WorldWideScience

Sample records for non-translational molecular diffusive

  1. Molecular dynamics simulation of diffusivity

    Institute of Scientific and Technical Information of China (English)

    Juanfang LIU; Danling ZENG; Qin LI; Hong GAO

    2008-01-01

    Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.

  2. Photoinduced diffusion molecular transport

    Science.gov (United States)

    Rozenbaum, Viktor M.; Dekhtyar, Marina L.; Lin, Sheng Hsien; Trakhtenberg, Leonid I.

    2016-08-01

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

  3. OH+ in Diffuse Molecular Clouds

    Science.gov (United States)

    Porras, A. J.; Federman, S. R.; Welty, D. E.; Ritchey, A. M.

    2014-01-01

    Near ultraviolet observations of OH+ and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH+ arises from a main component seen in CH+ (that with the highest CH+/CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH+ detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH+ as well, confirming OH+ and H2O+ observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for a high enough density and molecular fraction before detectable amounts are seen. Thus, while OH+ leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds.

  4. OH+ in Diffuse Molecular Clouds

    CERN Document Server

    Porras, A J; Welty, D E; Ritchey, A M

    2013-01-01

    Near ultraviolet observations of OH+ and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH+ arises from a main component seen in CH+ (that with the highest CH+/CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH+ detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH+ as well, confirming OH+ and H2O+ observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for high enough density and molecular fraction before detectable amounts are seen. Thus, while OH+ leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with differen...

  5. Visualization of molecular excitons diffusion

    Science.gov (United States)

    Salamatova, Evgeniia; Kozlov, Oleg V.; Luponosov, Yuriy N.; Solodukhin, Alexander N.; Toropynina, Viktoria Y.; Ponomarenko, Sergei A.; Pshenichnikov, Maxim S.

    2016-09-01

    Small organic molecules of the push-pull architecture are rapidly gaining their status in the organic electronics applications. In densely packed molecular films, both intra- and intermolecular interactions play an essential role for the device performance. Here we study two different molecules, a highly symmetric star-shaped one and its newly synthesized single arm analogue, for their photophysical properties. Both chromophores were dissolved in a solid matrix at different concentrations to vary their separation and therefore intermolecular coupling. We show that in both molecules the population relaxation accelerates by more than a factor of 10 at shorter intermolecular distances due to self-quenching thereby reducing the exciton survival time. The transient anisotropy dynamics are also quite similar, with their substantial acceleration at shorter interchromophore distances due to exciton diffusion caused by the Förster-like resonance energy transfer. However, the anisotropy values are noticeably lower for the star-shaped molecule because of intramolecular mixing of different polarization states. Finally, a model is presented that accounts for the observed results.

  6. Capacity of Discrete Molecular Diffusion Channels

    CERN Document Server

    Einolghozati, Arash; Beirami, Ahmad; Fekri, Faramarz

    2011-01-01

    In diffusion-based molecular communications, messages can be conveyed via the variation in the concentration of molecules in the medium. In this paper, we intend to analyze the achievable capacity in transmission of information from one node to another in a diffusion channel. We observe that because of the molecular diffusion in the medium, the channel possesses memory. We then model the memory of the channel by a two-step Markov chain and obtain the equations describing the capacity of the diffusion channel. By performing a numerical analysis, we obtain the maximum achievable rate for different levels of the transmitter power, i.e., the molecule production rate.

  7. Molecular diffusion in monolayer and submonolayer nitrogen

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Bruch, Ludwig Walter

    2001-01-01

    The orientational and translational motions in a monolayer fluid of physisorbed molecular nitrogen are treated using molecular dynamics simulations. Dynamical response functions and several approximations to the coefficient of translational diffusion are determined for adsorption on the basal pla...... where the ballistic approximation to the translational molecular self-correlation function is accurate....

  8. Dynamics Studies on Molecular Diffusion in Zeolites

    Institute of Scientific and Technical Information of China (English)

    王秋霞; 樊建芬; 肖鹤鸣

    2003-01-01

    A review about the applications of molecular dynamics(MD)simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.

  9. High efficiency diffusion molecular retention tumor targeting.

    Directory of Open Access Journals (Sweden)

    Yanyan Guo

    Full Text Available Here we introduce diffusion molecular retention (DMR tumor targeting, a technique that employs PEG-fluorochrome shielded probes that, after a peritumoral (PT injection, undergo slow vascular uptake and extensive interstitial diffusion, with tumor retention only through integrin molecular recognition. To demonstrate DMR, RGD (integrin binding and RAD (control probes were synthesized bearing DOTA (for (111 In(3+, a NIR fluorochrome, and 5 kDa PEG that endows probes with a protein-like volume of 25 kDa and decreases non-specific interactions. With a GFP-BT-20 breast carcinoma model, tumor targeting by the DMR or i.v. methods was assessed by surface fluorescence, biodistribution of [(111In] RGD and [(111In] RAD probes, and whole animal SPECT. After a PT injection, both probes rapidly diffused through the normal and tumor interstitium, with retention of the RGD probe due to integrin interactions. With PT injection and the [(111In] RGD probe, SPECT indicated a highly tumor specific uptake at 24 h post injection, with 352%ID/g tumor obtained by DMR (vs 4.14%ID/g by i.v.. The high efficiency molecular targeting of DMR employed low probe doses (e.g. 25 ng as RGD peptide, which minimizes toxicity risks and facilitates clinical translation. DMR applications include the delivery of fluorochromes for intraoperative tumor margin delineation, the delivery of radioisotopes (e.g. toxic, short range alpha emitters for radiotherapy, or the delivery of photosensitizers to tumors accessible to light.

  10. OH{sup +} IN DIFFUSE MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Porras, A. J.; Federman, S. R. [Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606 (United States); Welty, D. E. [Department of Astronomy and Astrophysics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Ritchey, A. M., E-mail: steven.federman@utoledo.edu, E-mail: aporras@live.unc.edu, E-mail: dwelty@oddjob.uchicago.edu, E-mail: aritchey@astro.washington.edu [Department of Astronomy, University of Washington, Seattle, WA 98195 (United States)

    2014-01-20

    Near ultraviolet observations of OH{sup +} and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH{sup +} arises from a main component seen in CH{sup +} (that with the highest CH{sup +}/CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH{sup +} detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH{sup +} as well, confirming OH{sup +} and H{sub 2}O{sup +} observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for a high enough density and molecular fraction before detectable amounts are seen. Thus, while OH{sup +} leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds.

  11. Diffusion in Liquids: Equilibrium Molecular Simulations and Predictive Engineering Models

    NARCIS (Netherlands)

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.

  12. Diffusion in Liquids: Equilibrium Molecular Simulations and Predictive Engineering Models

    OpenAIRE

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations. From a practical point of view, systems consisting more than two components are more interesting. However, experimental and simulation data on transport diffusion for such systems are scarce. There...

  13. A consistent transported PDF model for treating differential molecular diffusion

    Science.gov (United States)

    Wang, Haifeng; Zhang, Pei

    2016-11-01

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

  14. Molecular weight dependence of exciton diffusion in poly(3-hexylthiophene)

    DEFF Research Database (Denmark)

    Masri, Zarifi; Ruseckas, Arvydas; Emelianova, Evguenia V.

    2013-01-01

    A joint experimental and theoretical study of singlet exciton diffusion in spin-coated poly(3-hexylthiophene) (P3HT) films and its dependence on molecular weight is presented. The results show that exciton diffusion is fast along the co-facial π–π aggregates of polymer chromophores and about 100...

  15. Extending Molecular Theory to Steady-State Diffusing Systems

    Energy Technology Data Exchange (ETDEWEB)

    FRINK,LAURA J. D.; SALINGER,ANDREW G.; THOMPSON,AIDAN P.

    1999-10-22

    Predicting the properties of nonequilibrium systems from molecular simulations is a growing area of interest. One important class of problems involves steady state diffusion. To study these cases, a grand canonical molecular dynamics approach has been developed by Heffelfinger and van Swol [J. Chem. Phys., 101, 5274 (1994)]. With this method, the flux of particles, the chemical potential gradients, and density gradients can all be measured in the simulation. In this paper, we present a complementary approach that couples a nonlocal density functional theory (DFT) with a transport equation describing steady-state flux of the particles. We compare transport-DFT predictions to GCMD results for a variety of ideal (color diffusion), and nonideal (uphill diffusion and convective transport) systems. In all cases excellent agreement between transport-DFT and GCMD calculations is obtained with diffusion coefficients that are invariant with respect to density and external fields.

  16. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    Science.gov (United States)

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-08

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  17. Time scale of diffusion in molecular and cellular biology

    Science.gov (United States)

    Holcman, D.; Schuss, Z.

    2014-05-01

    Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

  18. A memory diffusion model for molecular anisotropic diffusion in siliceous β-zeolite.

    Science.gov (United States)

    Ji, Xiangfei; An, Zhuanzhuan; Yang, Xiaofeng

    2016-01-01

    A memory diffusion model of molecules on β-zeolite is proposed. In the model, molecular diffusion in β-zeolites is treated as jumping from one adsorption site to its neighbors and the jumping probability is a compound probability which includes that provided by the transitional state theory as well as that derived from the information about which direction the target molecule comes from. The proposed approach reveals that the diffusivities along two crystal axes on β-zeolite are correlated. The model is tested by molecular dynamics simulations on diffusion of benzene and other simple molecules in β-zeolites. The results show that the molecules with larger diameters fit the prediction much better and that the "memory effects" are important in all cases.

  19. Molecular dynamics simulations of diffusion mechanisms in NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Soule De Bas, B.; Farkas, D

    2003-03-14

    Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.

  20. The interstitialcy diffusion in FCC copper: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Bukkuru, S., E-mail: srinivasaraobukkuru@gmail.com; Rao, A. D. P. [Nucl. Phys Dept., Andhra University, Visakhapatnam– 530003 (India); Warrier, M. [Computational Analysis Division, Bhabha Atomic Research Centre, Visakhapatnam – 530012 (India)

    2015-06-24

    Damage of materials due to neutron irradiation occurs via energetic cascades caused by energetic primary knock-on atoms (PKA) created by the energetic neutron as it passes through the material. These cascades result in creation of Frenkel Pairs (interstitials and vacancies). The interstitials and vacancies diffuse and recombine to (I) nullify the damage when an interstitial recombines with a vacancy, (II) form interstitial clusters when two or more interstitials recombine, and (III) form vacancy clusters when several vacancies come together. The latter two processes result in change of material properties. Interstitial diffusion has reported time-scales of microseconds and vacancy diffusion has diffusion time-scales of the order of seconds. We have carried out molecular dynamics (MD) simulations of interstitial diffusion in crystal Cu to study the mechanism of diffusion. It is found that interstitialcy diffusion – wherein an interstitial displaces a lattice atom thereby making the lattice atom an interstitial – has time-scales of a few tens of pico-seconds. Therefore we propose that the “interstitialcy diffusion” mechanism could play a major part in the diffusive-recombinations of the Frenkel Pairs created during the cascade.

  1. On the coupling between molecular diffusion and solvation shell exchange

    DEFF Research Database (Denmark)

    Møller, Klaus Braagaard; Rey, Rossend; Masia, Marco;

    2005-01-01

    The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods are p...

  2. Gravitational instability of filamentary molecular clouds, including ambipolar diffusion

    CERN Document Server

    Hosseinirad, Mohammad; Abbassi, Shahram; Roshan, Mahmood

    2016-01-01

    The gravitational instability of a filamentary molecular cloud in non-ideal magnetohydrodynamics is investigated. The filament is assumed to be in hydrostatic equilibrium. We add the effect of ambipolar diffusion to the filament which is threaded by an initial uniform axial magnetic field along its axis. We write down the fluid equations in cylindrical coordinates and perform linear perturbation analysis. We integrate the resultant differential equations and then derive the numerical dispersion relation. We find that, a more efficient ambipolar diffusion leads to an enhancement of the growth of the most unstable mode, and to increase of the fragmentation scale of the filament.

  3. Post-processing interstitialcy diffusion from molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bukkuru, S. [Nuclear Physics Dept., Andhra University, Visakhapatnam, 530003 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India)

    2016-01-15

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.

  4. Properties of Diffuse Molecular Gas in the Magellanic Clouds

    Science.gov (United States)

    Welty, Daniel

    2012-10-01

    Studies of the interstellar medium in the lower-metallicity Magellanic Clouds explore somewhat different environmental conditions from those typically probed in our own Galactic ISM. Recent studies based on optical/UV spectra of SMC and LMC targets, for example, have revealed unexpected differences in gas-phase abundance patterns {for various atomic and molecular species} and have begun to explore the effects of differences in metallicity on the atomic-to-molecular transition and resulting molecular fraction f{H_2} - a key aspect in the formation of molecular clouds. We propose a more detailed study of the abundances, depletions, and local physical conditions characterizing diffuse molecular material in the Magellanic Clouds, using STIS E140H and E230M spectra of two sight lines with N{H_2} > 10^20 cm^-2 {both probing the outskirts of molecular clouds seen in CO emission}. The two STIS settings will include lines from various neutral and ionized species {with a range in depletion behavior}, several C I multiplets, and several bands of CO and C_2. By probing and characterizing the atomic-to-molecular transition in the Magellanic Clouds, we will address key issues regarding the effects of differences in metallicity on the relationship between the atomic and molecular gas in galaxies; on cloud structure, physical conditions, and diffuse cloud chemistry; and on the composition and properties of interstellar dust. The results of this project should thus aid in the interpretation of observations of atomic and molecular material in more distant low-metallicity systems.

  5. Active Versus Passive: Receiver Model Transforms for Diffusive Molecular Communication

    CERN Document Server

    Noel, Adam; Makrakis, Dimitrios; Hafid, Abdelhakim

    2016-01-01

    This paper presents an analytical comparison of the active and passive receiver models in diffusive molecular communication. In the active model, molecules are absorbed when they collide with the receiver surface. In the passive model, the receiver is a virtual boundary that does not affect molecule behavior. Two approaches are presented to derive transforms between the active and passive receiver signals. As an example, we unify the two models for an unbounded diffusion-only molecular communication system with a spherical receiver. As time increases in the three-dimensional system, the transform functions have constant scaling factors, such that the receiver models are effectively equivalent. Methods are presented to enable the transformation of stochastic simulations, which are used to verify the transforms and demonstrate that transforming the simulation of a passive receiver can be more efficient and more accurate than the direct simulation of an absorbing receiver.

  6. Molecular Diffusive Motion in a Monolayer of a Model Lubricant

    Science.gov (United States)

    Diama, A.; Criswell, L.; Mo, H.; Taub, H.; Herwig, K. W.; Hansen, F. Y.; Volkmann, U. G.; Dimeo, R.; Neumann, D.

    2003-03-01

    Squalane (C_30H_62), a branched alkane of intermediate length consisting of a tetracosane backbone (n-C_24H_50 or C24) and six symmetrically placed methyl sidegroups, is frequently taken as a model lubricant. We have conducted quasielastic neutron scattering (QNS) experiments to investigate the diffusive motion on different time scales in a squalane monolayer adsorbed on the (0001) surfaces of an exfoliated graphite substrate. Unlike tetracosane, high-energy resolution spectra (time scale ˜0.1 - 4 ns) at temperatures of 215 K and 230 K show the energy width of the QNS to have a maximum near Q = 1.2 ÅThis nonmonotonic Q dependence suggests a more complicated diffusive motion than the simple rotation about the long molecular axis believed to occur in a C24 monolayer at this temperature. Lower-energy-resolution spectra (time scale ˜4 - 40 ps) show evidence of two types of diffusive motion whose rates have opposite temperature dependences. The rate of the faster motion decreases as the monolayer is heated, and we speculate that it is due to hindered rotation of the methyl groups. The rate of the slower motion increases with temperature and may involve both uniaxial rotation and translational diffusion. Our experimental results will be compared with molecular dynamics simulations.

  7. In Vivo Diffuse Optical Tomography and Fluorescence Molecular Tomography

    Directory of Open Access Journals (Sweden)

    Mingze Li

    2010-01-01

    Full Text Available Diffuse optical tomography (DOT and fluorescence molecular tomography (FMT are two attractive imaging techniques for in vivo physiological and psychological research. They have distinct advantages such as non-invasiveness, non-ionizing radiation, high sensitivity and longitudinal monitoring. This paper reviews the key components of DOT and FMT. Light propagation model, mathematical reconstruction algorithm, imaging instrumentation and medical applications are included. Future challenges and perspective on optical tomography are discussed.

  8. Modeling of diffuse molecular gas applied to HD 102065 observations

    CERN Document Server

    Nehme, Cyrine; Boulanger, Francois; Forets, Guillaume Pineau des; Gry, Cecile

    2008-01-01

    Aims. We model a diffuse molecular cloud present along the line of sight to the star HD 102065. We compare our modeling with observations to test our understanding of physical conditions and chemistry in diffuse molecular clouds. Methods. We analyze an extensive set of spectroscopic observations which characterize the diffuse molecular cloud observed toward HD 102065. Absorption observations provide the extinction curve, H2, C I, CO, CH, and CH+ column densities and excitation. These data are complemented by observations of CII, CO and dust emission. Physical conditions are determined using the Meudon PDR model of UV illuminated gas. Results. We find that all observational results, except column densities of CH, CH+ and H2 in its excited (J > 2) levels, are consistent with a cloud model implying a Galactic radiation field (G~0.4 in Draine's unit), a density of 80 cm-3 and a temperature (60-80 K) set by the equilibrium between heating and cooling processes. To account for excited (J >2) H2 levels column densit...

