scale fluid flows. When the reagents diffuse through the capsules’ porous shells, they can react with enzymatic sites on the bottom surface. The ensuing reaction generates fluid density variations, which result in fluid flows. These flows carry the suspended microcapsules and drive them to aggregate into “colonies” on and near the enzyme-covered sites. This aggregation continues until the reagent has been depleted and the convection stops. We show that the shape of the assembled colonies can be tailored by patterning the distribution of enzymes on the surface. This fundamental physicochemical mechanism could have played a role in the self-organization of early biological cells (protocells) and can be used to regulate the autonomous motion and targeted delivery of microcarriers in microfluidic devices. PMID:27034990
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NASA Astrophysics Data System (ADS)
Komuro, Yoshitaka; Yamamoto, Hiroki; Kobayashi, Kazuo; Ohomori, Katsumi; Kozawa, Takahiro
2015-03-01
Extreme ultraviolet (EUV) lithography is the most promising candidate for the high-volume production of semiconductor devices with half-pitches of sub 10nm. An anion-bound polymer(ABP), in which at the anion part of onium salts is polymerized, has attracted much attention from the viewpoint of the control of acid diffusion. In this study, the acid generation mechanism in ABP films was investigated using γ and EUV radiolysis. On the basis of experimental results, the acid generation mechanism in anion-bound chemically amplified resists was proposed. The protons of acids are considered to be mainly generated through the reaction of phenyl radicals with diphenylsulfide radical cations that are produced through the hole transfer to the decomposition products of onium salts.
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NASA Astrophysics Data System (ADS)
Komuro, Yoshitaka; Yamamoto, Hiroki; Kobayashi, Kazuo; Utsumi, Yoshiyuki; Ohomori, Katsumi; Kozawa, Takahiro
2014-11-01
Extreme ultraviolet (EUV) lithography is the most promising candidate for the high-volume production of semiconductor devices with half-pitches of sub-10 nm. An anion-bound polymer (ABP), in which the anion part of onium salts is polymerized, has attracted much attention from the viewpoint of the control of acid diffusion. In this study, the acid generation mechanism in ABP films was investigated using electron (pulse), γ, and EUV radiolyses. On the basis of experimental results, the acid generation mechanism in anion-bound chemically amplified resists was proposed. The major path for proton generation in the absence of effective proton sources is considered to be the reaction of phenyl radicals with diphenylsulfide radical cations that are produced through hole transfer to the decomposition products of onium salts.
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Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel.
Reifenberger, Jeffrey G; Cao, Han; Dorfman, Kevin D
2018-02-13
We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.
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The OPGT/MJS plasma wave science team
NASA Technical Reports Server (NTRS)
Scarf, F. L.
1972-01-01
Some properties of a model magnetosphere for Saturn were studied in order to determine the bounds that can be set on surface field strength and trapped particle population. The primary observational constraint was that nonthermal radiation similar to the Jovian radio emissions must be undetectable from Earth. It is argued that for a Saturn surface field of approximately one gauss, particles that are energized as they diffuse in from the magnetopause with conservation of magnetic moment will produce synchrotron radiation levels that are undetectable at a range of 9.5 AU. The plasma instabilities that heat the oncoming wind particles at the bow shock and others that can limit the stably-trapped flux levels are also discussed.
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NASA Astrophysics Data System (ADS)
Cusimano, N.; Gerardo-Giorda, L.
2018-06-01
Classical models of electrophysiology do not typically account for the effects of high structural heterogeneity in the spatio-temporal description of excitation waves propagation. We consider a modification of the Monodomain model obtained by replacing the diffusive term of the classical formulation with a fractional power of the operator, defined in the spectral sense. The resulting nonlocal model describes different levels of tissue heterogeneity as the fractional exponent is varied. The numerical method for the solution of the fractional Monodomain relies on an integral representation of the nonlocal operator combined with a finite element discretisation in space, allowing to handle in a natural way bounded domains in more than one spatial dimension. Numerical tests in two spatial dimensions illustrate the features of the model. Activation times, action potential duration and its dispersion throughout the domain are studied as a function of the fractional parameter: the expected peculiar behaviour driven by tissue heterogeneities is recovered.
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Modelling Tethered Enzymatic Reactions
NASA Astrophysics Data System (ADS)
Solis Salas, Citlali; Goyette, Jesse; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel; Allard, Jun; Maini, Philip; Dushek, Omer
Enzymatic reactions are key to cell functioning, and whilst much work has been done in protein interaction in cases where diffusion is possible, interactions of tethered proteins are poorly understood. Yet, because of the large role cell membranes play in enzymatic reactions, several reactions may take place where one of the proteins is bound to a fixed point in space. We develop a model to characterize tethered signalling between the phosphatase SHP-1 interacting with a tethered, phosphorylated protein. We compare our model to experimental data obtained using surface plasmon resonance (SPR). We show that a single SPR experiment recovers 5 independent biophysical/biochemical constants. We also compare the results between a three dimensional model and a two dimensional model. The work gives the opportunity to use known techniques to learn more about signalling processes, and new insights into how enzyme tethering alters cellular signalling. With support from the Mexican Council for Science and Technology (CONACyT), the Public Education Secretariat (SEP), and the Mexican National Autonomous University's Foundation (Fundacion UNAM).
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Ionic liquids behave as dilute electrolyte solutions
Gebbie, Matthew A.; Valtiner, Markus; Banquy, Xavier; Fox, Eric T.; Henderson, Wesley A.; Israelachvili, Jacob N.
2013-01-01
We combine direct surface force measurements with thermodynamic arguments to demonstrate that pure ionic liquids are expected to behave as dilute weak electrolyte solutions, with typical effective dissociated ion concentrations of less than 0.1% at room temperature. We performed equilibrium force–distance measurements across the common ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C4mim][NTf2]) using a surface forces apparatus with in situ electrochemical control and quantitatively modeled these measurements using the van der Waals and electrostatic double-layer forces of the Derjaguin–Landau–Verwey–Overbeek theory with an additive repulsive steric (entropic) ion–surface binding force. Our results indicate that ionic liquids screen charged surfaces through the formation of both bound (Stern) and diffuse electric double layers, where the diffuse double layer is comprised of effectively dissociated ionic liquid ions. Additionally, we used the energetics of thermally dissociating ions in a dielectric medium to quantitatively predict the equilibrium for the effective dissociation reaction of [C4mim][NTf2] ions, in excellent agreement with the measured Debye length. Our results clearly demonstrate that, outside of the bound double layer, most of the ions in [C4mim][NTf2] are not effectively dissociated and thus do not contribute to electrostatic screening. We also provide a general, molecular-scale framework for designing ionic liquids with significantly increased dissociated charge densities via judiciously balancing ion pair interactions with bulk dielectric properties. Our results clear up several inconsistencies that have hampered scientific progress in this important area and guide the rational design of unique, high–free-ion density ionic liquids and ionic liquid blends. PMID:23716690
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Electrostatic Rate Enhancement and Transient Complex of Protein-Protein Association
Alsallaq, Ramzi; Zhou, Huan-Xiang
2012-01-01
The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to ~105 – 106 M−1s−1. Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys. J. 1997;73:2441–2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by kD = kD0 exp(−
*/ kBT), where kD and kD0 are the rates in the presence and absence of electrostatic interactions, respectively, * is the average electrostatic interaction energy in a “transient-complex” ensemble, and kBT is thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007, 15:215–224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. PMID:17932929 -
Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander
2011-01-01
The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.
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Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander
2011-01-01
Background The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. Methodology/Principal Findings This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Conclusions Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization. PMID:21858215
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Managed care and the diffusion of endoscopy in fee-for-service Medicare.
Mobley, Lee Rivers; Subramanian, Sujha; Koschinsky, Julia; Frech, H E; Trantham, Laurel Clayton; Anselin, Luc
2011-12-01
To determine whether Medicare managed care penetration impacted the diffusion of endoscopy services (sigmoidoscopy, colonoscopy) among the fee-for-service (FFS) Medicare population during 2001-2006. We model utilization rates for colonoscopy or sigmoidoscopy as impacted by both market supply and demand factors. We use spatial regression to perform ecological analysis of county-area utilization rates over two time intervals (2001-2003, 2004-2006) following Medicare benefits expansion in 2001 to cover colonoscopy for persons of average risk. We examine each technology in separate cross-sectional regressions estimated over early and later periods to assess differential effects on diffusion over time. We discuss selection factors in managed care markets and how failure to control perfectly for market selection might impact our managed care spillover estimates. Areas with worse socioeconomic conditions have lower utilization rates, especially for colonoscopy. Holding constant statistically the socioeconomic factors, we find that managed care spillover effects onto FFS Medicare utilization rates are negative for colonoscopy and positive for sigmoidoscopy. The spatial lag estimates are conservative and interpreted as a lower bound on true effects. Our findings suggest that managed care presence fostered persistence of the older technology during a time when it was rapidly being replaced by the newer technology. © Health Research and Educational Trust.
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Crowding and hopping in a protein’s diffusive transport on DNA
NASA Astrophysics Data System (ADS)
Koslover, Elena F.; Díaz de la Rosa, Mario; Spakowitz, Andrew J.
2017-02-01
Diffusion is a ubiquitous phenomenon that impacts virtually all processes that involve random fluctuations, and as such, the foundational work of Smoluchowski has proven to be instrumental in addressing innumerable problems. Here, we focus on a critical biological problem that relies on diffusive transport and is analyzed using a probabilistic treatment originally developed by Smoluchowski. The search of a DNA binding protein for its specific target site is believed to rely on non-specific binding to DNA with transient hops along the chain. In this work, we address the impact of protein crowding along the DNA on the transport of a DNA-binding protein. The crowders dramatically alter the dynamics of the protein while bound to the DNA, resulting in single-file transport that is subdiffusive in nature. However, transient unbinding and hopping results in a long-time behavior (shown to be superdiffusive) that is qualitatively unaffected by the crowding on the DNA. Thus, hopping along the chain mitigates the role that protein crowding has in restricting the translocation dynamics along the chain. The superdiffusion coefficient is influenced by the quantitative values of the effective binding rate, which is influenced by protein crowding. We show that vacancy fraction and superdiffusion coefficient exhibits a non-monotonic relationship under many circumstances. We leverage analytical theory and dynamic Monte Carlo simulations to address this problem. With several additional contributions, the core of our modeling work adopts a reaction-diffusion framework that is based on Smoluchowski’s original work.
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Reversible geminate recombination of hydrogen-bonded water molecule pair
NASA Astrophysics Data System (ADS)
Markovitch, Omer; Agmon, Noam
2008-08-01
The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.
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NASA Astrophysics Data System (ADS)
Korb, J.-P.; Xu, Shu; Jonas, J.
1993-02-01
A theory of dipolar relaxation by translational diffusion of a nonwetting liquid confined in model porous media is presented. We obtain expressions of the rates of spin-lattice relaxation 1/T1, spin-spin relaxation 1/T2, and spin-lattice relaxation in the rotating frame 1/T1ρ, which depend on the average pore size d. The frequency variations of these rates are intermediate between the two-dimensional and three-dimensional results. At small frequency they vary logarithmically for small d and tend progressively to a constant with increasing d. For small pore sizes we obtain quadratic confinement dependences of these rates (∝1/d2), at variance with the linear (∝1/d) relation coming from the biphasic fast exchange model usually applied for a wetting liquid in porous media. We apply such a theory to the 1H NMR relaxation of methylcyclohexane liquid in sol-gel porous silica glasses with a narrow pore-size distribution. The experiments confirm the theoretical predictions for very weak interacting solvent in porous silica glasses of pore sizes varying in the range of 18.4-87.2 Å and in the bulk. At the limit of small pores, the logarithmic frequency dependencies of 1/T1ρ and 1/T1 observed over several decades of frequency are interpreted with a model of unbounded two-dimensional diffusion in a layered geometry. The leveling off of the 1/T1ρ low-frequency dependence is interpreted in terms of the bounded two-dimensional diffusion due to the finite length L of the pores. An estimate of a finite size of L=100 Å is in excellent agreement with the experimental results of the transmission electron microscopy study of platinium-carbon replicated xerogels.
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Diffusion with resetting inside a circle
NASA Astrophysics Data System (ADS)
Chatterjee, Abhinava; Christou, Christos; Schadschneider, Andreas
2018-06-01
We study the Brownian motion of a particle in a bounded circular two-dimensional domain in search for a stationary target on the boundary of the domain. The process switches between two modes: one where it performs a two-dimensional diffusion inside the circle and one where it diffuses along the one-dimensional boundary. During the process, the Brownian particle resets to its initial position with a constant rate r . The Fokker-Planck formalism allows us to calculate the mean time to absorption (MTA) as well as the optimal resetting rate for which the MTA is minimized. From the derived analytical results the parameter regions where resetting reduces the search time can be specified. We also provide a numerical method for the verification of our results.
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Time series analysis of particle tracking data for molecular motion on the cell membrane.
Ying, Wenxia; Huerta, Gabriel; Steinberg, Stanly; Zúñiga, Martha
2009-11-01
Biophysicists use single particle tracking (SPT) methods to probe the dynamic behavior of individual proteins and lipids in cell membranes. The mean squared displacement (MSD) has proven to be a powerful tool for analyzing the data and drawing conclusions about membrane organization, including features like lipid rafts, protein islands, and confinement zones defined by cytoskeletal barriers. Here, we implement time series analysis as a new analytic tool to analyze further the motion of membrane proteins. The experimental data track the motion of 40 nm gold particles bound to Class I major histocompatibility complex (MHCI) molecules on the membranes of mouse hepatoma cells. Our first novel result is that the tracks are significantly autocorrelated. Because of this, we developed linear autoregressive models to elucidate the autocorrelations. Estimates of the signal to noise ratio for the models show that the autocorrelated part of the motion is significant. Next, we fit the probability distributions of jump sizes with four different models. The first model is a general Weibull distribution that shows that the motion is characterized by an excess of short jumps as compared to a normal random walk. We also fit the data with a chi distribution which provides a natural estimate of the dimension d of the space in which a random walk is occurring. For the biological data, the estimates satisfy 1 < d < 2, implying that particle motion is not confined to a line, but also does not occur freely in the plane. The dimension gives a quantitative estimate of the amount of nanometer scale obstruction met by a diffusing molecule. We introduce a new distribution and use the generalized extreme value distribution to show that the biological data also have an excess of long jumps as compared to normal diffusion. These fits provide novel estimates of the microscopic diffusion constant. Previous MSD analyses of SPT data have provided evidence for nanometer-scale confinement zones that restrict lateral diffusion, supporting the notion that plasma membrane organization is highly structured. Our demonstration that membrane protein motion is autocorrelated and is characterized by an excess of both short and long jumps reinforces the concept that the membrane environment is heterogeneous and dynamic. Autocorrelation analysis and modeling of the jump distributions are powerful new techniques for the analysis of SPT data and the development of more refined models of membrane organization. The time series analysis also provides several methods of estimating the diffusion constant in addition to the constant provided by the mean squared displacement. The mean squared displacement for most of the biological data shows a power law behavior rather the linear behavior of Brownian motion. In this case, we introduce the notion of an instantaneous diffusion constant. All of the diffusion constants show a strong consistency for most of the biological data.
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1981-01-01
skin; possibly the compound is bound to anionic polymers. These results do not allow appendageal diffusion (through hair follicles) to be...R.M. "Carbamylation and Decarbamylation of Acetylcholinesterase: Effect of Choline , 3,3-dimethyl-l-butanol and some Allosteric Effectors". J. Neurocnem
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Joanne Wang, C; Li, Xiong; Lin, Benjamin; Shim, Sangwoo; Ming, Guo-Li; Levchenko, Andre
2008-02-01
Neuronal growth cones contain sophisticated molecular machinery precisely regulating their migration in response to complex combinatorial gradients of diverse external cues. The details of this regulation are still largely unknown, in part due to limitations of the currently available experimental techniques. Microfluidic devices have been shown to be capable of generating complex, stable and precisely controlled chemical gradients, but their use in studying growth cone migration has been limited in part due to the effects of shear stress. Here we describe a microfluidics-based turning-assay chip designed to overcome this issue. In addition to generating precise gradients of soluble guidance cues, the chip can also fabricate complex composite gradients of diffusible and surface-bound guidance cues that mimic the conditions the growth cones realistically counter in vivo. Applying this assay to Xenopus embryonic spinal neurons, we demonstrate that the presence of a surface-bound laminin gradient can finely tune the polarity of growth cone responses (repulsion or attraction) to gradients of brain-derived neurotrophic factor (BDNF), with the guidance outcome dependent on the mean BDNF concentration. The flexibility inherent in this assay holds significant potential for refinement of our understanding of nervous system development and regeneration, and can be extended to elucidate other cellular processes involving chemotaxis of shear sensitive cells.
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Mantle dynamics in super-Earths: Post-perovskite rheology and self-regulation of viscosity
NASA Astrophysics Data System (ADS)
Tackley, P. J.; Ammann, M.; Brodholt, J. P.; Dobson, D. P.; Valencia, D.
2013-07-01
The discovery of extra-solar "super-Earth" planets with sizes up to twice that of Earth has prompted interest in their possible lithosphere and mantle dynamics and evolution. Simple scalings suggest that super-Earths are more likely than an equivalent Earth-sized planet to be undergoing plate tectonics. Generally, viscosity and thermal conductivity increase with pressure while thermal expansivity decreases, resulting in lower convective vigour in the deep mantle, which, if extralopated to the largest super-Earths might, according to conventional thinking, result in no convection in their deep mantles due to the very low effective Rayleigh number. Here we evaluate this. First, as the mantle of a super-Earth is made mostly of post-perovskite we here extend the density functional theory (DFT) calculations of post-perovskite activation enthalpy of to a pressure of 1 TPa, for both slowest diffusion (upper-bound rheology) and fastest diffusion (lower-bound rheology) directions. Along a 1600 K adiabat the upper-bound rheology would lead to a post-perovskite layer of a very high (˜1030 Pa s) but relatively uniform viscosity, whereas the lower-bound rheology leads to a post-perovskite viscosity increase of ˜7 orders of magnitude with depth; in both cases the deep mantle viscosity would be too high for convection. Second, we use these DFT-calculated values in statistically steady-state numerical simulations of mantle convection and lithosphere dynamics of planets with up to ten Earth masses. The models assume a compressible mantle including depth-dependence of material properties and plastic yielding induced plate-like lithospheric behaviour. Results confirm the likelihood of plate tectonics for planets with Earth-like surface conditions (temperature and water) and show a self-regulation of deep mantle temperature. The deep mantle is not adiabatic; instead feedback between internal heating, temperature and viscosity regulates the temperature such that the viscosity has the value needed to facilitate convective loss of the radiogenic heat, which results in a very hot perovskite layer for the upper-bound rheology, a super-adiabatic perovskite layer for the lower-bound rheology, and an azimuthally-averaged viscosity of no more than 1026 Pa s. Convection in large super-Earths is characterised by large upwellings (even with zero basal heating) and small, time-dependent downwellings, which for large super-Earths merge into broad downwellings. In the context of planetary evolution, if, as is likely, a super-Earth was extremely hot/molten after its formation, it is thus likely that even after billions of years its deep interior is still extremely hot and possibly substantially molten with a "super basal magma ocean" - a larger version of the proposal of Labrosse et al. (Labrosse, S., Hernlund, J.W., Coltice, N. [2007]. Nature 450, 866-869), although this depends on presently unknown melt-solid density contrast and solidus.
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NMR investigation of the short-chain ionic surfactant-water systems.
Popova, M V; Tchernyshev, Y S; Michel, D
2004-02-03
The structure and dynamics of surfactant molecules [CH3(CH2)7COOK] in heavy water solutions were investigated by 1H and 2H NMR. A double-exponential attenuation of the spin-echo amplitude in a Carr-Purcell-Meiboom-Gill experiment was found. We expect correspondence to both bounded and monomeric states. At high concentrations in the NMR self-diffusion measurements also a double-exponential decay of the spin-echo signal versus the square of the dc magnetic gradient was observed. The slow component of the diffusion process is caused by micellar aggregates, while the fast component is the result of the self-diffusion of the monomers through the micelles. The self-diffusion studies indicate that the form of micelles changes with increasing total surfactant concentration. The critical temperature range for self-association is reflected in the 1H transverse relaxation.
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Spatiotemporal evolution in a (2+1)-dimensional chemotaxis model
NASA Astrophysics Data System (ADS)
Banerjee, Santo; Misra, Amar P.; Rondoni, L.
2012-01-01
Simulations are performed to investigate the nonlinear dynamics of a (2+1)-dimensional chemotaxis model of Keller-Segel (KS) type, with a logistic growth term. Because of its ability to display auto-aggregation, the KS model has been widely used to simulate self-organization in many biological systems. We show that the corresponding dynamics may lead to steady-states, to divergencies in a finite time as well as to the formation of spatiotemporal irregular patterns. The latter, in particular, appears to be chaotic in part of the range of bounded solutions, as demonstrated by the analysis of wavelet power spectra. Steady-states are achieved with sufficiently large values of the chemotactic coefficient (χ) and/or with growth rates r below a critical value rc. For r>rc, the solutions of the differential equations of the model diverge in a finite time. We also report on the pattern formation regime, for different values of χ, r and of the diffusion coefficient D.
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A Lagrangian Simulation of Subsonic Aircraft Exhaust Emissions
NASA Technical Reports Server (NTRS)
Schoeberl, M. R.; Morris, G. A.
1999-01-01
To estimate the effect of subsonic and supersonic aircraft exhaust on the stratospheric concentration of NO(y), we employ a trajectory model initialized with air parcels based on the standard release scenarios. The supersonic exhaust simulations are in good agreement with 2D and 3D model results and show a perturbation of about 1-2 ppbv of NO(y) in the stratosphere. The subsonic simulations show that subsonic emissions are almost entirely trapped below the 380 K potential temperature surface. Our subsonic results contradict results from most other models, which show exhaust products penetrating above 380 K, as summarized. The disagreement can likely be attributed to an excessive vertical diffusion in most models of the strong vertical gradient in NO(y) that forms at the boundary between the emission zone and the stratosphere above 380 K. Our results suggest that previous assessments of the impact of subsonic exhaust emission on the stratospheric region above 380 K should be considered to be an upper bound.
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Parameter optimization for surface flux transport models
NASA Astrophysics Data System (ADS)
Whitbread, T.; Yeates, A. R.; Muñoz-Jaramillo, A.; Petrie, G. J. D.
2017-11-01
Accurate prediction of solar activity calls for precise calibration of solar cycle models. Consequently we aim to find optimal parameters for models which describe the physical processes on the solar surface, which in turn act as proxies for what occurs in the interior and provide source terms for coronal models. We use a genetic algorithm to optimize surface flux transport models using National Solar Observatory (NSO) magnetogram data for Solar Cycle 23. This is applied to both a 1D model that inserts new magnetic flux in the form of idealized bipolar magnetic regions, and also to a 2D model that assimilates specific shapes of real active regions. The genetic algorithm searches for parameter sets (meridional flow speed and profile, supergranular diffusivity, initial magnetic field, and radial decay time) that produce the best fit between observed and simulated butterfly diagrams, weighted by a latitude-dependent error structure which reflects uncertainty in observations. Due to the easily adaptable nature of the 2D model, the optimization process is repeated for Cycles 21, 22, and 24 in order to analyse cycle-to-cycle variation of the optimal solution. We find that the ranges and optimal solutions for the various regimes are in reasonable agreement with results from the literature, both theoretical and observational. The optimal meridional flow profiles for each regime are almost entirely within observational bounds determined by magnetic feature tracking, with the 2D model being able to accommodate the mean observed profile more successfully. Differences between models appear to be important in deciding values for the diffusive and decay terms. In like fashion, differences in the behaviours of different solar cycles lead to contrasts in parameters defining the meridional flow and initial field strength.
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Measuring binding of protein to gel-bound ligands using magnetic levitation.
Shapiro, Nathan D; Mirica, Katherine A; Soh, Siowling; Phillips, Scott T; Taran, Olga; Mace, Charles R; Shevkoplyas, Sergey S; Whitesides, George M
2012-03-28
This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (>70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems.
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Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation
Shapiro, Nathan D.; Mirica, Katherine A.; Soh, Siowling; Phillips, Scott T.; Taran, Olga; Mace, Charles R.; Shevkoplyas, Sergey S.; Whitesides, George M.
2012-01-01
This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (> 70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems. PMID:22364170
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Humplik, Thomas; Stirrup, Emily K.; Grillet, Anne M.; ...
2016-04-30
The transient transport of electrolytes in thermally-activated batteries is studied in this paper using electron probe micro-analysis (EPMA), demonstrating the robust capability of EPMA as a useful tool for studying and quantifying mass transport within porous materials, particularly in difficult environments where classical flow measurements are challenging. By tracking the mobility of bromine and potassium ions from the electrolyte stored within the separator into the lithium silicon anode and iron disulfide cathode, we are able to quantify the transport mechanisms and physical properties of the electrodes including permeability and tortuosity. Due to the micron to submicron scale porous structure ofmore » the initially dry anode, a fast capillary pressure driven flow is observed into the anode from which we are able to set a lower bound on the permeability of 10 -1 mDarcy. The transport into the cathode is diffusion-limited because the cathode originally contained some electrolyte before activation. Finally, using a transient one-dimensional diffusion model, we estimate the tortuosity of the cathode electrode to be 2.8 ± 0.8.« less
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Transient Ejector Analysis (TEA) code user's guide
NASA Technical Reports Server (NTRS)
Drummond, Colin K.
1993-01-01
A FORTRAN computer program for the semi analytic prediction of unsteady thrust augmenting ejector performance has been developed, based on a theoretical analysis for ejectors. That analysis blends classic self-similar turbulent jet descriptions with control-volume mixing region elements. Division of the ejector into an inlet, diffuser, and mixing region allowed flexibility in the modeling of the physics for each region. In particular, the inlet and diffuser analyses are simplified by a quasi-steady-analysis, justified by the assumption that pressure is the forcing function in those regions. Only the mixing region is assumed to be dominated by viscous effects. The present work provides an overview of the code structure, a description of the required input and output data file formats, and the results for a test case. Since there are limitations to the code for applications outside the bounds of the test case, the user should consider TEA as a research code (not as a production code), designed specifically as an implementation of the proposed ejector theory. Program error flags are discussed, and some diagnostic routines are presented.
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Biochemical transport modeling, estimation, and detection in realistic environments
NASA Astrophysics Data System (ADS)
Ortner, Mathias; Nehorai, Arye
2006-05-01
Early detection and estimation of the spread of a biochemical contaminant are major issues for homeland security applications. We present an integrated approach combining the measurements given by an array of biochemical sensors with a physical model of the dispersion and statistical analysis to solve these problems and provide system performance measures. We approximate the dispersion model of the contaminant in a realistic environment through numerical simulations of reflected stochastic diffusions describing the microscopic transport phenomena due to wind and chemical diffusion using the Feynman-Kac formula. We consider arbitrary complex geometries and account for wind turbulence. Localizing the dispersive sources is useful for decontamination purposes and estimation of the cloud evolution. To solve the associated inverse problem, we propose a Bayesian framework based on a random field that is particularly powerful for localizing multiple sources with small amounts of measurements. We also develop a sequential detector using the numerical transport model we propose. Sequential detection allows on-line analysis and detecting wether a change has occurred. We first focus on the formulation of a suitable sequential detector that overcomes the presence of unknown parameters (e.g. release time, intensity and location). We compute a bound on the expected delay before false detection in order to decide the threshold of the test. For a fixed false-alarm rate, we obtain the detection probability of a substance release as a function of its location and initial concentration. Numerical examples are presented for two real-world scenarios: an urban area and an indoor ventilation duct.