  9. DIFFUSE MOLECULAR CLOUD DENSITIES FROM UV MEASUREMENTS OF CO ABSORPTION

    Energy Technology Data Exchange (ETDEWEB)

    Goldsmith, Paul F. [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States)

    2013-09-10

    We use UV measurements of interstellar CO toward nearby stars to calculate the density in the diffuse molecular clouds containing the molecules responsible for the observed absorption. Chemical models and recent calculations of the excitation rate coefficients indicate that the regions in which CO is found have hydrogen predominantly in molecular form and that collisional excitation is by collisions with H{sub 2} molecules. We carry out statistical equilibrium calculations using CO-H{sub 2} collision rates to solve for the H{sub 2} density in the observed sources without including effects of radiative trapping. We have assumed kinetic temperatures of 50 K and 100 K, finding this choice to make relatively little difference to the lowest transition. For the sources having T{sup ex}{sub 10} only for which we could determine upper and lower density limits, we find (n(H{sub 2})) = 49 cm{sup -3}. While we can find a consistent density range for a good fraction of the sources having either two or three values of the excitation temperature, there is a suggestion that the higher-J transitions are sampling clouds or regions within diffuse molecular cloud material that have higher densities than the material sampled by the J = 1-0 transition. The assumed kinetic temperature and derived H{sub 2} density are anticorrelated when the J = 2-1 transition data, the J = 3-2 transition data, or both are included. For sources with either two or three values of the excitation temperature, we find average values of the midpoint of the density range that is consistent with all of the observations equal to 68 cm{sup -3} for T{sup k} = 100 K and 92 cm{sup -3} for T{sup k} = 50 K. The data for this set of sources imply that diffuse molecular clouds are characterized by an average thermal pressure between 4600 and 6800 K cm{sup -3}.

  10. The CH+ Abundance in Turbulent, Diffuse Molecular Clouds

    CERN Document Server

    Myers, Andrew; Li, Pak Shing

    2015-01-01

    The intermittent dissipation of interstellar turbulence is an important energy source in the diffuse ISM. Though on average smaller than the heating rates due to cosmic rays and the photoelectric effect on dust grains, the turbulent cascade can channel large amounts of energy into a relatively small fraction of the gas that consequently undergoes significant heating and chemical enrichment. In particular, this mechanism has been proposed as a solution to the long-standing problem of the high abundance of CH+ along diffuse molecular sight lines, which steady-state, low temperature models under-produce by over an order of magnitude. While much work has been done on the structure and chemistry of these small-scale dissipation zones, comparatively little attention has been paid to relating these zones to the properties of the large-scale turbulence. In this paper, we attempt to bridge this gap by estimating the temperature and CH+ column density along diffuse molecular sight-lines by post-processing 3-dimensional...

  11. Absorption from Diffuse Molecular Gas in the LMC

    Science.gov (United States)

    Welty, Dan; Murphy, Tara; Xue, Rui; Wong, Tony

    2011-04-01

    Observations of absorption from complex molecular species (e.g., HCO+, H2CO, HCN, C3H2, NH3) in the mm- and cm-wave spectra of extragalactic radio sources have revealed a surprisingly rich chemistry in relatively diffuse Galactic gas. Some of those same species have been detected, at redshifts z ~ 0.6-0.9, in similar spectra of several gravitationally lensed QSOs. It is not at all clear how such complex molecules are formed (and survive) in clouds characterized by such relatively low densities and extinctions. We propose to search for absorption from NH3 and C3H2 in the nearby, lower metallicity Large Magellanic Cloud, using ATCA/CABB observations of two of the brightest 20 GHz sources behind the main body of the LMC. Comparisons among the lowest NH3 inversion lines can yield estimates for the kinetic temperature in the gas; the ratio of linear- to cyclic-C3H2 can give an indication of the density. Via comparisons with existing observations of these species in our Galaxy and in several higher redshift systems, we aim to further understand (1) how complex molecules can be present in diffuse media, and (2) diffuse cloud chemistry and the atomic-to-molecular transition in lower metallicity systems.

  12. A molecular theory of large-solute diffusion

    Directory of Open Access Journals (Sweden)

    A.Yoshimori

    2007-12-01

    Full Text Available The limit of a large solute in the molecular theory of diffusion developed by Yamaguchi et al. [Yamaguchi T. et al., J. Chem. Phys., 2005, 123, 034504] is studied. By the limit, the Stokes approximation to the hydrodynamic equations is derived in the outside region of a diffusing solute. The limit of a large solute also leads to equations in the inside region of the solute. The analytical solution of the inside equation allows one to derive the boundary condition, which is needed on the surface of the solute when the hydrodynamic equations are calculated. The boundary condition includes stick and slip boundary conditions employed by the Stokes law, in the special case. Besides stick and slip conditions, other conditions can be expressed. The boundary condition depends on properties of a solvent.

  13. Multi-wavelength Study of Diffuse Atomic and Molecular Gas

    Science.gov (United States)

    Federman, Steven Robert; Rice, Johnathan; Flagey, Nicolas; Ritchey, Adam M.; Welty, Daniel E.; Goldsmith, Paul; Langer, William; Pineda, Jorge L.; Lambert, David L.; Lemaire, Jean-Louis

    2017-06-01

    Diffuse atomic and molecular gas is revealed through a combination of absorption lines against background targets and emission. We describe a project that combines results on ultraviolet (UV) and visible absorption with those obtained from the Herschel key program GOTC+ (Galactic Observations of Terahertz C+) to develop a comprehensive picture of neutral diffuse gas in the Galaxy. [C II], H I, and CO emission acquired for the GOTC+ survey reveal the presence of warm neutral atomic gas, cold neutral atomic gas, CO-dark H2 gas (molecular gas not seen in CO emission), and denser molecular gas in different kinematic components. We derive the component structure (number of clouds and their column densities) seen in absorption at visible wavelengths from Ca II, Ca I, K I, CH, CH+, and CN and compare that to the emission from [C II], H I, and CO and its isotopologues. Absorption lines from additional atoms (including C I, O I, and Ni II) and molecules (CO) from UV spectra obtained with the Hubble Space Telescope are used to expand the kinematic correspondences. Preliminary results on physical conditions (gas temperature and density) inferred from analyses of CN chemistry and excitation of neutral and singly-ionized carbon, neutral oxygen, and CO are also presented.

  14. Molecular simulation of protein dynamics in nanopores. II. Diffusion.

    Science.gov (United States)

    Javidpour, Leili; Tabar, M Reza Rahimi; Sahimi, Muhammad

    2009-02-28

    A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the alpha-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the experimental data, the computed diffusivities under the bulk conditions are of the correct order of magnitude. The diffusivities both in the bulk and in the pores follow a power law in the length [script-l] of the proteins and are larger in pores with repulsive walls. D(+)/D(-), the ratio of the diffusivities in pores with attractive and repulsive walls, exhibits two local maxima in its dependence on the pore size h, which are attributed to the pore sizes and protein configurations that induce long-lasting simultaneous interactions with both walls of the pores. Far from the folding temperature T(f), D increases about linearly with T, but due to the thermal fluctuations and their effect on the proteins' structure near T(f), the dependence of D on T in this region is nonlinear. We propose a novel and general "phase diagram," consisting of four regions, that describes qualitatively the effect of h, T, and interaction potentials with the walls on the diffusivity D of a protein.

  15. Diffuse Atomic and Molecular Gas near IC443

    CERN Document Server

    Hirschauer, A; Wallerstein, George; Means, T

    2009-01-01

    We present an analysis of results on absorption from Ca II, Ca I, K I, and the molecules CH+, CH, C2, and CN that probes gas interacting with the supernova remnant IC443. The eleven directions sample material across the visible nebula and beyond its eastern edge. Most of the neutral material, including the diatomic molecules, is associated with the ambient cloud detected via H I and CO emission. Analysis of excitation and chemistry yields gas densities that are typical of diffuse molecular gas. The low density gas probed by Ca II extends over a large range in velocities, from -120 to +80 km/s in the most extreme cases. This gas is distributed among several velocity components, unlike the situation for the shocked molecular clumps, whose emission occurs over much the same range but as very broad features. The extent of the high-velocity absorption suggests a shock velocity of 100 km/s for the expanding nebula.

  16. Renal water molecular diffusion characteristics in healthy native kidneys: assessment with diffusion tensor MR imaging.

    Directory of Open Access Journals (Sweden)

    Zhenfeng Zheng

    Full Text Available BACKGROUND: To explore the characteristics of diffusion tensor imaging (DTI and magnetic resonance (MR imaging in healthy native kidneys. METHODS: Seventy-three patients without chronic kidney disease underwent DTI-MRI with spin echo-echo planar (SE-EPI sequences accompanied by an array spatial sensitivity encoding technique (ASSET. Cortical and medullary mean, axial and radial diffusivity (MD, AD and RD, fractional anisotropy (FA and primary, secondary and tertiary eigenvalues (λ1, λ2, λ3 were analysed in both kidneys and in different genders. RESULTS: Cortical MD, λ2, λ3, and RD values were higher than corresponding medullary values. The cortical FA value was lower than the medullary FA value. Medullary λ1 and RD values in the left kidney were lower than in the right kidney. Medullary λ2, and λ3 values in women were higher than those in men. Medullary FA values in women were lower than those in men. Medullary FA (r = 0.351, P = 0.002 and λ1 (r = 0.277, P = 0.018 positively correlated with eGFR. Medullary FA (r = -0.25, P = 0.033 negatively correlated with age. CONCLUSIONS: Renal water molecular diffusion differences exist in human kidneys and genders. Age and eGFR correlate with medullary FA and primary eigenvalue.

  17. Combined role of molecular diffusion, mean streaming and helicity in the eddy diffusivity of short-correlated random flows

    CERN Document Server

    Afonso, Marco Martins; Gama, Sílvio

    2016-01-01

    We analytically investigate the effective-diffusivity tensor of a tracer particle in a fluid flow endowed with a short correlation time. By means of functional calculus and a multiscale expansion, we write down the main contributions to the eddy diffusivity due to each single physical effect and to their interplays. Namely, besides molecular diffusivity and a constant uniform mean streaming, we take into account the possibility for the (incompressible, Gaussian, stationary, homogeneous, isotropic) turbulent fluctuations to break parity invariance. With respect to the classical turbulence-driven diffusivity amplification for delta-correlated flows, we find that the presence of a short temporal correlation induces a diminution even when coupled with such effects, with two principal exceptions. Notably, the diffusivity is --- perturbatively --- enlarged not only by the helical contribution itself, but also by the interference between molecular diffusion and mean flow.

  18. A tentative study of the differences between Chinese-translated and non-translated English

    Institute of Scientific and Technical Information of China (English)

    杨乐

    2015-01-01

    Translated English is a distinctive variety of English with some special traits absent in non-translated English. This paper is an attempt to investigate the unique properties of Chinese-translated English, and categorize them in three aspects, namely, semantic, stylistic and syntactic, each of which is defined in light of non-translated English, and illustrated with proven data.

  19. Stokes-Einstein-Debye failure in molecular orientational diffusion: exception or rule?

    Science.gov (United States)

    Turton, David A; Wynne, Klaas

    2014-05-01

    The Stokes-Einstein-Debye (SED) expression is used routinely to relate orientational molecular diffusivity quantitatively to viscosity. However, it is well-known that Einstein's equations are derived from hydrodynamic theory for the diffusion of a Brownian particle in a homogeneous fluid and examples of SED breakdown and failure for molecular diffusion are not unusual. Here, using optical Kerr-effect spectroscopy to measure orientational diffusion for solutions of guanidine hydrochloride in water and mixtures of carbon disulfide with hexadecane, we show that these two contrasting systems each show pronounced exception to the SED relation and ask if it is reasonable to expect molecular diffusion to be a simple function of viscosity.

  20. A kinetic model for molecular diffusion through pores.

    Science.gov (United States)

    D'Agostino, Tommaso; Salis, Samuele; Ceccarelli, Matteo

    2016-07-01

    The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  1. Molecular Dynamics Simulation of Diffusion Coefficients of Oxygen, Nitrogen and Sodium Chloride in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    肖吉; 陆九芳; 陈健; 李以圭

    2001-01-01

    Molecular dynamics simulation has been performed to determine the infinite-dilution diffusion coefficients of oxygen and nitrogen, and the diffusion coefficients of NaCl in supercritical water from 703.2- 763.2 K and 30-45 MPa.The results obtained show that the diffusion coefficients in supercritical water increase with temperature, while decreasing with pressure. Nevertheless, the diffusion coefficients in supercritical water are much larger than those in normal water.

  2. Diffusion of Biomass Pyrolysis Products in H-ZSM-5 by Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; Kim, Seonah

    2017-01-12

    Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5 zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p-xylene:o-xylene:m-xylene almost equal to 83:3:1 at 700 K. Additionally, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.

  3. Invariant Fast Diffusion on the Surfaces of Ultrastable and Aged Molecular Glasses

    Science.gov (United States)

    Zhang, Yue; Fakhraai, Zahra

    2017-02-01

    Surface diffusion of molecular glasses is found to be orders of magnitude faster than bulk diffusion, with a stronger dependence on the molecular size and intermolecular interactions. In this study, we investigate the effect of variations in bulk dynamics on the surface diffusion of molecular glasses. Using the tobacco mosaic virus as a probe particle, we measure the surface diffusion on glasses of the same composition but with orders of magnitude of variations in bulk relaxation dynamics, produced by physical vapor deposition, physical aging, and liquid quenching. The bulk fictive temperatures of these glasses span over 35 K, indicating 13 to 20 orders of magnitude changes in bulk relaxation times. However, the surface diffusion coefficients on these glasses are measured to be identical at two temperatures below the bulk glass transition temperature Tg . These results suggest that surface diffusion has no dependence on the bulk relaxation dynamics when measured below Tg.

  4. Surface diffusion of molecular glasses: Material dependence and impact on physical stability

    Science.gov (United States)

    Ruan, Shigang; Zhang, Wei; Yu, Lian

    Surface diffusion coefficients have been measured for molecular glasses tris-naphthylbenzene (TNB) and PMMA oligomers by surface grating decay. Surface diffusion on TNB is vastly faster than bulk diffusion, by a factor of 107 at Tg, while the process is very slow on PMMA. Along with the previous results on o - terphenyl, nifedipine, indomethacin, and polystyrene oligomers, we find that surface diffusion slows down with increasing molecular size and intermolecular forces, whereas bulk diffusion has a weaker material dependence. The molecular glasses studied show fast crystal growth on the free surface. A general correlation is observed between the coefficient of surface diffusion and the velocity of surface crystal growth, indicating surface crystallization is supported by surface mobility. (Zhu, L., et al. Phys. Rev. Lett. 106 (2011): 256103; Zhang, W., et al. J. Phys. Chem. B 119 (2015): 5071-5078) Nsf.

  5. Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.

    Science.gov (United States)

    Liu, Xin; Schnell, Sondre K; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe; Bardow, André; Vlugt, Thijs J H

    2011-11-10

    A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic factor to convert MS into Fick diffusivities and vice versa, however, is usually difficult to extract from both simulations and experiments leaving a gap between theory and application. Here, we employ our novel method to compute the thermodynamic factor from small-scale density fluctuations in equilibrium MD simulations [Chem. Phys. Lett.2011, 504, 199-201]. Previously, this method was developed and validated for molecules with single interaction sites only. In this work, we applied this method to acetone-methanol and acetone-tetrachloromethane liquid mixtures and show that the method also works well in these more complex systems. This provides the missing step to extract Fick diffusion coefficients directly from equilibrium MD simulations. The computed Fick diffusivities of acetone-methanol and acetone-tetrachloromethane mixtures are in excellent agreement with experimental values. The suggested framework thus provides an efficient route to model diffusion in liquids on the basis of a consistent molecular picture.

  6. Chemistry in Magnetohydrodynamic Shock Waves in Diffuse Molecular Clouds

    Science.gov (United States)

    Peimbert, Antonio

    1998-09-01

    Absorption observations of the CH+ molecule with column densities of up to 1014 cm-2 in diffuse molecular clouds in many lines of sight are reviewed, and compared to the reddening and to abundances and velocity shifts of molecules like CH. Special attention is placed on the observations of the line of sight towards ς Ophiuchi where high quality observations of many chemical species are available. The problem of the required CH+ is described, and many formation mechanisms from the literature are reviewed, finding that none of them is particularly apt at describing the observations towards ς-Oph. Two fluid J-type shock models are studied as an alternative. The necessary conditions for their formation are discussed, and it is shown how they are expected to be present widely in the interstellar medium. Plane parallel numerical integrations, for the particular case in which the magnetic field is perpendicular to the shock velocity, are employed to study the region of phase-space of initial conditions that will produce 2 fluid shocks. A chemical network is developed and formation of key molecules like CH+, CH and OH, along with the excited roto-vibrational levels of H2, are studied under the shock dynamics. These models are then compared to the observations of the different lines of sight, showing they are capable of reproducing the features of the observations towards most of those clouds. An attempt to model the line of sight towards ς-Oph is done, finding that a shock with a shock speed vs = 9.0km/s going through a cloud with a density of nH = 14cm-3 with a magnetic field of B = 4.7μG does a reasonable job at satisfying most of the observations with the exception of the highest rotational excited states of molecular hydrogen for which observations are available. There is a small family of solutions capable of explaining the observed results which make specific predictions for the velocity profiles of the H2 lines of various excited levels. New observations with

  7. Crystal structural and diffusion property in titanium carbides: A molecular dynamics study

    Science.gov (United States)

    Lv, Yanan; Gao, Weimin

    2016-09-01

    Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.