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Study of moisture absorption by an organoplastic
NASA Astrophysics Data System (ADS)
Aniskevich, A. N.; Yanson, Yu. O.
1991-07-01
A complex experimental study of the state of sorbed moisture in a unidirectionally reinforced organoplastic was conducted. The methods of TG, DSC, DTA, and NMR showed that moisture absorption in OP is reversible up to 8%, the sorbed moisture does not crystallize in the temperature range from -70 to 0 °C, it is finely dispersely distributed and is in the strongly and weakly bound state, and there is almost no free moisture. The results of the sorption experiments conducted on OP and its structural components: microplastic and EDT-10 binder, in a wide range of temperature-humidity conditions and the data from physical studies showed that moisture absorption in the materials basically takes place by diffusion and is satisfactorily described by a phenomenological model based on the Fick equation. A method of accelerated determination of the sorption characteristics of anisotropic composite materials was developed, using the introduced concept of the fictitious diffusion coefficient and the extrapolation method of determining the limiting moisture content. The features of migration of moisture on the interface in a multiphase system were investigated, and the possibility of successive calculation estimation of the sorption characteristics of an organoplastic at different structural levels was demonstrated: components—unidirectionally reinforced composite—model laminated article. The tested phenomenological model of the sorption process and the experimentally obtained values of the characteristics of the material were the basis for a method of calculation determination of the resource of moisture-proofing properties of a model multilayer article of CM in nonstationary external conditions.
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Bounding species distribution models
Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.
2011-01-01
Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.
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Bounding Species Distribution Models
NASA Technical Reports Server (NTRS)
Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.
2011-01-01
Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].
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A reaction-diffusion within-host HIV model with cell-to-cell transmission.
Ren, Xinzhi; Tian, Yanni; Liu, Lili; Liu, Xianning
2018-06-01
In this paper, a reaction-diffusion within-host HIV model is proposed. It incorporates cell mobility, spatial heterogeneity and cell-to-cell transmission, which depends on the diffusion ability of the infected cells. In the case of a bounded domain, the basic reproduction number [Formula: see text] is established and shown as a threshold: the virus-free steady state is globally asymptotically stable if [Formula: see text] and the virus is uniformly persistent if [Formula: see text]. The explicit formula for [Formula: see text] and the global asymptotic stability of the constant positive steady state are obtained for the case of homogeneous space. In the case of an unbounded domain and [Formula: see text], the existence of the traveling wave solutions is proved and the minimum wave speed [Formula: see text] is obtained, providing the mobility of infected cells does not exceed that of the virus. These results are obtained by using Schauder fixed point theorem, limiting argument, LaSalle's invariance principle and one-side Laplace transform. It is found that the asymptotic spreading speed may be larger than the minimum wave speed via numerical simulations. However, our simulations show that it is possible either to underestimate or overestimate the spread risk [Formula: see text] if the spatial averaged system is used rather than one that is spatially explicit. The spread risk may also be overestimated if we ignore the mobility of the cells. It turns out that the minimum wave speed could be either underestimated or overestimated as long as the mobility of infected cells is ignored.
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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography
NASA Astrophysics Data System (ADS)
Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D'Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.
2017-01-01
Riboswitches are structural RNA elements that are generally located in the 5‧ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography
Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D’Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.
2017-01-01
Riboswitches are structural RNA elements that are generally located in the 5′ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform1–3. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time4. Here we use femtosecond X-ray free electron laser (XFEL) pulses5,6 to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes. PMID:27841871
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Exploring L1 model space in search of conductivity bounds for the MT problem
NASA Astrophysics Data System (ADS)
Wheelock, B. D.; Parker, R. L.
2013-12-01
Geophysical inverse problems of the type encountered in electromagnetic techniques are highly non-unique. As a result, any single inverted model, though feasible, is at best inconclusive and at worst misleading. In this paper, we use modified inversion methods to establish bounds on electrical conductivity within a model of the earth. Our method consists of two steps, each making use of the 1-norm in model regularization. Both 1-norm minimization problems are framed without approximation as non-negative least-squares (NNLS) problems. First, we must identify a parsimonious set of regions within the model for which upper and lower bounds on average conductivity will be sought. This is accomplished by minimizing the 1-norm of spatial variation, which produces a model with a limited number of homogeneous regions; in fact, the number of homogeneous regions will never be greater than the number of data, regardless of the number of free parameters supplied. The second step establishes bounds for each of these regions with pairs of inversions. The new suite of inversions also uses a 1-norm penalty, but applied to the conductivity values themselves, rather than the spatial variation thereof. In the bounding step we use the 1-norm of our model parameters because it is proportional to average conductivity. For a lower bound on average conductivity, the 1-norm within a bounding region is minimized. For an upper bound on average conductivity, the 1-norm everywhere outside a bounding region is minimized. The latter minimization has the effect of concentrating conductance into the bounding region. Taken together, these bounds are a measure of the uncertainty in the associated region of our model. Starting with a blocky inverse solution is key in the selection of the bounding regions. Of course, there is a tradeoff between resolution and uncertainty: an increase in resolution (smaller bounding regions), results in greater uncertainty (wider bounds). Minimization of the 1-norm of spatial variation delivers the fewest possible regions defined by a mean conductivity, the quantity we wish to bound. Thus, these regions present a natural set for which the most narrow and discriminating bounds can be found. For illustration, we apply these techniques to synthetic magnetotelluric (MT) data sets resulting from one-dimensional (1D) earth models. In each case we find that with realistic data coverage, any single inverted model can often stray from the truth, while the computed bounds on an encompassing region contain both the inverted and the true conductivities, indicating that our measure of model uncertainty is robust. Such estimates of uncertainty for conductivity can then be translated to bounds on important petrological parameters such as mineralogy, porosity, saturation, and fluid type.
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Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching
Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W.; Knoch, Tobias A.; Waldeck, Waldemar; Langowski, Jörg
2003-01-01
Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of ∼13 s. PMID:12719264
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Analyzing intracellular binding and diffusion with continuous fluorescence photobleaching.
Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W; Knoch, Tobias A; Waldeck, Waldemar; Langowski, Jörg
2003-05-01
Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of approximately 13 s.
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Supported Lipid Bilayer/Carbon Nanotube Hybrids
NASA Astrophysics Data System (ADS)
Zhou, Xinjian; Moran-Mirabal, Jose; Craighead, Harold; McEuen, Paul
2007-03-01
We form supported lipid bilayers on single-walled carbon nanotubes and use this hybrid structure to probe the properties of lipid membranes and their functional constituents. We first demonstrate membrane continuity and lipid diffusion over the nanotube. A membrane-bound tetanus toxin protein, on the other hand, sees the nanotube as a diffusion barrier whose strength depends on the diameter of the nanotube. Finally, we present results on the electrical detection of specific binding of streptavidin to biotinylated lipids with nanotube field effect transistors. Possible techniques to extract dynamic information about the protein binding events will also be discussed.
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NASA Astrophysics Data System (ADS)
Ginsberg, Naomi
2015-03-01
The migration of Frenkel excitons, tightly-bound electron-hole pairs, in polymeric organic semiconducting films is critical to the efficiency of bulk heterojunction solar cells. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton diffusion lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore.
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Narrow Escape of Interacting Diffusing Particles
NASA Astrophysics Data System (ADS)
Agranov, Tal; Meerson, Baruch
2018-03-01
The narrow escape problem deals with the calculation of the mean escape time (MET) of a Brownian particle from a bounded domain through a small hole on the domain's boundary. Here we develop a formalism which allows us to evaluate the nonescape probability of a gas of diffusing particles that may interact with each other. In some cases the nonescape probability allows us to evaluate the MET of the first particle. The formalism is based on the fluctuating hydrodynamics and the recently developed macroscopic fluctuation theory. We also uncover an unexpected connection between the narrow escape of interacting particles and thermal runaway in chemical reactors.
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Boggara, Mohan; Athmakuri, Krishna; Srivastava, Sunit; Cole, Richard; Kane, Ravi S
2013-02-01
A number of studies have shown that receptors of the epidermal growth factor receptor family (ErbBs) exist as higher-order oligomers (clusters) in cell membranes in addition to their monomeric and dimeric forms. Characterizing the lateral diffusion of such clusters may provide insights into their dynamics and help elucidate their functional relevance. To that end, we used single particle tracking to study the diffusion of clusters of the epidermal growth factor (EGF) receptor (EGFR; ErbB1) containing bound fluorescently-labeled ligand, EGF. EGFR clusters had a median diffusivity of 6.8×10(-11)cm(2)/s and were found to exhibit different modes of transport (immobile, simple, confined, and directed) similar to that previously reported for single EGFR molecules. Disruption of actin filaments increased the median diffusivity of EGFR clusters to 10.3×10(-11)cm(2)/s, while preserving the different modes of diffusion. Interestingly, disruption of microtubules rendered EGFR clusters nearly immobile. Our data suggests that microtubules may play an important role in the diffusion of EGFR clusters either directly or perhaps indirectly via other mechanisms. To our knowledge, this is the first report probing the effect of the cytoskeleton on the diffusion of EGFR clusters in the membranes of live cells. Copyright © 2012 Elsevier B.V. All rights reserved.
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Chemical Transport in a Fissured Rock: Verification of a Numerical Model
NASA Astrophysics Data System (ADS)
Rasmuson, A.; Narasimhan, T. N.; Neretnieks, I.
1982-10-01
Numerical models for simulating chemical transport in fissured rocks constitute powerful tools for evaluating the acceptability of geological nuclear waste repositories. Due to the very long-term, high toxicity of some nuclear waste products, the models are required to predict, in certain cases, the spatial and temporal distribution of chemical concentration less than 0.001% of the concentration released from the repository. Whether numerical models can provide such accuracies is a major question addressed in the present work. To this end we have verified a numerical model, TRUMP, which solves the advective diffusion equation in general three dimensions, with or without decay and source terms. The method is based on an integrated finite difference approach. The model was verified against known analytic solution of the one-dimensional advection-diffusion problem, as well as the problem of advection-diffusion in a system of parallel fractures separated by spherical particles. The studies show that as long as the magnitude of advectance is equal to or less than that of conductance for the closed surface bounding any volume element in the region (that is, numerical Peclet number <2), the numerical method can indeed match the analytic solution within errors of ±10-3% or less. The realistic input parameters used in the sample calculations suggest that such a range of Peclet numbers is indeed likely to characterize deep groundwater systems in granitic and ancient argillaceous systems. Thus TRUMP in its present form does provide a viable tool for use in nuclear waste evaluation studies. A sensitivity analysis based on the analytic solution suggests that the errors in prediction introduced due to uncertainties in input parameters are likely to be larger than the computational inaccuracies introduced by the numerical model. Currently, a disadvantage in the TRUMP model is that the iterative method of solving the set of simultaneous equations is rather slow when time constants vary widely over the flow region. Although the iterative solution may be very desirable for large three-dimensional problems in order to minimize computer storage, it seems desirable to use a direct solver technique in conjunction with the mixed explicit-implicit approach whenever possible. Work in this direction is in progress.
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Global behavior analysis for stochastic system of 1,3-PD continuous fermentation
NASA Astrophysics Data System (ADS)
Zhu, Xi; Kliemann, Wolfgang; Li, Chunfa; Feng, Enmin; Xiu, Zhilong
2017-12-01
Global behavior for stochastic system of continuous fermentation in glycerol bio-dissimilation to 1,3-propanediol by Klebsiella pneumoniae is analyzed in this paper. This bioprocess cannot avoid the stochastic perturbation caused by internal and external disturbance which reflect on the growth rate. These negative factors can limit and degrade the achievable performance of controlled systems. Based on multiplicity phenomena, the equilibriums and bifurcations of the deterministic system are analyzed. Then, a stochastic model is presented by a bounded Markov diffusion process. In order to analyze the global behavior, we compute the control sets for the associated control system. The probability distributions of relative supports are also computed. The simulation results indicate that how the disturbed biosystem tend to stationary behavior globally.
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Laboratory experiments were conducted to simulate radiopollutant effluents released to the atmosphere from two standard-design nuclear power plants. The main objective of the study was to compare the dispersion in the wakes of the plants with that in a simulated atmospheric bound...
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Coupling of active motion and advection shapes intracellular cargo transport.
Khuc Trong, Philipp; Guck, Jochen; Goldstein, Raymond E
2012-07-13
Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such cargo-motor motion. Active and advective transport are thus intrinsically coupled as related, yet different representations of the same underlying network structure. A reaction-advection-diffusion system is used here to show that this coupling affects the transport and localization of a passive tracer in a confined geometry. For sufficiently low diffusion, cargo localization to a target zone is optimized either by low reaction kinetics and decoupling of bound and unbound states, or by a mostly disordered cytoskeletal network with only weak directional bias. These generic results may help to rationalize subtle features of cytoskeletal networks, for example as observed for microtubules in fly oocytes.
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Complex Physical, Biophysical and Econophysical Systems
NASA Astrophysics Data System (ADS)
Dewar, Robert L.; Detering, Frank
1. Introduction to complex and econophysics systems: a navigation map / T. Aste and T. Di Matteo -- 2. An introduction to fractional diffusion / B. I. Henry, T.A.M. Langlands and P. Straka -- 3. Space plasmas and fusion plasmas as complex systems / R. O. Dendy -- 4. Bayesian data analysis / M. S. Wheatland -- 5. Inverse problems and complexity in earth system science / I. G. Enting -- 6. Applied fluid chaos: designing advection with periodically reoriented flows for micro to geophysical mixing and transport enhancement / G. Metcalfe -- 7. Approaches to modelling the dynamical activity of brain function based on the electroencephalogram / D. T. J. Liley and F. Frascoli -- 8. Jaynes' maximum entropy principle, Riemannian metrics and generalised least action bound / R. K. Niven and B. Andresen -- 9. Complexity, post-genomic biology and gene expression programs / R. B. H. Williams and O. J.-H. Luo -- 10. Tutorials on agent-based modelling with NetLogo and network analysis with Pajek / M. J. Berryman and S. D. Angus.
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Interaction of polymer-coated silicon nanocrystals with lipid bilayers and surfactant interfaces
NASA Astrophysics Data System (ADS)
Elbaradei, Ahmed; Brown, Samuel L.; Miller, Joseph B.; May, Sylvio; Hobbie, Erik K.
2016-10-01
We use photoluminescence (PL) microscopy to measure the interaction between polyethylene-glycol-coated (PEGylated) silicon nanocrystals (SiNCs) and two model surfaces: lipid bilayers and surfactant interfaces. By characterizing the photostability, transport, and size-dependent emission of the PEGylated nanocrystal clusters, we demonstrate the retention of red PL suitable for detection and tracking with minimal blueshift after a year in an aqueous environment. The predominant interaction measured for both interfaces is short-range repulsion, consistent with the ideal behavior anticipated for PEGylated phospholipid coatings. However, we also observe unanticipated attractive behavior in a small number of scenarios for both interfaces. We attribute this anomaly to defective PEG coverage on a subset of the clusters, suggesting a possible strategy for enhancing cellular uptake by controlling the homogeneity of the PEG corona. In both scenarios, the shape of the apparent potential is modeled through the free or bound diffusion of the clusters near the confining interface.
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Collective Surfing of Chemically Active Particles
NASA Astrophysics Data System (ADS)
Masoud, Hassan; Shelley, Michael J.
2014-03-01
We study theoretically the collective dynamics of immotile particles bound to a 2D surface atop a 3D fluid layer. These particles are chemically active and produce a chemical concentration field that creates surface-tension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. For a 3D diffusion-dominated concentration field and Stokesian fluid we show that the surface dynamics of active particle density can be determined using nonlocal 2D surface operators. Remarkably, we also show that for both deep or shallow fluid layers this surface dynamics reduces to the 2D Keller-Segel model for the collective chemotactic aggregation of slime mold colonies. Mathematical analysis has established that the Keller-Segel model can yield finite-time, finite-mass concentration singularities. We show that such singular behavior occurs in our finite-depth system, and study the associated 3D flow structures.
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NASA Astrophysics Data System (ADS)
Mesquita, Philippe C.; Oliveira, Alice R.; Pedrosa, Matheus F. Fernandes; de Oliveira, Anselmo Gomes; da Silva-Júnior, Arnóbio Antônio
2015-06-01
Spray dried methotrexate (MTX) loaded chitosan microparticles were prepared using different drug/copolymer ratios (9%, 18%, 27% and 45% w/w). The physicochemical aspects were assessed in order to select particles that were able to induce a sustained drug release effect. Particles were successfully produced which exhibited desired physicochemical aspects such as spherical shape and high drug loading. XRD and FT-IR analysis demonstrated that drug is not bound to copolymer and is only homogeneously dispersed in an amorphous state into polymeric matrix. Even the particles with higher drug loading levels presented a sustained drug release profile, which were mathematically modeled using adjusted Higuchi model. The drug release occurred predominantly with drug dissolution and diffusion through swollen polymeric matrix, with the slowest release occurring with particles containing 9% of drug, demonstrating an interesting and promising drug delivery system for MTX.
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Sommerfeld, Thomas; Ehara, Masahiro
2015-01-21
The energy of a temporary anion can be computed by adding a stabilizing potential to the molecular Hamiltonian, increasing the stabilization until the temporary state is turned into a bound state, and then further increasing the stabilization until enough bound state energies have been collected so that these can be extrapolated back to vanishing stabilization. The lifetime can be obtained from the same data, but only if the extrapolation is done through analytic continuation of the momentum as a function of the square root of a shifted stabilizing parameter. This method is known as analytic continuation of the coupling constant, and it requires--at least in principle--that the bound-state input data are computed with a short-range stabilizing potential. In the context of molecules and ab initio packages, long-range Coulomb stabilizing potentials are, however, far more convenient and have been used in the past with some success, although the error introduced by the long-rang nature of the stabilizing potential remains unknown. Here, we introduce a soft-Voronoi box potential that can serve as a short-range stabilizing potential. The difference between a Coulomb and the new stabilization is analyzed in detail for a one-dimensional model system as well as for the (2)Πu resonance of CO2(-), and in both cases, the extrapolation results are compared to independently computed resonance parameters, from complex scaling for the model, and from complex absorbing potential calculations for CO2(-). It is important to emphasize that for both the model and for CO2(-), all three sets of results have, respectively, been obtained with the same electronic structure method and basis set so that the theoretical description of the continuum can be directly compared. The new soft-Voronoi-box-based extrapolation is then used to study the influence of the size of diffuse and the valence basis sets on the computed resonance parameters.
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Electrostatic rate enhancement and transient complex of protein-protein association.
Alsallaq, Ramzi; Zhou, Huan-Xiang
2008-04-01
The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to approximately 10(5)-10(6) M(-1) s(-1). Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys J 1997;73:2441-2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by $k_{\\bf D}$ = $k_{D}0\\ {exp} ( - \\langle U_{el} \\rangle;{\\star}/k_{B} T),$ where k(D) and k(D0) are the rates in the presence and absence of electrostatic interactions, respectively, U(el) is the average electrostatic interaction energy in a "transient-complex" ensemble, and k(B)T is the thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with the experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007;15:215-224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. (c) 2007 Wiley-Liss, Inc.
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Gas production in the Barnett Shale obeys a simple scaling theory
Patzek, Tad W.; Male, Frank; Marder, Michael
2013-01-01
Natural gas from tight shale formations will provide the United States with a major source of energy over the next several decades. Estimates of gas production from these formations have mainly relied on formulas designed for wells with a different geometry. We consider the simplest model of gas production consistent with the basic physics and geometry of the extraction process. In principle, solutions of the model depend upon many parameters, but in practice and within a given gas field, all but two can be fixed at typical values, leading to a nonlinear diffusion problem we solve exactly with a scaling curve. The scaling curve production rate declines as 1 over the square root of time early on, and it later declines exponentially. This simple model provides a surprisingly accurate description of gas extraction from 8,294 wells in the United States’ oldest shale play, the Barnett Shale. There is good agreement with the scaling theory for 2,057 horizontal wells in which production started to decline exponentially in less than 10 y. The remaining 6,237 horizontal wells in our analysis are too young for us to predict when exponential decline will set in, but the model can nevertheless be used to establish lower and upper bounds on well lifetime. Finally, we obtain upper and lower bounds on the gas that will be produced by the wells in our sample, individually and in total. The estimated ultimate recovery from our sample of 8,294 wells is between 10 and 20 trillion standard cubic feet. PMID:24248376
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Gas production in the Barnett Shale obeys a simple scaling theory.
Patzek, Tad W; Male, Frank; Marder, Michael
2013-12-03
Natural gas from tight shale formations will provide the United States with a major source of energy over the next several decades. Estimates of gas production from these formations have mainly relied on formulas designed for wells with a different geometry. We consider the simplest model of gas production consistent with the basic physics and geometry of the extraction process. In principle, solutions of the model depend upon many parameters, but in practice and within a given gas field, all but two can be fixed at typical values, leading to a nonlinear diffusion problem we solve exactly with a scaling curve. The scaling curve production rate declines as 1 over the square root of time early on, and it later declines exponentially. This simple model provides a surprisingly accurate description of gas extraction from 8,294 wells in the United States' oldest shale play, the Barnett Shale. There is good agreement with the scaling theory for 2,057 horizontal wells in which production started to decline exponentially in less than 10 y. The remaining 6,237 horizontal wells in our analysis are too young for us to predict when exponential decline will set in, but the model can nevertheless be used to establish lower and upper bounds on well lifetime. Finally, we obtain upper and lower bounds on the gas that will be produced by the wells in our sample, individually and in total. The estimated ultimate recovery from our sample of 8,294 wells is between 10 and 20 trillion standard cubic feet.
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Anomalous Surface Diffusion of Protons on Lipid Membranes
Wolf, Maarten G.; Grubmüller, Helmut; Groenhof, Gerrit
2014-01-01
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. PMID:24988343
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Anomalous surface diffusion of protons on lipid membranes.
Wolf, Maarten G; Grubmüller, Helmut; Groenhof, Gerrit
2014-07-01
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Ultrafast dynamics of low-energy electron attachment via a non-valence correlation-bound state
NASA Astrophysics Data System (ADS)
Rogers, Joshua P.; Anstöter, Cate S.; Verlet, Jan R. R.
2018-03-01
The primary electron-attachment process in electron-driven chemistry represents one of the most fundamental chemical transformations with wide-ranging importance in science and technology. However, the mechanistic detail of the seemingly simple reaction of an electron and a neutral molecule to form an anion remains poorly understood, particularly at very low electron energies. Here, time-resolved photoelectron imaging was used to probe the electron-attachment process to a non-polar molecule using time-resolved methods. An initially populated diffuse non-valence state of the anion that is bound by correlation forces evolves coherently in ∼30 fs into a valence state of the anion. The extreme efficiency with which the correlation-bound state serves as a doorway state for low-energy electron attachment explains a number of electron-driven processes, such as anion formation in the interstellar medium and electron attachment to fullerenes.
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Radionuclide Transport in Fracture-Granite Interface Zones
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hu, Q; Mori, A
In situ radionuclide migration experiments, followed by excavation and sample characterization, were conducted in a water-conducting shear zone at the Grimsel Test Site (GTS) in Switzerland to study diffusion paths of radionuclides in fractured granite. In this work, we employed a micro-scale mapping technique that interfaces laser ablation sampling with inductively coupled plasma-mass spectrometry (LA/ICP-MS) to measure the fine-scale (micron-range) distribution of actinides ({sup 234}U, {sup 235}U, and {sup 237}Np) in the fracture-granite interface zones. Long-lived {sup 234}U, {sup 235}U, and {sup 237}Np were detected in flow channels, as well as in the adjacent rock matrix, using the sensitive, feature-basedmore » mapping of the LA/ICP-MS technique. The injected sorbing actinides are mainly located within the advective flowing fractures and the immediately adjacent regions. The water-conducting fracture studied in this work is bounded on one side by mylonite and the other by granitic matrix regions. These actinides did not penetrate into the mylonite side as much as the relatively higher-porosity granite matrix, most likely due to the low porosity, hydraulic conductivity, and diffusivity of the fracture wall (a thickness of about 0.4 mm separates the mylonite region from the fracture) and the mylonite region itself. Overall, the maximum penetration depth detected with this technique for the more diffusive {sup 237}Np over the field experimental time scale of about 60 days was about 10 mm in the granitic matrix, illustrating the importance of matrix diffusion in retarding radionuclide transport from the advective fractures. Laboratory tests and numerical modeling of radionuclide diffusion into granitic matrix was conducted to complement and help interpret the field results. Measured apparent diffusivity of multiple tracers in granite provided consistent predictions for radionuclide transport in the fractured granitic rock.« less
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When clusters collide: constraints on antimatter on the largest scales
DOE Office of Scientific and Technical Information (OSTI.GOV)
Steigman, Gary, E-mail: steigman@mps.ohio-state.edu
2008-10-15
Observations have ruled out the presence of significant amounts of antimatter in the Universe on scales ranging from the solar system, to the Galaxy, to groups and clusters of galaxies, and even to distances comparable to the scale of the present horizon. Except for the model-dependent constraints on the largest scales, the most significant upper limits to diffuse antimatter in the Universe are those on the {approx}Mpc scale of clusters of galaxies provided by the EGRET upper bounds to annihilation gamma rays from galaxy clusters whose intracluster gas is revealed through its x-ray emission. On the scale of individual clustersmore » of galaxies the upper bounds to the fraction of mixed matter and antimatter for the 55 clusters from a flux-limited x-ray survey range from 5 Multiplication-Sign 10{sup -9} to <1 Multiplication-Sign 10{sup -6}, strongly suggesting that individual clusters of galaxies are made entirely of matter or of antimatter. X-ray and gamma-ray observations of colliding clusters of galaxies, such as the Bullet Cluster, permit these constraints to be extended to even larger scales. If the observations of the Bullet Cluster, where the upper bound to the antimatter fraction is found to be <3 Multiplication-Sign 10{sup -6}, can be generalized to other colliding clusters of galaxies, cosmologically significant amounts of antimatter will be excluded on scales of order {approx}20 Mpc (M{approx}5 Multiplication-Sign 10{sup 15}M{sub sun})« less
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Local Group dSph radio survey with ATCA - II. Non-thermal diffuse emission
NASA Astrophysics Data System (ADS)
Regis, Marco; Richter, Laura; Colafrancesco, Sergio; Profumo, Stefano; de Blok, W. J. G.; Massardi, Marcella
2015-04-01
Our closest neighbours, the Local Group dwarf spheroidal (dSph) galaxies, are extremely quiescent and dim objects, where thermal and non-thermal diffuse emissions lack, so far, of detection. In order to possibly study the dSph interstellar medium, deep observations are required. They could reveal non-thermal emissions associated with the very low level of star formation, or to particle dark matter annihilating or decaying in the dSph halo. In this work, we employ radio observations of six dSphs, conducted with the Australia Telescope Compact Array in the frequency band 1.1-3.1 GHz, to test the presence of a diffuse component over typical scales of few arcmin and at an rms sensitivity below 0.05 mJy beam-1. We observed the dSph fields with both a compact array and long baselines. Short spacings led to a synthesized beam of about 1 arcmin and were used for the extended emission search. The high-resolution data mapped background sources, which in turn were subtracted in the short-baseline maps, to reduce their confusion limit. We found no significant detection of a diffuse radio continuum component. After a detailed discussion on the modelling of the cosmic ray (CR) electron distribution and on the dSph magnetic properties, we present bounds on several physical quantities related to the dSphs, such that the total radio flux, the angular shape of the radio emissivity, the equipartition magnetic field, and the injection and equilibrium distributions of CR electrons. Finally, we discuss the connection to far-infrared and X-ray observations.
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Tijink, Marlon S L; Wester, Maarten; Sun, Junfen; Saris, Anno; Bolhuis-Versteeg, Lydia A M; Saiful, Saiful; Joles, Jaap A; Borneman, Zandrie; Wessling, Matthias; Stamatialis, Dimitris F
2012-07-01
Hemodialysis is a commonly used blood purification technique in patients requiring kidney replacement therapy. Sorbents could increase uremic retention solute removal efficiency but, because of poor biocompatibility, their use is often limited to the treatment of patients with acute poisoning. This paper proposes a novel membrane concept for combining diffusion and adsorption of uremic retention solutes in one step: the so-called mixed-matrix membrane (MMM). In this concept, adsorptive particles are incorporated in a macro-porous membrane layer whereas an extra particle-free membrane layer is introduced on the blood-contacting side of the membrane to improve hemocompatibility and prevent particle release. These dual-layer mixed-matrix membranes have high clean-water permeance and high creatinine adsorption from creatinine model solutions. In human plasma, the removal of creatinine and of the protein-bound solute para-aminohippuric acid (PAH) by single and dual-layer membranes is in agreement with the removal achieved by the activated carbon particles alone, showing that under these experimental conditions the accessibility of the particles in the MMM is excellent. This study proves that the combination of diffusion and adsorption in a single step is possible and paves the way for the development of more efficient blood purification devices, excellently combining the advantages of both techniques. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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Parsons, T.; Thatcher, W.
2011-01-01
Geodetic measurements tell us that the eastern part of the Basin and Range Province expands in an east-west direction relative to stable North America, whereas the western part of the province moves to the northwest. We develop three-dimensional finite element representations of the western United States lithosphere in an effort to understand the global positioning system (GPS) signal. The models are constrained by known bounding-block velocities and topography, and Basin and Range Province deformation is represented by simple plastic (thermal creep) rheology. We show that active Basin and Range spreading by gravity collapse is expected to have a strong southward component that does not match the GPS signal. We can reconcile the gravitational component of displacement with observed velocity vectors if the Pacific plate applies northwest-directed shear stress to the Basin and Range via the Sierra Nevada block. This effect reaches at least 1000 km east of the San Andreas fault in our models. ?? 2011 Geological Society of America.
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Wavefunctions, quantum diffusion, and scaling exponents in golden-mean quasiperiodic tilings.
Thiem, Stefanie; Schreiber, Michael
2013-02-20
We study the properties of wavefunctions and the wavepacket dynamics in quasiperiodic tight-binding models in one, two, and three dimensions. The atoms in the one-dimensional quasiperiodic chains are coupled by weak and strong bonds aligned according to the Fibonacci sequence. The associated d-dimensional quasiperiodic tilings are constructed from the direct product of d such chains, which yields either the hypercubic tiling or the labyrinth tiling. This approach allows us to consider fairly large systems numerically. We show that the wavefunctions of the system are multifractal and that their properties can be related to the structure of the system in the regime of strong quasiperiodic modulation by a renormalization group (RG) approach. We also study the dynamics of wavepackets to get information about the electronic transport properties. In particular, we investigate the scaling behaviour of the return probability of the wavepacket with time. Applying again the RG approach we show that in the regime of strong quasiperiodic modulation the return probability is governed by the underlying quasiperiodic structure. Further, we also discuss lower bounds for the scaling exponent of the width of the wavepacket and propose a modified lower bound for the absolute continuous regime.
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CO Depletion: A Microscopic Perspective
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cazaux, S.; Martín-Doménech, R.; Caro, G. M. Muñoz
In regions where stars form, variations in density and temperature can cause gas to freeze out onto dust grains forming ice mantles, which influences the chemical composition of a cloud. The aim of this paper is to understand in detail the depletion (and desorption) of CO on (from) interstellar dust grains. Experimental simulations were performed under two different (astrophysically relevant) conditions. In parallel, Kinetic Monte Carlo simulations were used to mimic the experimental conditions. In our experiments, CO molecules accrete onto water ice at temperatures below 27 K, with a deposition rate that does not depend on the substrate temperature.more » During the warm-up phase, the desorption processes do exhibit subtle differences, indicating the presence of weakly bound CO molecules, therefore highlighting a low diffusion efficiency. IR measurements following the ice thickness during the TPD confirm that diffusion occurs at temperatures close to the desorption. Applied to astrophysical conditions, in a pre-stellar core, the binding energies of CO molecules, ranging between 300 and 850 K, depend on the conditions at which CO has been deposited. Because of this wide range of binding energies, the depletion of CO as a function of A{sub V} is much less important than initially thought. The weakly bound molecules, easily released into the gas phase through evaporation, change the balance between accretion and desorption, which result in a larger abundance of CO at high extinctions. In addition, weakly bound CO molecules are also more mobile, and this could increase the reactivity within interstellar ices.« less
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Luterbacher, Jeremy S; Moran-Mirabal, Jose M; Burkholder, Eric W; Walker, Larry P
2015-01-01
Enzymatic hydrolysis is one of the critical steps in depolymerizing lignocellulosic biomass into fermentable sugars for further upgrading into fuels and/or chemicals. However, many studies still rely on empirical trends to optimize enzymatic reactions. An improved understanding of enzymatic hydrolysis could allow research efforts to follow a rational design guided by an appropriate theoretical framework. In this study, we present a method to image cellulosic substrates with complex three-dimensional structure, such as filter paper, undergoing hydrolysis under conditions relevant to industrial saccharification processes (i.e., temperature of 50°C, using commercial cellulolytic cocktails). Fluorescence intensities resulting from confocal images were used to estimate parameters for a diffusion and reaction model. Furthermore, the observation of a relatively constant bound enzyme fluorescence signal throughout hydrolysis supported our modeling assumption regarding the structure of biomass during hydrolysis. The observed behavior suggests that pore evolution can be modeled as widening of infinitely long slits. The resulting model accurately predicts the concentrations of soluble carbohydrates obtained from independent saccharification experiments conducted in bulk, demonstrating its relevance to biomass conversion work. © 2014 Wiley Periodicals, Inc.
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Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian
DOE Office of Scientific and Technical Information (OSTI.GOV)
Pittman, S. M.; Tannenbaum, E.; Heller, E. J.
This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm{sup −1} peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol’d diffusion, which connects different regions of phase-space by a resonance network known as the Arnol’d web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep.more » Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol’d web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.« less
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Langdon, Blake B.; Kastantin, Mark; Schwartz, Daniel K.
2012-01-01
With the use of single-molecule total internal reflection fluorescence microscopy (TIRFM), the dynamics of bovine serum albumin (BSA) and human fibrinogen (Fg) at low concentrations were observed at the solid-aqueous interface as a function of temperature on hydrophobic trimethylsilane (TMS) and hydrophilic fused silica (FS) surfaces. Multiple dynamic modes and populations were observed and characterized by their surface residence times and squared-displacement distributions (surface diffusion). Characteristic desorption and diffusion rates for each population/mode were generally found to increase with temperature, and apparent activation energies were determined from Arrhenius analyses. The apparent activation energies of desorption and diffusion were typically higher on FS than on TMS surfaces, suggesting that protein desorption and mobility were hindered on hydrophilic surfaces due to favorable protein-surface and solvent-surface interactions. The diffusion of BSA on TMS appeared to be activationless for several populations, whereas diffusion on FS always exhibited an apparent activation energy. All activation energies were small in absolute terms (generally only a few kBT), suggesting that most adsorbed protein molecules are weakly bound and move and desorb readily under ambient conditions. PMID:22713578
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Notes on hyperscaling violating Lifshitz and shear diffusion
NASA Astrophysics Data System (ADS)
Kolekar, Kedar S.; Mukherjee, Debangshu; Narayan, K.
2017-07-01
We explore in greater detail our investigations of shear diffusion in hyperscaling violating Lifshitz theories in Phys. Lett. B 760, 86 (2016), 10.1016/j.physletb.2016.06.046. This adapts and generalizes the membrane-paradigm-like analysis of Kovtun, Son, and Starinets for shear gravitational perturbations in the near horizon region given certain self-consistent approximations, leading to the shear diffusion constant on an appropriately defined stretched horizon. In theories containing a gauge field, some of the metric perturbations mix with some of the gauge field perturbations and the above analysis is somewhat more complicated. We find a similar near-horizon analysis can be obtained in terms of new field variables involving a linear combination of the metric and the gauge field perturbation resulting in a corresponding diffusion equation. Thereby as before, for theories with Lifshitz and hyperscaling violating exponents z , θ satisfying z <4 -θ in four bulk dimensions, our analysis here results in a similar expression for the shear diffusion constant with power-law scaling with temperature suggesting universal behavior in relation to the viscosity bound. For z =4 -θ , we find logarithmic behavior.
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Modeling diffuse phosphorus emissions to assist in best management practice designing
NASA Astrophysics Data System (ADS)
Kovacs, Adam; Zessner, Matthias; Honti, Mark; Clement, Adrienne
2010-05-01
A diffuse emission modeling tool has been developed, which is appropriate to support decision-making in watershed management. The PhosFate (Phosphorus Fate) tool allows planning best management practices (BMPs) in catchments and simulating their possible impacts on the phosphorus (P) loads. PhosFate is a simple fate model to calculate diffuse P emissions and their transport within a catchment. The model is a semi-empirical, catchment scale, distributed parameter and long-term (annual) average model. It has two main parts: (a) the emission and (b) the transport model. The main input data of the model are digital maps (elevation, soil types and landuse categories), statistical data (crop yields, animal numbers, fertilizer amounts and precipitation distribution) and point information (precipitation, meteorology, soil humus content, point source emissions and reservoir data). The emission model calculates the diffuse P emissions at their source. It computes the basic elements of the hydrology as well as the soil loss. The model determines the accumulated P surplus of the topsoil and distinguishes the dissolved and the particulate P forms. Emissions are calculated according to the different pathways (surface runoff, erosion and leaching). The main outputs are the spatial distribution (cell values) of the runoff components, the soil loss and the P emissions within the catchment. The transport model joins the independent cells based on the flow tree and it follows the further fate of emitted P from each cell to the catchment outlets. Surface runoff and P fluxes are accumulated along the tree and the field and in-stream retention of the particulate forms are computed. In case of base flow and subsurface P loads only the channel transport is taken into account due to the less known hydrogeological conditions. During the channel transport, point sources and reservoirs are also considered. Main results of the transport algorithm are the discharge, dissolved and sediment-bounded P load values at any arbitrary point within the catchment. Finally, a simple design procedure has been built up to plan BMPs in the catchments and simulate their possible impacts on diffuse P fluxes as well as calculate their approximately costs. Both source and transport controlling measures have been involved into the planning procedure. The model also allows examining the impacts of alterations of fertilizer application, point source emissions as well as the climate change on the river loads. Besides this, a simple optimization algorithm has been developed to select the most effective source areas (real hot spots), which should be targeted by the interventions. The fate model performed well in Hungarian pilot catchments. Using the calibrated and validated model, different management scenarios were worked out and their effects and costs evaluated and compared to each other. The results show that the approach is suitable to effectively design BMP measures at local scale. Combinative application of the source and transport controlling BMPs can result in high P reduction efficiency. Optimization of the interventions can remarkably reduce the area demand of the necessary BMPs, consequently the establishment costs can be decreased. The model can be coupled with a larger scale catchment model to form a "screening and planning" modeling system.
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Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E
2015-01-29
Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.
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Desorption of oxygen from YBa2Cu3O6+x films studied by Raman spectroscopy
NASA Astrophysics Data System (ADS)
Bock, A.; Kürsten, R.; Brühl, M.; Dieckmann, N.; Merkt, U.
1996-08-01
Phonons of laser-deposited YBa2Cu3O6+x films on MgO(100) substrates are investigated in a Raman setup as a function of laser power density. Investigations of YBa2Cu3O7 films allow us to study oxygen out-diffusion, where the onset of out-diffusion is indicated by the appearance of disorder-induced modes in the Raman spectra. At a pressure of 5×10-6 mbar the temperature threshold of the out-diffusion is (490+/-15) K. With increasing oxygen pressure the observed temperature thresholds rise only moderately in contrast to the behavior expected from the pox-T phase diagram of YBa2Cu3O6+x. Even at 1 bar oxygen partial pressure out-diffusion is observed and tetragonal sites with x=0 develop. These observations can be explained by photon-stimulated desorption of oxygen. Investigations of YBa2Cu3O6 films allow us to study oxygen in-diffusion. In 1 bar oxygen we observe competing oxygen fluxes due to thermally activated diffusion and photon-stimulated desorption. From these measurements we determine an upper bound of the thermal activation energy of the oxygen in-diffusion into YBa2Cu3O6 films of (0.19+/-0.01) eV.
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Physical Uncertainty Bounds (PUB)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Vaughan, Diane Elizabeth; Preston, Dean L.
2015-03-19
This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switchingmore » out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.« less
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New Numerical Approaches To thermal Convection In A Compositionally Stratified Fluid
NASA Astrophysics Data System (ADS)
Puckett, E. G.; Turcotte, D. L.; Kellogg, L. H.; Lokavarapu, H. V.; He, Y.; Robey, J.
2016-12-01
Seismic imaging of the mantle has revealed large and small scale heterogeneities in the lower mantle; specifically structures known as large low shear velocity provinces (LLSVP) below Africa and the South Pacific. Most interpretations propose that the heterogeneities are compositional in nature, differing from the overlying mantle, an interpretation that would be consistent with chemical geodynamic models. The LLSVP's are thought to be very old, meaning they have persisted thoughout much of Earth's history. Numerical modeling of persistent compositional interfaces present challenges to even state-of-the-art numerical methodology. It is extremely difficult to maintain sharp composition boundaries which migrate and distort with time dependent fingering without compositional diffusion and / or artificial diffusion. The compositional boundary must persist indefinitely. In this work we present computations of an initial compositionally stratified fluid that is subject to a thermal gradient ΔT = T1 - T0 across the height D of a rectangular domain over a range of buoyancy numbers B and Rayleigh numbers Ra. In these computations we compare three numerical approaches to modeling the movement of two distinct, thermally driven, compositional fields; namely, a high-order Finte Element Method (FEM) that employs artifical viscosity to preserve the maximum and minimum values of the compositional field, a Discontinous Galerkin (DG) method with a Bound Preserving (BP) limiter, and a Volume-of-Fluid (VOF) interface tracking algorithm. Our computations demonstrate that the FEM approach has far too much numerical diffusion to yield meaningful results, the DGBP method yields much better resuts but with small amounts of each compositional field being (numerically) entrained within the other compositional field, while the VOF method maintains a sharp interface between the two compositions throughout the computation. In the figure we show a comparison of between the three methods for a computation made with B = 1.111 and Ra = 10,000 after the flow has reached 'steady state'. (R) the images computed with the standard FEM method (with artifical viscosity), (C) the images computed with the DGBP method (with no artifical viscosity or diffusion due to discretization errors) and (L) the images computed with the VOF algorithm.
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NASA Astrophysics Data System (ADS)
Chung, So Hyun
Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. A bound water index (BWI) was developed that quantifies the spectral shift and shape changes observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopic imaging (DOSI). DOSI quantitatively measures light absorption and scattering spectra in cm-deep tissues and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOSI to MRI and a conductivity cell using bound water phantoms. Non-invasive BWI measurements of malignant and normal tissues in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p<0.0001) compared to normal tissues. BWI showed potential as a prognostic index based on high correlations with tumor grade and size. An algorithm for absolute temperature measurements in deep tissues was developed based on resolving opposing effects of water vibrational frequency shifts due to macromolecular binding. DOSI measures absolute temperature with a difference of 1.1+/-0.91°C from a thermistor. Deep tissue temperature measured in forearms during cold-stress was consistent with previously reported invasively-measured deep tissue temperature. Finally, the BWI was compared to Apparent Diffusion Coefficient (ADC) of diffusion weighted MRI in 9 breast cancer patients. The BWI and ADC correlated (R=0.8, p=<0.01) and both parameters decreased with increasing bulk water content in cancer tissues. Although BWI and ADC are positively correlated in vivo, BWI appears to be more sensitive to free water in the extracellular matrix while ADC reflects increased tumor cellularity. The relationship between ADC, BWI and bulk water concentration suggests that both parameters have potential for assessing tumor histopathological grade. My results confirm the importance of water as a critical tissue component that can potentially provide unique insight into the molecular pathophysiology of cancer.
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Dharani, S; Rakkiyappan, R; Cao, Jinde; Alsaedi, Ahmed
2017-08-01
This paper explores the problem of synchronization of a class of generalized reaction-diffusion neural networks with mixed time-varying delays. The mixed time-varying delays under consideration comprise of both discrete and distributed delays. Due to the development and merits of digital controllers, sampled-data control is a natural choice to establish synchronization in continuous-time systems. Using a newly introduced integral inequality, less conservative synchronization criteria that assure the global asymptotic synchronization of the considered generalized reaction-diffusion neural network and mixed delays are established in terms of linear matrix inequalities (LMIs). The obtained easy-to-test LMI-based synchronization criteria depends on the delay bounds in addition to the reaction-diffusion terms, which is more practicable. Upon solving these LMIs by using Matlab LMI control toolbox, a desired sampled-data controller gain can be acuqired without any difficulty. Finally, numerical examples are exploited to express the validity of the derived LMI-based synchronization criteria.
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Robust Bounded Influence Tests in Linear Models
1988-11-01
sensitivity analysis and bounded influence estimation. In: Evaluation of Econometric Models, J. Kmenta and J.B. Ramsey (eds.) Academic Press, New York...1R’OBUST bOUNDED INFLUENCE TESTS IN LINEA’ MODELS and( I’homas P. [lettmansperger* Tim [PennsylvanLa State UJniversity A M i0d fix pu111 rsos.p JJ 1 0...November 1988 ROBUST BOUNDED INFLUENCE TESTS IN LINEAR MODELS Marianthi Markatou The University of Iowa and Thomas P. Hettmansperger* The Pennsylvania
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Improving receiver performance of diffusive molecular communication with enzymes.
Noel, Adam; Cheung, Karen C; Schober, Robert
2014-03-01
This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules and then degrade them so that they cannot interfere with future transmissions. A lower bound expression on the expected number of molecules measured at the receiver is derived. A simple binary receiver detection scheme is proposed where the number of observed molecules is sampled at the time when the maximum number of molecules is expected. Insight is also provided into the selection of an appropriate bit interval. The expected bit error probability is derived as a function of the current and all previously transmitted bits. Simulation results show the accuracy of the bit error probability expression and the improvement in communication performance by having active enzymes present.
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Reynolds-number dependence of the longitudinal dispersion in turbulent pipe flow.
Hawkins, Christopher; Angheluta, Luiza; Krotkiewski, Marcin; Jamtveit, Bjørn
2016-04-01
In Taylor's theory, the longitudinal dispersion in turbulent pipe flows approaches, on long time scales, a diffusive behavior with a constant diffusivity K_{L}, which depends empirically on the Reynolds number Re. We show that the dependence on Re can be determined from the turbulent energy spectrum. By using the intimate connection between the friction factor and the longitudinal dispersion in wall-bounded turbulence, we predict different asymptotic scaling laws of K_{L}(Re) depending on the different turbulent cascades in two-dimensional turbulence. We also explore numerically the K_{L}(Re) dependence in turbulent channel flows with smooth and rough walls using a lattice Boltzmann method.
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NASA Technical Reports Server (NTRS)
Atkins, H. L.; Shu, Chi-Wang
2001-01-01
The explicit stability constraint of the discontinuous Galerkin method applied to the diffusion operator decreases dramatically as the order of the method is increased. Block Jacobi and block Gauss-Seidel preconditioner operators are examined for their effectiveness at accelerating convergence. A Fourier analysis for methods of order 2 through 6 reveals that both preconditioner operators bound the eigenvalues of the discrete spatial operator. Additionally, in one dimension, the eigenvalues are grouped into two or three regions that are invariant with order of the method. Local relaxation methods are constructed that rapidly damp high frequencies for arbitrarily large time step.
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Diffusion approximation-based simulation of stochastic ion channels: which method to use?
Pezo, Danilo; Soudry, Daniel; Orio, Patricio
2014-01-01
To study the effects of stochastic ion channel fluctuations on neural dynamics, several numerical implementation methods have been proposed. Gillespie's method for Markov Chains (MC) simulation is highly accurate, yet it becomes computationally intensive in the regime of a high number of channels. Many recent works aim to speed simulation time using the Langevin-based Diffusion Approximation (DA). Under this common theoretical approach, each implementation differs in how it handles various numerical difficulties—such as bounding of state variables to [0,1]. Here we review and test a set of the most recently published DA implementations (Goldwyn et al., 2011; Linaro et al., 2011; Dangerfield et al., 2012; Orio and Soudry, 2012; Schmandt and Galán, 2012; Güler, 2013; Huang et al., 2013a), comparing all of them in a set of numerical simulations that assess numerical accuracy and computational efficiency on three different models: (1) the original Hodgkin and Huxley model, (2) a model with faster sodium channels, and (3) a multi-compartmental model inspired in granular cells. We conclude that for a low number of channels (usually below 1000 per simulated compartment) one should use MC—which is the fastest and most accurate method. For a high number of channels, we recommend using the method by Orio and Soudry (2012), possibly combined with the method by Schmandt and Galán (2012) for increased speed and slightly reduced accuracy. Consequently, MC modeling may be the best method for detailed multicompartment neuron models—in which a model neuron with many thousands of channels is segmented into many compartments with a few hundred channels. PMID:25404914
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Chowdhury, Mohammad Mahfuz; Fujii, Teruo; Sakai, Yasuyuki
2013-07-01
In our previous studies, we observed that cell-secreted BMP4 had a prominent influence on mouse embryonic stem cell (mESC) behaviors in a membrane-based two-chambered microbioreactor (MB), but not in a macro-scale culture (6-well plate/6WP). In this study, we investigated how the physical aspects of these cultures regulated BMP4 signaling by developing mathematical models of the cultures. The models estimated signaling activity in the cultures by considering size of the undifferentiated mESC colonies and their growth, diffusion of BMP4, and BMP4 trafficking process in the colonies. The models successfully depicted measured profile of BMP4 concentration in the culture medium which was two times higher in the MB than that in the 6WP during 5-day culture. The models estimated that, owing to the small volume and the membrane, cells were exposed to a higher BMP4 concentration in the top chamber of the MB than that in the 6WP culture. The higher concentration of BMP4 induced a higher concentration of BMP4-bound receptor in the colony in the MB than in the 6WP, thereby leading to the higher activation of BMP4 signaling in the MB. The models also predicted that the size of the MB, but not that of the 6WP, was suitable for maximizing BMP4 accumulation and upregulating its signaling. This study will be helpful in analyzing culture systems, designing microfluidic devices for controlling ESC or other cell behavior. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
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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.
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Scaling Limits and Generic Bounds for Exploration Processes
NASA Astrophysics Data System (ADS)
Bermolen, Paola; Jonckheere, Matthieu; Sanders, Jaron
2017-12-01
We consider exploration algorithms of the random sequential adsorption type both for homogeneous random graphs and random geometric graphs based on spatial Poisson processes. At each step, a vertex of the graph becomes active and its neighboring nodes become blocked. Given an initial number of vertices N growing to infinity, we study statistical properties of the proportion of explored (active or blocked) nodes in time using scaling limits. We obtain exact limits for homogeneous graphs and prove an explicit central limit theorem for the final proportion of active nodes, known as the jamming constant, through a diffusion approximation for the exploration process which can be described as a unidimensional process. We then focus on bounding the trajectories of such exploration processes on random geometric graphs, i.e., random sequential adsorption. As opposed to exploration processes on homogeneous random graphs, these do not allow for such a dimensional reduction. Instead we derive a fundamental relationship between the number of explored nodes and the discovered volume in the spatial process, and we obtain generic bounds for the fluid limit and jamming constant: bounds that are independent of the dimension of space and the detailed shape of the volume associated to the discovered node. Lastly, using coupling techinques, we give trajectorial interpretations of the generic bounds.
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Observatory enabled discovery of diffuse discharge temperature structure
NASA Astrophysics Data System (ADS)
Bemis, K. G.; Lee, R.; Ivakin, A. N.
2016-12-01
Underwater cabled observatories provide long term but short time and spatial scale measurements of hydrothermal discharge properties. For the first time, an intricate picture of diffuse discharge has been captured at both Axial Volcano (Axial) and the Main Endeavour Field (MEF) on the Juan de Fuca Ridge. This study combines thermistor (3D array, 2D array and spot) and acoustic data to compare the statistical and distribution characteristics of diffuse discharge for narrow crack flow (at ASHES field on Axial) and distributive flow out of a sulfide structure (at Grotto vent in MEF). Two surprising observations seem to apply to both styles of diffuse discharge: (1) thermal variance scales with the mean temperature suggesting coherent flow structures exist in the form of plumes, wakes or boundary layers, and (2) thermal hot spots are persistently localized in space, despite tidal current disruption. Thermal variance was measured at ASHES using a 3D thermistor array (TMPSF) with 10 s sampling over two years and at Grotto using 2D thermistor arrays with 1 hr sampling over several years and a ROV-held CTD (Seabird 39plus) with 0.5 second sampling over several minutes. For locations with temperatures greater than ambient, the variance in temperature scales with the mean temperature. This unusual statistical property is characteristic of self-similar flows like plumes, wakes, and boundary layers and arises from the bounded mixing of a cooling high temperature fluid with a cold ambient fluid. Thus this observation implies an underlying coherence to the diffuse discharge that has not yet been adequately captured or described. A coherent flow like a plume should have a discoverable spatial pattern, albeit one that may vary with the influence of tides. Acoustic observations ( 1m diameter footprint) of the Grotto sulfide edifice found stable local hot spots of diffuse discharge that sway with tides. In contrast, the 3D thermistor array at ASHES sees very localized (single thermistor) hot spots that persist for months. Is this a fundamental difference between two styles of diffuse discharge? Alternate conceptual models of diffuse discharge are used to place localized observations in a spatial context and develop a rigorous understanding of the spatial and temporal pattern of diffuse discharge for both crack and distributive styles.
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A Literature Review on the Study of Moisture in Polymers
DOE Office of Scientific and Technical Information (OSTI.GOV)
Trautschold, Olivia Carol
2016-05-25
This literature review covers the main chemical and physical interactions between moisture and the polymer matrix. Fickian versus Non-Fickian diffusion behaviors are discussed in approximating the characteristics of moisture sorption. Also, bound water and free water sorbed in polymers are distinguished. Methods to distinguish between bound and free water include differential scanning calorimetry, infrared spectroscopy, and time-domain nuclear magnetic resonance spectroscopy. The difference between moisture sorption and water sorption is considered, as well as the difficulties associated with preventing moisture sorption. Furthermore, specific examples of how moisture sorption influences polymers include natural fiber-polymer composites, starch-based biodegradable thermoplastics, and thermoset polyurethanemore » and epoxies.« less
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Local bounds preserving stabilization for continuous Galerkin discretization of hyperbolic systems
NASA Astrophysics Data System (ADS)
Mabuza, Sibusiso; Shadid, John N.; Kuzmin, Dmitri
2018-05-01
The objective of this paper is to present a local bounds preserving stabilized finite element scheme for hyperbolic systems on unstructured meshes based on continuous Galerkin (CG) discretization in space. A CG semi-discrete scheme with low order artificial dissipation that satisfies the local extremum diminishing (LED) condition for systems is used to discretize a system of conservation equations in space. The low order artificial diffusion is based on approximate Riemann solvers for hyperbolic conservation laws. In this case we consider both Rusanov and Roe artificial diffusion operators. In the Rusanov case, two designs are considered, a nodal based diffusion operator and a local projection stabilization operator. The result is a discretization that is LED and has first order convergence behavior. To achieve high resolution, limited antidiffusion is added back to the semi-discrete form where the limiter is constructed from a linearity preserving local projection stabilization operator. The procedure follows the algebraic flux correction procedure usually used in flux corrected transport algorithms. To further deal with phase errors (or terracing) common in FCT type methods, high order background dissipation is added to the antidiffusive correction. The resulting stabilized semi-discrete scheme can be discretized in time using a wide variety of time integrators. Numerical examples involving nonlinear scalar Burgers equation, and several shock hydrodynamics simulations for the Euler system are considered to demonstrate the performance of the method. For time discretization, Crank-Nicolson scheme and backward Euler scheme are utilized.