  8. Simulation of dimer diffusion on metal fcc (001)surfaces by molecular dynamics

    Institute of Scientific and Technical Information of China (English)

    LIU; Qingwei; ZHUANG; Jun

    2004-01-01

    We study systematically the dimer diffusion on metal fcc (001) surfaces through molecular dynamics calculations based on embedded atom method. Besides the conventional hopping and exchange mechanisms, some other interesting diffusion mechanisms are observed, such as the exchange rotation mechanism, the cooperative hopping mechanism, and the cooperative exchange mechanism. On the different kinds of metal surfaces, we find that not only the dominant diffusion mechanism but also the physical model for the exchange mechanism is different.

  9. Tested Demonstrations: Diffusion of Gases--Kinetic Molecular Theory of Gases.

    Science.gov (United States)

    Gilbert, George L., Ed.

    1984-01-01

    Provided are procedures and list of materials needed to demonstrate that the pressure inside a container with a porous surface can be changed due to the rate of diffusion of low molecular weight gases. Typical results obtained are included. (JN)

  10. Developing a Macroscopic Mechanistic Model for Low Molecular Weight Diffusion through Polymers in the Rubbery State

    DEFF Research Database (Denmark)

    Martinez-Lopez, Brais; Huguet, P.; Gontard, N.

    2016-01-01

    frequency of their bonds by reconstructing their theoretical spectra. Results showed that the use of molecular descriptors that take into account flexibility rather than the most stable conformation of the diffusing molecules may improve the description of the diffusion behavior caused by variations...... in shape and size of the free volumes of the polymeric matrix in the rubbery state....

  11. The use of parentheses in Arabic translated and non-translated texts

    Directory of Open Access Journals (Sweden)

    El-Hussein Ali Yehia Ali

    2012-07-01

    Full Text Available The study aims at comparing the functions of parentheses in Arabic translated and non-translated texts. The study is carried out across genres; it includes texts from science, medicine, education, computers, and literary criticism. The texts constitute two corpora: a monolingual comparable corpus and bilingual parallel corpus. The monolingual comparable corpus is used to identify differences between Arabic translated and non-translated language in the uses of parentheses. The findings are then tested against a bilingual parallel corpus consisting of original English texts and their translations into Arabic. The study looks at the qualitative and quantitative differences between the uses of parentheses in translated and non-translated Arabic. Furthermore, the paper does not deal only with translation anomalies, but focuses as well on correct parallels. The paper can be seen then as a guide on the uses of parentheses in Arabic and in translation between Arabic and English.

  12. A dirty window diffuse and translucent molecular gas in the interstellar medium

    CERN Document Server

    Magnani, Loris

    2017-01-01

    This book provides an introduction to the physics of interstellar gas in the Galaxy. It deals with the diffuse interstellar medium which supplies a complex environment for exploring the neutral gas content of a galaxy like the Milky Way and the techniques necessary for studying this non-stellar component. After an initial exposition of the phases of the interstellar medium and the role of gas in a spiral galaxy, the authors discuss the transition from atomic to molecular gas. They then consider basic radiative transfer and molecular spectroscopy with particular emphasis on the molecules useful for studying low-density molecular gas. Observational techniques for investigating the gas and the dust component of the diffuse interstellar medium throughout the electromagnetic spectrum are explored emphasizing results from the recent Herschel and Planck missions. A brief exposition on dust in the diffuse interstellar medium is followed by a discussion of molecular clouds in general and high-latitude molecular clouds...

  13. Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution%Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution

    Institute of Scientific and Technical Information of China (English)

    曾建平; 王爱民; 贡雪东; 陈景文; 陈松; 薛锋

    2012-01-01

    Under different temperatures and concentrations, the diffusion of Vitamin C (VC) in water solution was exam- ined by molecular dynamics simulation. The diffusion coefficients were calculated based on the Einstein equation. The influences of temperature, concentration, and simulation time on the diffusion coefficient were discussed. The results showed that at higher temperature and lower concentration the normal diffusions appear relatively late, but the linear range of mean square displacement curves continues longer than that at lower temperature and higher concentration. At the same temperature, the normal diffusion time increases and the diffusion coefficient decreases as the simulation concentration increases. These simulation results are in good agreement with experiments. Analyses of the pair correlation functions of the simulation systems showed that hydrogen bonds are mainly formed be- tween the hydrogen atoms of VC molecules and oxygen atoms of H20 molecules, rather than between the O atoms of VC molecules and H atoms of H20 molecules. The diffusion coefficient is higher as the interaction between water molecules and VC molecules is stronger when VC concentration is lower. The water in the model systems affects the diffusion of VC molecules by the short-range repulsion of O(H20)-O(H20) pairs and the non-bond interaction of H(H20)-H(H20) pairs. The short-range repulsion of O(H20)-O(H20) pairs is greater when VC concentration is higher, the diffusion of VC is weaker. The greater the non-bond interaction of H(H20)-H(H20) pairs is, the higher the VC diffusion is. It is expected that this study can provide a theoretical direction for the experiments on the mass transfer of VC in water solution.

  14. Diffusion of Pt in molecular beam epitaxy grown ZnSe

    Science.gov (United States)

    Slotte, J.; Salonen, R.; Ahlgren, T.; Räisänen, J.; Rauhala, E.; Uusimaa, P.

    1998-05-01

    Diffusion of platinum in zinc selenide has been studied by the use of the 4He and 12C ion backscattering techniques. The samples were thin films grown by molecular beam epitaxy on GaAs (100) epitaxial layers followed by evaporation of platinum and annealing in the temperature range 500-800 °C. The diffusion coefficients were determined by the fitting of a concentration independent solution of the diffusion equation to the experimental depth profiles. The activation energy and the pre-exponential factor of the diffusion process were found to be 1.7 eV and 6.4×10-6 cm2/s, respectively.

  15. Diffusion measurements for molecular capsules: pulse sequences effect on water signal decay.

    Science.gov (United States)

    Avram, Liat; Cohen, Yoram

    2005-04-20

    Diffusion NMR and, more recently, diffusion ordered spectroscopy (DOSY) are gaining popularity as efficient tools for the characterization of supramolecular systems in solution. Here, using diffusion NMR of hydrogen-bond molecular capsules, we demonstrate that the use of different diffusion sequences may have a dramatic effect on exchanging peaks. In fact, we found that the signal decay of the water peak in [(1a)(6)(H(2)O)(8)] is monoexponential in the pulsed gradient spin-echo (PGSE) and stimulated echo (PGSTE) sequences and biexponential in the longitudinal eddy current delay (LED) and the bipolar longitudinal eddy current delay (BPLED) sequences, routinely used in modern DOSY experiments. By performing these diffusion measurements on molecular capsules, in which water is not part of the molecular capsules, we demonstrate that this phenomenon is observed only for water molecules that exchange between two sites that differ considerably in their diffusion coefficients. Degeneration of the LED or the BPLED sequences into PGSTE-type sequences by shortening the te period resulted in the disappearance of the extra slow diffusing component. The origin, as well as the implications of the different results obtained from conventional diffusion sequences, such as the PGSE and PGSTE as compared with the LED and BPLED sequences generally used in DOSY experiments, are briefly discussed.

  16. The static dipole polarizabilities of helium and molecular hydrogen by differential diffusion Monte Carlo

    NARCIS (Netherlands)

    Huiszoon, C.; Briels, W.J.

    1993-01-01

    The differential diffusion Monte Carlo method, involving correlated random walks, is used to calculate the static polarizabilities of molecular hydrogen and helium by application of a finite electrostatic field. The results are for molecular hydrogen (alpha)=4.60(3) au; (alpha)|=6.38(5) au; for heli

  17. Transport diffusion in one dimensional molecular systems: Power law and validity of Fick's law

    Science.gov (United States)

    Xu, Zhi-cheng; Zheng, Dong-qin; Ai, Bao-quan; Hu, Bambi; Zhong, Wei-rong

    2015-10-01

    The transport diffusion in one-dimensional molecular systems is investigated through non-equilibrium molecular dynamics and Monte Carlo methods. We have proposed the power law relationship of the transport diffusion coefficient with the temperature, the mass and the transport length, D* ∝ T*m*-1L*β, where β equals to 0.8 for small systems and zero for large systems. It is found that Fick's law is valid in long transport length but invalid in short transport length. Our results can provide a new perspective for understanding the microscopic mechanism of the molecular transport phenomena in low-dimensional systems.

  18. Molecular dynamics simulation on diffusion properties of Pb-Mg alloy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A new method to calculate mutual-diffusion coefficients of the binary alloy has been proposed in this report.At first self-diffusion coefficient of the constituent element was calculated using molecular dynamics method,thermodynamic factor of the alloy was got with the NRTL (non-random-two-liquid) equation,then mutual-diffusion coefficient was obtained with Darken formula.Using this method the mutual-diffusion coefficient of Pb-Mg alloy with different Pb content was calculated.The calculated values were compared with the available experimental ones and the reason of the maximal mutual-diffusion coefficient appearing at 33.3 at.%Pb was discussed.Partial pair correlation function and partial coordination number were calculated to analyze the effect of the melt structure on mutual-diffusion coefficient.

  19. Diffusion coefficients of molecular iodine in aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Cantrel, L. [CEA Cadarache, Saint Paul lez Durance (France). Inst. de Protection et de Surete Nucleaire; Chaouche, R.; Chopin-Dumas, J. [Ecole Nationale Superieure de Syntheses, Marseille (France)

    1997-01-01

    In the event of a severe accident on a light water nuclear reactor (LWR), resulting in overheating of the core, the fission products would be released into the containment building. Among the fission products, iodine represents a biological hazard for the environment by reason of the {sup 131}I radioactive isotope. As iodine is a highly reactive and volatile compound, it is involved in mass transfer from the liquid phase to the gas phase of the containment vessel. In order to determine the quantity of iodine present in the gas phase, it is necessary to know the diffusion coefficient of iodine in water at several temperatures. The diffusion coefficients of iodine in 0.075 mol/dm{sup 3} sulfuric acid have been determined between 298 K and 358 K, by measuring the limiting reduction currents at a platinum rotating disk electrode. A Stokes-Einstein relation is verified over the range of temperature studied. The experimental value obtained at 298 K is compared with some available relations for the estimation of diffusion coefficients at infinite dilution. The agreement is good.

  20. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  1. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

    Science.gov (United States)

    Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.

    2013-07-01

    The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.

  2. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    Science.gov (United States)

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

  3. Molecular simulation of adsorption and diffusion of hydrogen in metal-organic frameworks.

    Science.gov (United States)

    Yang, Qingyuan; Zhong, Chongli

    2005-06-23

    Metal-organic frameworks (MOFs) are thought to be a set of promising hydrogen storage materials; however, little is known about the interactions between hydrogen molecules and pore walls as well as the diffusivities of hydrogen in MOFs. In this work, we performed a systematic molecular simulation study on the adsorption and diffusion of hydrogen in MOFs to provide insight into molecular-level details of the underlying mechanisms. This work shows that metal-oxygen clusters are preferential adsorption sites for hydrogen in MOFs, and the effect of the organic linkers becomes evident with increasing pressure. The hydrogen storage capacity of MOFs is similar to carbon nanotubes, which is higher than zeolites. Diffusion of hydrogen in MOFs is an activated process that is similar to diffusion in zeolites. The information derived in this work is useful to guide the future rational design and synthesis of tailored MOF materials with improved hydrogen adsorption capability.

  4. Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics

    Directory of Open Access Journals (Sweden)

    COELHO L. A. F.

    1999-01-01

    Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.

  5. Glitters of warm H2 in cold diffuse molecular gas

    NARCIS (Netherlands)

    Falgarone, Edith; Beichman, Chaz; Boulanger, Francois; Combes, Francoise; Gry, Cecile; Helou, Georges; Laureijs, Rene; Pineau Des Forets, Guillaume; Valentijn, Edwin; Verstraete, Laurent

    2004-01-01

    Cold molecular hydrogen, a possibly dominant gas fraction in galaxies, does not radiate due to the symmetry and small moment of inertia of the molecule. The only tracers of cold H2, the rotational lines of CO and dust thermal emission operate only in metal-rich environments. By detecting the lowest

  6. How Effective Are Simulated Molecular-level Experiments for Teaching Diffusion and Osmosis?

    OpenAIRE

    Meir, Eli; Perry, Judith; Stal, Derek; Maruca, Susan; Klopfer, Eric

    2005-01-01

    Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger et al., 2001; and results herein). Students have deep-rooted misconceptions about how diffusion and osmosis work, especially at the molecular level. We hypothesized that this might be in part due t...

  7. Application of the Clustering Method in Molecular Dynamics Simulation of the Diffusion Coefficient

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Using molecular dynamics (MD) simulation, the diffusion of oxygen, methane, ammonia and carbon dioxide in water was simulated in the canonical NVT ensemble, and the diffusion coefficient was analyzed by the clustering method. By comparing to the conventional method (using the Einstein model) and the differentiation-interval variation method, we found that the results obtained by the clustering method used in this study are more close to the experimental values. This method proved to be more reasonable than the other two methods.

  8. Influence of molecular diffusion on alignment of vector fields: Eulerian analysis

    Science.gov (United States)

    Gonzalez, M.

    2016-11-01

    The effect of diffusive processes on the structure of passive vector and scalar gradient fields is investigated by analyzing the corresponding terms in the orientation and norm equations. Numerical simulation is used to solve the transport equations for both vectors in a two-dimensional, parameterized model flow. The study highlights the role of molecular diffusion in the vector orientation process and shows its subsequent action on the geometric features of vector fields.

  9. Molecular dynamics simulations of gas diffusion in metal-organic frameworks: argon in CuBTC.

    Science.gov (United States)

    Skoulidas, Anastasios I

    2004-02-11

    The class of coordination polymers known as metal-organic frameworks (MOFs) has three-dimensional porous structures that are considered as a promising alternative to zeolites and other nanoporous materials for catalysis, gas adsorption, and gas separation applications. In this paper, we present the first study of gas diffusion inside an MOF and compare the observed diffusion to known behaviors in zeolites. Using grand canonical Monte Carlo and equilibrium molecular dynamics, we calculate the adsorption isotherm and self-, corrected, and transport diffusivities for argon in the CuBTC metal-organic framework. Our results indicate that diffusion of Ar in CuBTC is very similar to Ar diffusion in silica zeolites in magnitude, concentration, and temperature dependence. This conclusion appears to apply to a broad range of MOF structures.

  10. Enhanced Diffusion of Molecular Motors in the Presence of Adenosine Triphosphate and External Force

    Science.gov (United States)

    Shinagawa, Ryota; Sasaki, Kazuo

    2016-06-01

    The diffusion of a molecular motor in the presence of a constant external force is considered on the basis of a simple theoretical model. The motor is represented by a Brownian particle moving in a series of parabolic potentials placed periodically on a line, and the potential is switched stochastically from one parabola to another by a chemical reaction, which corresponds to the hydrolysis or synthesis of adenosine triphosphate (ATP) in motor proteins. It is found that the diffusion coefficient as a function of the force exhibits peaks. The mechanism of this diffusion enhancement and the possibility of observing it in F1-ATPase, a biological rotary motor, are discussed.

  11. Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations.

    Science.gov (United States)

    Ryabov, Yaroslav; Clore, G Marius; Schwieters, Charles D

    2012-01-21

    We present a general formalism for the computation of orientation correlation functions involving a molecular system undergoing rotational diffusion in the presence of transitions between discrete conformational states. In this formalism, there are no proscriptions on the time scales of conformational rearrangement relative to that for rotational diffusion, and the rotational diffusion tensors of the different states can be completely arbitrary. Although closed-form results are limited to the frequency domain, this is generally useful for many spectroscopic observables as the result allows the computation of the spectral density function. We specialize the results for the computation of the frequency-domain correlation function associated with the NMR relaxation.

  12. The study of Cu/Nb interface diffusion using molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Ivan V. Nelasov

    2016-06-01

    Full Text Available The peculiarities of interfacial boundary diffusion where the boundary goes between nonmiscible metals with body-centered cubic (BCC and face-centered cubic (FCC lattices have been studied taking, as a case in point, the Cu/Nb system, and using the molecular dynamics method. The diffusion atomic displacements were shown to occur mainly near the mismatch dislocations and their intersections. The diffusion of the high-melting component was found to be characterized by high anisotropy with the predominant atomic displacement along the dense-packed direction in the interfacial boundary plane being common to FCC and BCC lattices with the Kurdyumov–Sachs mutual orientation.

  13. Molecular dynamics simulations of NMR relaxation and diffusion of bulk hydrocarbons and water

    Science.gov (United States)

    Singer, Philip M.; Asthagiri, Dilip; Chapman, Walter G.; Hirasaki, George J.

    2017-04-01

    Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1,2 in the fast motion regime where T1 =T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.