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(Bio)Sensing Using Nanoparticle Arrays: On the Effect of Analyte Transport on Sensitivity.
Lynn, N Scott; Homola, Jiří
2016-12-20
There has recently been an extensive amount of work regarding the development of optical, electrical, and mechanical (bio)sensors employing planar arrays of surface-bound nanoparticles. The sensor output for these systems is dependent on the rate at which analyte is transported to, and interacts with, each nanoparticle in the array. There has so far been little discussion on the relationship between the design parameters of an array and the interplay of convection, diffusion, and reaction. Moreover, current methods providing such information require extensive computational simulation. Here we demonstrate that the rate of analyte transport to a nanoparticle array can be quantified analytically. We show that such rates are bound by both the rate to a single NP and that to a planar surface (having equivalent size as the array), with the specific rate determined by the fill fraction: the ratio between the total surface area used for biomolecular capture with respect to the entire sensing area. We characterize analyte transport to arrays with respect to changes in numerous parameters relevant to experiment, including variation of the nanoparticle shape and size, packing density, flow conditions, and analyte diffusivity. We also explore how analyte capture is dependent on the kinetic parameters related to an affinity-based biosensor, and furthermore, we classify the conditions under which the array might be diffusion- or reaction-limited. The results obtained herein are applicable toward the design and optimization of all (bio)sensors based on nanoparticle arrays.
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Meridional overturning and large-scale circulation of the Indian Ocean
NASA Astrophysics Data System (ADS)
Ganachaud, Alexandre; Wunsch, Carl; Marotzke, Jochem; Toole, John
2000-11-01
The large scale Indian Ocean circulation is estimated from a global hydrographic inverse geostrophic box model with a focus on the meridional overturning circulation (MOC). The global model is based on selected recent World Ocean Circulation Experiment (WOCE) sections which in the Indian Basin consist of zonal sections at 32°S, 20°S and 8°S, and a section between Bali and Australia from the Java-Australia Dynamic Experiment (JADE). The circulation is required to conserve mass, salinity, heat, silica and "PO" (170PO4+O2). Near-conservation is imposed within layers bounded by neutral surfaces, while permitting advective and diffusive exchanges between the layers. Conceptually, the derived circulation is an estimate of the average circulation for the period 1987-1995. A deep inflow into the Indian Basin of 11±4 Sv is found, which is in the lower range of previous estimates, but consistent with conservation requirements and the global data set. The Indonesian Throughflow (ITF) is estimated at 15±5 Sv. The flow in the Mozambique Channel is of the same magnitude, implying a weak net flow between Madagascar and Australia. A net evaporation of -0.6±0.4 Sv is found between 32°S and 8°S, consistent with independent estimates. No net heat gain is found over the Indian Basin (0.1 ± 0.2PW north of 32°S) as a consequence of the large warm water influx from the ITF. Through the use of anomaly equations, the average dianeutral upwelling and diffusion between the sections are required and resolved, with values in the range 1-3×10-5 cm s-1 for the upwelling and 2-10 cm2 s-1 for the diffusivity.
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Multilevel Sequential Monte Carlo Samplers for Normalizing Constants
Moral, Pierre Del; Jasra, Ajay; Law, Kody J. H.; ...
2017-08-24
This article considers the sequential Monte Carlo (SMC) approximation of ratios of normalizing constants associated to posterior distributions which in principle rely on continuum models. Therefore, the Monte Carlo estimation error and the discrete approximation error must be balanced. A multilevel strategy is utilized to substantially reduce the cost to obtain a given error level in the approximation as compared to standard estimators. Two estimators are considered and relative variance bounds are given. The theoretical results are numerically illustrated for two Bayesian inverse problems arising from elliptic partial differential equations (PDEs). The examples involve the inversion of observations of themore » solution of (i) a 1-dimensional Poisson equation to infer the diffusion coefficient, and (ii) a 2-dimensional Poisson equation to infer the external forcing.« less
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On Instability of Geostrophic Current with Linear Vertical Shear at Length Scales of Interleaving
NASA Astrophysics Data System (ADS)
Kuzmina, N. P.; Skorokhodov, S. L.; Zhurbas, N. V.; Lyzhkov, D. A.
2018-01-01
The instability of long-wave disturbances of a geostrophic current with linear velocity shear is studied with allowance for the diffusion of buoyancy. A detailed derivation of the model problem in dimensionless variables is presented, which is used for analyzing the dynamics of disturbances in a vertically bounded layer and for describing the formation of large-scale intrusions in the Arctic basin. The problem is solved numerically based on a high-precision method developed for solving fourth-order differential equations. It is established that there is an eigenvalue in the spectrum of eigenvalues that corresponds to unstable (growing with time) disturbances, which are characterized by a phase velocity exceeding the maximum velocity of the geostrophic flow. A discussion is presented to explain some features of the instability.
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Implications of the pseudo-Dirac scenario for ultra high energy neutrinos from GRBs
DOE Office of Scientific and Technical Information (OSTI.GOV)
Esmaili, Arman; Farzan, Yasaman, E-mail: aesmaili@ifi.unicamp.br, E-mail: yasaman@theory.ipm.ac.ir
2012-12-01
The source of Ultra High Energy Cosmic Rays (UHECR) is still an unresolved mystery. Up until recently, sources of Gamma Ray Bursts (GRBs) had been considered as a suitable source for UHECR. Within the fireball model, the UHECR produced at GRBs should be accompanied with a neutrino flux detectable at the neutrino telescope such as IceCube. Recently, IceCube has set an upper bound on the neutrino flux accompanied by GRBs about 3.7 times below the prediction. We investigate whether this deficit can be explained by the oscillation of the active neutrinos to sterile neutrinos en route from the source tomore » the detectors within the pseudo-Dirac scenario. We then discuss the implication of this scenario for diffuse supernova relic neutrinos.« less
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Multispecies diffusion models: A study of uranyl species diffusion
NASA Astrophysics Data System (ADS)
Liu, Chongxuan; Shang, Jianying; Zachara, John M.
2011-12-01
Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energy's Hanford 300A, where intragranular diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that had been previously described using a semiempirical, multirate model. Compared with the multirate model, the diffusion models have the advantage to provide spatiotemporal speciation evolution within the diffusion domains.
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NASA Astrophysics Data System (ADS)
Tang, Tie-Qiao; Luo, Xiao-Feng; Liu, Kai
2016-09-01
The driver's bounded rationality has significant influences on the micro driving behavior and researchers proposed some traffic flow models with the driver's bounded rationality. However, little effort has been made to explore the effects of the driver's bounded rationality on the trip cost. In this paper, we use our recently proposed car-following model to study the effects of the driver's bounded rationality on his running cost and the system's total cost under three traffic running costs. The numerical results show that considering the driver's bounded rationality will enhance his each running cost and the system's total cost under the three traffic running costs.
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A numerical study of confined turbulent jets
NASA Technical Reports Server (NTRS)
Zhu, J.; Shih, T.-H.
1993-01-01
A numerical investigation is reported of turbulent incompressible jets confined in two ducts, one cylindrical and the other conical with a 5 degree divergence. In each case, three Craya-Curtet numbers are considered which correspond, respectively, to flow situations with no moderate and strong recirculation. Turbulence closure is achieved by using the k-epsilon model and a recently proposed realizable Reynolds stress algebraic equation model that relates the Reynolds stresses explicitly to the quadratic terms of the mean velocity gradients and ensures the positiveness of each component of the turbulent kinetic energy. Calculations are carried out with a finite-volume procedure using boundary-fitted curvilinear coordinates. A second-order accurate, bounded convection scheme and sufficiently fine grids are used to prevent the solutions from being contaminated by numerical diffusion. The calculated results are compared extensively with the available experimental data. It is shown that the numerical methods presented are capable of capturing the essential flow features observed in the experiments and that the realizable Reynolds stress algebraic equation model performs much better than the k-epsilon model for this class of flows of great practical importance.
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Models of human platelet thrombospondin in solution. A dynamic light-scattering study.
Vuillard, L; Clezardin, P; Miller, A
1991-01-01
The translational diffusion coefficient (D20,w) of human platelet thrombospondin was measured by dynamic light-scattering. D20,w, measured in 20 mM-Hepes buffer, pH 7.4, containing 350 mM-NaCl and 2 mM-CaCl2, was 1.73(+/- 0.02) x 10(-7) cm2.s-1. After removal of bound Ca2+ by addition of EDTA, D20,w decreased to 1.56(+/- 0.04) x 10(-7) cm2.s-1; this was not a consequence of aggregation. D20,w showed little sensitivity to NaCl concentration between 130 and 550 mM. Through hydrodynamic analysis combining D20,w and other parameters taken from the literature, two major types of models for thrombospondin can be proposed: either classic compact models (i.e. low degree of hydration) such as prolate or oblate ellipsoids with a high axial ratio (greater than 20) or models of low axial ratio made of multiple subunits with significant cavities (i.e. high degree of hydration). PMID:1902085
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Lee, Yu; Yu, Chanki; Lee, Sang Wook
2018-01-10
We present a sequential fitting-and-separating algorithm for surface reflectance components that separates individual dominant reflectance components and simultaneously estimates the corresponding bidirectional reflectance distribution function (BRDF) parameters from the separated reflectance values. We tackle the estimation of a Lafortune BRDF model, which combines a nonLambertian diffuse reflection and multiple specular reflectance components with a different specular lobe. Our proposed method infers the appropriate number of BRDF lobes and their parameters by separating and estimating each of the reflectance components using an interval analysis-based branch-and-bound method in conjunction with iterative K-ordered scale estimation. The focus of this paper is the estimation of the Lafortune BRDF model. Nevertheless, our proposed method can be applied to other analytical BRDF models such as the Cook-Torrance and Ward models. Experiments were carried out to validate the proposed method using isotropic materials from the Mitsubishi Electric Research Laboratories-Massachusetts Institute of Technology (MERL-MIT) BRDF database, and the results show that our method is superior to a conventional minimization algorithm.
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The effect of stimulus strength on the speed and accuracy of a perceptual decision.
Palmer, John; Huk, Alexander C; Shadlen, Michael N
2005-05-02
Both the speed and the accuracy of a perceptual judgment depend on the strength of the sensory stimulation. When stimulus strength is high, accuracy is high and response time is fast; when stimulus strength is low, accuracy is low and response time is slow. Although the psychometric function is well established as a tool for analyzing the relationship between accuracy and stimulus strength, the corresponding chronometric function for the relationship between response time and stimulus strength has not received as much consideration. In this article, we describe a theory of perceptual decision making based on a diffusion model. In it, a decision is based on the additive accumulation of sensory evidence over time to a bound. Combined with simple scaling assumptions, the proportional-rate and power-rate diffusion models predict simple analytic expressions for both the chronometric and psychometric functions. In a series of psychophysical experiments, we show that this theory accounts for response time and accuracy as a function of both stimulus strength and speed-accuracy instructions. In particular, the results demonstrate a close coupling between response time and accuracy. The theory is also shown to subsume the predictions of Piéron's Law, a power function dependence of response time on stimulus strength. The theory's analytic chronometric function allows one to extend theories of accuracy to response time.
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Limits on Log Cross-Product Ratios for Item Response Models. Research Report. ETS RR-06-10
ERIC Educational Resources Information Center
Haberman, Shelby J.; Holland, Paul W.; Sinharay, Sandip
2006-01-01
Bounds are established for log cross-product ratios (log odds ratios) involving pairs of items for item response models. First, expressions for bounds on log cross-product ratios are provided for unidimensional item response models in general. Then, explicit bounds are obtained for the Rasch model and the two-parameter logistic (2PL) model.…
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gay, C. D.; Porter, R. L.; Stancil, P. C.
Using ab initio potential curves and dipole transition moments, cross-section calculations were performed for the direct continuum photodissociation of H{sub 2} through the B{sup 1}{Sigma}{sup +}{sub u} <- X{sup 1}{Sigma}{sup +}{sub g} (Lyman) and C{sup 1}{Pi}{sub u} <- X{sup 1}{Sigma}{sup +}{sub g} (Werner) transitions. Partial cross-sections were obtained for wavelengths from 100 A to the dissociation threshold between the upper electronic state and each of the 301 bound rovibrational levels v''J'' within the ground electronic state. The resulting cross-sections are incorporated into three representative classes of interstellar gas models: diffuse clouds, photon-dominated regions, and X-ray-dominated regions (XDRs). The models, whichmore » used the CLOUDY plasma/molecular spectra simulation code, demonstrate that direct photodissociation is comparable to fluorescent dissociation (or spontaneous radiative dissociation, the Solomon process) as an H{sub 2} destruction mechanism in intense far-ultraviolet or X-ray-irradiated gas. In particular, changes in H{sub 2} rotational column densities are found to be as large as 20% in the XDR model with the inclusion of direct photodissociation. The photodestruction rate from some high-lying rovibrational levels can be enhanced by pumping from H Ly{beta} due to a wavelength coincidence with cross-section resonances resulting from quasi-bound levels of the upper electronic states. Given the relatively large size of the photodissociation data set, a strategy is described to create truncated, but reliable, cross-section data consistent with the wavelength resolving power of typical observations.« less
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Wu, Zhihao; Wang, Shengrui; He, Mengchang; Zhang, Li; Jiao, Lixin
2015-10-01
Labile P, Fe, and sulfide with the high spatial resolution in sediment porewater of five sites (A-E) of Dianchi Lake (China) were measured at same locations using AgI/Chelex-100, Chelex-100, and ferrihydrite DGT (diffusive gradients in thin films) probes. DGT derived P/Fe/S concentrations in sediment porewater on millimeter or sub-millimeter scale in order to reveal the element remobilization process and the mechanism of "internal P-loading" of sediments in Dianchi Lake. Decomposition of alga biomass in the uppermost sediment layer and the reductive dissolution of Fe-bound P in the anoxic sediment were the two main processes causing P release. A dynamic numerical model-DIFS (DGT-induced flux in sediments) was used to assess sediment-P reactivity (capacity of solid pool and rate of transfer) and P release risk by kinetic parameter-T C (1089∼20,450 s), distribution coefficient-K d (167.09∼502.0 cm(3) g(-1)), resupply parameter-R (from 0.242 to 0.518), and changes of dissolved/sorbed concentration, R and M at the microzone of DGT/porewater/sediment.
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Linear ground-water flow, flood-wave response program for programmable calculators
Kernodle, John Michael
1978-01-01
Two programs are documented which solve a discretized analytical equation derived to determine head changes at a point in a one-dimensional ground-water flow system. The programs, written for programmable calculators, are in widely divergent but commonly encountered languages and serve to illustrate the adaptability of the linear model to use in situations where access to true computers is not possible or economical. The analytical method assumes a semi-infinite aquifer which is uniform in thickness and hydrologic characteristics, bounded on one side by an impermeable barrier and on the other parallel side by a fully penetrating stream in complete hydraulic connection with the aquifer. Ground-water heads may be calculated for points along a line which is perpendicular to the impermeable barrie and the fully penetrating stream. Head changes at the observation point are dependent on (1) the distance between that point and the impermeable barrier, (2) the distance between the line of stress (the stream) and the impermeable barrier, (3) aquifer diffusivity, (4) time, and (5) head changes along the line of stress. The primary application of the programs is to determine aquifer diffusivity by the flood-wave response technique. (Woodard-USGS)
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The breakup mechanism of biomolecular and colloidal aggregates in a shear flow
NASA Astrophysics Data System (ADS)
Ó Conchúir, Breanndán; Zaccone, Alessio
2014-03-01
The theory of self-assembly of colloidal particles in shear flow is incomplete. Previous analytical approaches have failed to capture the microscopic interplay between diffusion, shear and intermolecular interactions which controls the aggregates fate in shear. In this work we analytically solved the drift-diffusion equation for the breakup rate of a dimer in flow. Then applying rigidity percolation theory, we found that the lifetime of a generic cluster formed under shear is controlled by the typical lifetime of a single bond in its interior, which in turn depends on the efficiency of the stress transmitted from other bonds in the cluster. We showed that aggregate breakup is a thermally-activated process where the activation energy is controlled by the interplay between intermolecular forces and the shear drift, and where structural parameters determine whether cluster fragmentation or surface erosion prevails. In our latest work, we analyzed floppy modes and nonaffine deformations to derive a lower bound on the fractal dimension df below which aggregates are mechanically unstable, ie. for large aggregates df ~= 2.4. This theoretical framework is in quantitative agreement with experiments and can be used for population balance modeling of colloidal and protein aggregation.
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ERIC Educational Resources Information Center
Welch, Olga M.; And Others
In order to examine the relationship between the development of academic self-esteem and a climate of excellence in the classroom this study compared the experiences of a group of high school students in their two inner-city Knoxville (Tennessee) high schools with their corresponding experiences in a University of Tennessee (Knoxville) sponsored…
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Laminar Soot Processes Experiment Shedding Light on Flame Radiation
NASA Technical Reports Server (NTRS)
Urban, David L.
1998-01-01
The Laminar Soot Processes (LSP) experiment investigated soot processes in nonturbulent, round gas jet diffusion flames in still air. The soot processes within these flames are relevant to practical combustion in aircraft propulsion systems, diesel engines, and furnaces. However, for the LSP experiment, the flames were slowed and spread out to allow measurements that are not tractable for practical, Earth-bound flames.
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Induced mitochondrial membrane potential for modeling solitonic conduction of electrotonic signals
Poznanski, R. R.; Cacha, L. A.; Ali, J.; Rizvi, Z. H.; Yupapin, P.; Salleh, S. H.; Bandyopadhyay, A.
2017-01-01
A cable model that includes polarization-induced capacitive current is derived for modeling the solitonic conduction of electrotonic potentials in neuronal branchlets with microstructure containing endoplasmic membranes. A solution of the nonlinear cable equation modified for fissured intracellular medium with a source term representing charge ‘soakage’ is used to show how intracellular capacitive effects of bound electrical charges within mitochondrial membranes can influence electrotonic signals expressed as solitary waves. The elastic collision resulting from a head-on collision of two solitary waves results in localized and non-dispersing electrical solitons created by the nonlinearity of the source term. It has been shown that solitons in neurons with mitochondrial membrane and quasi-electrostatic interactions of charges held by the microstructure (i.e., charge ‘soakage’) have a slower velocity of propagation compared with solitons in neurons with microstructure, but without endoplasmic membranes. When the equilibrium potential is a small deviation from rest, the nonohmic conductance acts as a leaky channel and the solitons are small compared when the equilibrium potential is large and the outer mitochondrial membrane acts as an amplifier, boosting the amplitude of the endogenously generated solitons. These findings demonstrate a functional role of quasi-electrostatic interactions of bound electrical charges held by microstructure for sustaining solitons with robust self-regulation in their amplitude through changes in the mitochondrial membrane equilibrium potential. The implication of our results indicate that a phenomenological description of ionic current can be successfully modeled with displacement current in Maxwell’s equations as a conduction process involving quasi-electrostatic interactions without the inclusion of diffusive current. This is the first study in which solitonic conduction of electrotonic potentials are generated by polarization-induced capacitive current in microstructure and nonohmic mitochondrial membrane current. PMID:28880876
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Induced mitochondrial membrane potential for modeling solitonic conduction of electrotonic signals.
Poznanski, R R; Cacha, L A; Ali, J; Rizvi, Z H; Yupapin, P; Salleh, S H; Bandyopadhyay, A
2017-01-01
A cable model that includes polarization-induced capacitive current is derived for modeling the solitonic conduction of electrotonic potentials in neuronal branchlets with microstructure containing endoplasmic membranes. A solution of the nonlinear cable equation modified for fissured intracellular medium with a source term representing charge 'soakage' is used to show how intracellular capacitive effects of bound electrical charges within mitochondrial membranes can influence electrotonic signals expressed as solitary waves. The elastic collision resulting from a head-on collision of two solitary waves results in localized and non-dispersing electrical solitons created by the nonlinearity of the source term. It has been shown that solitons in neurons with mitochondrial membrane and quasi-electrostatic interactions of charges held by the microstructure (i.e., charge 'soakage') have a slower velocity of propagation compared with solitons in neurons with microstructure, but without endoplasmic membranes. When the equilibrium potential is a small deviation from rest, the nonohmic conductance acts as a leaky channel and the solitons are small compared when the equilibrium potential is large and the outer mitochondrial membrane acts as an amplifier, boosting the amplitude of the endogenously generated solitons. These findings demonstrate a functional role of quasi-electrostatic interactions of bound electrical charges held by microstructure for sustaining solitons with robust self-regulation in their amplitude through changes in the mitochondrial membrane equilibrium potential. The implication of our results indicate that a phenomenological description of ionic current can be successfully modeled with displacement current in Maxwell's equations as a conduction process involving quasi-electrostatic interactions without the inclusion of diffusive current. This is the first study in which solitonic conduction of electrotonic potentials are generated by polarization-induced capacitive current in microstructure and nonohmic mitochondrial membrane current.
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Alexandrescu, A. T.; Rathgeb-Szabo, K.; Rumpel, K.; Jahnke, W.; Schulthess, T.; Kammerer, R. A.
1998-01-01
Backbone 15N relaxation parameters (R1, R2, 1H-15N NOE) have been measured for a 22-residue recombinant variant of the S-peptide in its free and S-protein bound forms. NMR relaxation data were analyzed using the "model-free" approach (Lipari & Szabo, 1982). Order parameters obtained from "model-free" simulations were used to calculate 1H-15N bond vector entropies using a recently described method (Yang & Kay, 1996), in which the form of the probability density function for bond vector fluctuations is derived from a diffusion-in-a-cone motional model. The average change in 1H-15N bond vector entropies for residues T3-S15, which become ordered upon binding of the S-peptide to the S-protein, is -12.6+/-1.4 J/mol.residue.K. 15N relaxation data suggest a gradient of decreasing entropy values moving from the termini toward the center of the free peptide. The difference between the entropies of the terminal and central residues is about -12 J/mol residue K, a value comparable to that of the average entropy change per residue upon complex formation. Similar entropy gradients are evident in NMR relaxation studies of other denatured proteins. Taken together, these observations suggest denatured proteins may contain entropic contributions from non-local interactions. Consequently, calculations that model the entropy of a residue in a denatured protein as that of a residue in a di- or tri-peptide, might over-estimate the magnitude of entropy changes upon folding. PMID:9521116
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Miralles, Francesc; Öfverstedt, Lars-Göran; Sabri, Nafiseh; Aissouni, Youssef; Hellman, Ulf; Skoglund, Ulf; Visa, Neus
2000-01-01
Using electron tomography, we have analyzed whether the Balbiani ring (BR) pre-mRNP particles in transit from the gene to the nuclear pore complex (NPC) are bound to any structure that could impair free diffusion through the nucleoplasm. We show that one-third of the BR particles are in contact with thin connecting fibers (CFs), which in some cases merge into large fibrogranular clusters. The CFs have a specific protein composition different from that of BR particles, as shown by immuno-EM. Moreover, we have identified hrp65 as one of the protein components of the CFs. The sequencing of hrp65 cDNA reveals similarities with hnRNP proteins and splicing factors. However, hrp65 is likely to have a different function because it does not bind to nascent pre-mRNA and is not part of the pre-mRNP itself. Taken together, our observations indicate that pre-mRNPs are not always freely diffusible in the nucleoplasm but interact with fibers of specific structure and composition, which implies that some of the posttranscriptional events that the pre-mRNPs undergo before reaching the NPC occur in a bound state. PMID:10648560
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NASA Astrophysics Data System (ADS)
Moshammer, Hanns; Neuberger, Manfred
At a central elementary school in the capital of Upper Austria children aged 7-10 years underwent repeated respiratory health checkups (questionnaires, diaries, spirometry). Between March and May 2001 the daily means of the signals of a diffusion charging sensor, measuring the "active surface" of suspended particles, and a photoelectric aerosol sensor, measuring the particle-bound polycyclic aromatic hydrocarbons, were related to spirometric results of the total 164 children examined and to the daily symptom scores of a susceptible subgroup. Significant reductions of forced vital capacity ( p=0.006) and forced expiratory volume in the first second ( p=0.001) and significant increases of wheezing ( p=0.001), shortness of breath ( p=0.041), cough in the evening ( p=0.031) and at night ( p=0.018) were found with increase of "active surface" of suspended particles measured at the adjacent outdoor monitoring station, but not with the increase of particle-bound polycyclic aromatic hydrocarbons. Monitoring "active surface" of particles with diameters of about 10 nm-1 μm by means of a diffusion charging sensor might provide additional information in surveillance of particulate matter for prevention of acute effects on respiratory health.
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Report on simulation of fission gas and fission product diffusion in UO 2
DOE Office of Scientific and Technical Information (OSTI.GOV)
Andersson, Anders David; Perriot, Romain Thibault; Pastore, Giovanni
2016-07-22
In UO 2 nuclear fuel, the retention and release of fission gas atoms such as xenon (Xe) are important for nuclear fuel performance by, for example, reducing the fuel thermal conductivity, causing fuel swelling that leads to mechanical interaction with the clad, increasing the plenum pressure and reducing the fuel–clad gap thermal conductivity. We use multi-scale simulations to determine fission gas diffusion mechanisms as well as the corresponding rates in UO 2 under both intrinsic and irradiation conditions. In addition to Xe and Kr, the fission products Zr, Ru, Ce, Y, La, Sr and Ba have been investigated. Density functionalmore » theory (DFT) calculations are used to study formation, binding and migration energies of small clusters of Xe atoms and vacancies. Empirical potential calculations enable us to determine the corresponding entropies and attempt frequencies for migration as well as investigate the properties of large clusters or small fission gas bubbles. A continuum reaction-diffusion model is developed for Xe and point defects based on the mechanisms and rates obtained from atomistic simulations. Effective fission gas diffusivities are then obtained by solving this set of equations for different chemical and irradiation conditions using the MARMOT phase field code. The predictions are compared to available experimental data. The importance of the large Xe U3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequence of its high mobility and high binding energy. We find that the Xe U3O cluster gives Xe diffusion coefficients that are higher for intrinsic conditions than under irradiation over a wide range of temperatures. Under irradiation the fast-moving Xe U3O cluster recombines quickly with irradiation-induced interstitial U ions, while this mechanism is less important for intrinsic conditions. The net result is higher concentration of the Xe U3O cluster for intrinsic conditions than under irradiation. We speculate that differences in the irradiation conditions and their impact on the Xe U3O cluster can explain the wide range of diffusivities reported in experimental studies. However, all vacancy-mediated mechanisms underestimate the Xe diffusivity compared to the empirical radiation-enhanced rate used in most fission gas release models. We investigate the possibility that diffusion of small fission gas bubbles or extended Xe-vacancy clusters may give rise to the observed radiation-enhanced diffusion coefficient. These studies highlight the importance of U divacancies and an octahedron coordination of uranium vacancies encompassing a Xe fission gas atom. The latter cluster can migrate via a multistep mechanism with a rather low effective barrier, which together with irradiation-induced clusters of uranium vacancies, gives rise to the irradiation-enhanced diffusion coefficient observed in experiments.« less
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Bounds on low scale gravity from RICE data and cosmogenic neutrino flux models
NASA Astrophysics Data System (ADS)
Hussain, Shahid; McKay, Douglas W.