  14. Diffusion of Molecular Diagnostic Lung Cancer Tests: A Survey of German Oncologists

    Directory of Open Access Journals (Sweden)

    Julius Alexander Steffen

    2014-03-01

    Full Text Available This study was aimed at examining the diffusion of diagnostic lung cancer tests in Germany. It was motivated by the high potential of detecting and targeting oncogenic drivers. Recognizing that the diffusion of diagnostic tests is a conditio sine qua non for the success of personalized lung cancer therapies, this study analyzed the diffusion of epidermal growth factor receptor (EGFR and anaplastic lymphoma kinase (ALK tests in Germany. Qualitative and quantitative research strategies were combined in a mixed-method design. A literature review and subsequent Key Opinion Leader interviews identified a set of qualitative factors driving the diffusion process, which were then translated into an online survey. The survey was conducted among a sample of 961 oncologists (11.34% response rate. The responses were analyzed in a multiple linear regression which identified six statistically significant factors driving the diffusion of molecular diagnostic lung cancer tests: reimbursement, attitude towards R&D, information self-assessment, perceived attitudes of colleagues, age and test-pathway strategies. Besides the important role of adequate reimbursement and relevant guidelines, the results of this study suggest that an increasing usage of test-pathway strategies, especially in an office-based setting, can increase the diffusion of molecular diagnostic lung cancer tests in the future.

  15. Diffusion of molecular diagnostic lung cancer tests: a survey of german oncologists.

    Science.gov (United States)

    Steffen, Julius Alexander

    2014-03-21

    This study was aimed at examining the diffusion of diagnostic lung cancer tests in Germany. It was motivated by the high potential of detecting and targeting oncogenic drivers. Recognizing that the diffusion of diagnostic tests is a conditio sine qua non for the success of personalized lung cancer therapies, this study analyzed the diffusion of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) tests in Germany. Qualitative and quantitative research strategies were combined in a mixed-method design. A literature review and subsequent Key Opinion Leader interviews identified a set of qualitative factors driving the diffusion process, which were then translated into an online survey. The survey was conducted among a sample of 961 oncologists (11.34% response rate). The responses were analyzed in a multiple linear regression which identified six statistically significant factors driving the diffusion of molecular diagnostic lung cancer tests: reimbursement, attitude towards R&D, information self-assessment, perceived attitudes of colleagues, age and test-pathway strategies. Besides the important role of adequate reimbursement and relevant guidelines, the results of this study suggest that an increasing usage of test-pathway strategies, especially in an office-based setting, can increase the diffusion of molecular diagnostic lung cancer tests in the future.

  16. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  17. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  18. Apparent Rate Constant for Diffusion-Controlled Three molecular (catalytic) reaction

    OpenAIRE

    Burlatsky, S. F.; Moreau, M

    1996-01-01

    We present simple explicit estimates for the apparent reaction rate constant for three molecular reactions, which are important in catalysis. For small concentrations and $d> 1$, the apparent reaction rate constant depends only on the diffusion coefficients and sizes of the particles. For small concentrations and $d\\le 1$, it is also time -- dependent. For large concentrations, it gains the dependence on concentrations.

  19. Molecular Simulation of Solubility and Diffusion of Hindered-Amine Light Stabilizers (HALS) in Polyethylene

    Science.gov (United States)

    Nath, Shyamal K.; de Pablo, Juan J.; Debellis, Anthony

    1997-03-01

    Hindered-amine light stabilizers (HALS) are some of the most common additives employed for prevention of photooxidation in polymers. One of the major problems encountered in polymer stabilization is that of physical loss of the additives. Such loss limits the life of the polymer and, more importantly, it can have serious consequences when the polymer is to be used for food packaging and other toxicity-sensitive applications. The loss of additives is related to their solubility and diffusion coefficient in polymers. In this work, a novel Monte Carlo formalism is proposed to determine the solubility of commercially available HALS (Tinuvin 770) in polyethylene. Diffusion coefficients is also determined by conventional molecular dynamics simulations. We report results for the solubility and diffusion of HALS in polyethylene as a function of temperature, pressure and density. We also examine the effects of branching on these quantities, and we use our findings to propose HALS structures with attractive compatibility and diffusive characteristics.

  20. Molecular dynamics simulation of tensile behavior of diffusion bonded Ni/Al nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Zhenjiang; Yan, Yongda; Yan, Jiuchun; Zhang, Junjie; Sun, Tao [Harbin Institute of Technology, Harbin (China)

    2013-01-15

    Interfaces play key roles in determining mechanical properties of materials. In current work we perform molecular dynamics simulations of diffusion bonding to evaluate the effect of temperature on the morphology of the Ni/Al interface and the strength of the diffusion bonded Ni/Al nanowires. The centro-symmetry parameter is adopted to identify defect atoms generated. Simulation results show that the thickness of the Ni/Al interface has strong dependence on the temperature of diffusion bonding. Following uniaxial tension tests indicate that the yield strength of Ni/Al nanowires is smaller than both the single crystalline Ni and Al nanowires, because of the Ni/Al interface acting as dislocation source and the mobilization of pre-existing dislocations at high temperature. It is shown that the mechanical properties of diffusion bonded Ni/Al nanowires strongly depend on the temperature.

  1. Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes

    Science.gov (United States)

    Kondratyuk, Nikolay D.; Norman, Genri E.; Stegailov, Vladimir V.

    2016-11-01

    Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.

  2. On the Statistics of Reaction-Diffusion Simulations for Molecular Communication

    CERN Document Server

    Noel, Adam; Schober, Robert

    2015-01-01

    A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular diffusion, are well understood. However, the coupling of multiple interactions can impede closed-form analysis, such that simulations are required to determine the statistics. This paper compares the statistics of molecular reaction-diffusion simulation models from the perspective of molecular communication systems. Microscopic methods track the location and state of every molecule, whereas mesoscopic methods partition the environment into virtual containers that hold molecules. The properties of each model are described and compared with a hybrid of both models. Simulation results also assess the accuracy of Poisson and Gaussian approximations of the underlying Binomial statistics.

  3. Diffusion of light gases in 6FDA/BPDA-DAM Carbon Molecular Sieve membranes by Pulsed Field Gradient NMR

    OpenAIRE

    Mueller, Robert; Kanungo, Rohit; Kiyono-Shimobe, Mayumi; Koros, William J.; Vasenkov, Sergey

    2015-01-01

    In this paper, we demonstrate the potential of pulsed field gradient (PFG) NMR spectroscopy to reveal detailed knowledge of self-diffusion of light gases and light gas mixtures in carbon molecular sieve membranes on small length scales. PFG NMR is used to investigate intra-membrane diffusion of carbon dioxide and methane for a broad range of temperatures and mean square displacements in a carbon molecular sieve membrane derived from a 6FDA/BPDA-DAM polyimide film. Diffusion is investigated...

  4. Hydrogen in diffuse molecular clouds in the Milky Way. Atomic column densities and molecular fraction along prominent lines of sight

    Science.gov (United States)

    Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.

    2017-03-01

    Context. Recent submillimeter and far-infrared wavelength observations of absorption in the rotational ground-state lines of various simple molecules against distant Galactic continuum sources have opened the possibility of studying the chemistry of diffuse molecular clouds throughout the Milky Way. In order to calculate abundances, the column densities of molecular and atomic hydrogen, H i, must be known. Aims: We aim at determining the atomic hydrogen column densities for diffuse clouds located on the sight lines toward a sample of prominent high-mass star-forming regions that were intensely studied with the HIFI instrument onboard Herschel. Methods: Based on Jansky Very Large Array data, we employ the 21 cm H i absorption-line technique to construct profiles of the H i opacity versus radial velocity toward our target sources. These profiles are combined with lower resolution archival data of extended H i emission to calculate the H i column densities of the individual clouds along the sight lines. We employ Bayesian inference to estimate the uncertainties of the derived quantities. Results: Our study delivers reliable estimates of the atomic hydrogen column density for a large number of diffuse molecular clouds at various Galactocentric distances. Together with column densities of molecular hydrogen derived from its surrogates observed with HIFI, the measurements can be used to characterize the clouds and investigate the dependence of their chemistry on the molecular fraction, for example. The data sets are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/600/A2

  5. Diffusion and separation of CH4/N2 in pillared graphene nanomaterials: A molecular dynamics investigation

    Science.gov (United States)

    Zhou, Sainan; Lu, Xiaoqing; Wu, Zhonghua; Jin, Dongliang; Guo, Chen; Wang, Maohuai; Wei, Shuxian

    2016-09-01

    Diffusion and separation of CH4/N2 in pillared graphene were investigated by molecular dynamics. The pillared graphene with (6, 6) carbon nanotube (CNT) exhibited the higher diffusion and selectivity of CH4 over N2 than that with (7, 7) CNT due to the cooperative effect of pore topological characteristics and interaction energy. The stronger interaction facilitated CH4 to enter CNT prior to N2, and higher pressure promoted CH4 to pass CNT more easily. The relative concentrations profiles showed that CH4 reached equilibrium state faster than N2 at low pressure. Our results highlight potential use of pillared graphene in gas purification and separation.

  6. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    Institute of Scientific and Technical Information of China (English)

    Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; Muhammad Ismail; Hafeez Ullah; Yongqing Cai; M Arshad Javid; Ejaz Ahmad; S A Ahmad

    2016-01-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion;whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process;however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.

  7. molecular dynamics study of the gallium vacancy diffusion in GaAs

    Science.gov (United States)

    Bockstedte, Michel; Scheffler, Matthias

    1996-03-01

    Experimentally(T. Y. Tan et al.), Rev. Solid State Mater. Sci. 17, 47 (1991). it is well established that cation self-diffusion in GaAs proceeds by gallium vacancies. An analysis(J-L. Rouviere et al.), Phys. Rev. Lett. 68, 2798 (1992). of diffusion experiments yielded an exceptionally high value for the formation entropy of 32.9 kB and a migration energy barrier of 1.7 eV. The physics underlying this result is quite puzzling. Even the question whether the diffusion involves only the gallium sublattice or whether it proceeds by nearest neighbor hops is unanswered. Employing ab initio molecular dynamics simulations we analyze the motion of atoms and evaluate the free energy of vacancy formation and the diffusion constant. For the Ga vacancy we obtain a value for the formation entropy of 8 kB - comparable to that of the vacancy in silicon - but significantly lower than that extracted from experimentfootnotemark[2]. Based on our studies we therefore dare to question the experimental analysis. The calculated motion of a gallium vacancy close to the melting temperature of GaAs and the analysis of the different diffusion events exclude a diffusion mechanism by nearest neighbor hops. We discuss the microscopic picture of the second nearest neighbor hop, and determine its rate constant.

  8. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    Science.gov (United States)

    Muhammad, Imran; Fayyaz, Hussain; Muhammad, Rashid; Muhammad, Ismail; Hafeez, Ullah; Yongqing, Cai; M Arshad, Javid; Ejaz, Ahmad; S, A. Ahmad

    2016-07-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.

  9. Speciation of copper diffused in a bi-porous molecular sieve

    Energy Technology Data Exchange (ETDEWEB)

    Huang, C.-H. [Department of Environmental Engineering, National Cheng Kung University, Tainan 70101, Taiwan (China); Paul Wang, H., E-mail: wanghp@mail.ncku.edu.t [Department of Environmental Engineering, National Cheng Kung University, Tainan 70101, Taiwan (China); Sustainable Environmental Research Center, National Cheng Kung University, Tainan 70101, Taiwan (China); Wei, Y.-L. [Department of Environmental Science and Engineering, Tunghai University, Taichung 40704, Taiwan (China); Chang, J.-E. [Department of Environmental Engineering, National Cheng Kung University, Tainan 70101, Taiwan (China); Sustainable Environmental Research Center, National Cheng Kung University, Tainan 70101, Taiwan (China)

    2010-07-21

    To better understand diffusion of copper in the micro- and mesopores, speciation of copper in a bi-porous molecular sieve (BPMS) possessing inter-connecting 3-D micropores (0.50-0.55 nm) and 2-D mesopores (4.1 nm) has been studied by X-ray absorption near edge structure (XANES) spectroscopy. It is found that about 77% (16% of CuO nanoparticles and 61% of CuO clusters) and 23% (CuO{sub ads}) of copper can be diffused into the meso- and micropores, respectively, in the BPMS. At least two diffusion steps in the BPMS may be involved: (i) free diffusion of copper in the mesopores and (ii) diffusion-controlled copper migrating into the micropores of the BPMS. The XANES data also indicate that diffusion rate of copper in the BPMS (4.68x10{sup -5} g/s) is greater than that in the ZSM-5 (1.11x10{sup -6} g/s) or MCM-41 (1.17x10{sup -5} g/s).

  10. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

    Directory of Open Access Journals (Sweden)

    Le Novère Nicolas

    2010-03-01

    Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.

  11. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)

    2015-08-18

    Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  12. Molecular dynamics simulation of hydrogen dissolution and diffusion in a tungsten grain boundary

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yi; Shu, Xiaolin; Liu, Yi-Nan; Lu, Guang-Hong, E-mail: lgh@buaa.edu.cn

    2014-12-15

    We employ a classic molecular dynamics method to investigate the dissolution and diffusion properties of hydrogen (H) in a Σ5(3 1 0) tilt grain boundary (GB). A maximum binding energy of 2.5 eV and a diffusion barrier of 1.65 eV indicate that GB plays an important role in H trapping. Dynamic simulations with temperature ranging from 600 K to 1200 K verify the diffusion and the aggregation of H in the GB are closely associated with the temperature. Pair radius distribution function analysis suggests a high local GB concentration of H such as 30% at 900 K can lead to a disordered GB structure.

  13. Molecular simulation of translational and rotational diffusion of Janus nanoparticles at liquid interfaces

    CERN Document Server

    Rezvantalab, Hossein; Shojaei-Zadeh, Shahab

    2014-01-01

    We perform molecular dynamics simulations to understand the translational and rotational diffusion of Janus nanoparticles at the interface between two immiscible fluids. Considering spherical particles with different affinity to fluid phases, both their dynamics as well as the fluid structure around them are evaluated as a function of particle size, amphiphilicity, fluid density, and interfacial tension. We show that as the particle amphiphilicity increases due to enhanced wetting of each side with its favorite fluid, the rotational thermal motion decreases. Moreover, the in-plane diffusion of nanoparticles at the interface becomes slower for more amphiphilic particles, mainly due to formation of a denser adsorption layer. The particles induce an ordered structure in the surrounding fluid that becomes more pronounced for highly amphiphilic nanoparticles, leading to increased resistance against nanoparticle motion. A similar phenomenon is observed for homogeneous particles diffusing in bulk upon increasing the...

  14. A comparative molecular dynamics study of diffusion of -decane and 3-methyl pentane in Y zeolite

    Indian Academy of Sciences (India)

    F G Pazzona; B J Borah; P Demontis; G B Suffritti; S Yashonath

    2009-09-01

    Molecular dynamics simulations are reported on the structure and dynamics of -decane and 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We have also analysed trajectory to obtain diffusivity and velocity autocorrelation function (VACF). Surprisingly, the diffusivity of 3-methylpentane which is having larger cross-section perpendicular to the long molecular axis is higher than -decane at 300 K. Activation energies have been obtained from simulations performed at 200 K, 300 K, 350 K, 400 K and 450 K in the NVE ensemble. These results can be understood in terms of the previously known levitation effect. Arrhenious plot has higher value of slope for -decane (5.9 kJ/mol) than 3-methylpentane (3.7 kJ/mol) in agreement with the prediction of levitation effect.

  15. On the Symmetry of Molecular Flows Through the Pipe of an Arbitrary Shape (I) Diffusive Reflection

    Science.gov (United States)

    Kusumoto, Yoshiro

    Molecular gas flows through the pipe of an arbitrary shape is mathematically considered based on a diffusive reflection model. To avoid a perpetual motion, the magnitude of the molecular flow rate must remain invariant under the exchange of inlet and outlet pressures. For this flow symmetry, the cosine law reflection at the pipe wall was found to be sufficient and necessary, on the assumption that the molecular flux is conserved in a collision with the wall. It was also shown that a spontaneous flow occurs in a hemispherical apparatus, if the reflection obeys the n-th power of cosine law with n other than unity. This apparatus could work as a molecular pump with no moving parts.

  16. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

    Energy Technology Data Exchange (ETDEWEB)

    Kekenes-Huskey, P. M., E-mail: pkekeneshuskey@ucsd.edu [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Gillette, A. K. [Department of Mathematics, University of Arizona, Tucson, Arizona 85721-0089 (United States); McCammon, J. A. [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Department of Chemistry, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0636 (United States)

    2014-05-07

    The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute “obstacles” and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as “buffers” that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events

  17. Insights into diffusion of gases in zeolites gained from molecular dynamics simulations

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2008-01-01

    The Maxwell-Stefan (M-S) diffusivities Đi of a variety of gases (He, Ne, Ar, Kr, H2, N2, CO2, CH4) in six different all-silica zeolite structures (MFI, AFI, FAU, CHA, DDR, and LTA) have been determined using molecular dynamics (MD) simulations for a range of molar loadings, qi. In all cases the Đi

  18. Insights into diffusion of gases in zeolites gained from molecular dynamics simulations

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2008-01-01

    The Maxwell-Stefan (M-S) diffusivities Đi of a variety of gases (He, Ne, Ar, Kr, H2, N2, CO2, CH4) in six different all-silica zeolite structures (MFI, AFI, FAU, CHA, DDR, and LTA) have been determined using molecular dynamics (MD) simulations for a range of molar loadings, qi. In all cases the Đi a

  19. Analytical solutions for a soil vapor extraction model that incorporates gas phase dispersion and molecular diffusion

    Science.gov (United States)

    Huang, Junqi; Goltz, Mark N.

    2017-06-01

    To greatly simplify their solution, the equations describing radial advective/dispersive transport to an extraction well in a porous medium typically neglect molecular diffusion. While this simplification is appropriate to simulate transport in the saturated zone, it can result in significant errors when modeling gas phase transport in the vadose zone, as might be applied when simulating a soil vapor extraction (SVE) system to remediate vadose zone contamination. A new analytical solution for the equations describing radial gas phase transport of a sorbing contaminant to an extraction well is presented. The equations model advection, dispersion (including both mechanical dispersion and molecular diffusion), and rate-limited mass transfer of dissolved, separate phase, and sorbed contaminants into the gas phase. The model equations are analytically solved by using the Laplace transform with respect to time. The solutions are represented by confluent hypergeometric functions in the Laplace domain. The Laplace domain solutions are then evaluated using a numerical Laplace inversion algorithm. The solutions can be used to simulate the spatial distribution and the temporal evolution of contaminant concentrations during operation of a soil vapor extraction well. Results of model simulations show that the effect of gas phase molecular diffusion upon concentrations at the extraction well is relatively small, although the effect upon the distribution of concentrations in space is significant. This study provides a tool that can be useful in designing SVE remediation strategies, as well as verifying numerical models used to simulate SVE system performance.

  20. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    Science.gov (United States)

    Liao, Rui-Jin; Zhu, Meng-Zhao; Yang, Li-Jun; Zhou, Xin; Gong, Chun-Yan

    2011-03-01

    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  1. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

    Science.gov (United States)

    García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

    2014-08-14

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

  2. Structure and diffusion of nanoparticle monolayers floating at liquid/vapor interfaces: a molecular dynamics study.

    Science.gov (United States)

    Cheng, Shengfeng; Grest, Gary S

    2012-06-07

    Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles floating on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short-range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short-range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions.

  3. Water self-diffusivity confined in graphene nanogap using molecular dynamics simulations

    Science.gov (United States)

    Moulod, M.; Hwang, G.

    2016-11-01

    Fundamental understanding of water confined in graphene is crucial to optimally design and operate sustainable energy, water desalination, and bio-medical systems. However, the current understanding predominantly remains in the static properties near the graphene surfaces. In this paper, a key water transport property, i.e., self-diffusivity, is examined under confinement by various graphene nanogap sizes (Lz = 0.7-4.17 nm), using molecular dynamics simulations with various graphene-water interatomic potentials (Simple Point Charge (SPC/E) and TIP3P water models). It is found that the water self-diffusivity nearly linearly decreases as the graphene-water interatomic potential energy increases at a given nanogap size. It also decreases as the graphene nanogap size decreases down to Lz = 1.34 nm; however, it shows the peak water self-diffusivity at Lz = 0.8 nm and then continues to decrease. The peak water self-diffusivity is related to the significant change of the overlapping surface force, and associated, nonlinear local water density distribution. The in-plane water self-diffusivity is higher up to nearly an order of magnitude than that of the out-of-plane due to the geometrical confinement effect by the graphene nanogap. The obtained results provide a roadmap to fundamentally understand the water transport properties in the graphene geometries and surface interactions.

  4. Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

    Science.gov (United States)

    Fuson, Michael M.

    2017-01-01

    Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

  5. Diffusion-coupled molecular assembly: structuring of coordination polymers across multiple length scales.

    Science.gov (United States)

    Hirai, Kenji; Reboul, Julien; Morone, Nobuhiro; Heuser, John E; Furukawa, Shuhei; Kitagawa, Susumu

    2014-10-22

    Porous coordination polymers (PCPs) are an intriguing class of molecular-based materials because of the designability of framework scaffolds, pore sizes and pore surface functionalities. Besides the structural designability at the molecular scale, the structuring of PCPs into mesoscopic/macroscopic morphologies has attracted much attention due to the significance for the practical applications. The structuring of PCPs at the mesoscopic/macroscopic scale has been so far demonstrated by the spatial localization of coordination reactions on the surface of templates or at the phase boundaries. However, these methodologies have never been applied to the fabrication of solid-solution or multivariate metal-organic frameworks (MOFs), in which multiple components are homogeneously mixed. Herein, we demonstrate the structuring of a box-type superstructure comprising of a solid-solution PCP by integrating a bidirectional diffusion of multiple organic ligands into molecular assembly. The parent crystals of [Zn2(ndc)2(bpy)]n were placed in the DMF solution of additional organic component of H2bdc, and the temperature was rapidly elevated up to 80 °C (ndc = 1,4-naphthalenedicarboxylate, bpy = 4,4'-bipyridyl, bdc = 1,4-benzenedicarboxylate). The dissolution of the parent crystals induced the outward diffusion of components; contrariwise, the accumulation of the other organic ligand of H2bdc induced the inward diffusion toward the surface of the parent crystals. This bidirectional diffusion of multiple components spatially localized the recrystallization at the surface of cuboid parent crystals; therefore, the nanocrystals of a solid-solution PCP ([Zn2(bdc)1.5(ndc)0.5(bpy)]n) were organized into a mesoscopic box superstructure. Furthermore, we demonstrated that the box superstructures enhanced the mass transfer kinetics for the separation of hydrocarbons.

  6. Anisotropy of self-diffusion in forsterite grain boundaries derived from molecular dynamics simulations

    Science.gov (United States)

    Wagner, Johannes; Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

    2016-12-01

    Diffusion rates and associated deformation behaviour in olivine have been subjected to many studies, due to the major abundance of this mineral group in the Earth's upper mantle. However, grain boundary (GB) transport studies yield controversial results. The relation between transport rate, energy, and geometry of individual GBs is the key to understand transport in aggregates with lattice preferred orientation that favours the presence and/or alignment of specific GBs over random ones in an undeformed rock. In this contribution, we perform classical molecular dynamics simulations of a series of symmetric and one asymmetric tilt GBs of Mg_2 SiO_4 forsterite, ranging from 9.58° to 90° in misorientation and varying surface termination. Our emphasis lies on unravelling structural characteristics of high- and low-angle grain boundaries and how the atomic structure influences grain boundary excess volume and self-diffusion processes. To obtain diffusion rates for different GB geometries, we equilibrate the respective systems at ambient pressure and temperatures from 1900 to 2200 K and trace their evolution for run durations of at least 1000 ps. We then calculate the mean square displacement of the different atomic species within the GB interface to estimate self-diffusion coefficients in the individual systems. Grain boundary diffusion coefficients for Mg, Si and O range from 10^{-18} to 10^{-21} m^3/s, falling in line with extrapolations from lower temperature experimental data. Our data indicate that higher GB excess volumes enable faster diffusion within the GB. Finally, we discuss two types of transport mechanisms that may be distinguished in low- and high-angle GBs.

  7. A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface.

    Science.gov (United States)

    Yang, Hua; Lu, Zhong-Yuan; Li, Ze-Sheng; Sun, Chia-Chung

    2006-03-01

    Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid-liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. [Figure: see text].

  8. Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu

    2016-07-15

    Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.

  9. Multicomponent Diffusion of Penetrant Mixtures in Rubbery Polymers: A Molecular Dynamics Study

    Science.gov (United States)

    Bringuier, Stefan; Varady, Mark; Knox, Craig; Cabalo, Jerry; Pearl, Thomas; Mantooth, Brent

    The importance of understanding transport of chemical species across liquid-solid boundaries is of particular interest in the decontamination of harmful chemicals absorbed within polymeric materials. To characterize processes associated with liquid-phase extraction of absorbed species from polymers, it is necessary to determine an appropriate physical description of species transport in multicomponent systems. The Maxwell-Stefan (M-S) formulation is a rigorous description of mass transport in multicomponent solutions, in which, mutual diffusivities determine the degree of relative motion between interacting molecules in response to a chemical potential gradient. The work presented focuses on the determination of M-S diffusivities from molecular dynamics (MD) simulations of nerve agent O-ethyl S-[2(diisopropylamino)ethyl] methylphosphonothioate (VX), water, and methanol mixtures within a poly(dimethylsiloxane) matrix. We investigate the composition dependence of M-S diffusivities and compare the results to values predicted using empirical relations for binary and ternary mixtures. Finally, we highlight the pertinent differences in molecular mechanisms associated with species transport and employ non-equilibrium MD to probe transport across the mixture-polymer interface.

  10. The C$^{14}$N/C$^{15}$N Ratio in Diffuse Molecular Clouds

    CERN Document Server

    Ritchey, Adam M; Lambert, David L

    2015-01-01

    We report the first detection of C$^{15}$N in diffuse molecular gas from a detailed examination of CN absorption lines in archival VLT/UVES spectra of stars probing local diffuse clouds. Absorption from the C$^{15}$N isotopologue is confidently detected (at $\\gtrsim4\\sigma$) in three out of the four directions studied and appears as a very weak feature between the main $^{12}$CN and $^{13}$CN absorption components. Column densities for each CN isotopologue are determined through profile fitting, after accounting for weak additional line-of-sight components of $^{12}$CN, which are seen in the absorption profiles of CH and CH$^+$ as well. The weighted mean value of C$^{14}$N/C$^{15}$N for the three sight lines with detections of C$^{15}$N is $274\\pm18$. Since the diffuse molecular clouds toward our target stars have relatively high gas kinetic temperatures and relatively low visual extinctions, their C$^{14}$N/C$^{15}$N ratios should not be affected by chemical fractionation. The mean C$^{14}$N/C$^{15}$N ratio ...

  11. Molecular Simulation of Oxygen Sorption and Diffusion in the Poly (lactic acid)

    Institute of Scientific and Technical Information of China (English)

    SUN Delin; ZHOU Jian

    2013-01-01

    Grand canonical Monte Carlo and molecular dynamics simulation methods are used to simulate oxygen sorption and diffusion in amorphous poly(lactic acid) (PLA).The simulated solubility coefficient of oxygen is close to experimental data obtained from the quartz crystal microbalance but much higher than those from the time-lag method.This discrepancy is explained by using the dual-mode sorption model.It is found that oxygen sorption in PLA is predominantly Langmuir type controlled,i.e.,through the process of filling holes.The time-lag method only takes into account oxygen molecules that participate the diffusion process whereas a large proportion of oxygen molecules trapped in the void have little chance to execute hopping due to the glassy nature of PLA at room temperature.The simulated diffusion coefficient of oxygen is reasonably close to the data obtained from the time-lag method.The solubility coefficient of oxygen decreases linearly with increasing relative humidity while its diffusion coefficient firstly decreases and then increases as a function of relative humidity.

  12. Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale

    Science.gov (United States)

    Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong

    2016-12-01

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.

  13. Molecular dynamics study of strain-induced diffusivity of nitrogen in pure iron nanocrystalline

    Science.gov (United States)

    Mohammadzadeh, Roghayeh; Razmara, Naiyer; Razmara, Fereshteh

    2016-12-01

    In the present study, the self-diffusion process of nitrogen in pure iron nanocrystalline under strain conditions has been investigated by Molecular Dynamics (MD). The interactions between particles are modeled using Modified Embedded Atom Method (MEAM). Mean Square Displacement (MSD) of nitrogen in iron structure under strain is calculated. Strain is applied along [ 11 2 ¯ 0 ] and [ 0001 ] directions in both tensile and compression conditions. The activation energy and pre-exponential diffusion factor for nitrogen diffusion is comparatively high along [ 0001 ] direction of compressed structure of iron. The strain-induced diffusion coefficient at 973 K under the compression rate of 0.001 Å/ps along [ 0001 ] direction is about 6.72E-14 m2/s. The estimated activation energy of nitrogen under compression along [ 0001 ] direction is equal to 12.39 kcal/mol. The higher activation energy might be due to the fact that the system transforms into a more dense state when compressive stress is applied.

  14. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    Science.gov (United States)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

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

    DEFF Research Database (Denmark)

    Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander

    2005-01-01

    Mutual diffusion in condensed phases is a theoretically and practically important subject of active research. One of the most rigorous and theoretically advanced approaches to the problem is a recently developed approach based on the concept of penetration lengths (Physica A 320 (2003) 211; Physi...... fluctuation theory and molecular dynamics scheme exhibit consistent trends and average deviations from experimental data around 10-20%. (c) 2004 Elsevier B.V. All rights reserved....... binary liquid mixtures of non-polar components that computed penetration lengths, for various temperatures and compositions, are consistent with those deduced from experiments in the framework of the formalism of the fluctuation theory. Moreover, the mutual diffusion coefficients obtained from a coupled...

  16. Molecular Dynamics Simulation of Formaldehyde Adsorption and Diffusion in Single-Wall Carbon Nanotube

    Institute of Scientific and Technical Information of China (English)

    Pin Lv; Zhenan Tang; Jun Yu; Yanbing Xue

    2006-01-01

    For gas sensor application, adsorption and diffusion of formaldehyde gas in single-wall carbon nanotube were investigated by using molecular dynamics simulation. The conformations of formaldehyde molecule adsorbed in carbon nanotube were optimized according to principle of minimum energy. The axis of conformatiot is parallel to the axis of carbon nanotube and about 0.3 nm~0.4 nm away from carbon nanotube wall. The conformation, which is different from that of the formaldehyde molecule in the gas-phase, rotates around carbon nanotube axis. The adsorption energy and diffusivity of formaldehyde molecule in single-wall carbon nanotube is of-56.2 kJ/mol and of 0.2× 10-4 cm2/s, respectively.

  17. Molecular dynamics study on ion diffusion in LiFePO4 olivine materials.

    Science.gov (United States)

    Zhang, Peixin; Wu, Yanpeng; Zhang, Dongyun; Xu, Qiming; Liu, Jianhong; Ren, Xiangzhong; Luo, Zhongkuan; Wang, Mingliang; Hong, Weiliang

    2008-06-19

    Molecular dynamics (MD) simulations have been employed to investigate the ionic diffusion and the structure of LiFePO 4 cathode material. The results correspond well with the published experimental observations. The simulation results indicated that the diffusion of lithium ions was thermally activated and more significant than those of other ions. Compared with other cathode materials, the shifts of ions were less significant in LiFePO 4. This suggested that LiFePO 4 was more thermally stable. The snapshots of the positions of lithium atoms over a range of the steps provided a microscopic picture and the picture showed the lithium ions migrated through one-dimension channels.

  18. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

    Science.gov (United States)

    Hepburn, I.; Chen, W.; De Schutter, E.

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  19. Microelectrode Studies of Seasonal Oxygen-Uptake in a Coastal Sediment - Role of Molecular-Diffusion

    DEFF Research Database (Denmark)

    RASMUSSEN, H.; JØRGENSEN, BB

    1992-01-01

    Oxygen uptake rates and microdistributions of O2 in sediment of Aarhus Bay, Denmark, were studied over a year. Oxygen uptake was determined in the laboratory by 3 methods: (a) total O2 uptake in closed cores, (b) O2 flux through the diffusive boundary layer and (c) O2 consumption within the oxic...... surface zone. The O2 consumption rates in the oxic surface layer, calculated from (b) and (c) using molecular diffusion coefficients of O2, closely agreed and accounted for 70 % of the total O2 uptake. The O2 uptake rates strongly depended on in situ O2 concentrations in the overlying seawater, which...... in the bay varied from 100 % air saturation during winter to 23 % during summer. The potentially higher O2 respiration during the summer months was counteracted by a lower O2 concentration in the bottom water, which led to a small seasonal variation in O2 uptake. Depth of the oxic sediment zone reached 5...

  20. Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach

    Science.gov (United States)

    Shamloo, Amir; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria

    2016-07-01

    Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted.

  1. Thermodiffusion, molecular diffusion and Soret coefficients of aromatic+n-alkane binary mixtures

    Science.gov (United States)

    Larrañaga, Miren; Bou-Ali, M. Mounir; Lapeira, Estela; Lizarraga, Ion; Santamaría, Carlos

    2016-10-01

    In the present work, we have measured the thermodiffusion coefficient of 51 binary liquid mixtures at 25 oC. These mixtures correspond to the series of the aromatics toluene and 1-methylnaphthalene with n-alkanes nCi (i = 6, 8, 10, 12, and 14) at different mass fractions in the whole range. For that, we have used the thermogravitational technique. It is shown that the thermodiffusion coefficient is a linear function of the mass fraction in all the mixtures. Extrapolating the lines, we obtain the thermodiffusion coefficient in dilute solutions of n-alkanes for both toluene and 1-methylnaphthalene. These limiting values show a linear dependence with the inverse of the product of the molecular weights. In addition, we have measured the molecular diffusion coefficient of all the mixtures at 0.5 of mass fraction and at 25 oC, by the sliding symmetric tubes technique. It is observed that the product of this coefficient with the viscosity at the same concentrations takes a constant value for each of the series considered. Finally, we have also determined the Soret coefficient of the equimass mixtures by the combination of the measurements of thermodiffusion and molecular diffusion coefficients.

  2. The chemistry of interstellar argonium and other probes of the molecular fraction in diffuse clouds

    CERN Document Server

    Neufeld, David A

    2016-01-01

    We present a general parameter study, in which the abundance of interstellar argonium (ArH$^+$) is predicted using a model for the physics and chemistry of diffuse interstellar gas clouds. Results have been obtained as a function of UV radiation field, cosmic-ray ionization rate, and cloud extinction. No single set of cloud parameters provides an acceptable fit to the typical ArH$^+$, OH$^+$ and $\\rm H_2O^+$ abundances observed in diffuse clouds within the Galactic disk. Instead, the observed abundances suggest that ArH$^+$ resides primarily in a separate population of small clouds of total visual extinction of at most 0.02 mag per cloud, within which the column-averaged molecular fraction is in the range $10^{-5} - 10^{-2}$, while OH$^+$ and $\\rm H_2O^+$ reside primarily in somewhat larger clouds with a column-averaged molecular fraction $\\sim 0.2$. This analysis confirms our previous suggestion that the argonium molecular ion is a unique tracer of almost purely atomic gas.