2006-03-01
We explore limits on low scale gravity models set by results from the Radio Ice Cherenkov Experiment's (RICE) ongoing search for cosmic ray neutrinos in the cosmogenic, or GZK, energy range. The bound on M, the fundamental scale of gravity, depends upon cosmogenic flux model, black hole formation and decay treatments, inclusion of graviton mediated elastic neutrino processes, and the number of large extra dimensions, d. Assuming proton-based cosmogenic flux models that cover a broad range of flux possibilities, we find bounds in the interval 0.9 TeV
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An error bound for a discrete reduced order model of a linear multivariable system
NASA Technical Reports Server (NTRS)
Al-Saggaf, Ubaid M.; Franklin, Gene F.
1987-01-01
The design of feasible controllers for high dimension multivariable systems can be greatly aided by a method of model reduction. In order for the design based on the order reduction to include a guarantee of stability, it is sufficient to have a bound on the model error. Previous work has provided such a bound for continuous-time systems for algorithms based on balancing. In this note an L-infinity bound is derived for model error for a method of order reduction of discrete linear multivariable systems based on balancing.
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NASA Astrophysics Data System (ADS)
Chen, Kewei; Zhan, Hongbin
2018-06-01
The reactive solute transport in a single fracture bounded by upper and lower matrixes is a classical problem that captures the dominant factors affecting transport behavior beyond pore scale. A parallel fracture-matrix system which considers the interaction among multiple paralleled fractures is an extension to a single fracture-matrix system. The existing analytical or semi-analytical solution for solute transport in a parallel fracture-matrix simplifies the problem to various degrees, such as neglecting the transverse dispersion in the fracture and/or the longitudinal diffusion in the matrix. The difficulty of solving the full two-dimensional (2-D) problem lies in the calculation of the mass exchange between the fracture and matrix. In this study, we propose an innovative Green's function approach to address the 2-D reactive solute transport in a parallel fracture-matrix system. The flux at the interface is calculated numerically. It is found that the transverse dispersion in the fracture can be safely neglected due to the small scale of fracture aperture. However, neglecting the longitudinal matrix diffusion would overestimate the concentration profile near the solute entrance face and underestimate the concentration profile at the far side. The error caused by neglecting the longitudinal matrix diffusion decreases with increasing Peclet number. The longitudinal matrix diffusion does not have obvious influence on the concentration profile in long-term. The developed model is applied to a non-aqueous-phase-liquid (DNAPL) contamination field case in New Haven Arkose of Connecticut in USA to estimate the Trichloroethylene (TCE) behavior over 40 years. The ratio of TCE mass stored in the matrix and the injected TCE mass increases above 90% in less than 10 years.
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D'Angelo, E
2017-12-01
Tetracycline (TET) is commonly used to treat bacterial diseases in humans and chickens (Gallus gallus domesticus), is largely excreted, and is found at elevated concentrations in treated sewage sludge (biosolids) and poultry litter (excrement plus bedding materials). Routine application of these nutrient-and carbon-enriched materials to soils improves fertility and other characteristics, but the presence of antibiotics (and other pharmaceuticals) in amendments raises questions about potential adverse effects on biota and development of antibiotic resistance in the environment. Hazard risks are largely dictated by sorption-desorption and diffusion behavior in amendments, so these processes were evaluated from sorption-desorption equilibrium isotherm and diffusion cell experiments with four types amendments (biosolids, poultry manure, wood chip litter, and rice hull litter) at three temperatures (8 °C, 20 °C and 32 °C). Linear sorption-desorption equilibrium distribution constants (Kd) in native amendments ranged between 124-2418 L kg -1 . TET sorption was significantly increased after treatment with alum, and there was a strong exponential relationship between Kd and the concentration of bound Al 3+ in amendments (R 2 = 0.94), which indicated that amendments contained functional groups capable of chelating Al 3+ and forming metal bridges with TET. Effective diffusion coefficients of TET in amendments ranged between 0.1 and 5.2 × 10 -6 cm 2 s -1 , which were positively related to temperature and inversely related to Kd by a multiple regression model (R 2 = 0.86). Treatment of organic amendments with alum greatly increased Kd, would decrease D s , and so would greatly reduce hazard risks of applying these organic amendments with this antibiotic to soils. Copyright © 2017 Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wazawa, Tetsuichi; CREST, JST, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012; Sagawa, Takashi
2011-01-28
Research highlights: {yields} Translationally hyper-mobile water has been detected around actin filaments. {yields} Translationally hyper-mobile water is formed upon polymerization of actin. {yields} Low water viscosity was found around F-actin using fluorescence anisotropy. {yields} Formation of hyper-mobile water may explain endothermic actin polymerization. -- Abstract: This paper reports that water molecules around F-actin, a polymerized form of actin, are more mobile than those around G-actin or in bulk water. A measurement using pulse-field gradient spin-echo {sup 1}H NMR showed that the self-diffusion coefficient of water in aqueous F-actin solution increased with actin concentration by {approx}5%, whereas that in G-actin solutionmore » was close to that of pure water. This indicates that an F-actin/water interaction is responsible for the high self-diffusion of water. The local viscosity around actin was also investigated by fluorescence measurements of Cy3, a fluorescent dye, conjugated to Cys 374 of actin. The steady-state fluorescence anisotropy of Cy3 attached to F-actin was 0.270, which was lower than that for G-actin, 0.334. Taking into account the fluorescence lifetimes of the Cy3 bound to actin, their rotational correlation times were estimated to be 3.8 and 9.1 ns for F- and G-actin, respectively. This indicates that Cy3 bound to F-actin rotates more freely than that bound to G-actin, and therefore the local water viscosity is lower around F-actin than around G-actin.« less
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NASA Astrophysics Data System (ADS)
Zhou, Xinjian; Moran-Mirabal, Jose Manuel; Craighead, Harold; McEuen, Paul
2006-03-01
We have formed supported lipid bilayers (SLBs) by small unilamellar vesicle fusion on substrates containing single-walled carbon nanotube field-effect transistors (SWNT-FETs). We are able to detect the self-assembly of SLBs electrically with SWNT-FETs since their threshold voltages are shifted by this event. The SLB fully covers the NT surface and lipid molecules can diffuse freely in the bilayer surface across the NT. To study the interactions of important biological entities with receptors imbedded within the membrane, we have also integrated a membrane protein, GT1b ganglioside, in the bilayer. While bare gangliosides can diffuse freely across the NT, interestingly the NT acts as a diffusion barrier for the gangliosides when they are bound with tetanus toxin. This experiment opens the possibility of using SWNT-FETs as biosensors for label-free detection.
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Motion-induced phase error estimation and correction in 3D diffusion tensor imaging.
Van, Anh T; Hernando, Diego; Sutton, Bradley P
2011-11-01
A multishot data acquisition strategy is one way to mitigate B0 distortion and T2∗ blurring for high-resolution diffusion-weighted magnetic resonance imaging experiments. However, different object motions that take place during different shots cause phase inconsistencies in the data, leading to significant image artifacts. This work proposes a maximum likelihood estimation and k-space correction of motion-induced phase errors in 3D multishot diffusion tensor imaging. The proposed error estimation is robust, unbiased, and approaches the Cramer-Rao lower bound. For rigid body motion, the proposed correction effectively removes motion-induced phase errors regardless of the k-space trajectory used and gives comparable performance to the more computationally expensive 3D iterative nonlinear phase error correction method. The method has been extended to handle multichannel data collected using phased-array coils. Simulation and in vivo data are shown to demonstrate the performance of the method.
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Weyl corrections to diffusion and chaos in holography
NASA Astrophysics Data System (ADS)
Li, Wei-Jia; Liu, Peng; Wu, Jian-Pin
2018-04-01
Using holographic methods in the Einstein-Maxwell-dilaton-axion (EMDA) theory, it was conjectured that the thermal diffusion in a strongly coupled metal without quasi-particles saturates an universal lower bound that is associated with the chaotic property of the system at infrared (IR) fixed points [1]. In this paper, we investigate the thermal transport and quantum chaos in the EMDA theory with a small Weyl coupling term. It is found that the Weyl coupling correct the thermal diffusion constant D Q and butterfly velocity v B in different ways, hence resulting in a modified relation between the two at IR fixed points. Unlike that in the EMDA case, our results show that the ratio D Q /( v B 2 τ L ) always contains a non-universal Weyl correction which depends also on the bulk fields as long as the U(1) current is marginally relevant in the IR.
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Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...
2014-12-19
We report that lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF more » $$\\bar{6}$$ anion. Li + prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li + solvation. Corresponding analysis for the PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less
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Nanostructures and nanosecond dynamics at the polymer/filler interface
NASA Astrophysics Data System (ADS)
Koga, Tad; Barkley, Deborah; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Taniguchi, Takashi
We report in-situ nanostructures and nanosecond dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in polymer solutions (from dilute to concentrated solutions). The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene (a good solvent) to label the BPL for ``contrast-matching'' small-angle neutron scattering (SANS) and neutron spin echo (NSE) techniques. The SANS results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. In addition, the NSE results show that the dynamics of the swollen bound chains in the polymer solutions can be explained by the collective dynamics, the so-called ``breathing mode''. Intriguingly, it was also indicative that the collective dynamics is independent of the polymer concentrations and is much faster than that predicted from the solution viscosity. We will discuss the mechanism at the bound polymer-free polymer interface at the nanometer scale. T.K. acknowledges the financial support from NSF Grant (CMMI-1332499).
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Nanostructures and dynamics of macromolecules bound to attractive filler surfaces
NASA Astrophysics Data System (ADS)
Koga, Tad; Barkley, Deborah; Jiang, Naisheng; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Satija, Sushil; Taniguchi, Takashi
We report in-situ nanostructures and dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in a good solvent. The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene to label the BPL for small-angle neutron scattering and neutron spin echo techniques. Intriguingly, the results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of ~ 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. This two-layer formation on the filler surface is similar to that reported for polymer chains adsorbed on planar substrates from melts. In addition, the results show that the dynamics of the swollen bound chains can be explained by the so-called ``breathing mode'' and is generalized with the thickness of the swollen BPL. Furthermore, we will discuss how the breathing collective dynamics is affected by the presence of polymer chains in a matrix solution. We acknowledge the financial support from NSF Grant No. CMMI-1332499.
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On Entropy Production in the Madelung Fluid and the Role of Bohm's Potential in Classical Diffusion
NASA Astrophysics Data System (ADS)
Heifetz, Eyal; Tsekov, Roumen; Cohen, Eliahu; Nussinov, Zohar
2016-07-01
The Madelung equations map the non-relativistic time-dependent Schrödinger equation into hydrodynamic equations of a virtual fluid. While the von Neumann entropy remains constant, we demonstrate that an increase of the Shannon entropy, associated with this Madelung fluid, is proportional to the expectation value of its velocity divergence. Hence, the Shannon entropy may grow (or decrease) due to an expansion (or compression) of the Madelung fluid. These effects result from the interference between solutions of the Schrödinger equation. Growth of the Shannon entropy due to expansion is common in diffusive processes. However, in the latter the process is irreversible while the processes in the Madelung fluid are always reversible. The relations between interference, compressibility and variation of the Shannon entropy are then examined in several simple examples. Furthermore, we demonstrate that for classical diffusive processes, the "force" accelerating diffusion has the form of the positive gradient of the quantum Bohm potential. Expressing then the diffusion coefficient in terms of the Planck constant reveals the lower bound given by the Heisenberg uncertainty principle in terms of the product between the gas mean free path and the Brownian momentum.
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Wu, Zhihao; Wang, Shengrui; Luo, Jun
2018-05-15
DGT (diffusive gradients in thin films) technique and DIFS (DGT induced fluxes in sediment) model are firstly designed for macrophyte-rhizobox system and in-situ macrophytes in Lake Erhai. Dynamics of phosphorus (P) transfer in Zizania latifolia (ZL) and Myriophyllum verticiilatur (MV) rhizosphere is revealed and phytoremediation performance for P in sediment is evaluated. Dynamic transfer process of P at DGT/sediment interface includes (i) diffusion flux and concentration gradients at DGT(root)/porewater interface leading to porewater concentration (C 0 ) depletion and (ii) P desorption from labile P pool in sediment solid to resupply C 0 depletion. Fe-redox controlled P release from Fe-bound P (BD-P2) and then NH 4 Cl-P1 in rhizosphere sediment resupplies porewater depletion due to DGT (root) sink. K d (labile P pool size in solid phase), r (resupply ratio) and kinetic exchange (Tc and k -1 ) lead to change characters of DIFS curves of (1) r against deployment time and (2) C solu (dissolved concentration) against distance at 24 h. They include two opposite types of "fast" and "slow" rate of resupplies. Sediment properties and DIFS parameters control P diffusion and resupply in rhizosphere sediment. Phytoremoval ability for sediment P in lake is estimated to be 23.4 (ZL) or 15.0 t a -1 (MV) by "DGT-flux" method. Copyright © 2018 Elsevier B.V. All rights reserved.
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An Experimental Investigation of the Laminar Flamelet Concept for Soot Properties
NASA Technical Reports Server (NTRS)
Diez, F. J.; Aalburg, C.; Sunderland, P. B.; Urban, D. L.; Yuan, Z.-G.; Faeth, G. M.
2007-01-01
The soot properties of round, nonbuoyant, laminar jet diffusion flames are described, based on experiments at microgravity carried out on orbit during three flights of the Space Shuttle Columbia, (Flights STS-83, 94 and 107). Experimental conditions included ethylene- and propane-fueled flames burning in still air at an ambient temperature of 300 K and ambient pressures of 35-100 kPa. Measurements included soot volume fraction distributions using deconvoluted laser extinction imaging, and soot temperature distributions using deconvoluted multiline emission imaging. Flowfield modeling based on the work of Spalding is presented. The present work explores whether soot properties of these flames are universal functions of mixture fraction, i.e., whether they satisfy soot state relationships. Measurements are presented, including radiative emissions and distributions of soot temperature and soot volume fraction. It is shown that most of the volume of these flames is bounded by the dividing streamline and thus should follow residence time state relationships. Most streamlines from the fuel supply to the surroundings are found to exhibit nearly the same maximum soot volume fraction and temperature. The radiation intensity along internal streamlines also is found to have relatively uniform values. Finally, soot state relationships were observed, i.e., soot volume fraction was found to correlate with estimated mixture fraction for each fuel/pressure selection. These results support the existence of soot property state relationships for steady nonbuoyant laminar diffusion flames, and thus in a large class of practical turbulent diffusion flames through the application of the laminar flamelet concept.
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Ignition Delay Associated with a Strained Strip
NASA Technical Reports Server (NTRS)
Gerk, T. J.; Karagozian, A. R.
1996-01-01
Ignition processes associated with two adjacent fuel-oxidizer interferences bounding a strained fuel strip are explored here using single-step activation energy asymptotics. Calculations are made for constant as well as temporally decaying strain fields. There possible models of ignition are determined: one in which the two interfaces ignite independently as diffusion flames; one in which the two interfaces ignite dependently and in which ignition occurs to form a single , premixed flame at very high strain rates before ignition is completely prevented. In contrast to a single, isolated interface in which ignition can be prevented by overmatching heat production with heat convection due to strain, ignition of a strained fuel strip can also be prevented if the finite extend of fuel is diluted by oxidizer more quickly than heat production can cause a positive feedback thermal runaway. These behaviors are dependent on the relative sizes of timescales associated with species and heat diffusion, with convection due to strain, and with the chemical reaction. The result here indicate that adjacent, strained species interfaces may ignite quite differently in nature from ignition of a single, strained intrface and that their interdependence should be considered as the interfaces are brought closer together in complex strain fields. Critical strain rates leading to complete ignition delay are found to be considerably smaller for the fuel strip than those for single interfaces as the fuel strip is made thin in comparison to diffusion and chemical length scales.
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The hydrogeology of Kilauea volcano
Ingebritsen, S.E.; Scholl, M.A.
1993-01-01
The hydrogeology of Kilauea volcano and adjacent areas has been studied since the turn of this century. However, most studies to date have focused on the relatively shallow, low-salinity parts of the ground-water system, and the deeper hydrothermal system remains poorly understood. The rift zones of adjacent Mauna Loa volcano bound the regional ground-water flow system that includes Kilauea, and the area bounded by the rift zones of Kilauea and the ocean may comprise a partly isolated subsystem. Rates of ground-water recharge vary greatly over the area and discharge is difficult to measure, because streams are ephemeral and most ground-water discharges diffusely at or below sea level. Hydrothermal systems exist at depth in Kilauea's cast and southwest rift zone, as evidenced by thermal springs at the coast and wells in the lower east-rift zone. Available data suggest that dike-impounded, heated ground water occurs at relatively high elevations in the upper east-and southwest-rift zones of Kilauea, and that permeability at depth in the rift zones (probably 10 10 m2). Substantial variations in permeability and the presence of magmatic heat sources influence the structure of the fresh water-salt water interface, so the Ghyben-Herzberg model will often fail to predict its position. Numerical modeling studies have considered only subsets of the hydrothermal system, because no existing computer code solves the coupled fluid-flow, heat- and solute-transport problem over the temperature and salinity range encountered at Kilauea. ?? 1993.
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An invariance property of generalized Pearson random walks in bounded geometries
NASA Astrophysics Data System (ADS)
Mazzolo, Alain
2009-03-01
Invariance properties of random walks in bounded domains are a topic of growing interest since they contribute to improving our understanding of diffusion in confined geometries. Recently, limited to Pearson random walks with exponentially distributed straight paths, it has been shown that under isotropic uniform incidence, the average length of the trajectories through the domain is independent of the random walk characteristic and depends only on the ratio of the volume's domain over its surface. In this paper, thanks to arguments of integral geometry, we generalize this property to any isotropic bounded stochastic process and we give the conditions of its validity for isotropic unbounded stochastic processes. The analytical form for the traveled distance from the boundary to the first scattering event that ensures the validity of the Cauchy formula is also derived. The generalization of the Cauchy formula is an analytical constraint that thus concerns a very wide range of stochastic processes, from the original Pearson random walk to a Rayleigh distribution of the displacements, covering many situations of physical importance.
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Chemical transport in a fissured rock: Verification of a numerical model
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rasmuson, A.; Narasimhan, T. N.; Neretnieks, I.
1982-10-01
Numerical models for simulating chemical transport in fissured rocks constitute powerful tools for evaluating the acceptability of geological nuclear waste repositories. Due to the very long-term, high toxicity of some nuclear waste products, the models are required to predict, in certain cases, the spatial and temporal distribution of chemical concentration less than 0.001% of the concentration released from the repository. Whether numerical models can provide such accuracies is a major question addressed in the present work. To this end, we have verified a numerical model, TRUMP, which solves the advective diffusion equation in general three dimensions with or without decaymore » and source terms. The method is based on an integrated finite-difference approach. The model was verified against known analytic solution of the one-dimensional advection-diffusion problem as well as the problem of advection-diffusion in a system of parallel fractures separated by spherical particles. The studies show that as long as the magnitude of advectance is equal to or less than that of conductance for the closed surface bounding any volume element in the region (that is, numerical Peclet number <2), the numerical method can indeed match the analytic solution within errors of ±10{sup -3} % or less. The realistic input parameters used in the sample calculations suggest that such a range of Peclet numbers is indeed likely to characterize deep groundwater systems in granitic and ancient argillaceous systems. Thus TRUMP in its present form does provide a viable tool for use in nuclear waste evaluation studies. A sensitivity analysis based on the analytic solution suggests that the errors in prediction introduced due to uncertainties in input parameters is likely to be larger than the computational inaccuracies introduced by the numerical model. Currently, a disadvantage in the TRUMP model is that the iterative method of solving the set of simultaneous equations is rather slow when time constants vary widely over the flow region. Although the iterative solution may be very desirable for large three-dimensional problems in order to minimize computer storage, it seems desirable to use a direct solver technique in conjunction with the mixed explicit-implicit approach whenever possible. work in this direction is in progress.« less
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Pham, Anh Le-Tuan; Johnson, Carol; Manley, Devon; Hsu-Kim, Heileen
2015-11-03
Diffusive gradient in thin-film (DGT) passive samplers are frequently used to monitor the concentrations of metals such as mercury and zinc in sediments and other aquatic environments. The application of these samplers generally presumes that they quantify only the dissolved fraction and not particle-bound metal species that are too large to migrate into the sampler. However, metals associated with very small nanoparticles (smaller than the pore size of DGT samplers) can be abundant in certain environments, yet the implications of these nanoparticles for DGT measurements are unclear. The objective of this study was to determine how the performance of the DGT sampler is affected by the presence of nanoparticulate species of Hg and Zn. DGT samplers were exposed to solutions containing known amounts of dissolved Hg(II) and nanoparticulate HgS (or dissolved Zn(II) and nanoparticulate ZnS). The amounts of Hg and Zn accumulated onto the DGT samplers were quantified over hours to days, and the rates of diffusion of the dissolved metal (i.e., the effective diffusion coefficient D) into the sampler's diffusion layer were calculated and compared for solutions containing varying concentrations of nanoparticles. The results suggested that the nanoparticles deposited on the surface of the samplers might have acted as sorbents, slowing the migration of the dissolved species into the samplers. The consequence was that the DGT sampler data underestimated the dissolved metal concentration in the solution. In addition, X-ray absorption spectroscopy was employed to determine the speciation of the Hg accumulated on the sampler binding layer, and the results indicated that HgS nanoparticles did not appear to directly contribute to the DGT measurement. Overall, our findings suggest that the deployment of DGT samplers in settings where nanoparticles are relevant (e.g., sediments) may result in DGT data that incorrectly estimated the dissolved metal concentrations. Models for metal uptake into the sampler may need to be reconsidered.
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Mechanisms Underlying the Confined Diffusion of Cholera Toxin B-Subunit in Intact Cell Membranes
Day, Charles A.; Kenworthy, Anne K.
2012-01-01
Multivalent glycolipid binding toxins such as cholera toxin have the capacity to cluster glycolipids, a process thought to be important for their functional uptake into cells. In contrast to the highly dynamic properties of lipid probes and many lipid-anchored proteins, the B-subunit of cholera toxin (CTxB) diffuses extremely slowly when bound to its glycolipid receptor GM1 in the plasma membrane of living cells. In the current study, we used confocal FRAP to examine the origins of this slow diffusion of the CTxB/GM1 complex at the cell surface, relative to the behavior of a representative GPI-anchored protein, transmembrane protein, and fluorescent lipid analog. We show that the diffusion of CTxB is impeded by actin- and ATP-dependent processes, but is unaffected by caveolae. At physiological temperature, the diffusion of several cell surface markers is unchanged in the presence of CTxB, suggesting that binding of CTxB to membranes does not alter the organization of the plasma membrane in a way that influences the diffusion of other molecules. Furthermore, diffusion of the B-subunit of another glycolipid-binding toxin, Shiga toxin, is significantly faster than that of CTxB, indicating that the confined diffusion of CTxB is not a simple function of its ability to cluster glycolipids. By identifying underlying mechanisms that control CTxB dynamics at the cell surface, these findings help to delineate the fundamental properties of toxin-receptor complexes in intact cell membranes. PMID:22511973
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NASA Technical Reports Server (NTRS)
1979-01-01
A reflectometer which can separately evaluate the spectral and diffuse reflectivities of surfaces is described. A phase locked detection system for the reflectometer is also described. A selective coating on aluminum potentially useful for flat plate solar collector applications is presented. The coating is composed of strongly bound copper oxide (divalent) and is formed by an etching process performed on an aluminum alloy with high copper content. Fabrication costs are expected to be small due to the one stop fabrication process. A number of conclusions gathered from the literature as to the required optical properties of flat plate solar collectors are discussed.
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Effect of temperature and pressure on the dynamics of nanoconfined propane
NASA Astrophysics Data System (ADS)
Gautam, Siddharth; Liu, Tingting; Rother, Gernot; Jalarvo, Niina; Mamontov, Eugene; Welch, Susan; Cole, David
2014-04-01
We report the effect of temperature and pressure on the dynamical properties of propane confined in nanoporous silica aerogel studied using quasielastic neutron scattering (QENS). Our results demonstrate that the effect of a change in the pressure dominates over the effect of temperature variation on the dynamics of propane nano-confined in silica aerogel. At low pressures, most of the propane molecules are strongly bound to the pore walls, only a small fraction is mobile. As the pressure is increased, the fraction of mobile molecules increases. A change in the mechanism of motion, from continuous diffusion at low pressures to jump diffusion at higher pressures has also been observed.
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Reduced equations of motion for quantum systems driven by diffusive Markov processes.
Sarovar, Mohan; Grace, Matthew D
2012-09-28
The expansion of a stochastic Liouville equation for the coupled evolution of a quantum system and an Ornstein-Uhlenbeck process into a hierarchy of coupled differential equations is a useful technique that simplifies the simulation of stochastically driven quantum systems. We expand the applicability of this technique by completely characterizing the class of diffusive Markov processes for which a useful hierarchy of equations can be derived. The expansion of this technique enables the examination of quantum systems driven by non-Gaussian stochastic processes with bounded range. We present an application of this extended technique by simulating Stark-tuned Förster resonance transfer in Rydberg atoms with nonperturbative position fluctuations.
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Outward Bound Outcome Model Validation and Multilevel Modeling
ERIC Educational Resources Information Center
Luo, Yuan-Chun
2011-01-01
This study was intended to measure construct validity for the Outward Bound Outcomes Instrument (OBOI) and to predict outcome achievement from individual characteristics and course attributes using multilevel modeling. A sample of 2,340 participants was collected by Outward Bound USA between May and September 2009 using the OBOI. Two phases of…
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Dependence in probabilistic modeling Dempster-Shafer theory and probability bounds analysis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ferson, Scott; Nelsen, Roger B.; Hajagos, Janos
2015-05-01
This report summarizes methods to incorporate information (or lack of information) about inter-variable dependence into risk assessments that use Dempster-Shafer theory or probability bounds analysis to address epistemic and aleatory uncertainty. The report reviews techniques for simulating correlated variates for a given correlation measure and dependence model, computation of bounds on distribution functions under a specified dependence model, formulation of parametric and empirical dependence models, and bounding approaches that can be used when information about the intervariable dependence is incomplete. The report also reviews several of the most pervasive and dangerous myths among risk analysts about dependence in probabilistic models.
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Density Large Deviations for Multidimensional Stochastic Hyperbolic Conservation Laws
NASA Astrophysics Data System (ADS)
Barré, J.; Bernardin, C.; Chetrite, R.
2018-02-01
We investigate the density large deviation function for a multidimensional conservation law in the vanishing viscosity limit, when the probability concentrates on weak solutions of a hyperbolic conservation law. When the mobility and diffusivity matrices are proportional, i.e. an Einstein-like relation is satisfied, the problem has been solved in Bellettini and Mariani (Bull Greek Math Soc 57:31-45, 2010). When this proportionality does not hold, we compute explicitly the large deviation function for a step-like density profile, and we show that the associated optimal current has a non trivial structure. We also derive a lower bound for the large deviation function, valid for a more general weak solution, and leave the general large deviation function upper bound as a conjecture.