  3. Molecular Simulation of the Diffusion of Uranyl Carbonate Species in Aqueous Solution

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Liu, Chongxuan

    2010-09-01

    Molecular dynamics simulations of aqueous uranyl carbonate species were carried out with two different potential models to gain molecular-level insight into the hydration properties of these species and evaluate the ability of the two models to reproduce published ab initio and experimental data. The simulation results were used to estimate the self-diffusion coefficients of uranyl carbonate species that often dominate uranyl speciation in groundwater systems. The first potential model was based on a series of shell models developed by Parker and co-workers (including (DE LEEUW and PARKER, 1998; KERISIT and PARKER, 2004; PAVESE et al., 1996). The second potential model was a rigid-ion model based on the flexible SPC water model (TELEMAN et al., 1987), the uranyl model of Guilbaud and Wipff (GUILBAUD and WIPFF, 1996), and the parameters for the carbonate ion given by Greathouse and co-workers (GREATHOUSE and CYGAN, 2005; GREATHOUSE et al., 2002). Analysis of structural (mean interatomic distances and coordination numbers) and dynamical (water residence times in hydration shell and self-diffusion coefficients) properties showed that, overall, the first potential model performed best when compared to published data, although the only major discrepancy with the second model was a misrepresentation of the configuration adopted by the alkaline-earth uranyl carbonate ions. The diffusion coefficients obtained for the alkaline-earth cations and the uranyl ion were compared with three variants of the Stokes-Einstein (SE) equation and it was found that none of the three SE models were able to reproduce both the absolute values and the overall trend determined from the molecular dynamics simulations. However, as would be expected based on the SE equation, a plot of the diffusion coefficients of the uranyl carbonate complexes as a function of the inverse of the equivalent spherical radius showed a general linear dependence with the two models yielding almost identical gradients

  4. Molecular dynamics investigation of the self-diffusion of binary mixture diffusion in the metal-organic framework Zn(tbip) accounting for framework flexibility

    NARCIS (Netherlands)

    Seehamart, K.; Chmelik, C.; Krishna, R.; Fritzsche, S.

    2011-01-01

    The self-diffusion of three equimolar mixtures in the metal-organic framework Zn(tbip) has been investigated by molecular dynamics simulations. The simulations take due account of lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice

  5. Molecular dynamics study of Ar flow and He flow inside carbon nanotube junction as a molecular nozzle and diffuser

    Directory of Open Access Journals (Sweden)

    Itsuo Hanasaki, Akihiro Nakatani and Hiroshi Kitagawa

    2004-01-01

    Full Text Available A carbon nanotube junction consists of two connected nanotubes with different diameters. It has been extensively investigated as a molecular electronic device since carbon nanotubes can be metallic and semiconductive, depending on their structure. However, a carbon nanotube junction can also be viewed as a nanoscale nozzle andv diffuser. Here, we focus on the nanotube junction from the perspective of an intersection between machine, material and device. We have conducted a molecular dynamics simulation of the molecular flow inside a modeled (12,12–(8,8 nanotube junction. A strong gravitational field and a periodic boundary condition are applied in the flow direction. We investigated dense-Ar flows and dense-He flows while controlling the temperature of the nanotube junction. The results show that Ar atoms tend to be near to the wall and the density of the Ar is higher in the wide (12,12 nanotube than in the narrow (8,8 nanotube, while it is lower in the wide tube when no flow occurs. The streaming velocities of both the Ar and the He are higher in the narrow nanotube than in the wide nanotube, but the velocity of the Ar is higher than the velocity of the He and the temperature of the flowing Ar is higher than the temperature of the He when the same magnitude of gravitational field is applied.

  6. Sorbate Transport in Carbon Molecular Sieve Membranes and FAU/EMT Intergrowth by Diffusion NMR

    Directory of Open Access Journals (Sweden)

    John J. Low

    2012-02-01

    Full Text Available In this paper we present and discuss selected results of our recent studies of sorbate self-diffusion in microporous materials. The main focus is given to transport properties of carbon molecular sieve (CMS membranes as well as of the intergrowth of FAU-type and EMT-type zeolites. CMS membranes show promise for applications in separations of mixtures of small gas molecules, while FAU/EMT intergrowth can be used as an active and selective cracking catalyst. For both types of applications diffusion of guest molecules in the micropore networks of these materials is expected to play an important role. Diffusion studies were performed by a pulsed field gradient (PFG NMR technique that combines advantages of high field (17.6 T NMR and high magnetic field gradients (up to 30 T/m. This technique has been recently introduced at the University of Florida in collaboration with the National Magnet Lab. In addition to a more conventional proton PFG NMR, also carbon-13 PFG NMR was used.

  7. Molecular simulation of translational and rotational diffusion of Janus nanoparticles at liquid interfaces.

    Science.gov (United States)

    Rezvantalab, Hossein; Drazer, German; Shojaei-Zadeh, Shahab

    2015-01-07

    We perform molecular dynamics simulations to understand the translational and rotational diffusion of Janus nanoparticles at the interface between two immiscible fluids. Considering spherical particles with different affinity to fluid phases, both their dynamics as well as the fluid structure around them are evaluated as a function of particle size, amphiphilicity, fluid density, and interfacial tension. We show that as the particle amphiphilicity increases due to enhanced wetting of each side with its favorite fluid, the rotational thermal motion decreases. Moreover, the in-plane diffusion of nanoparticles at the interface becomes slower for more amphiphilic particles, mainly due to the formation of a denser adsorption layer. The particles induce an ordered structure in the surrounding fluid that becomes more pronounced for highly amphiphilic nanoparticles, leading to increased resistance against nanoparticle motion. A similar phenomenon is observed for homogeneous particles diffusing in bulk upon increasing their wettability. Our findings can provide fundamental insight into the dynamics of drugs and protein molecules with anisotropic surface properties at biological interfaces including cell membranes.

  8. Molecular simulation study of adsorption and diffusion on silicalite for a benzene/CO2 mixture.

    Science.gov (United States)

    Yue, Xiaopeng; Yang, Xiaoning

    2006-03-28

    The adsorption and diffusion of a binary mixture of supercritical CO2 and benzene on silicalite (MFI-type) have been studied through the grand canonical Monte Carlo and molecular dynamics (MD) simulations. The adsorption behavior of pure CO2 on silicalite was discussed in detail from the adsorption isotherms, adsorption sites, interaction energies, and isosteric heats of adsorption. For the mixture, the influences of temperature, pressure and composition on the adsorption isotherms have been examined. The adsorption site behavior of the mixture has been analyzed, and benzene molecules get adsorbed preferentially in the more spacious channel intersection positions. These simulation results suggest that SC-CO2 fluid can be used as an efficient desorbent of larger aromatics in the zeolite material. The diffusion characteristic for the benzene/CO2 mixture was studied on the basis of MD simulation. It was found that the large coadsorbed benzene molecule has a pronounced effect on the CO2 diffusion in the mixture, while the mobility of benzene molecules is very small due to geometrical restrictions.

  9. Molecular Simulation of Shale Gas Adsorption and Diffusion in Clay Nanopores

    Directory of Open Access Journals (Sweden)

    Hongguang Sui

    2015-12-01

    Full Text Available The present work aims to study the adsorption behavior and dynamical properties of CH4 in clay slit pore with or without cation exchange structures at sizes of 1.0 nm–4.0 nm using grand canonical Monte Carlo (GCMC and molecular dynamics (MD methods. The adsorption isotherms of CH4 have been investigated by GCMC simulations at different temperatures and various pore sizes. In the montmorillonite (MMT clays without a cation exchange structure, from the density profile, we find the molecules preferentially adsorb onto the surface, and only an obvious single layer was observed. The general trend within slit pores is that with increasing pore width, the adsorbed amount will increase. However, the larger pores exhibit lower excess density and the smaller pores exhibit higher excess density. The preloaded water will reduce CH4 sorption. The in plane self-diffusion coefficient of CH4 which is investigated by MD simulations combined with Einstein fluid equation increases rapidly with the pore size increasing at low pressure. Under these given conditions, the effect of temperature has little influence on the in-plane self-diffusion coefficient. In the MMT clays with cation exchange structure, cation exchange has little effect on CH4 adsorption and self-diffusion.

  10. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  11. Direct molecular diffusion and micro-mixing for rapid dewatering of LiBr solution

    Energy Technology Data Exchange (ETDEWEB)

    Bigham, S; Isfahani, RN; Moghaddam, S

    2014-03-01

    A slow molecular diffusion rate often limits the desorption process of an absorbate molecule from a liquid absorbent. To enhance the desorption rate, the absorbent is often boiled to increase the liquid vapor interfacial area. However, the growth of bubbles generated during the nucleate boiling process still remains mass-diffusion limited. Here, it is shown that a desorption rate higher than that of boiling can be achieved, if the vapor absorbent interface is continuously replenished with the absorbate-rich solution to limit the concentration boundary layer growth. The study is conducted in a LiBr-water-solution, in which the water molecules' diffusion rate is quite slow. The manipulation of the vapor solution interface concentration distribution is enabled by the mechanical confinement of the solution flow within microchannels, using a hydrophobic vapor-venting membrane and the implementation of microstructures on the flow channel's bottom wall. The microstructures stretch and fold the laminar streamlines within the solution film and produce vortices. The vortices continuously replace the concentrated solution at the vapor solution interface with the water-rich solution brought from the bottom and middle of the flow channel. The physics of the process is described using a combination of experimental and numerical studies. Published by Elsevier Ltd.

  12. Molecular Simulations of the Diffusion of Uranyl Carbonate Species in Nanosized Mineral Fractures

    Science.gov (United States)

    Kerisit, S.; Liu, C.

    2010-12-01

    Uranium is a major groundwater contaminant at uranium processing and mining sites as a result of intentional and accidental discharges of uranium-containing waste products into subsurface environments. Recent characterization has shown that uranium preferentially associates with intragrain and intra-aggregate domains in some of the uranium-contaminated sediments collected from the US Department of Energy Hanford Site [1, 2]. In these sediments, uranium existed as precipitated and/or adsorbed phases in grain micropores with nano- to microscale sizes. Desorption and diffusion characterization studies and continuum-scale modeling indicated that ion diffusion in the microfractures is a major mechanism that led to preferential uranium concentration in the microfracture regions and will control the future mobility of uranium in the subsurface sediments [1, 3-4]. However, the diffusion properties of uranyl species in the intragrain regions, especially at the solid-liquid interface, are still poorly understood. Therefore, a general aim of this work is to provide atomic-level insights into the contribution of microscopic surface effects to the slow diffusion process of uranyl species in porous media with nano- to microsized fractures. In this presentation, we will first present molecular dynamics (MD) simulations of feldspar-water interfaces to investigate their interfacial structure and dynamics and establish a theoretical framework for subsequent simulations of water and ion diffusion at these interfaces [5]. We will then report on MD simulations carried out to probe the effects of confinement and of the presence of the mineral surface on the diffusion of water and electrolyte ions in nanosized feldspar fractures [6]. Several properties of the mineral-water interface were varied, such as the fracture width, the ionic strength of the contacting solution, and the surface charge. Our calculations reveal a 2.0-2.5 nm interfacial region within which the diffusion properties of

  13. Molecular Hydrogen in Diffuse Interstellar Clouds of Arbitrary Three-Dimensional Geometry

    CERN Document Server

    Spaans, M; Spaans, Marco; Neufeld, David A.

    1997-01-01

    We have constructed three-dimensional models for the equilibrium abundance of molecular hydrogen within diffuse interstellar clouds of arbitrary geometry that are illuminated by ultraviolet radiation. The position-dependent photo- dissociation rate of H$_2$ within such clouds was computed using a 26-ray approximation to model the attenuation of the incident ultraviolet radiation field by dust and by H$_2$ line absorption. We have applied our modeling technique to the isolated diffuse cloud G236+39, assuming that the cloud has a constant density and that the thickness of the cloud along the line of sight is at every point proportional to the 100 um continuum intensity measured by IRAS. We find that our model can successfully account for observed variations in the ratio of 100 umu continuum intensity to HI column density, with larger values of that ratio occurring along lines of sight in which the molecular hydrogen fraction is expected to be largest. Using a standard chi^2 analysis to assess the goodness of fi...

  14. Diffusion-driven growth of nanowires by low-temperature molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Rueda-Fonseca, P.; Orrù, M. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CNRS, Institut NEEL, F-38000 Grenoble (France); CEA, INAC, F-38000 Grenoble (France); Bellet-Amalric, E.; Robin, E. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, INAC, F-38000 Grenoble (France); Den Hertog, M.; Genuist, Y.; André, R.; Tatarenko, S.; Cibert, J., E-mail: joel.cibert@neel.cnrs.fr [Univ. Grenoble Alpes, F-38000 Grenoble (France); CNRS, Institut NEEL, F-38000 Grenoble (France)

    2016-04-28

    With ZnTe as an example, we use two different methods to unravel the characteristics of the growth of nanowires (NWs) by gold-catalyzed molecular beam epitaxy at low temperature. In the first approach, CdTe insertions have been used as markers, and the nanowires have been characterized by scanning transmission electron microscopy, including geometrical phase analysis and energy dispersive electron spectrometry; the second approach uses scanning electron microscopy and the statistics of the relationship between the length of the tapered nanowires and their base diameter. Axial and radial growth are quantified using a diffusion-limited model adapted to the growth conditions; analytical expressions describe well the relationship between the NW length and the total molecular flux (taking into account the orientation of the effusion cells), and the catalyst-nanowire contact area. A long incubation time is observed. This analysis allows us to assess the evolution of the diffusion lengths on the substrate and along the nanowire sidewalls, as a function of temperature and deviation from stoichiometric flux.

  15. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

    Science.gov (United States)

    Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia

    2013-10-24

    The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

  16. Is now the time for molecular driven therapy for diffuse large B-cell lymphoma?

    Science.gov (United States)

    Di Rocco, Alice; De Angelis, Federico; Ansuinelli, Michela; Foà, Robin; Martelli, Maurizio

    2017-09-01

    Recent genetic and molecular discoveries regarding alterations in diffuse large B-cell lymphoma (DLBCL) deeply changed the approach to this lymphoproliferative disorder. Novel additional predictors of outcomes and new therapeutic strategies are being introduced to improve outcomes. Areas covered: This review aims to analyse the recent molecular discoveries in DLBCL, the rationale of novel molecular driven treatments and their impact on DLBCL prognosis, especially in ABC-DLBCL and High Grade B Cell Lymphoma. Pre-clinical and clinical evidences are reviewed to critically evaluate the novel DLBCL management strategies. Expert commentary: New insights in DLBCL molecular characteristics should guide the therapeutic approach; the results of the current studies which are investigating safety and efficacy of novel 'X-RCHOP' will probably lead, in future, to a cell of origin (COO) based upfront therapy. Moreover, it is necessary to identify early patients with DLBCL who carried MYC, BCL2 and/or BCL6 rearrangements double hit lymphomas (DHL) because they should not receive standard R-CHOP but high intensity treatment as reported in many retrospective studies. New prospective trials are needed to investigate the more appropriate treatment of DHL.

  17. Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

    Science.gov (United States)

    Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

    2016-09-01

    A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

  18. Theoretical, experimental and field studies concerning molecular diffusion of radioisotopes in sediments and suspended solid particles of the sea Part A: Theories and mathematical calculations

    NARCIS (Netherlands)

    Duursma, E.K.; Hoede, C.

    1967-01-01

    The best way to describe the kinetics of the uptake of radioisotopes from sea water by bottom sediments and suspended solid matter is by molecular diffusion. The basic diffusion laws can be applied for finding the important parameter of the diffusion, the diffusion coefficient, which will characteri

  19. INFLUENCE VARIOUS REAGENTS ON THE MOLECULAR DIFFUSION INDEX OF SUCROSE FROM BEET

    Directory of Open Access Journals (Sweden)

    N. G. Kulneva

    2015-01-01

    Full Text Available Food products from vegetable raw materials play a special role in the food industry. Sugar is one of the strategically important products. The significance of its is great due to its wide use in confectionery, bakery, liquor, canning, biochemical, pharmaceutical and other branches of human activity. Effective development of the domestic sugar industry depends on the terms of competition with European partners. Production of granulated sugar includes a significant amount of energy-intensive and technologically complex operations, one of which is the extraction of sucrose from beet chips by means of hot countercurrent extraction. The most important criterion for the extraction process efficiency evaluation is the coefficient of molecular diffusion. The efficiency of using of beet chips thermo chemical processing before extraction depending on the quality of processed beet was investigated. It was found out that when using a low quality beet the diffusion coefficient decreases compared to healthy beet. The use of solutio ns of some salts for beet chips heat treatment has an overall positive effect on the diffusion coefficient. A method for recovering sucrose from beet with the use of compounds of Al2(SO4, Ca(SO4, and (NH42SO4 as the extractants was proposed. It was found out that beet samples treatment with solutions of proposed salts provides a sucrose smooth transition from the pores of sugar beet tissue into the extractant due to intense convective washout. It is caused by the high degree of tissue cells plasmolysis achieved in its processing with solutions of proposed reagents. The results obtained indicate a significant increase of the sucrose diffusion coefficient in the ammonium sulfate solution used as the extractant.