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Separation of Membrane-Bound Compounds by Solid-Supported Bilayer Electrophoresis
Daniel, Susan; Diaz, Arnaldo J.; Martinez, Kelly M.; Bench, Bennie J.; Albertorio, Fernando; Cremer, Paul S.
2008-01-01
A new method was developed to purify membrane bound species within a supported lipid bilayer (SLB) environment. SLBs consisting of phosphatidylcholine lipids and cholesterol were employed as the separation matrix. Cholesterol was used to reduce the diffusion of lipids within the bilayer and, therefore, substantially reduce mixing of the dye-conjugated lipids to be separated. These molecules were introduced into an SLB adjacent to the separations SLB and electrophoresis was employed to move these species through it. The method was powerful enough to completely resolve two isomers of Texas Red DHPE from each other. Moreover, these isomers could be separated from a BODIPY-conjugated lipid as well. Such procedures could be extended to the purification of peripheral and transmembrane proteins. PMID:17564451
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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.
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Long-Time Behavior and Critical Limit of Subcritical SQG Equations in Scale-Invariant Sobolev Spaces
NASA Astrophysics Data System (ADS)
Coti Zelati, Michele
2018-02-01
We consider the subcritical SQG equation in its natural scale-invariant Sobolev space and prove the existence of a global attractor of optimal regularity. The proof is based on a new energy estimate in Sobolev spaces to bootstrap the regularity to the optimal level, derived by means of nonlinear lower bounds on the fractional Laplacian. This estimate appears to be new in the literature and allows a sharp use of the subcritical nature of the L^∞ bounds for this problem. As a by-product, we obtain attractors for weak solutions as well. Moreover, we study the critical limit of the attractors and prove their stability and upper semicontinuity with respect to the strength of the diffusion.
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Bordallo, Heloisa N; Aldridge, Laurence P; Desmedt, Arnaud
2006-09-14
Portland cement reacts with water to form an amorphous paste through a chemical reaction called hydration. In concrete the formation of pastes causes the mix to harden and gain strength to form a rock-like mass. Within this process lies the key to a remarkable peculiarity of concrete: it is plastic and soft when newly mixed, strong and durable when hardened. These qualities explain why one material, concrete, can build skyscrapers, bridges, sidewalks and superhighways, houses, and dams. The character of the concrete is determined by the quality of the paste. Creep and shrinkage of concrete specimens occur during the loss and gain of water from cement paste. To better understand the role of water in mature concrete, a series of quasielastic neutron scattering (QENS) experiments were carried out on cement pastes with water/cement ratio varying between 0.32 and 0.6. The samples were cured for about 28 days in sealed containers so that the initial water content would not change. These experiments were carried out with an actual sample of Portland cement rather than with the components of cement studied by other workers. The QENS spectra differentiated between three different water interactions: water that was chemically bound into the cement paste, the physically bound or "glassy water" that interacted with the surface of the gel pores in the paste, and unbound water molecules that are confined within the larger capillary pores of cement paste. The dynamics of the "glassy" and "unboud" water in an extended time scale, from a hundred picoseconds to a few nanoseconds, could be clearly differentiated from the data. While the observed motions on the picosecond time scale are mainly stochastic reorientations of the water molecules, the dynamics observed on the nanosecond range can be attributed to long-range diffusion. Diffusive motion was characterized by diffusion constants in the range of (0.6-2) 10(-9) m(2)/s, with significant reduction compared to the rate of diffusion for bulk water. This reduction of the water diffusion is discussed in terms of the interaction of the water with the calcium silicate gel and the ions present in the pore water.
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Sine-gordon type field in spacetime of arbitrary dimension. II: Stochastic quantization
NASA Astrophysics Data System (ADS)
Kirillov, A. I.
1995-11-01
Using the theory of Dirichlet forms, we prove the existence of a distribution-valued diffusion process such that the Nelson measure of a field with a bounded interaction density is its invariant probability measure. A Langevin equation in mathematically correct form is formulated which is satisfied by the process. The drift term of the equation is interpreted as a renormalized Euclidean current operator.
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Perez-Garmendia, Roxanna; Ibarra-Bracamontes, Vanessa; Vasilevko, Vitaly; Luna-Muñoz, Jose; Mena, Raul; Govezensky, Tzipe; Acero, Gonzalo; Manoutcharian, Karen; Cribbs, David H.; Gevorkian, Goar
2010-01-01
N-truncated/modified forms of amyloid beta (Aß) peptide are found in diffused and dense core plaques in Alzheimer's disease (AD) and Down's syndrome patients as well as animal models of AD, and represent highly desirable therapeutic targets. In the present study we have focused on Ntruncated/modified Aβ peptide bearing amino-terminal pyroglutamate at position 11 (AβN11(pE)). We identified two B-cell epitopes recognized by rabbit anti-AβN11(pE) polyclonal antibodies. Interestingly, rabbit anti-AβN11(pE) polyclonal antibodies bound also to full-length Aβ1-42 and N-truncated/modified AβN3(pE), suggesting that the three peptides may share a common B-cell epitope. Importantly, rabbit anti-AβN11(pE) antibodies bound to naturally occurring Aβ aggregates present in brain samples from AD patients. These results are potentially important for developing novel immunogens for targeting N-truncated/modified Aβ aggregates as well, since the most commonly used immunogens in the majority of vaccine studies have been shown to induce antibodies that recognize the N-terminal immunodominant epitope (EFRH) of the full length Aβ, which is absent in N-amino truncated peptides. PMID:20864186
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NASA Astrophysics Data System (ADS)
Lopez, Benjamin
2015-03-01
EB1 is an important microtubule associating protein (MAP) that acts as a master coordinator of protein activity at the growing plus-end of the microtubule. We can recapitulate the plus-end binding behavior of EB1 along the entire length of a static microtubule using microtubules polymerized in the presence of the nonhydrolyzable GTP analogs GMPCPP and GTP γS instead of GTP. Through the use of single-molecule TIRF imaging we find that EB1 is highly dynamic (with a sub-second characteristic binding lifetime) and continuously diffusive while bound to the microtubule. We measure the diffusion coefficient, D, through linear fitting to mean-squared displacement of individually labeled proteins, and the binding lifetime, τ, by fitting a single exponential decay to the probability distribution of trajectory lifetimes. In agreement with measurements of other diffusive MAPs, we find that D increases and τ decreases with increasing ionic strength. We also find that D is sensitive to the choice of GTP analog: EB1 proteins bound to GTP γS polymerized microtubules have a D half of that found with GMPCPP polymerized microtubules. To compare these single-molecule measurements to the bulk binding behavior of EB1, we use TIRF imaging to measure the intensity of microtubules coated with EB1-GFP as a function of EB1 concentration. We find that EB1 binding is cooperative and both the quantity of EB1 bound and the dissociation constant are sensitive to GTP analog and ionic concentration. The correlation between binding affinity and D and the cooperative nature of EB1-microtubule binding leads to a decrease in D with increasing EB1 concentration. Interestingly, we also find an increase in τ at high EB1 concentrations, consistent with attractive EB1-microtubule interactions driving the cooperativity. To further understand the nature of the cooperativity we estimate the interaction energy by measuring the association and dissociation rates (kon and koff respectively) at different concentrations of EB1.
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Bootstrapping Least Squares Estimates in Biochemical Reaction Networks
Linder, Daniel F.
2015-01-01
The paper proposes new computational methods of computing confidence bounds for the least squares estimates (LSEs) of rate constants in mass-action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large volume limit of a reaction network, to network’s partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769
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NASA Astrophysics Data System (ADS)
Johnson, Lawrence; Ferry, Cécile; Poinssot, Christophe; Lovera, Patrick
2005-11-01
A source-term model for the short-term release of radionuclides from spent nuclear fuel (SNF) has been developed. It provides quantitative estimates of the fraction of various radionuclides that are expected to be released rapidly (the instant release fraction, or IRF) when water contacts the UO 2 or MOX fuel after container breaching in a geological repository. The estimates are based on correlation of leaching data for radionuclides with fuel burnup and fission gas release. Extrapolation of the data to higher fuel burnup values is based on examination of data on fuel restructuring, such as rim development, and on fission gas release data, which permits bounding IRF values to be estimated assuming that radionuclide releases will be less than fission gas release. The consideration of long-term solid-state changes influencing the IRF prior to canister breaching is addressed by evaluating alpha self-irradiation enhanced diffusion, which may gradually increase the accumulation of fission products at grain boundaries.
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Xu, Hongyang; Frankenberg, Noni T; Lamb, Graham D; Gooley, Paul R; Stapleton, David I; Murphy, Robyn M
2016-07-01
The 5'-AMP-activated protein kinase (AMPK), a heterotrimeric complex that functions as an intracellular fuel sensor that affects metabolism, is activated in skeletal muscle in response to exercise and utilization of stored energy. The diffusibility properties of α- and β-AMPK were examined in isolated skeletal muscle fiber segments dissected from rat fast-twitch extensor digitorum longus and oxidative soleus muscles from which the surface membranes were removed by mechanical dissection. After the muscle segments were washed for 1 and 10 min, ∼60% and 75%, respectively, of the total AMPK pools were found in the diffusible fraction. After in vitro stimulation of the muscle, which resulted in an ∼80% decline in maximal force, 20% of the diffusible pool became bound in the fiber. This bound pool was not associated with glycogen, as determined by addition of a wash step containing amylase. Stimulation of extensor digitorum longus muscles resulted in 28% glycogen utilization and a 40% increase in phosphorylation of the downstream AMPK target acetyl carboxylase-CoA. This, however, had no effect on the proportion of total β2-AMPK that was phosphorylated in whole muscle homogenates measured by immunoprecipitation. These findings suggest that, in rat skeletal muscle, β2-AMPK is not associated with glycogen and that activation of AMPK by muscle contraction does not dephosphorylate β2-AMPK. These findings question the physiological relevance of the carbohydrate-binding function of β2-AMPK in skeletal muscle. Copyright © 2016 the American Physiological Society.
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Assessment of dynamic surface leaching of monolithic surface road materials.
Paulus, Hélène; Schick, Joachim; Poirier, Jean-Eric
2016-07-01
Construction materials have to satisfy, among others, health and environment requirements. To check the environmental compatibility of road construction materials, release of hazardous substances into water must be assessed. Literature mostly describes the leaching behaviour of recycled aggregates for potential use in base or sub-base layers of roads. But little is known about the release of soluble substances by materials mixed with binders and compacted for intended use on road surface. In the present study, we thus performed a diffusion test with sequential renewal of water during a 64 day period according to CEN/TS 16637-2 specifications, on asphalt concretes and hydraulically bound monoliths, two common surface road materials. It is shown that release of dangerous substances is limited in these hydrodynamic conditions. It was particularly true for asphalt concrete leachates where no metallic trace element, sulphate, chloride or fluoride ion could be quantified. This is because of the low hydraulic conductivity and the low polarity of the petroleum hydrocarbon binder of these specimens. For hydraulically bound materials around 20,000 mg/m(2) of sulphate diffused from the monoliths. It is one order of magnitude higher than chloride diffusion and two orders of magnitude higher than fluoride release. No metallic trace element, except small quantities of copper in the last eluate could be quantified. No adverse effect is to be expected for human and environmental health from the leachates of these compacted surface road construction materials, because all the measured parameters were below EU (Council Directive 98/83/EC) or WHO guidelines for drinking water standards. Copyright © 2016 Elsevier Ltd. All rights reserved.
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A Model for Selection of Eyespots on Butterfly Wings.
Sekimura, Toshio; Venkataraman, Chandrasekhar; Madzvamuse, Anotida
2015-01-01
The development of eyespots on the wing surface of butterflies of the family Nympalidae is one of the most studied examples of biological pattern formation.However, little is known about the mechanism that determines the number and precise locations of eyespots on the wing. Eyespots develop around signaling centers, called foci, that are located equidistant from wing veins along the midline of a wing cell (an area bounded by veins). A fundamental question that remains unsolved is, why a certain wing cell develops an eyespot, while other wing cells do not. We illustrate that the key to understanding focus point selection may be in the venation system of the wing disc. Our main hypothesis is that changes in morphogen concentration along the proximal boundary veins of wing cells govern focus point selection. Based on previous studies, we focus on a spatially two-dimensional reaction-diffusion system model posed in the interior of each wing cell that describes the formation of focus points. Using finite element based numerical simulations, we demonstrate that variation in the proximal boundary condition is sufficient to robustly select whether an eyespot focus point forms in otherwise identical wing cells. We also illustrate that this behavior is robust to small perturbations in the parameters and geometry and moderate levels of noise. Hence, we suggest that an anterior-posterior pattern of morphogen concentration along the proximal vein may be the main determinant of the distribution of focus points on the wing surface. In order to complete our model, we propose a two stage reaction-diffusion system model, in which an one-dimensional surface reaction-diffusion system, posed on the proximal vein, generates the morphogen concentrations that act as non-homogeneous Dirichlet (i.e., fixed) boundary conditions for the two-dimensional reaction-diffusion model posed in the wing cells. The two-stage model appears capable of generating focus point distributions observed in nature. We therefore conclude that changes in the proximal boundary conditions are sufficient to explain the empirically observed distribution of eyespot focus points on the entire wing surface. The model predicts, subject to experimental verification, that the source strength of the activator at the proximal boundary should be lower in wing cells in which focus points form than in those that lack focus points. The model suggests that the number and locations of eyespot foci on the wing disc could be largely controlled by two kinds of gradients along two different directions, that is, the first one is the gradient in spatially varying parameters such as the reaction rate along the anterior-posterior direction on the proximal boundary of the wing cells, and the second one is the gradient in source values of the activator along the veins in the proximal-distal direction of the wing cell.
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Al-Mur, Bandar A; Quicksall, Andrew N; Kaste, James M
2017-09-15
The Red Sea is a unique ecosystem with high biodiversity in one of the warmest regions of the world. In the last five decades, Red Sea coastal development has rapidly increased. Sediments from continental margins are delivered to depths by advection and diffusion-like processes which are difficult to quantify yet provide invaluable data to researchers. Beryllium-7, lead-210 and ceseium-137 were analyzed from sediment cores from the near-coast Red Sea near Jeddah, Saudi Arabia. The results of this work are the first estimates of diffusion, mixing, and sedimentation rates of the Red Sea coastal sediments. Maximum chemical diffusion and particle mixing rates range from 69.1 to 380cm -2 y -1 and 2.54 to 6.80cm -2 y -1 , respectively. Sedimentation rate is constrained to approximately 0.6cm/yr via multiple methods. These data provide baselines for tracking changes in various environmental problems including erosion, marine benthic ecosystem silting, and particle-bound contaminant delivery to the seafloor. Copyright © 2017. Published by Elsevier Ltd.
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Bao, Shanyong; Ma, Chunrui; Chen, Garry; Xu, Xing; Enriquez, Erik; Chen, Chonglin; Zhang, Yamei; Bettis, Jerry L; Whangbo, Myung-Hwan; Dong, Chuang; Zhang, Qingyu
2014-04-22
Surface exchange and oxygen vacancy diffusion dynamics were studied in double-perovskites LnBaCo2O5.5+δ (LnBCO) single-crystalline thin films (Ln = Er, Pr; -0.5 < δ < 0.5) by carefully monitoring the resistance changes under a switching flow of oxidizing gas (O2) and reducing gas (H2) in the temperature range of 250 ~ 800 °C. A giant resistance change ΔR by three to four orders of magnitude in less than 0.1 s was found with a fast oscillation behavior in the resistance change rates in the ΔR vs. t plots, suggesting that the oxygen vacancy exchange diffusion with oxygen/hydrogen atoms in the LnBCO thin films is taking the layer by layer oxygen-vacancy-exchange mechanism. The first principles density functional theory calculations indicate that hydrogen atoms are present in LnBCO as bound to oxygen forming O-H bonds. This unprecedented oscillation phenomenon provides the first direct experimental evidence of the layer by layer oxygen vacancy exchange diffusion mechanism.
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Bianchi, Frans; Syga, Łukasz; Moiset, Gemma; Spakman, Dian; Schavemaker, Paul E; Punter, Christiaan M; Seinen, Anne-Bart; van Oijen, Antoine M; Robinson, Andrew; Poolman, Bert
2018-02-05
The plasma membrane (PM) of Saccharomyces cerevisiae contains membrane compartments, MCC/eisosomes and MCPs, named after the protein residents Can1 and Pma1, respectively. Using high-resolution fluorescence microscopy techniques we show that Can1 and the homologous transporter Lyp1 are able to diffuse into the MCC/eisosomes, where a limited number of proteins are conditionally trapped at the (outer) edge of the compartment. Upon addition of substrate, the immobilized proteins diffuse away from the MCC/eisosomes, presumably after taking a different conformation in the substrate-bound state. Our data indicate that the mobile fraction of all integral plasma membrane proteins tested shows extremely slow Brownian diffusion through most of the PM. We also show that proteins with large cytoplasmic domains, such as Pma1 and synthetic chimera of Can1 and Lyp1, are excluded from the MCC/eisosomes. We hypothesize that the distinct localization patterns found for these integral membrane proteins in S. cerevisiae arises from a combination of slow lateral diffusion, steric exclusion, and conditional trapping in membrane compartments.
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Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret
2016-01-01
The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.
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The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion
Bassingthwaighte, James B.; Raymond, Gary M.; Dash, Ranjan K.; Beard, Daniel A.; Nolan, Margaret
2016-01-01
The ‘Pathway for Oxygen’ is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system’s basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: 1) a ‘one-alveolus lung’ with airway resistance, lung volume compliance, 2) bidirectional transport of solute gasses like O2 and CO2, 3) gas exchange between alveolar air and lung capillary blood, 4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and 5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there. PMID:26782201
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Excitons in Single-Walled Carbon Nanotubes and Their Dynamics
NASA Astrophysics Data System (ADS)
Amori, Amanda R.; Hou, Zhentao; Krauss, Todd D.
2018-04-01
Understanding exciton dynamics in single-walled carbon nanotubes (SWCNTs) is essential to unlocking the many potential applications of these materials. This review summarizes recent progress in understanding exciton photophysics and, in particular, exciton dynamics in SWCNTs. We outline the basic physical and electronic properties of SWCNTs, as well as bright and dark transitions within the framework of a strongly bound one-dimensional excitonic model. We discuss the many facets of ultrafast carrier dynamics in SWCNTs, including both single-exciton states (bright and dark) and multiple-exciton states. Photophysical properties that directly relate to excitons and their dynamics, including exciton diffusion lengths, chemical and structural defects, environmental effects, and photoluminescence photon statistics as observed through photon antibunching measurements, are also discussed. Finally, we identify a few key areas for advancing further research in the field of SWCNT excitons and photonics.
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The Brain: An Intriguing Piece of Condensed Matter
NASA Astrophysics Data System (ADS)
Cotterill, Rodney M. J.
1986-01-01
The human brain consists of approximately one hundred thousand million cells, arranged in a variety of structures, the largest of which is the familiar neocortex. These cells, or neurons, possess the vital property of excitability, which is dependent upon the differential diffusion characteristics of their bounding membranes. The cells receive and transmit electrical impulses through their numerous tentacle-like extensions, and the signals are passed from one cell to another by the chemical messengers called neurotransmitters, which diffuse across the narrow inter-cell gaps known as synapses. The efficiency of the transmission process is chemically modifiable, and this is believed to imbue the neural network with the ability to learn and remember. The response to a variety of input patterns has been studied in a vector model assembly of interconnected neurons. The time evolution of the injected signal is followed, attention being paid to both its subsequent topology and phase. The model is realistic in that it includes action potential impulses in the axon regions, statistically distributed synaptic delays, and electronics waves in the dendrites. Of particular interest were the frequency response of the system, and its dependence on the proportions of excitatory and inhibitory synapses. The relevance of the concept of coherence length was also critically examined, in such disparate contexts as association autism and the primary visual processes in the retina. Coherence, and the more general issue of correction, were also considered in connection with memory models, including those of the holographics type. This brief account also includes reference to such unlikely topics as fever and the dreaming state.
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Scale-Invariant Transition Probabilities in Free Word Association Trajectories
Costa, Martin Elias; Bonomo, Flavia; Sigman, Mariano
2009-01-01
Free-word association has been used as a vehicle to understand the organization of human thoughts. The original studies relied mainly on qualitative assertions, yielding the widely intuitive notion that trajectories of word associations are structured, yet considerably more random than organized linguistic text. Here we set to determine a precise characterization of this space, generating a large number of word association trajectories in a web implemented game. We embedded the trajectories in the graph of word co-occurrences from a linguistic corpus. To constrain possible transport models we measured the memory loss and the cycling probability. These two measures could not be reconciled by a bounded diffusive model since the cycling probability was very high (16% of order-2 cycles) implying a majority of short-range associations whereas the memory loss was very rapid (converging to the asymptotic value in ∼7 steps) which, in turn, forced a high fraction of long-range associations. We show that memory loss and cycling probabilities of free word association trajectories can be simultaneously accounted by a model in which transitions are determined by a scale invariant probability distribution. PMID:19826622
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cao, Y., E-mail: yxc238@psu.edu; Randall, C. A.; Chen, L. Q.
2014-05-05
A self-consistent model has been proposed to study the switchable current-voltage (I-V) characteristics in Cu/BaTiO{sub 3}/Cu sandwiched structure combining the phase-field model of ferroelectric domains and diffusion equations for ionic/electronic transport. The electrochemical transport equations and Ginzburg-Landau equations are solved using the Chebyshev collocation algorithm. We considered a single parallel plate capacitor configuration which consists of a single layer BaTiO{sub 3} containing a single tetragonal domain orientated normal to the plate electrodes (Cu) and is subject to a sweep of ac bias from −1.0 to 1.0 V at 25 °C. Our simulation clearly shows rectifying I-V response with rectification ratios amount tomore » 10{sup 2}. The diode characteristics are switchable with an even larger rectification ratio after the polarization direction is flipped. The effects of interfacial polarization charge, dopant concentration, and dielectric constant on current responses were investigated. The switchable I-V behavior is attributed to the polarization bound charges that modulate the bulk conduction.« less
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Richards, Mark J; Daniel, Susan
2017-02-07
The supported lipid bilayer has been portrayed as a useful model of the cell membrane compatible with many biophysical tools and techniques that demonstrate its appeal in learning about the basic features of the plasma membrane. However, some of its potential has yet to be realized, particularly in the area of bilayer patterning and phase/composition heterogeneity. In this work, we generate contiguous bilayer patterns as a model system that captures the general features of membrane domains and lipid rafts. Micropatterned polymer templates of two types are investigated for generating patterned bilayer formation: polymer blotting and polymer lift-off stenciling. While these approaches have been used previously to create bilayer arrays by corralling bilayers patches with various types of boundaries impenetrable to bilayer diffusion, unique to the methods presented here, there are no physical barriers to diffusion. In this work, interfaces between contiguous lipid phases define the pattern shapes, with continuity between them allowing transfer of membrane-bound biomolecules between the phases. We examine effectors of membrane domain stability including temperature and cholesterol content to investigate domain dynamics. Contiguous patterning of supported bilayers as a model of lipid rafts expands the application of the SLB to an area with current appeal and brings with it a useful toolset for characterization and analysis. These combined tools should be helpful to researchers investigating lipid raft dynamics and function and biomolecule partitioning studies. Additionally, this patterning technique may be useful for applications such as bioseparations that exploit differences in lipid phase partitioning or creation of membranes that bind species like viruses preferentially at lipid phase boundaries, to name a few.
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Towner, Rheal A; Smith, Nataliya; Saunders, Debra; Lupu, Florea; Silasi-Mansat, Robert; West, Melinda; Ramirez, Dario C; Gomez-Mejiba, Sandra E; Bonini, Marcelo G; Mason, Ronald P; Ehrenshaft, Marilyn; Hensley, Kenneth
2013-10-01
Free radicals associated with oxidative stress play a major role in amyotrophic lateral sclerosis (ALS). By combining immuno-spin trapping and molecular magnetic resonance imaging, in vivo trapped radical adducts were detected in the spinal cords of SOD1(G93A)-transgenic (Tg) mice, a model for ALS. For this study, the nitrone spin trap DMPO (5,5-dimethyl-1-pyrroline N-oxide) was administered (ip) over 5 days before administration (iv) of an anti-DMPO probe (anti-DMPO antibody covalently bound to an albumin-gadolinium-diethylenetriamine pentaacetic acid-biotin MRI contrast agent) to trap free radicals. MRI was used to detect the presence of the anti-DMPO radical adducts by a significant sustained increase in MR signal intensities (p < 0.05) or anti-DMPO probe concentrations measured from T₁ relaxations (p < 0.01). The biotin moiety of the anti-DMPO probe was targeted with fluorescence-labeled streptavidin to locate the probe in excised tissues. Negative controls included either Tg ALS mice initially administered saline rather than DMPO followed by the anti-DMPO probe or non-Tg mice initially administered DMPO and then the anti-DMPO probe. The anti-DMPO probe was found to bind to neurons via colocalization fluorescence microscopy. DMPO adducts were also confirmed in diseased/nondiseased tissues from animals administered DMPO. Apparent diffusion coefficients from diffusion-weighted images of spinal cords from Tg mice were significantly elevated (p < 0.001) compared to wild-type controls. This is the first report regarding the detection of in vivo trapped radical adducts in an ALS model. This novel, noninvasive, in vivo diagnostic method can be applied to investigate the involvement of free radical mechanisms in ALS rodent models. Copyright © 2013 Elsevier Inc. All rights reserved.
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Chapman, Brian
2017-06-01
This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.
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2017-01-01
This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687
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Lieb-Robinson bounds for spin-boson lattice models and trapped ions.
Jünemann, J; Cadarso, A; Pérez-García, D; Bermudez, A; García-Ripoll, J J
2013-12-06
We derive a Lieb-Robinson bound for the propagation of spin correlations in a model of spins interacting through a bosonic lattice field, which satisfies a Lieb-Robinson bound in the absence of spin-boson couplings. We apply these bounds to a system of trapped ions and find that the propagation of spin correlations, as mediated by the phonons of the ion crystal, can be faster than the regimes currently explored in experiments. We propose a scheme to test the bounds by measuring retarded correlation functions via the crystal fluorescence.
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NASA Astrophysics Data System (ADS)
Tzou, J. C.; Ward, M. J.
2018-06-01
Spot patterns, whereby the activator field becomes spatially localized near certain dynamically-evolving discrete spatial locations in a bounded multi-dimensional domain, is a common occurrence for two-component reaction-diffusion (RD) systems in the singular limit of a large diffusivity ratio. In previous studies of 2-D localized spot patterns for various specific well-known RD systems, the domain boundary was assumed to be impermeable to both the activator and inhibitor, and the reaction-kinetics were assumed to be spatially uniform. As an extension of this previous theory, we use formal asymptotic methods to study the existence, stability, and slow dynamics of localized spot patterns for the singularly perturbed 2-D Brusselator RD model when the domain boundary is only partially impermeable, as modeled by an inhomogeneous Robin boundary condition, or when there is an influx of inhibitor across the domain boundary. In our analysis, we will also allow for the effect of a spatially variable bulk feed term in the reaction kinetics. By applying our extended theory to the special case of one-spot patterns and ring patterns of spots inside the unit disk, we provide a detailed analysis of the effect on spot patterns of these three different sources of heterogeneity. In particular, when there is an influx of inhibitor across the boundary of the unit disk, a ring pattern of spots can become pinned to a ring-radius closer to the domain boundary. Under a Robin condition, a quasi-equilibrium ring pattern of spots is shown to exhibit a novel saddle-node bifurcation behavior in terms of either the inhibitor diffusivity, the Robin constant, or the ambient background concentration. A spatially variable bulk feed term, with a concentrated source of "fuel" inside the domain, is shown to yield a saddle-node bifurcation structure of spot equilibria, which leads to qualitatively new spot-pinning behavior. Results from our asymptotic theory are validated from full numerical simulations of the Brusselator model.
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The EZ diffusion model provides a powerful test of simple empirical effects.
van Ravenzwaaij, Don; Donkin, Chris; Vandekerckhove, Joachim
2017-04-01
Over the last four decades, sequential accumulation models for choice response times have spread through cognitive psychology like wildfire. The most popular style of accumulator model is the diffusion model (Ratcliff Psychological Review, 85, 59-108, 1978), which has been shown to account for data from a wide range of paradigms, including perceptual discrimination, letter identification, lexical decision, recognition memory, and signal detection. Since its original inception, the model has become increasingly complex in order to account for subtle, but reliable, data patterns. The additional complexity of the diffusion model renders it a tool that is only for experts. In response, Wagenmakers et al. (Psychonomic Bulletin & Review, 14, 3-22, 2007) proposed that researchers could use a more basic version of the diffusion model, the EZ diffusion. Here, we simulate experimental effects on data generated from the full diffusion model and compare the power of the full diffusion model and EZ diffusion to detect those effects. We show that the EZ diffusion model, by virtue of its relative simplicity, will be sometimes better able to detect experimental effects than the data-generating full diffusion model.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fox, Zachary; Neuert, Gregor; Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232
2016-08-21
Emerging techniques now allow for precise quantification of distributions of biological molecules in single cells. These rapidly advancing experimental methods have created a need for more rigorous and efficient modeling tools. Here, we derive new bounds on the likelihood that observations of single-cell, single-molecule responses come from a discrete stochastic model, posed in the form of the chemical master equation. These strict upper and lower bounds are based on a finite state projection approach, and they converge monotonically to the exact likelihood value. These bounds allow one to discriminate rigorously between models and with a minimum level of computational effort.more » In practice, these bounds can be incorporated into stochastic model identification and parameter inference routines, which improve the accuracy and efficiency of endeavors to analyze and predict single-cell behavior. We demonstrate the applicability of our approach using simulated data for three example models as well as for experimental measurements of a time-varying stochastic transcriptional response in yeast.« less
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Kleckner, Ian R.; McElroy, Craig A.; Kuzmic, Petr; Gollnick, Paul; Foster, Mark P.
2014-01-01
The trp RNA-binding Attenuation Protein (TRAP) assembles into an 11-fold symmetric ring that regulates transcription and translation of trp-mRNA in bacilli via heterotropic allosteric activation by the amino acid tryptophan (Trp). Whereas nuclear magnetic resonance studies have revealed that Trp-induced activation coincides with both μs-ms rigidification and local structural changes in TRAP, the pathway of binding of the 11 Trp ligands to the TRAP ring remains unclear. Moreover, because each of eleven bound Trp molecules is completely surrounded by protein, its release requires flexibility of Trp-bound (holo) TRAP. Here, we used stopped-flow fluorescence to study the kinetics of Trp binding by Bacillus stearothermophilus TRAP over a range of temperatures and we observed well-separated kinetic steps. These data were analyzed using non-linear least-squares fitting of several two- and three-step models. We found that a model with two binding steps best describes the data, although the structural equivalence of the binding sites in TRAP implies a fundamental change in the time-dependent structure of the TRAP rings upon Trp binding. Application of the two binding step model reveals that Trp binding is much slower than the diffusion limit, suggesting a gating mechanism that depends on the dynamics of apo TRAP. These data also reveal that Trp dissociation from the second binding mode is much slower than after the first Trp binding mode, revealing insight into the mechanism for positive homotropic allostery, or cooperativity. Temperature dependent analyses reveal that both binding modes imbue increases in bondedness and order toward a more compressed active state. These results provide insight into mechanisms of cooperative TRAP activation, and underscore the importance of protein dynamics for ligand binding, ligand release, protein activation, and allostery. PMID:24224873
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Ab initio based study of the ArO- photoelectron spectra: Selectivity of spin-orbit transitions
NASA Astrophysics Data System (ADS)
Buchachenko, A. A.; Jakowski, Jacek; Chałasiński, Grzegorz; Szczȩśniak, M. M.; Cybulski, S. M.
2000-04-01
A combined ab initio atoms-in-molecule approach was implemented to model the photoelectron spectra of the ArO- anion. The lowest adiabatic states of Σ and Π symmetry of ArO and ArO- were investigated using the fourth-order Møller-Plessett perturbation theory including bond functions. The total energies were dissected into electrostatic, exchange, induction, and dispersion components. The complex of Ar with atomic oxygen is only weakly bound, primarily by dispersion interaction. The Π state possesses a deeper minimum (Re=3.4Å,De=380μEh) than the Σ state (Re=3.8Å,De=220μEh). In contrast, the anion complex is fairly strongly bound, primarily by ion-induced dipole induction forces, and the Σ state possesses a deeper minimum at shorter interatomic distances (Re=3.02Å,De=3600μEh) than the Π state (Re=3.35Å,De=2400μEh). The Σ-Π splittings in both systems are mainly due to differences in the exchange repulsion terms. Atoms-in-molecule models were used to account for the spin-orbit interaction, and to generate adiabatic relativistic potentials and wave functions. Collisional properties, diffusion, and mobility coefficients of O and O- in Ar, and absolute total Ar+O scattering cross sections, were calculated and found to agree well with the available experimental data. The photoelectron spectra were simulated within vibronic model, and were found in excellent agreement with the experimental measurements. The bimodal electron kinetic energy distribution was shown to stem from the strong selectivity of spin-orbit transitions, which split into two dense groups, depending on the initial electronic state of the anion. The latter feature cannot be described without explicit consideration of electronic intensity factor.
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The nature of water within bacterial spores: protecting life in extreme environments
NASA Astrophysics Data System (ADS)
Rice, Charles V.; Friedline, Anthony; Johnson, Karen; Zachariah, Malcolm M.; Thomas, Kieth J., III
2011-10-01
The bacterial spore is a formidable container of life, protecting the vital contents from chemical attack, antimicrobial agents, heat damage, UV light degradation, and water dehydration. The exact role of the spore components remains in dispute. Nevertheless, water molecules are important in each of these processes. The physical state of water within the bacterial spore has been investigated since the early 1930's. The water is found two states, free or bound, in two different areas, core and non-core. It is established that free water is accessible to diffuse and exchange with deuterated water and that the diffusible water can access all areas of the spore. The presence of bound water has come under recent scrutiny and has been suggested the water within the core is mobile, rather than bound, based on the analysis of deuterium relaxation rates. Using an alternate method, deuterium quadrupole-echo spectroscopy, we are able to distinguish between mobile and immobile water molecules. In the absence of rapid motion, the deuterium spectrum of D2O is dominated by a broad line, whose line shape is used as a characteristic descriptor of molecular motion. The deuterium spectrum of bacterial spores reveals three distinct features: the broad peak of immobilized water, a narrow line of water in rapid motion, and a signal of intermediate width. This third signal is assigned this peak from partially deuterated proteins with the spore in which N-H groups have undergone exchange with water deuterons to form N-D species. As a result of these observations, the nature of water within the spore requires additional explanation to understand how the spore and its water preserve life.
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Characterization of muscle ankyrin repeat proteins in human skeletal muscle.
Wette, Stefan G; Smith, Heather K; Lamb, Graham D; Murphy, Robyn M
2017-09-01
Muscle ankyrin repeat proteins (MARPs) are a family of titin-associated, stress-response molecules and putative transducers of stretch-induced signaling in skeletal muscle. In cardiac muscle, cardiac ankyrin repeat protein (CARP) and diabetes-related ankyrin repeat protein (DARP) reportedly redistribute from binding sites on titin to the nucleus following a prolonged stretch. However, it is unclear whether ankyrin repeat domain protein 2 (Ankrd 2) shows comparable stretch-induced redistribution to the nucleus. We measured the following in rested human skeletal muscle: 1 ) the absolute amount of MARPs and 2 ) the distribution of Ankrd 2 and DARP in both single fibers and whole muscle preparations. In absolute amounts, Ankrd 2 is the most abundant MARP in human skeletal muscle, there being ~3.1 µmol/kg, much greater than DARP and CARP (~0.11 and ~0.02 µmol/kg, respectively). All DARP was found to be tightly bound at cytoskeletal (or possibly nuclear) sites. In contrast, ~70% of the total Ankrd 2 is freely diffusible in the cytosol [including virtually all of the phosphorylated (p)Ankrd 2-Ser99 form], ~15% is bound to non-nuclear membranes, and ~15% is bound at cytoskeletal sites, likely at the N2A region of titin. These data are not consistent with the proposal that Ankrd 2, per se, or pAnkrd 2-Ser99 mediates stretch-induced signaling in skeletal muscle, dissociating from titin and translocating to the nucleus, because the majority of these forms of Ankrd 2 are already free in the cytosol. It will be necessary to show that the titin-associated Ankrd 2 is modified by stretch in some as-yet-unidentified way, distinct from the diffusible pool, if it is to act as a stretch-sensitive signaling molecule. Copyright © 2017 the American Physiological Society.
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Validation of the SURE Program, phase 1
NASA Technical Reports Server (NTRS)
Dotson, Kelly J.
1987-01-01
Presented are the results of the first phase in the validation of the SURE (Semi-Markov Unreliability Range Evaluator) program. The SURE program gives lower and upper bounds on the death-state probabilities of a semi-Markov model. With these bounds, the reliability of a semi-Markov model of a fault-tolerant computer system can be analyzed. For the first phase in the validation, fifteen semi-Markov models were solved analytically for the exact death-state probabilities and these solutions compared to the corresponding bounds given by SURE. In every case, the SURE bounds covered the exact solution. The bounds, however, had a tendency to separate in cases where the recovery rate was slow or the fault arrival rate was fast.
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Bounded Linear Stability Analysis - A Time Delay Margin Estimation Approach for Adaptive Control
NASA Technical Reports Server (NTRS)
Nguyen, Nhan T.; Ishihara, Abraham K.; Krishnakumar, Kalmanje Srinlvas; Bakhtiari-Nejad, Maryam
2009-01-01
This paper presents a method for estimating time delay margin for model-reference adaptive control of systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent the conventional model-reference adaptive law by a locally bounded linear approximation within a small time window using the comparison lemma. The locally bounded linear approximation of the combined adaptive system is cast in a form of an input-time-delay differential equation over a small time window. The time delay margin of this system represents a local stability measure and is computed analytically by a matrix measure method, which provides a simple analytical technique for estimating an upper bound of time delay margin. Based on simulation results for a scalar model-reference adaptive control system, both the bounded linear stability method and the matrix measure method are seen to provide a reasonably accurate and yet not too conservative time delay margin estimation.
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MinE conformational dynamics regulate membrane binding, MinD interaction, and Min oscillation
Park, Kyung-Tae; Villar, Maria T.; Artigues, Antonio; Lutkenhaus, Joe
2017-01-01
In Escherichia coli MinE induces MinC/MinD to oscillate between the ends of the cell, contributing to the precise placement of the Z ring at midcell. To do this, MinE undergoes a remarkable conformational change from a latent 6β-stranded form that diffuses in the cytoplasm to an active 4β-stranded form bound to the membrane and MinD. How this conformational switch occurs is not known. Here, using hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) we rule out a model in which the two forms are in rapid equilibrium. Furthermore, HDX-MS revealed that a MinE mutant (D45A/V49A), previously shown to produce an aberrant oscillation and unable to assemble a MinE ring, is more rigid than WT MinE. This mutant has a defect in interaction with MinD, suggesting it has difficulty in switching to the active form. Analysis of intragenic suppressors of this mutant suggests it has difficulty in releasing the N-terminal membrane targeting sequences (MTS). These results indicate that the dynamic association of the MTS with the β-sheet is fine-tuned to balance MinE’s need to sense MinD on the membrane with its need to diffuse in the cytoplasm, both of which are necessary for the oscillation. The results lead to models for MinE activation and MinE ring formation. PMID:28652337
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NASA Technical Reports Server (NTRS)
Glownia, James H.; Sorokin, Peter P.
1994-01-01
In this paper, a new model is proposed to account for the DIB's (Diffuse Interstellar Bands). In this model, the DIB's result from a non-linear effect: resonantly-enhanced two-photon absorption of H(2+) ions located near the surface of the Stromgren sphere that surrounds an O- or B- type star. The strong light that is required to 'drive' the two-photon transition is provided by L(alpha) light emerging from the Stromgren sphere that bounds the H II region surrounding the star. A value of approximately 100 micro W/sq cm is estimated for the L(alpha) flux at the Stromgren radius, R(s), of a strong (O5) star. It is shown that a c.w. L(alpha) flux of this intensity should be sufficient to induce a few percent absorption for visible light radiated by the same star at a frequency (omega2) that completes an allowed two-photon transition, provided (1) the L(alpha) radiation happens to be nearly resonant with the frequency of a fully-allowed absorber transition that effectively represents the first step in the two-photon transition, and (2) an effective column density approximately 10(sup18)/sq cm of the absorber is present near the Stromgren sphere radius, R(sub s).
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Directed and persistent movement arises from mechanochemistry of the ParA/ParB system.
Hu, Longhua; Vecchiarelli, Anthony G; Mizuuchi, Kiyoshi; Neuman, Keir C; Liu, Jian
2015-12-22
The segregation of DNA before cell division is essential for faithful genetic inheritance. In many bacteria, segregation of low-copy number plasmids involves an active partition system composed of a nonspecific DNA-binding ATPase, ParA, and its stimulator protein ParB. The ParA/ParB system drives directed and persistent movement of DNA cargo both in vivo and in vitro. Filament-based models akin to actin/microtubule-driven motility were proposed for plasmid segregation mediated by ParA. Recent experiments challenge this view and suggest that ParA/ParB system motility is driven by a diffusion ratchet mechanism in which ParB-coated plasmid both creates and follows a ParA gradient on the nucleoid surface. However, the detailed mechanism of ParA/ParB-mediated directed and persistent movement remains unknown. Here, we develop a theoretical model describing ParA/ParB-mediated motility. We show that the ParA/ParB system can work as a Brownian ratchet, which effectively couples the ATPase-dependent cycling of ParA-nucleoid affinity to the motion of the ParB-bound cargo. Paradoxically, this resulting processive motion relies on quenching diffusive plasmid motion through a large number of transient ParA/ParB-mediated tethers to the nucleoid surface. Our work thus sheds light on an emergent phenomenon in which nonmotor proteins work collectively via mechanochemical coupling to propel cargos-an ingenious solution shaped by evolution to cope with the lack of processive motor proteins in bacteria.
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Atomistic Molecular Dynamics Simulations of Charged Latex Particle Surfaces in Aqueous Solution.
Li, Zifeng; Van Dyk, Antony K; Fitzwater, Susan J; Fichthorn, Kristen A; Milner, Scott T
2016-01-19
Charged particles in aqueous suspension form an electrical double layer at their surfaces, which plays a key role in suspension properties. For example, binder particles in latex paint remain suspended in the can because of repulsive forces between overlapping double layers. Existing models of the double layer assume sharp interfaces bearing fixed uniform charge, and so cannot describe aqueous binder particle surfaces, which are soft and diffuse, and bear mobile charge from ionic surfactants as well as grafted multivalent oligomers. To treat this industrially important system, we use atomistic molecular dynamics simulations to investigate a structurally realistic model of commercial binder particle surfaces, informed by extensive characterization of particle synthesis and surface properties. We determine the interfacial profiles of polymer, water, bound and free ions, from which the charge density and electrostatic potential can be calculated. We extend the traditional definitions of the inner and outer Helmholtz planes to our diffuse interfaces. Beyond the Stern layer, the simulated electrostatic potential is well described by the Poisson-Boltzmann equation. The potential at the outer Helmholtz plane compares well to the experimental zeta potential. We compare particle surfaces bearing two types of charge groups, ionic surfactant and multivalent oligomers, with and without added salt. Although the bare charge density of a surface bearing multivalent oligomers is much higher than that of a surfactant-bearing surface at realistic coverage, greater counterion condensation leads to similar zeta potentials for the two systems.
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Temperature effects on multiphase reactions of organic molecular markers: A modeling study
NASA Astrophysics Data System (ADS)
Pratap, Vikram; Chen, Ying; Yao, Guangming; Nakao, Shunsuke
2018-04-01
Various molecular markers are used in source apportionment studies. In early studies, molecular markers were assumed to be inert. However, recent studies suggest that molecular markers can decay rapidly through multiphase reactions, which makes interpretation of marker measurements challenging. This study presents a simplified model to account for the effects of temperature and relative humidity on the lifetime of molecular markers through a shift in gas-particle partitioning as well as a change in viscosity of the condensed phase. As a model case, this study examines the stability of levoglucosan, a key marker species of biomass burning, over a wide temperature range relevant to summertime and wintertime. Despite the importance of wood combustion for space heating in winter, the lifetime of levoglucosan in wintertime is not well understood. The model predicts that in low-temperature conditions, levoglucosan predominantly remains in the particle phase, and therefore its loss due to gas-phase oxidation reactions is significantly reduced. Furthermore, the movement of the levoglucosan from the bulk of the particle to the particle surface is reduced due to low diffusivity in the semi-solid state. The simplified model developed in this study reasonably reproduces upper and lower bounds of the lifetime of levoglucosan investigated in previous studies. The model results show that the levoglucosan depletion after seven days reduces significantly from ∼98% at 25 °C to <1% at 0 °C under dry conditions. The depletion of levoglucosan increases at higher relative humidities. However, at temperatures below 0 °C, levoglucosan appears to be a useful marker (lifetime > 1 week) even at 60% relative humidity irrespective of the assumed fragility parameter D that controls estimated diffusivity. The model shows that lifetime of an organic molecular marker strongly depends on assumed D especially when a semi-volatile marker is in semi-solid organic aerosol.
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Cadmium, an effector in the synthesis of thionein.
Bryan, S E; Hidalgo, H A; Koppa, V; Smith, H A
1979-01-01
Cadmium can elicit the synthesis of thionein in liver cells independent of tissue-organ interactions. The metal diffuses across the plasma membrane and is partitioned between subcellular components in a time dependent manner such that thionein synthesis responds to levels of nonspecifically and specifically bound cytoplasmic metal. Cadmium appears to function at the transcriptional level, and the metal may act to increase the pool of specific m-RNA's. PMID:488043
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Dynamic Decision Making under Uncertainty and Partial Information
2013-11-14
integral under the natural filtration generated by the Brownian motions . This compact expression potentially enables us to design sub- optimal penalties...bounds on bermudan option price under jump diffusion processes. Quantitative Finance , 2013. Under review, available at http://arxiv.org/abs/1305.4321... Finance , 19:53 – 71, 2009. [3] D.P. Bertsekas. Dynamic Programming and Optimal Control. Athena Scientific, 4th edition, 2012. [4] D.B. Brown and J.E
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Single-particle tracking: applications to membrane dynamics.
Saxton, M J; Jacobson, K
1997-01-01
Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.
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ERIC Educational Resources Information Center
McPeake, John D.; And Others
1991-01-01
Describes adolescent chemical dependency treatment model developed at Beech Hill Hospital (New Hampshire) which integrated Twelve Step-oriented alcohol and drug rehabilitation program with experiential education school, Hurricane Island Outward Bound School. Describes Beech Hill Hurricane Island Outward Bound School Adolescent Chemical Dependency…
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NASA Astrophysics Data System (ADS)
Kilinc, Devrim; Blasiak, Agata; O'Mahony, James J.; Lee, Gil U.
2014-11-01
Growth cones, dynamic structures at axon tips, integrate chemical and physical stimuli and translate them into coordinated axon behaviour, e.g., elongation or turning. External force application to growth cones directs and enhances axon elongation in vitro; however, direct mechanical stimulation is rarely combined with chemotactic stimulation. We describe a microfluidic device that exposes isolated cortical axons to gradients of diffusing and substrate-bound molecules, and permits the simultaneous application of piconewton (pN) forces to multiple individual growth cones via magnetic tweezers. Axons treated with Y-27632, a RhoA kinase inhibitor, were successfully towed against Semaphorin 3A gradients, which repel untreated axons, with less than 12 pN acting on a small number of neural cell adhesion molecules. Treatment with Y-27632 or monastrol, a kinesin-5 inhibitor, promoted axon towing on substrates coated with chondroitin sulfate proteoglycans, potent axon repellents. Thus, modulating key molecular pathways that regulate contractile stress generation in axons counteracts the effects of repellent molecules and promotes tension-induced growth. The demonstration of parallel towing of axons towards inhibitory environments with minute forces suggests that mechanochemical stimulation may be a promising therapeutic approach for the repair of the damaged central nervous system, where regenerating axons face repellent factors over-expressed in the glial scar.
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NASA Astrophysics Data System (ADS)
Rustichelli, Andrea; Di Celma, Claudio; Tondi, Emanuele; Baud, Patrick; Vinciguerra, Sergio
2016-04-01
New knowledge on patterns of fibrous gypsum veins, their genetic mechanisms, deformation style and weathering are provided by a field- and laboratory-based study carried out on the Neogene to Quaternary Pisco Basin sedimentary strata (porous sandstones, siltstones and diatomites) exposed in the Ica desert, southern Peru. Gypsum veins vary considerably in dimensions, attitudes and timing and can develop in layered and moderately fractured rocks also in the absence of evaporitic layers. Veins occur both as diffuse features, confined to certain stratigraphic levels, and localised within fault zones. Arrays formed by layer-bounded, mutually orthogonal sets of steeply-dipping gypsum veins are reported for the first time. Vein length, height and spacing depend on the thickness of the bed packages in which they are confined. Within fault zones, veins are partly a product of faulting but also inherited layer-bounded features along which faults are superimposed. Due to the different petrophysical properties with respect to the parent rocks and their susceptibility to textural and mineralogical modifications, water dissolution and rupture, gypsum veins may have a significant role in geofluid management. Depending on their patterns and grade of physical and chemical alteration, veins may influence geofluid circulation and storage, acting as barriers to flow and possibly also as conduits.
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Time-dependent water dynamics in hydrated uranyl fluoride
Miskowiec, Andrew J.; Anderson, Brian B.; Herwig, Kenneth W.; ...
2015-09-15
In this study, uranyl fluoride is a three-layer, hexagonal structure with significant stacking disorder in the c-direction. It supports a range of unsolved ‘thermodynamic’ hydrates with 0–2.5 water molecules per uranium atom, and perhaps more. However, the relationship between water, hydrate crystal structures, and thermodynamic results, collectively representing the chemical pathway through these hydrate structures, has not been sufficiently elucidated. We used high-resolution quasielastic neutron scattering to study the dynamics of water in partially hydrated uranyl fluoride powder over the course of 4 weeks under closed conditions. The spectra are composed of two quasielastic components: one is associated with translationalmore » diffusive motion of water that is approximately five to six times slower than bulk water, and the other is a slow (on the order of 2–300 ps), spatially bounded water motion. The translational component represents water diffusing between the weakly bonded layers in the crystal, while the bounded component may represent water trapped in subnanometre ‘pockets’ formed by the space between uranium-centred polymerisation units. Complementary neutron diffraction measurements do not show any significant structural changes, suggesting that a chemical conversion of the material does not occur in the thermodynamically isolated system on this timescale.« less
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Lysosome Transport as a Function of Lysosome Diameter
Bandyopadhyay, Debjyoti; Cyphersmith, Austin; Zapata, Jairo A.; Kim, Y. Joseph; Payne, Christine K.
2014-01-01
Lysosomes are membrane-bound organelles responsible for the transport and degradation of intracellular and extracellular cargo. The intracellular motion of lysosomes is both diffusive and active, mediated by motor proteins moving lysosomes along microtubules. We sought to determine how lysosome diameter influences lysosome transport. We used osmotic swelling to double the diameter of lysosomes, creating a population of enlarged lysosomes. This allowed us to directly examine the intracellular transport of the same organelle as a function of diameter. Lysosome transport was measured using live cell fluorescence microscopy and single particle tracking. We find, as expected, the diffusive component of intracellular transport is decreased proportional to the increased lysosome diameter. Active transport of the enlarged lysosomes is not affected by the increased lysosome diameter. PMID:24497985
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Regularity of random attractors for fractional stochastic reaction-diffusion equations on Rn
NASA Astrophysics Data System (ADS)
Gu, Anhui; Li, Dingshi; Wang, Bixiang; Yang, Han
2018-06-01
We investigate the regularity of random attractors for the non-autonomous non-local fractional stochastic reaction-diffusion equations in Hs (Rn) with s ∈ (0 , 1). We prove the existence and uniqueness of the tempered random attractor that is compact in Hs (Rn) and attracts all tempered random subsets of L2 (Rn) with respect to the norm of Hs (Rn). The main difficulty is to show the pullback asymptotic compactness of solutions in Hs (Rn) due to the noncompactness of Sobolev embeddings on unbounded domains and the almost sure nondifferentiability of the sample paths of the Wiener process. We establish such compactness by the ideas of uniform tail-estimates and the spectral decomposition of solutions in bounded domains.
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1987-05-01
condition at the wall: v( x , y,.)/Uo = dri/dx results in the following bound- ary condition for R( x , y): 3 (OR) 2 1 [2S _ q] d2r (1 0) y X2 ; -PGo __ 2P d...i - X - 30 bar (downward triangles) for T = 20 *C (water temperature) and Dt = 1 mm (throat diameter). Figure 2.9. Bubble detection length L! necessary...diffuser of the venturi of Fig. 2.14 without incurring in laminar separation as a function of the distance x from the diffuser inlet. Figure 3.1. Schematic
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Dynamics and cluster formation in charged and uncharged Ficoll70 solutions
NASA Astrophysics Data System (ADS)
Palit, Swomitra; Yethiraj, Anand
2017-08-01
We apply pulsed-field-gradient NMR (PFG NMR) technique to measure the translational diffusion for both uncharged and charged polysaccharide (Ficoll70) in water. Analysis of the data indicates that the NMR signal attenuation above a certain packing fraction can be adequately fitted with a bi-exponential function. The self-diffusion measurements also show that the Ficoll70, an often-used compact, spherical polysucrose molecule, is itself nonideal, exhibiting signs of both softness and attractive interactions in the form of a stable suspension consisting of monomers and clusters. Further, we can quantify the fraction of monomers and clusters. This work strengthens the picture of the existence of a bound water layer within and around a porous Ficoll70 particle.
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NASA Astrophysics Data System (ADS)
Selvi, Canan; Nartop, Dilek
2012-09-01
New polymer-bound Schiff bases and Cr(III) complexes have been synthesized by the reaction of 4-benzyloxybenzaldehyde, polymer-bound with 2-aminophenol, 2-amino-4-chlorophenol and 2-amino-4-methylphenol. The structure of polymeric-Schiff bases and their Cr(III) complexes have been characterized by elemental analyses, magnetic measurements, IR, UV-Vis, TG-DTA and 1H-NMR. All these compounds have also been investigated for antibacterial activity by the well-diffusion method against Staphylococcus aureus (RSKK-07035), Shigella dysenteria type 10 (RSKK 1036), Listeria monocytogenes 4b(ATCC 19115, Escherichia coli (ATCC 1230), Salmonella typhi H (NCTC 901.8394), Staphylococcus epidermis (ATCC 12228), Brucella abortus (RSKK-03026), Micrococcs luteus (ATCC 93419, Bacillus cereus sp., Pseudomonas putida sp. and for antifungal activity against Candida albicans (Y-1200-NIH).