  20. Molecular dynamics simulation of diffusion of gases in a carbon-nanotube-polymer composite

    Science.gov (United States)

    Lim, Seong Y.; Sahimi, Muhammad; Tsotsis, Theodore T.; Kim, Nayong

    2007-07-01

    Extensive molecular dynamics (MD) simulations were carried out to compute the solubilities and self-diffusivities of CO2 and CH4 in amorphous polyetherimide (PEI) and mixed-matrix PEI generated by inserting single-walled carbon nanotubes into the polymer. Atomistic models of PEI and its composites were generated using energy minimizations, MD simulations, and the polymer-consistent force field. Two types of polymer composite were generated by inserting (7,0) and (12,0) zigzag carbon nanotubes into the PEI structure. The morphologies of PEI and its composites were characterized by their densities, radial distribution functions, and the accessible free volumes, which were computed with probe molecules of different sizes. The distributions of the cavity volumes were computed using the Voronoi tessellation method. The computed self-diffusivities of the gases in the polymer composites are much larger than those in pure PEI. We find, however, that the increase is not due to diffusion of the gases through the nanotubes which have smooth energy surfaces and, therefore, provide fast transport paths. Instead, the MD simulations indicate a squeezing effect of the nanotubes on the polymer matrix that changes the composite polymers’ free-volume distributions and makes them more sharply peaked. The presence of nanotubes also creates several cavities with large volumes that give rise to larger diffusivities in the polymer composites. This effect is due to the repulsive interactions between the polymer and the nanotubes. The solubilities of the gases in the polymer composites are also larger than those in pure PEI, hence indicating larger gas permeabilities for mixed-matrix PEI than PEI itself.

  1. Detection of hydrogen fluoride absorption in diffuse molecular clouds with Herschel/HIFI: a ubiquitous tracer of molecular gas

    CERN Document Server

    Sonnentrucker, P; Phillips, T G; Gerin, M; Lis, D C; De Luca, M; Goicoechea, J R; Black, J H; Bell, T A; Boulanger, F; Cernicharo, J; Coutens, A; Dartois, E; Kazmierczak, M; Encrenaz, P; Falgarone, E; Geballe, T R; Giesen, T; Godard, B; Goldsmith, P F; Gry, C; Gupta, H; Hennebelle, P; Herbst, E; Hily-Blant, P; Joblin, C; Kolos, R; Krelowski, J; Mart\\in-Pintado, J; Menten, K M; Monje, R; Mookerjea, B; Pearson, J; Perault, M; Persson, C M; Plume, R; Salez, M; Schlemmer, S; Schmidt, M; Stutzki, J; Teyssier, D; Vastel, C; Yu, S; Caux, E; Gusten, R; Hatch, W A; Klein, T; Mehdi, I; Morris, P; Ward, J S

    2010-01-01

    We discuss the detection of absorption by interstellar hydrogen fluoride (HF) along the sight line to the submillimeter continuum sources W49N and W51. We have used Herschel's HIFI instrument in dual beam switch mode to observe the 1232.4762 GHz J = 1 - 0 HF transition in the upper sideband of the band 5a receiver. We detected foreground absorption by HF toward both sources over a wide range of velocities. Optically thin absorption components were detected on both sight lines, allowing us to measure - as opposed to obtain a lower limit on - the column density of HF for the first time. As in previous observations of HF toward the source G10.6-0.4, the derived HF column density is typically comparable to that of water vapor, even though the elemental abundance of oxygen is greater than that of fluorine by four orders of magnitude. We used the rather uncertain N(CH)-N(H2) relationship derived previously toward diffuse molecular clouds to infer the molecular hydrogen column density in the clouds exhibiting HF abs...

  2. Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12

    Science.gov (United States)

    Chen, Chi; Lu, Ziheng; Ciucci, Francesco

    2017-01-01

    Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations.

  3. Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12

    Science.gov (United States)

    Chen, Chi; Lu, Ziheng; Ciucci, Francesco

    2017-01-01

    Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations. PMID:28094317

  4. Molecular simulation of the diffusion of uranyl carbonate species in aqueous solution

    Science.gov (United States)

    Kerisit, Sebastien; Liu, Chongxuan

    2010-09-01

    Potential-based molecular dynamics simulations of aqueous uranyl carbonate species (M xUO 2(CO 3) y2+2x-2y with M = Mg, Ca, or Sr) were carried out to gain molecular-level insight into the hydration properties of these species. The simulation results were used to estimate the self-diffusion coefficients of these uranyl carbonate species, which often dominate uranyl speciation in groundwater systems. The diffusion coefficients obtained for the monoatomic alkaline-earth cations and polyatomic ions (uranyl, carbonate, and uranyl tri-carbonate) were compared with those calculated from the Stokes-Einstein (SE) equation and its variant formulation by Impey et al. (1983). Our results show that the equation of Impey et al. (1983), originally formulated for monovalent monoatomic ions, can be extended to divalent monoatomic ions, with some success in reproducing the absolute values and the overall trend determined from the molecular dynamics simulations, but not to polyatomic ions, for which the hydration shell is not spherically symmetrical. Despite the quantitative failure of both SE formulations, a plot of the diffusion coefficients of the uranyl carbonate complexes as a function of the inverse of the equivalent spherical radius showed that a general linear dependence is observed for these complexes as expected from the SE equation. The nature of the alkaline-earth cation in the uranyl carbonate complexes was not found to have a significant effect on the ion's diffusion coefficient, which suggests that the use of a single diffusion coefficient for different alkaline-earth uranyl carbonate complexes in microscopic diffusion models is appropriate. The potential model reproduced well published quantum mechanical and experimental data of UO(CO)32x-4 and of the individual constituent ions, and therefore is expected to offer reliable predictions of the structure of magnesium and strontium uranyl carbonate aqueous species, for which there is no structural data available to date

  5. Variation of diffusivity with the cation radii in molten salts of superionic conductors containing iodine anion: A molecular dynamics study

    Indian Academy of Sciences (India)

    Srinivasa R Varanasi; S Yashonath

    2012-01-01

    A molecular dynamics study of the dependence of diffusivity of the cation on ionic radii in molten AgI is reported.We have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo and Kobayashi. Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several structural and dynamical properties are reported.

  6. Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12

    OpenAIRE

    Chi Chen; Ziheng Lu; Francesco Ciucci

    2017-01-01

    Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate c...

  7. Decreases in molecular diffusion, perfusion fraction and perfusion-related diffusion in fibrotic livers: a prospective clinical intravoxel incoherent motion MR imaging study.

    Directory of Open Access Journals (Sweden)

    Pu-Xuan Lu

    Full Text Available PURPOSE: This study was aimed to determine whether pure molecular-based diffusion coefficient (D and perfusion-related diffusion parameters (perfusion fraction f, perfusion-related diffusion coefficient D* differ in healthy livers and fibrotic livers through intra-voxel incoherent motion (IVIM MR imaging. MATERIAL AND METHODS: 17 healthy volunteers and 34 patients with histopathologically confirmed liver fibrosis patients (stage 1 = 14, stage 2 = 8, stage 3 & 4 = 12, METAVIR grading were included. Liver MR imaging was performed at 1.5-T. IVIM diffusion weighted imaging sequence was based on standard single-shot DW spin echo-planar imaging, with ten b values of 10, 20, 40, 60, 80, 100, 150, 200, 400, 800 sec/mm2 respectively. Pixel-wise realization and regions-of-interest based quantification of IVIM parameters were performed. RESULTS: D, f, and D* in healthy volunteer livers and patient livers were 1.096±0.155 vs 0.917±0.152 (10(-3 mm2/s, p = 0.0015, 0.164±0.021 vs 0.123±0.029 (p<0.0001, and 13.085±2.943 vs 9.423±1.737 (10(-3 mm2/s, p<0.0001 respectively, all significantly lower in fibrotic livers. As the fibrosis severity progressed, D, f, and D* values decreased, with a trend significant for f and D*. CONCLUSION: Fibrotic liver is associated with lower pure molecular diffusion, lower perfusion volume fraction, and lower perfusion-related diffusion. The decrease of f and D* in the liver is significantly associated liver fibrosis severity.

  8. Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media.

    Science.gov (United States)

    Bourg, Ian C; Sposito, Garrison

    2010-03-15

    In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations, which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer "compartments." We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D(interlayer) of water tracers and representative cations (Na(+), Cs(+), Sr(2+)) in Na-smectite interlayers. We find that a remarkably simple expression relates D(interlayer) to the pore-scale parameter δ(nanopore) ≤ 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: δ(nanopore) = D(interlayer)/D(0), where D(0) is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracers H(2)0, Na(+), Sr(2+), and Cs(+) in compacted Na-smectite-rich materials.

  9. Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media

    Energy Technology Data Exchange (ETDEWEB)

    Bourg, I.C.; Sposito, G.

    2009-12-01

    In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer 'compartments.' We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D{sub interlayer} of water tracers and representative cations (Na{sup +}, Cs{sup +}, Sr{sup 2+}) in Na-smectite interlayers. We find that a remarkably simple expression relates D{sub interlayer} to the pore-scale parameter {delta}{sub nanopore} {<=} 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: {delta}{sub nanopore} = D{sub interlayer}/D{sub 0}, where D{sub 0} is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracer H{sub 2}O, Na{sup +}, Sr{sup 2+} and Cs{sup +}+ in compacted Na-smectite-rich materials.

  10. Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media

    Energy Technology Data Exchange (ETDEWEB)

    Bourg, I.C.; Sposito, G.

    2009-12-01

    In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer 'compartments.' We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D{sub interlayer} of water tracers and representative cations (Na{sup +}, Cs{sup +}, Sr{sup 2+}) in Na-smectite interlayers. We find that a remarkably simple expression relates D{sub interlayer} to the pore-scale parameter {delta}{sub nanopore} {<=} 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: {delta}{sub nanopore} = D{sub interlayer}/D{sub 0}, where D{sub 0} is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracer H{sub 2}O, Na{sup +}, Sr{sup 2+} and Cs{sup +}+ in compacted Na-smectite-rich materials.

  11. Molecular structure effects on the post irradiation diffusion in polymer gel dosimeters

    Energy Technology Data Exchange (ETDEWEB)

    Mattea, F.; Romero, M.; Strumia, M. [Instituto Multidisciplinario de Biologia Vegetal / CONICET, Universidad Nacional de Cordoba, Departamento de Quimica Organica, Ciudad Universitaria, 5000 Cordoba (Argentina); Vedelago, J. [Laboratorio de Investigaciones e Instrumentacion en Fisica Aplicada a la Medicina e Imagenes por Rayos X, Laboratorio 448 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Quiroga, A. [Centro de Investigacion y Estudios de Matematica / CONICET, Oficina 318 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Valente, M., E-mail: fmattea@gmail.com [Instituto de Fisica E. Gaviola / CONICET, LIIFAMIRx, Oficina 102 FaMAF - UNC, 5000 Cordoba (Argentina)

    2014-08-15

    Polymer gel dosimeters have specific advantages for recording 3D radiation dose distribution representing a key factor for most of the therapeutic and diagnostic radiation techniques. Radiation-induced polymerization and crosslinking reactions that take place in the dosimeter have been studied for different monomers like acrylamide and N,N-methylene-bis acrylamide (Bis) and most recently for less toxic monomers like N-isopropylacrylamide and Bis. In this work a novel system based on itaconic acid and Bis is proposed, the radical polymerization or gel formation of these monomers has been already studied for the formation of an hydrogel for non dosimetric applications and their reactivity are comparable with the already mentioned systems. Although the 3D structure is maintained after the dosimeter has been irradiated, it is not possible to eliminate the diffusion of the reacted and monomer species in regions of dose gradients within the gel after irradiation. As a consequence the dose information of the dosimeters loose quality over time. The mobility within the gelatin structure of the already mentioned species is related to their chemical structure, and nature. In this work the effect of changes in the chemical structure of the monomers over the dosimetric sensitivity and over the post-irradiation diffusion of species is studied. One of the acrylic acid groups of the itaconic acid molecule is modified to obtain molecules with similar reactivity but different molecular sizes. Dosimetric systems with these modified species, Bis, an antioxidant to avoid oxygen polymerization inhibition, water and gelatin are irradiated in an X-ray tomography at different doses, and the resulting dosimeters are characterized by Raman spectroscopy and optical absorbance to study their feasibility and capabilities as dosimetric systems, and by optical-CT to analyze the diffusion degree after being irradiated. (Author)

  12. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    Science.gov (United States)

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  13. The effect of ambipolar diffusion on low-density molecular ISM filaments

    CERN Document Server

    Ntormousi, Evangelia; André, Philippe; Masson, Jacques

    2016-01-01

    The filamentary structure of the molecular interstellar medium and the potential link of this morphology to star formation have been brought into focus recently by high resolution observational surveys. An especially puzzling matter is that local interstellar filaments appear to have the same thickness, independent of their column density. This requires a theoretical understanding of their formation process and the physics that governs their evolution. In this work we explore a scenario in which filaments are dissipative structures of the large-scale interstellar turbulence cascade and ion-neutral friction (also called ambipolar diffusion) is affecting their sizes by preventing small-scale compressions. We employ high-resolution, 3D MHD simulations, performed with the grid code RAMSES, to investigate non-ideal MHD turbulence as a filament formation mechanism. We focus the analysis on the mass and thickness distributions of the resulting filamentary structures. Simulations of both driven and decaying MHD turbu...

  14. Diffusion effects on formation process of mesoporous molecular sieve MCM-41

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The regular mesoporous molecular sieve MCM-41 has been investigated at different stages during its formation,using high resolution transmission electron microscopy and powder X-ray diffraction.The results not only support the liquid-crystal templating mechanism previously postulated,but allow the extension fo its scope to discribe ditails of MCM-41 formation.It has been observed that formation of the hexagonal liquid crystal phase on the one hand and of silica aggregates on the other,occurs simultaneously at the inception of gel formation and throughout the crystallisation.This process is most probably affected by diffusion of both the surfactant molecules and the oligomeric silicate ions.With this postulate it becomes possible to explain several experimental observation(both old and new)and to develop a multi-step synthesis method to grow large particles of MCM-41 using small calcined crystals of MCM-41 as seeds.

  15. Three-dimensional simulations of molecular cloud fragmentation regulated by magnetic fields and ambipolar diffusion

    CERN Document Server

    Kudoh, Takahiro; Ogata, Youichi; Yabe, Takashi

    2007-01-01

    We employ the first fully three-dimensional simulation to study the role of magnetic fields and ion-neutral friction in regulating gravitationally-driven fragmentation of molecular clouds. The cores in an initially subcritical cloud develop gradually over an ambipolar diffusion time while the cores in an initially supercritical cloud develop in a dynamical time. The infall speeds on to cores are subsonic in the case of an initially subcritical cloud, while an extended (\\ga 0.1 pc) region of supersonic infall exists in the case of an initially supercritical cloud. These results are consistent with previous two-dimensional simulations. We also found that a snapshot of the relation between density (rho) and the strength of the magnetic field (B) at different spatial points of the cloud coincides with the evolutionary track of an individual core. When the density becomes large, both relations tend to B \\propto \\rho^{0.5}.

  16. An adult multifocal medulloblastoma with diffuse acute postoperative cerebellar swelling: immunohistochemical and molecular genetics analysis.

    Science.gov (United States)

    Balik, Vladimir; Trojanec, Radek; Holzerova, Milena; Tuckova, Lucie; Sulla, Igor; Megova, Magdalena; Vaverka, Miroslav; Hrabalek, Lumir; Ehrmann, Jiri

    2015-01-01

    Medulloblastoma (MB), the most common malignant tumor typically affecting children, occurs only exceptionally in adults. Multifocal presentation of this malignancy in adulthood is even much rarer—only four cases with favorable postoperative course have been reported, so far. The study illustrates a very rare rapid postoperative clinical deterioration due to diffuse cerebellar swelling (DCS) in an adult multifocal MB (MMB). To the best of their knowledge, authors for the first time performed genetic analysis of MMB and demonstrated expression patterns of selected markers that put the patient within the sonic hedgehog (SHH) molecular subgroup and at least partially explain her unsatisfactory clinical course. Herein, authors summarized the relevant literature concerning this issue with the aim to determine features that would facilitate diagnosis and therapy of such a scarce clinical entity.

  17. Quantum Diffusion on Molecular Tubes: Universal Scaling of the 1D to 2D Transition

    Science.gov (United States)

    Chuang, Chern; Lee, Chee Kong; Moix, Jeremy M.; Knoester, Jasper; Cao, Jianshu

    2016-05-01

    The transport properties of disordered systems are known to depend critically on dimensionality. We study the diffusion coefficient of a quantum particle confined to a lattice on the surface of a tube, where it scales between the 1D and 2D limits. It is found that the scaling relation is universal and independent of the temperature, disorder, and noise parameters, and the essential order parameter is the ratio between the localization length in 2D and the circumference of the tube. Phenomenological and quantitative expressions for transport properties as functions of disorder and noise are obtained and applied to real systems: In the natural chlorosomes found in light-harvesting bacteria the exciton transfer dynamics is predicted to be in the 2D limit, whereas a family of synthetic molecular aggregates is found to be in the homogeneous limit and is independent of dimensionality.

  18. Modeling sorption and diffusion of organic sorbate in hexadecyltrimethylammonium-modified clay nanopores - a molecular dynamics simulation study.