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LISA pathfinder appreciably constrains collapse models
NASA Astrophysics Data System (ADS)
Helou, Bassam; Slagmolen, B. J. J.; McClelland, David E.; Chen, Yanbei
2017-04-01
Spontaneous collapse models are phenomological theories formulated to address major difficulties in macroscopic quantum mechanics. We place significant bounds on the parameters of the leading collapse models, the continuous spontaneous localization (CSL) model, and the Diosi-Penrose (DP) model, by using LISA Pathfinder's measurement, at a record accuracy, of the relative acceleration noise between two free-falling macroscopic test masses. In particular, we bound the CSL collapse rate to be at most (2.96 ±0.12 ) ×10-8 s-1 . This competitive bound explores a new frequency regime, 0.7 to 20 mHz, and overlaps with the lower bound 10-8 ±2 s-1 proposed by Adler in order for the CSL collapse noise to be substantial enough to explain the phenomenology of quantum measurement. Moreover, we bound the regularization cutoff scale used in the DP model to prevent divergences to be at least 40.1 ±0.5 fm , which is larger than the size of any nucleus. Thus, we rule out the DP model if the cutoff is the size of a fundamental particle.
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iGen: An automated generator of simplified models with provable error bounds.
NASA Astrophysics Data System (ADS)
Tang, D.; Dobbie, S.
2009-04-01
Climate models employ various simplifying assumptions and parameterisations in order to increase execution speed. However, in order to draw conclusions about the Earths climate from the results of a climate simulation it is necessary to have information about the error that these assumptions and parameterisations introduce. A novel computer program, called iGen, is being developed which automatically generates fast, simplified models by analysing the source code of a slower, high resolution model. The resulting simplified models have provable bounds on error compared to the high resolution model and execute at speeds that are typically orders of magnitude faster. iGen's input is a definition of the prognostic variables of the simplified model, a set of bounds on acceptable error and the source code of a model that captures the behaviour of interest. In the case of an atmospheric model, for example, this would be a global cloud resolving model with very high resolution. Although such a model would execute far too slowly to be used directly in a climate model, iGen never executes it. Instead, it converts the code of the resolving model into a mathematical expression which is then symbolically manipulated and approximated to form a simplified expression. This expression is then converted back into a computer program and output as a simplified model. iGen also derives and reports formal bounds on the error of the simplified model compared to the resolving model. These error bounds are always maintained below the user-specified acceptable error. Results will be presented illustrating the success of iGen's analysis of a number of example models. These extremely encouraging results have lead on to work which is currently underway to analyse a cloud resolving model and so produce an efficient parameterisation of moist convection with formally bounded error.
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Twisting, supercoiling and stretching in protein bound DNA
NASA Astrophysics Data System (ADS)
Lam, Pui-Man; Zhen, Yi
2018-04-01
We have calculated theoretical results for the torque and slope of the twisted DNA, with various proteins bound on it, using the Neukirch-Marko model, in the regime where plectonemes exist. We found that the torque in the protein bound DNA decreases compared to that in the bare DNA. This is caused by the decrease in the free energy g(f) , and hence the smaller persistence lengths, in the case of protein bound DNA. We hope our results will encourage experimental investigations of supercoiling in protein bound DNA, which can provide further tests of the Neukirch-Marko model.
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Self diffusion of interacting membrane proteins.
Abney, J R; Scalettar, B A; Owicki, J C
1989-01-01
A two-dimensional version of the generalized Smoluchowski equation is used to analyze the time (or distance) dependent self diffusion of interacting membrane proteins in concentrated membrane systems. This equation provides a well established starting point for descriptions of the diffusion of particles that interact through both direct and hydrodynamic forces; in this initial work only the effects of direct interactions are explicitly considered. Data describing diffusion in the presence of hard-core repulsions, soft repulsions, and soft repulsions with weak attractions are presented. The effect that interactions have on the self-diffusion coefficient of a real protein molecule from mouse liver gap junctions is also calculated. The results indicate that self diffusion is always inhibited by direct interactions; this observation is interpreted in terms of the caging that will exist at finite protein concentration. It is also noted that, over small distance scales, the diffusion coefficient is determined entirely by the very strong Brownian forces; therefore, as a function of displacement the self-diffusion coefficient decays (rapidly) from its value at infinite dilution to its steady-state interaction-averaged value. The steady-state self-diffusion coefficient describes motion over distance scales that range from approximately 10 nm to cellular dimensions and is the quantity measured in fluorescence recovery after photobleaching experiments. The short-ranged behavior of the diffusion coefficient is important on the interparticle-distance scale and may therefore influence the rate at which nearest-neighbor collisional processes take place. The hard-disk theoretical results presented here are in excellent agreement with lattice Monte-Carlo results obtained by other workers. The concentration dependence of experimentally measured diffusion coefficients of antibody-hapten complexes bound to the membrane surface is consistent with that predicted by the theory. The variation in experimental diffusion coefficients of integral membrane proteins is greater than that predicted by the theory, and may also reflect protein-induced perturbations in membrane viscosity. PMID:2720077
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Exact solutions to a spatially extended model of kinase-receptor interaction.
Szopa, Piotr; Lipniacki, Tomasz; Kazmierczak, Bogdan
2011-10-01
B and Mast cells are activated by the aggregation of the immune receptors. Motivated by this phenomena we consider a simple spatially extended model of mutual interaction of kinases and membrane receptors. It is assumed that kinase activates membrane receptors and in turn the kinase molecules bound to the active receptors are activated by transphosphorylation. Such a type of interaction implies positive feedback and may lead to bistability. In this study we apply the Steklov eigenproblem theory to analyze the linearized model and find exact solutions in the case of non-uniformly distributed membrane receptors. This approach allows us to determine the critical value of receptor dephosphorylation rate at which cell activation (by arbitrary small perturbation of the inactive state) is possible. We found that cell sensitivity grows with decreasing kinase diffusion and increasing anisotropy of the receptor distribution. Moreover, these two effects are cooperating. We showed that the cell activity can be abruptly triggered by the formation of the receptor aggregate. Since the considered activation mechanism is not based on receptor crosslinking by polyvalent antigens, the proposed model can also explain B cell activation due to receptor aggregation following binding of monovalent antigens presented on the antigen presenting cell.
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Step Permeability on the Pt(111) Surface
NASA Astrophysics Data System (ADS)
Altman, Michael
2005-03-01
Surface morphology will be affected, or even dictated, by kinetic limitations that may be present during growth. Asymmetric step attachment is recognized to be an important and possibly common cause of morphological growth instabilities. However, the impact of this kinetic limitation on growth morphology may be hindered by other factors such as the rate limiting step and step permeability. This strongly motivates experimental measurements of these quantities in real systems. Using low energy electron microscopy, we have measured step flow velocities in growth on the Pt(111) surface. The dependence of step velocity upon adjacent terrace width clearly shows evidence of asymmetric step attachment and step permeability. Step velocity is modeled by solving the diffusion equation simultaneously on several adjacent terraces subject to boundary conditions at intervening steps that include asymmetric step attachment and step permeability. This analysis allows a quantitative evaluation of step permeability and the kinetic length, which characterizes the rate limiting step continuously between diffusion and attachment-detachment limited regimes. This work provides information that is greatly needed to set physical bounds on the parameters that are used in theoretical treatments of growth. The observation that steps are permeable even on a simple metal surface should also stimulate more experimental measurements and theoretical treatments of this effect.
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Yamamoto, Eiji
2017-01-01
Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multiscale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctuations. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:29159013
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Chara, Osvaldo; Borges, Augusto; Milhiet, Pierre-Emmanuel; Nöllmann, Marcelo; Cattoni, Diego I
2018-03-27
Transport of cellular cargo by molecular motors requires directionality to ensure proper biological functioning. During sporulation in Bacillus subtilis, directionality of chromosome transport is mediated by the interaction between the membrane-bound DNA translocase SpoIIIE and specific octameric sequences (SRS). Whether SRS regulate directionality by recruiting and orienting SpoIIIE or by simply catalyzing its translocation activity is still unclear. By using atomic force microscopy and single-round fast kinetics translocation assays we determined the localization and dynamics of diffusing and translocating SpoIIIE complexes on DNA with or without SRS. Our findings combined with mathematical modelling revealed that SpoIIIE directionality is not regulated by protein recruitment to SRS but rather by a fine-tuned balance among the rates governing SpoIIIE-DNA interactions and the probability of starting translocation modulated by SRS. Additionally, we found that SpoIIIE can start translocation from non-specific DNA, providing an alternative active search mechanism for SRS located beyond the exploratory length defined by 1D diffusion. These findings are relevant in vivo in the context of chromosome transport through an open channel, where SpoIIIE can rapidly explore DNA while directionality is modulated by the probability of translocation initiation upon interaction with SRS versus non-specific DNA.
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Directed and persistent movement arises from mechanochemistry of the ParA/ParB system
NASA Astrophysics Data System (ADS)
Hu, Longhua; Vecchiarelli, Anthony G.; Mizuuchi, Kiyoshi; Neuman, Keir C.; Liu, Jian
The segregation of DNA prior to cell division is essential for faithful genetic inheritance. In many bacteria, segregation of the low-copy-number plasmids involves an active partition system composed of ParA ATPase and its stimulator protein ParB. Recent experiments suggest that ParA/ParB system motility is driven by a diffusion-ratchet mechanism in which ParB-coated plasmid both creates and follows a ParA gradient on the nucleoid surface. However, the detailed mechanism of ParA/ParB-mediated directed and persistent movement remains unknown. We develop a theoretical model describing ParA/ParB-mediated motility. We show that the ParA/ParB system can work as a Brownian ratchet, which effectively couples the ATPase-dependent cycling of ParA-nucleoid affinity to the motion of the ParB bound cargo. Paradoxically, the resulting processive motion relies on quenching diffusive plasmid motion through a large number of transient ParA/ParB-mediated tethers to the nucleoid surface. Our work sheds light on a new emergent phenomenon in which non-motor proteins work collectively via mechanochemical coupling to propel cargos -- an ingenious solution shaped by evolution to cope with the lack of processive motor proteins in bacteria.
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A Quasi-Elastic Neutron Scattering Study of the Dynamics of Electrically Constrained Water.
Fuchs, Elmar C; Bitschnau, Brigitte; Wexler, Adam D; Woisetschläger, Jakob; Freund, Friedemann T
2015-12-31
We have measured the quasi-elastic neutron scattering (QENS) of an electrohydrodynamic liquid bridge formed between two beakers of pure water when a high voltage is applied, a setup allowing to investigate water under high-voltage without high currents. From this experiment two proton populations were distinguished: one consisting of protons strongly bound to oxygen atoms (immobile population, elastic component) and a second one of quasi-free protons (mobile population, inelastic component) both detected by QENS. The diffusion coefficient of the quasi-free protons was found to be D = (26 ± 10) × 10(-5) cm(2) s(-1) with a jump length lav ∼ 3 Å and an average residence time of τ0 = 0.55 ± 0.08 ps. The associated proton mobility in the proton channel of the bridge is ∼9.34 × 10(-7) m(2) V(-1) s(-1), twice as fast as diffusion-based proton mobility in bulk water. It also matches the so-called electrohydrodynamic or "apparent" charge mobility, an experimental quantity which so far has lacked molecular interpretation. These results further corroborate the proton channel model for liquid water under high voltage and give new insights into the molecular mechanisms behind electrohydrodynamic charge transport phenomena and delocalization of protons in liquid water.
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Approximate Model Checking of PCTL Involving Unbounded Path Properties
NASA Astrophysics Data System (ADS)
Basu, Samik; Ghosh, Arka P.; He, Ru
We study the problem of applying statistical methods for approximate model checking of probabilistic systems against properties encoded as
PCTL formulas. Such approximate methods have been proposed primarily to deal with state-space explosion that makes the exact model checking by numerical methods practically infeasible for large systems. However, the existing statistical methods either consider a restricted subset ofPCTL , specifically, the subset that can only express bounded until properties; or rely on user-specified finite bound on the sample path length. We propose a new method that does not have such restrictions and can be effectively used to reason about unbounded until properties. We approximate probabilistic characteristics of an unbounded until property by that of a bounded until property for a suitably chosen value of the bound. In essence, our method is a two-phase process: (a) the first phase is concerned with identifying the bound k 0; (b) the second phase computes the probability of satisfying the k 0-bounded until property as an estimate for the probability of satisfying the corresponding unbounded until property. In both phases, it is sufficient to verify bounded until properties which can be effectively done using existing statistical techniques. We prove the correctness of our technique and present its prototype implementations. We empirically show the practical applicability of our method by considering different case studies including a simple infinite-state model, and large finite-state models such as IPv4 zeroconf protocol and dining philosopher protocol modeled as Discrete Time Markov chains. -
An improved bounded semi-Lagrangian scheme for the turbulent transport of passive scalars
NASA Astrophysics Data System (ADS)
Verma, Siddhartha; Xuan, Y.; Blanquart, G.
2014-09-01
An improved bounded semi-Lagrangian scalar transport scheme based on cubic Hermite polynomial reconstruction is proposed in this paper. Boundedness of the scalar being transported is ensured by applying derivative limiting techniques. Single sub-cell extrema are allowed to exist as they are often physical, and help minimize numerical dissipation. This treatment is distinct from enforcing strict monotonicity as done by D.L. Williamson and P.J. Rasch [5], and allows better preservation of small scale structures in turbulent simulations. The proposed bounding algorithm, although a seemingly subtle difference from strict monotonicity enforcement, is shown to result in significant performance gain in laminar cases, and in three-dimensional turbulent mixing layers. The scheme satisfies several important properties, including boundedness, low numerical diffusion, and high accuracy. Performance gain in the turbulent case is assessed by comparing scalar energy and dissipation spectra produced by several bounded and unbounded schemes. The results indicate that the proposed scheme is capable of furnishing extremely accurate results, with less severe resolution requirements than all the other bounded schemes tested. Additional simulations in homogeneous isotropic turbulence, with scalar timestep size unconstrained by the CFL number, show good agreement with spectral scheme results available in the literature. Detailed analytical examination of gain and phase error characteristics of the original cubic Hermite polynomial is also included, and points to dissipation and dispersion characteristics comparable to, or better than, those of a fifth order upwind Eulerian scheme.
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Mixed and Mixture Regression Models for Continuous Bounded Responses Using the Beta Distribution
ERIC Educational Resources Information Center
Verkuilen, Jay; Smithson, Michael
2012-01-01
Doubly bounded continuous data are common in the social and behavioral sciences. Examples include judged probabilities, confidence ratings, derived proportions such as percent time on task, and bounded scale scores. Dependent variables of this kind are often difficult to analyze using normal theory models because their distributions may be quite…
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NASA Astrophysics Data System (ADS)
Thelen, Brian J.; Xique, Ismael J.; Burns, Joseph W.; Goley, G. Steven; Nolan, Adam R.; Benson, Jonathan W.
2017-04-01
In Bayesian decision theory, there has been a great amount of research into theoretical frameworks and information- theoretic quantities that can be used to provide lower and upper bounds for the Bayes error. These include well-known bounds such as Chernoff, Battacharrya, and J-divergence. Part of the challenge of utilizing these various metrics in practice is (i) whether they are "loose" or "tight" bounds, (ii) how they might be estimated via either parametric or non-parametric methods, and (iii) how accurate the estimates are for limited amounts of data. In general what is desired is a methodology for generating relatively tight lower and upper bounds, and then an approach to estimate these bounds efficiently from data. In this paper, we explore the so-called triangle divergence which has been around for a while, but was recently made more prominent in some recent research on non-parametric estimation of information metrics. Part of this work is motivated by applications for quantifying fundamental information content in SAR/LIDAR data, and to help in this, we have developed a flexible multivariate modeling framework based on multivariate Gaussian copula models which can be combined with the triangle divergence framework to quantify this information, and provide approximate bounds on Bayes error. In this paper we present an overview of the bounds, including those based on triangle divergence and verify that under a number of multivariate models, the upper and lower bounds derived from triangle divergence are significantly tighter than the other common bounds, and often times, dramatically so. We also propose some simple but effective means for computing the triangle divergence using Monte Carlo methods, and then discuss estimation of the triangle divergence from empirical data based on Gaussian Copula models.
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Diffusion models for innovation: s-curves, networks, power laws, catastrophes, and entropy.
Jacobsen, Joseph J; Guastello, Stephen J
2011-04-01
This article considers models for the diffusion of innovation would be most relevant to the dynamics of early 21st century technologies. The article presents an overview of diffusion models and examines the adoption S-curve, network theories, difference models, influence models, geographical models, a cusp catastrophe model, and self-organizing dynamics that emanate from principles of network configuration and principles of heat diffusion. The diffusion dynamics that are relevant to information technologies and energy-efficient technologies are compared. Finally, principles of nonlinear dynamics for innovation diffusion that could be used to rehabilitate the global economic situation are discussed.
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Bounded rationality alters the dynamics of paediatric immunization acceptance.
Oraby, Tamer; Bauch, Chris T
2015-06-02
Interactions between disease dynamics and vaccinating behavior have been explored in many coupled behavior-disease models. Cognitive effects such as risk perception, framing, and subjective probabilities of adverse events can be important determinants of the vaccinating behaviour, and represent departures from the pure "rational" decision model that are often described as "bounded rationality". However, the impact of such cognitive effects in the context of paediatric infectious disease vaccines has received relatively little attention. Here, we develop a disease-behavior model that accounts for bounded rationality through prospect theory. We analyze the model and compare its predictions to a reduced model that lacks bounded rationality. We find that, in general, introducing bounded rationality increases the dynamical richness of the model and makes it harder to eliminate a paediatric infectious disease. In contrast, in other cases, a low cost, highly efficacious vaccine can be refused, even when the rational decision model predicts acceptance. Injunctive social norms can prevent vaccine refusal, if vaccine acceptance is sufficiently high in the beginning of the vaccination campaign. Cognitive processes can have major impacts on the predictions of behaviour-disease models, and further study of such processes in the context of vaccination is thus warranted.
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Bounded rationality alters the dynamics of paediatric immunization acceptance
Oraby, Tamer; Bauch, Chris T.
2015-01-01
Interactions between disease dynamics and vaccinating behavior have been explored in many coupled behavior-disease models. Cognitive effects such as risk perception, framing, and subjective probabilities of adverse events can be important determinants of the vaccinating behaviour, and represent departures from the pure “rational” decision model that are often described as “bounded rationality”. However, the impact of such cognitive effects in the context of paediatric infectious disease vaccines has received relatively little attention. Here, we develop a disease-behavior model that accounts for bounded rationality through prospect theory. We analyze the model and compare its predictions to a reduced model that lacks bounded rationality. We find that, in general, introducing bounded rationality increases the dynamical richness of the model and makes it harder to eliminate a paediatric infectious disease. In contrast, in other cases, a low cost, highly efficacious vaccine can be refused, even when the rational decision model predicts acceptance. Injunctive social norms can prevent vaccine refusal, if vaccine acceptance is sufficiently high in the beginning of the vaccination campaign. Cognitive processes can have major impacts on the predictions of behaviour-disease models, and further study of such processes in the context of vaccination is thus warranted. PMID:26035413
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Dark matter and color octets beyond the Standard Model
NASA Astrophysics Data System (ADS)
Krnjaic, Gordan Z.
Although the Standard Model (SM) of particles and interactions has survived forty years of experimental tests, it does not provide a complete description of nature. From cosmological and astrophysical observations, it is now clear that the majority of matter in the universe is not baryonic and interacts very weakly (if at all) via non-gravitational forces. The SM does not provide a dark matter candidate, so new particles must be introduced. Furthermore, recent Tevatron results suggest that SM predictions for benchmark collider observables are in tension with experimental observations. In this thesis, we will propose extensions to the SM that address each of these issues. Although there is abundant indirect evidence for the existence of dark matter, terrestrial efforts to observe its interactions have yielded conflicting results. We address this situation with a simple model of dark matter that features hydrogen-like bound states that scatter off SM nuclei by undergoing inelastic hyperfine transitions. We explore the available parameter space that results from demanding that DM self-interactions satisfy experimental bounds and ameliorate the tension between positive and null signals at the DAMA and CDMS experiments respectively. However, this simple model does not explain the cosmological abundance of dark matter and also encounters a Landau pole at a low energy scale. We, therefore, extend the field content and gauge group of the dark sector to resolve these issues with a renormalizable UV completion. We also explore the galactic dynamics of unbound dark matter and find that "dark ions" settle into a diffuse isothermal halo that differs from that of the bound states. This suppresses the local dark-ion density and expands the model's viable parameter space. We also consider the > 3σ excess in W plus dijet events recently observed at the Tevatron collider. We show that decays of a color-octet, electroweak-triplet scalar particle ("octo-triplet") can yield the requisite final state to explain the data. We also find that octotriplets can induce mixing in the B - B¯ system and may give rise to additional CP violation. The model makes concrete predictions for several final states accessible at the LHC, so it can promptly be discovered or falsified. Finally we address the anomalous top forward-backward asymmetry observed the Tevatron. We find that a spin-1 color octet particle with flavor blind axial interactions can explain this anomaly if the mass is in the 50 - 90 GeV range. We explore the multitude of experimental constrains in this mass window and present the viable parameter space as a function of the axigluon mass and coupling constant.
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Velocity relaxation of a particle in a confined compressible fluid
NASA Astrophysics Data System (ADS)
Tatsumi, Rei; Yamamoto, Ryoichi
2013-05-01
The velocity relaxation of an impulsively forced spherical particle in a fluid confined by two parallel plane walls is studied using a direct numerical simulation approach. During the relaxation process, the momentum of the particle is transmitted in the ambient fluid by viscous diffusion and sound wave propagation, and the fluid flow accompanied by each mechanism has a different character and affects the particle motion differently. Because of the bounding walls, viscous diffusion is hampered, and the accompanying shear flow is gradually diminished. However, the sound wave is repeatedly reflected and spreads diffusely. As a result, the particle motion is governed by the sound wave and backtracks differently in a bulk fluid. The time when the backtracking of the particle occurs changes non-monotonically with respect to the compressibility factor ɛ = ν/ac and is minimized at the characteristic compressibility factor. This factor depends on the wall spacing, and the dependence is different at small and large wall spacing regions based on the different mechanisms causing the backtracking.
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A magnetic gradient induced force in NMR restricted diffusion experiments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ghadirian, Bahman; Stait-Gardner, Tim; Castillo, Reynaldo
2014-03-28
We predict that the phase cancellation of a precessing magnetisation field carried by a diffusing species in a bounded geometry under certain nuclear magnetic resonance pulsed magnetic field gradient sequences results in a small force over typically micrometre length scales. Our calculations reveal that the total magnetisation energy in a pore under the influence of a pulsed gradient will be distance-dependent thus resulting in a force acting on the boundary. It is shown that this effect of the magnetisation of diffusing particles will appear as either an attractive or repulsive force depending on the geometry of the pore and magneticmore » properties of the material. A detailed analysis is performed for the case of a pulsed gradient spin-echo experiment on parallel planes. It is shown that the force decays exponentially in terms of the spin-spin relaxation. The proof is based on classical electrodynamics. An application of this effect to soft matter is suggested.« less
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Dang, Zhiya; Shamsi, Javad; Palazon, Francisco; Imran, Muhammad; Akkerman, Quinten A; Park, Sungwook; Bertoni, Giovanni; Prato, Mirko; Brescia, Rosaria; Manna, Liberato
2017-02-28
An increasing number of studies have recently reported the rapid degradation of hybrid and all-inorganic lead halide perovskite nanocrystals under electron beam irradiation in the transmission electron microscope, with the formation of nanometer size, high contrast particles. The nature of these nanoparticles and the involved transformations in the perovskite nanocrystals are still a matter of debate. Herein, we have studied the effects of high energy (80/200 keV) electron irradiation on colloidal cesium lead bromide (CsPbBr 3 ) nanocrystals with different shapes and sizes, especially 3 nm thick nanosheets, a morphology that facilitated the analysis of the various ongoing processes. Our results show that the CsPbBr 3 nanocrystals undergo a radiolysis process, with electron stimulated desorption of a fraction of bromine atoms and the reduction of a fraction of Pb 2+ ions to Pb 0 . Subsequently Pb 0 atoms diffuse and aggregate, giving rise to the high contrast particles, as previously reported by various groups. The diffusion is facilitated by both high temperature and electron beam irradiation. The early stage Pb nanoparticles are epitaxially bound to the parent CsPbBr 3 lattice, and evolve into nonepitaxially bound Pb crystals upon further irradiation, leading to local amorphization and consequent dismantling of the CsPbBr 3 lattice. The comparison among CsPbBr 3 nanocrystals with various shapes and sizes evidences that the damage is particularly pronounced at the corners and edges of the surface, due to a lower diffusion barrier for Pb 0 on the surface than inside the crystal and the presence of a larger fraction of under-coordinated atoms.
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Planck limits on non-canonical generalizations of large-field inflation models
DOE Office of Scientific and Technical Information (OSTI.GOV)
Stein, Nina K.; Kinney, William H., E-mail: ninastei@buffalo.edu, E-mail: whkinney@buffalo.edu
2017-04-01
In this paper, we consider two case examples of Dirac-Born-Infeld (DBI) generalizations of canonical large-field inflation models, characterized by a reduced sound speed, c {sub S} < 1. The reduced speed of sound lowers the tensor-scalar ratio, improving the fit of the models to the data, but increases the equilateral-mode non-Gaussianity, f {sup equil.}{sub NL}, which the latest results from the Planck satellite constrain by a new upper bound. We examine constraints on these models in light of the most recent Planck and BICEP/Keck results, and find that they have a greatly decreased window of viability. The upper bound onmore » f {sup equil.}{sub NL} corresponds to a lower bound on the sound speed and a corresponding lower bound on the tensor-scalar ratio of r ∼ 0.01, so that near-future Cosmic Microwave Background observations may be capable of ruling out entire classes of DBI inflation models. The result is, however, not universal: infrared-type DBI inflation models, where the speed of sound increases with time, are not subject to the bound.« less
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Zhang, Guangwen; Wang, Shuangshuang; Wen, Didi; Zhang, Jing; Wei, Xiaocheng; Ma, Wanling; Zhao, Weiwei; Wang, Mian; Wu, Guosheng; Zhang, Jinsong
2016-12-09
Water molecular diffusion in vivo tissue is much more complicated. We aimed to compare non-Gaussian diffusion models of diffusion-weighted imaging (DWI) including intra-voxel incoherent motion (IVIM), stretched-exponential model (SEM) and Gaussian diffusion model at 3.0 T MRI in patients with rectal cancer, and to determine the optimal model for investigating the water diffusion properties and characterization of rectal carcinoma. Fifty-nine consecutive patients with pathologically confirmed rectal adenocarcinoma underwent DWI with 16 b-values at a 3.0 T MRI system. DWI signals were fitted to the mono-exponential and non-Gaussian diffusion models (IVIM-mono, IVIM-bi and SEM) on primary tumor and adjacent normal rectal tissue. Parameters of standard apparent diffusion coefficient (ADC), slow- and fast-ADC, fraction of fast ADC (f), α value and distributed diffusion coefficient (DDC) were generated and compared between the tumor and normal tissues. The SEM exhibited the best fitting results of actual DWI signal in rectal cancer and the normal rectal wall (R 2 = 0.998, 0.999 respectively). The DDC achieved relatively high area under the curve (AUC = 0.980) in differentiating tumor from normal rectal wall. Non-Gaussian diffusion models could assess tissue properties more accurately than the ADC derived Gaussian diffusion model. SEM may be used as a potential optimal model for characterization of rectal cancer.