    Science.gov (United States)

    Zhao, Qian; Burns, Susan E

    2013-03-19

    Organoclays are highly sorptive engineered materials that can be used as amendments in barrier systems or geosynthetic liners. The performance of confining and isolating the nonpolar organic contaminants by those barrier/lining systems is essentially controlled by the process of organic contaminant mass transport in nanopores of organoclays. In this article, we use molecular dynamics (MD) simulations to study the sorption and diffusion of organic sorbates in interlayers of sodium montmorillonite and hexadecyltrimethylammonium (HDTMA(+))-modified montmorillonite clays. Simulated system consisted of the clay framework, interlayer organic cation, water, and organic sorbate. Their interactions were addressed by the combined force field of ClayFF, constant-valence force field, and SPC water model. Simulation results indicated that in HDTMA coated clay nanopores, diffusion of nonpolar species benzene was slowed because they were subjected to influence of both the pore wall and the HDTMA surfactant. This suggested the nonpolar organic compound diffusion in organophilic clays can be affected by molecular size of diffusive species, clay pore size, and organic surfactant loading. Additionally, a model that connected the diffusion rate of organic compounds in the bulk organoclay matrix with macropores and nanopores was established. The impact of intercalated organic cations on the diffusion dominated mass transport of organic compounds yielded insight into the prediction of the apparent diffusion behavior of organic compounds in organic-modified clays.

  19. Influence of Molecular Hydrogen Diffusion on Concentration and Distribution of Hydroxyl Groups in Silica Fibers

    Science.gov (United States)

    Plotnichenko, Victor G.; Ivanov, Gennadii A.; Kryukova, Elena B.; Aksenov, Vyacheslav A.; Sokolov, Vyacheslav O.; Isaev, Victor A.

    2005-01-01

    To study the hydroxyl (OH)-group contamination mechanisms in silica-based optical fibers, the transmission spectra of substrate tubes and fiber preforms made from various types of silica glasses ("Suprasil F-300," KS-4V, and KUVI) are measured by the method of infrared Fourier spectroscopy in a wavelength region of 2-5 μm. Due to the intensity of the fundamental OH stretching vibration band, the absorption coefficient, concentration, and a distribution profile of OH groups across the aforesaid samples are calculated. It is found that using an oxyhydrogen burner in the modified chemical vapor deposition (MCVD) process of manufacturing preforms and fiber drawing, the main source of impurity OH groups can be the molecular hydrogen H2 penetrating into glass much deeper than the OH groups diffusing from the substrate tube surface. A simple model explaining the formation and diffusion of OH groups into a fiber core and cladding is proposed. It is shown that heating tubes and preforms in a flame of oxyhydrogen burner during fiber fabrication causes a significant OH-group content growth (almost by two orders of magnitude) near to the outer preform surface. Using substrate tubes made from Suprasil F-300 glass, optical fibers are fabricated having a silica core and fluorosilicate reflecting cladding with optical losses of 0.3 dB/km at 1.55 μm and a refractive-index difference between core and cladding ~ 1 . 10^-2.

  20. Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems

    Directory of Open Access Journals (Sweden)

    Xiunan Wang

    2015-01-01

    Full Text Available Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS. In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of graphene sheets as well as the number and types of drug molecules. Our study shows that the binding of graphene-drug complex is favorable when the drug molecules and finite graphene sheets become comparable in sizes. The boundaries of finite sized graphene sheets restrict the movement of drug molecules. The double-side loading often slows down the diffusion of drug molecules compared with the single-side loading. The drug molecules bind more strongly with GO-PEG than with pristine graphene sheets, demonstrating the advantages of functionalization in improving the stability and biocompatibility of graphene-based DDS.

  1. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow

    Science.gov (United States)

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.

    2016-07-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.

  2. Interstellar CN and CH+ in Diffuse Molecular Clouds: 12C/13C Ratios and CN Excitation

    CERN Document Server

    Ritchey, A M; Lambert, D L

    2010-01-01

    We present very high signal-to-noise ratio absorption-line observations of CN and CH+ along 13 lines of sight through diffuse molecular clouds. The data are examined to extract precise isotopologic ratios of 12CN/13CN and 12CH+/13CH+ in order to assess predictions of diffuse cloud chemistry. Our results on 12CH+/13CH+ confirm that this ratio does not deviate from the ambient 12C/13C ratio in local interstellar clouds, as expected if the formation of CH+ involves nonthermal processes. We find that 12CN/13CN, however, can be significantly fractionated away from the ambient value. The dispersion in our sample of 12CN/13CN ratios is similar to that found in recent surveys of 12CO/13CO. For sight lines where both ratios have been determined, the 12CN/13CN ratios are generally fractionated in the opposite sense compared to 12CO/13CO. Chemical fractionation in CO results from competition between selective photodissociation and isotopic charge exchange. An inverse relationship between 12CN/13CN and 12CO/13CO follows ...

  3. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bhatia, Harsh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gyulassy, Attila [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ong, Mitchell [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Draeger, Erik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pask, John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-09-27

    The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.

  4. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

    Science.gov (United States)

    Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  5. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

    Science.gov (United States)

    Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C

    2014-12-16

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

  6. Diffusion of methane and carbon dioxide in carbon molecular sieve membranes by multinuclear pulsed field gradient NMR.

    Science.gov (United States)

    Mueller, Robert; Kanungo, Rohit; Kiyono-Shimobe, Mayumi; Koros, William J; Vasenkov, Sergey

    2012-07-10

    Carbon molecular sieve (CMS) membranes are promising materials for energy efficient separations of light gases. In this work, we report a detailed microscopic study of carbon dioxide and methane self-diffusion in three CMS membrane derived from 6FDA/BPDA(1:1)-DAM and Matrimid polymers. In addition to diffusion of one-component sorbates, diffusion of a carbon dioxide/methane mixture was investigated. Self-diffusion studies were performed by the multinuclear (i.e., (1)H and (13)C) pulsed field gradient (PFG) NMR technique which combines the advantages of high field (17.6 T) NMR and high magnetic field gradients (up to 30 T/m). Diffusion measurements were carried out at different temperatures and for a broad range of the root-mean-square displacements of gas molecules inside the membranes. The diffusion data obtained from PFG NMR are compared with the corresponding results of membrane permeation measurements reported previously for the same membrane types. The observed differences between the transport diffusivities and self-diffusion coefficients of carbon dioxide and methane are discussed.

  7. Insight into the topology effect on the diffusion of ethene and propene in zeolites: A molecular dynamics simulation study

    Institute of Scientific and Technical Information of China (English)

    Chuanming; Wang; Bowei; Li; Yangdong; Wang; Zaiku; Xie

    2013-01-01

    Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of products.Besides the topology effect on reaction kinetics,the topology influences the diffusion of reactants and products in catalysts as well.In this work,by using COMPASS force-field molecular dynamics method,we investigated the intracrystalline diffusion of ethene and propene in four different zeolites,CHA,MFI,BEA and FAU,at different temperatures.The self-diffusion coefficients and diffusion activation barriers were calculated.A strong restriction on the diffusion of propene in CHA was observed because the self-diffusion coefficient ratio of ethene to propene is larger than 18 and the diffusion activation barrier of propene is more than 20 kJ/mol in CHA.This ratio decreases with the increase of temperature in the four investigated zeolites.The shape selectivity on products from diffusion perspective can provide some implications on the understanding of the selectivity difference between HSAPO-34 and HZSM-5 catalysts for the MTO conversion.

  8. Structure, hydrolysis and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

    CERN Document Server

    Jiang, Zhen; Alexandrov, Vitaly

    2016-01-01

    A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries (RFB). Here, we employ Car-Parrinello molecular dynamics (CPMD) simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction and diffusion of aqueous V$^{2+}$, V$^{3+}$, VO$^{2+}$, and VO$_2^+$ ions at 300 K. The results indicate that the first hydration shell of both V$^{2+}$ and V$^{3+}$ contains six water molecules, while VO$^{2+}$ is coordinated to five and VO$_2^+$ to three water ligands. The first acidity constants (p$K_\\mathrm{a}$) estimated using metadynamics simulations are 2.47, 3.06 and 5.38 for aqueous V$^{3+}$, VO$_2^+$ and VO$^{2+}$, respectively, while V$^{2+}$ is predicted to be a fairly weak acid in aqueous solution with a p$K_\\mathrm{a}$ value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO$_2^+$ ion has a...

  9. Receivers for Diffusion-Based Molecular Communication: Exploiting Memory and Sampling Rate

    CERN Document Server

    Mosayebi, Reza; Gohari, Amin; Kenari, Masoumeh Nasiri; Mitra, Urbashi

    2014-01-01

    In this paper, a diffusion-based molecular communication channel between two nano-machines is considered. The effect of the amount of memory on performance is characterized, and a simple memory-limited decoder is proposed and its performance is shown to be close to that of the best possible imaginable decoder (without any restriction on the computational complexity or its functional form), using Genie-aided upper bounds. This effect is specialized for the case of Molecular Concentration Shift Keying; it is shown that a four-bits memory achieved nearly the same performance as infinite memory. Then a general class of threshold decoders is considered and shown not to be optimal for Poisson channel with memory, unless SNR is higher than a value specified in the paper. Another contribution is to show that receiver sampling at a rate higher than the transmission rate, i.e., a multi-read system, can significantly improve the performance. The associated decision rule for this system is shown to be a weighted sum of t...

  10. Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations

    Science.gov (United States)

    Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

    2017-09-01

    The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

  11. VizieR Online Data Catalog: Hydrogen in diffuse molecular clouds (Winkel+, 2017)

    Science.gov (United States)

    Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.

    2017-01-01

    To study the Hydrogen in diffuse molecular clouds in the Milky Way, eight sources were observed with the Jansky Very Large Array in spectral line mode at 21-cm. The targets have bright continuum emission and were used as background sources for HI absorption spectroscopy. The brightest positions in the background continuum images were used to define several sight lines per source and to extract associated HI absorption spectra. To obtain spin temperatures and corrected HI column densities, suitable Off-position spectra were acquired, making use of the three Galactic plane surveys: Canadian Galactic Plane Survey (CGPS, Taylor et al., 2003AJ....125.3145T), Southern Galactic Plane Survey (SGPS, McClure-Griffiths et al., 2005ApJS..158..178M), and VLA Galactic Plane Survey (VGPS, Stil et al., 2006AJ....132.1158S). Furthermore, for some of the sight lines 550-GHz HF spectra are available, observed with the Herschel space telescope. With these, the molecular hydrogen column density can be estimated, and in combination with the HI column densities, the molecular fraction is determined. The calculation of all result spectra was done with Bayesian Markov-Chain Monte Carlo using the Python PyMC3 framework (Patil, Huard, and Fonnesbeck, DOI: 10.18637/jss.v035.i04). In the FITS binary tables, provided here, the results of our Bayes sampling are contained. For each sight line, we provide seven spectra per quantity (i.e, the -3, -2, -1, 0, 1, 2, and 3 confidence levels) plus the full Bayes chains (1000 steps) for the following variables: Tcsou, Tcbg, tau, Tspin, NHI, NH2, and F{H2/H}, because the latter are not Normal distributed. (3 data files).

  12. Two-dimensional assembly based on flow supramolecular chemistry: kinetic control of molecular interactions under solvent diffusion.

    Science.gov (United States)

    Numata, Munenori; Kozawa, Tomohiro

    2014-05-19

    Self-assembly of porphyrin molecules can be controlled kinetically to form structures with lengths extending from the nano- to the micrometer scale, through a programmed solvent-diffusion process in designed microflow spaces. Temporal solvent structures generated in the microflow were successfully transcribed into molecular architectures.

  13. Intramolecular diffusive motion in alkane monolayers studied by high-resolution quasielastic neutron scattering and molecular dynamics simulations

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D;

    2004-01-01

    Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence that these rel...

  14. Adsorption and diffusion of alkanes in CuBTC crystals investigated using infra-red microscopy and molecular simulations

    NARCIS (Netherlands)

    Chmelik, C.; Kärger, J.; Wiebcke, M.; Caro, J.; van Baten, J.M.; Krishna, R.

    2009-01-01

    The adsorption and intra-crystalline diffusion of n-butane (nC4), iso-butane (iC4), 2-methylbutane (2MB), and 2,2-dimethylpropane (neoP) in CuBTC (Cu-3(BTC)(2) where BTC = benzene-1,3,5-tricarboxylate) has been investigated using infrared microscopy (IRM), combined with molecular simulations. Both e

  15. Effect of bending and torsion rigidity on self-diffusion in polymer melts : A molecular-dynamics study

    NARCIS (Netherlands)

    Bulacu, M; van der Giessen, E

    2005-01-01

    Extensive molecular-dynamics simulations have been performed to study the effect of chain conformational rigidity, controlled by bending and torsion potentials, on self-diffusion in polymer melts. The polymer model employs a novel torsion potential that avoids computational singularities without the

  16. Investigating the relative influences of molecular dimensions and binding energies on diffusivities of guest species inside nanoporous crystalline materials

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2012-01-01

    The primary objective of this article is to investigate the relative influences of molecular dimensions and adsorption binding energies on unary diffusivities of guest species inside nanoporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). The investigations are based o

  17. Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations.

    Science.gov (United States)

    Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf

    2017-03-22

    Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.

  18. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    Energy Technology Data Exchange (ETDEWEB)

    Wyrick, Jonathan; Bartels, Ludwig, E-mail: ludwig.bartels@ucr.edu [Pierce Hall, University of California-Riverside, Riverside, California 92521 (United States); Einstein, T. L. [Department of Physics and Condensed Matter Theory Center, University of Maryland, College Park, Maryland 20742-4111 (United States)

    2015-03-14

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  19. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    Science.gov (United States)

    Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

    2015-03-01

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  20. Molecular dynamics study on the diffusion behavior of Li in the grain boundaries of α-Fe

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Xingang, E-mail: xgyu@ucas.ac.cn [School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049 (China); Liu, Chengrui [Beijing Institute of Control Engineering, Beijing 100190 (China); Han, Tiansi [Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 (China); Gan, Xianglai [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

    2016-11-01

    Highlights: • Confirmed the strong binding effect between the grain boundaries and lithium interstitials. • Determined the critical temperatures for a lithium atom to diffuse in the grain boundaries. • Revealed that the diffusion mechanism of a lithium atom depends on the grain boundary structure. - Abstract: Liquid lithium has been considered as a candidate material for several components of future fusion devices. Since the containment materials are usually ferrous alloys, molecular dynamics simulations were performed to study the diffusion behavior of lithium atoms along <110> tilt grain boundaries (GB) including Σ9{114}, Σ11{113}, Σ3{112} and Σ11{332} in α-Fe. The binding energies of a Li interstitial to the GBs were calculated. The results suggest that all the GBs have strong binding effect on the Li atom. The critical temperatures for the Li atom to diffuse were determined. The diffusion process of a Li interstitial in the GBs was systematically analyzed. It turns out that the diffusion mechanism depends on the GB structures. For Σ11{113} and GB Σ9{114}, the Li atom was trapped by the Frenkel defect around the GBs at 300 K and 400 K respectively and therefore the diffusion was slowed down rapidly. For Σ3{112}, no defects were formed around GB and the Li atom diffused into Fe bulk at 700 K and above. For Σ3{112}, the diffusion process is driven by the movement of the GB. Finally, the diffusion coefficient, as well as the activation energy, was evaluated.

  1. A rain induced landslide 3D model based on molecular dynamics with fractal and fractional water diffusion

    CERN Document Server

    Martelloni, Gianluca; Guarino, Alessio

    2016-01-01

    We present a three-dimensional model, based on cohesive spherical particles, of rain-induced landslides. The rainwater infiltration into the soil follow the either the fractional or the fractal diffusion equations. We solve analytically the fractal diffusion partial differential equation (PDE) with particular boundary conditions to simulate a rainfall event. Then, for the PDE, we developed a numerical integration scheme that we integrate with MD (Molecular Dynamics) algorithm for the triggering and propagation of the simulated landslide. Therefore we test the numerical integration scheme of fractal diffusion equation with the analytical solution. We adopt the fractal diffusion equation in term of gravimetric water content that we use as input of triggering scheme based on Mohr-Coulomb limit-equilibrium criterion, adapted to particle level. Moreover, taking into account an interacting force Lennard-Jones inspired, we use a standard MD algorithm to update particle positions and velocities. Then we present resul...

  2. Molecular Diffusion of Volatiles in Lunar Regolith during the Resource Prospector Mission Sample Acquisition

    Science.gov (United States)

    Teodoro, L. A.; Colaprete, A.; Roush, T. L.; Elphic, R. C.; Cook, A.; Kleinhenz, J.; Fritzler, E.; Smith, J. T.; Zacny, K.

    2016-12-01

    In the context of NASA's Resource Prospector (RP) mission to the high latitudes and permanently shadowed regions of the Moon, we study 3D models of volatile transport in the lunar regolith. This mission's goal is to extract and identify volatile species in the top meter of the lunar regolith layer. Roughly, RP consists of 5 elements: i) the Neutron Spectrometer System will search for high hydrogen concentrations and in turn select optimum drilling locations; ii) The Near Infrared Volatile Spectrometer System (NIRVSS) will characterize the nature of the surficial water ice; iii) The Drill Sub-system will extract samples from the top meter of the lunar surface and deliver them to the Oxygen and Volatile Extraction Node (OVEN); iv) OVEN will heat up the sample and extract the volatiles therein, that will be v) transferred to the Lunar Advanced Volatiles Analysis system for chemical composition analysis. A series of vacuum cryogenic experiments have been carried out at Glenn Research Center with the aim of quantifying the volatile losses during the drilling/sample acquisition phase and sample delivery to crucibles steps. These experiments' outputs include: i) Pressure measurements of several chemical species (e.g. H2O, Ar); ii) Temperature measurements within and at the surface of the lunar simulant using thermocouples; and iii) Surficial temperature NIRVSS measurements. Here, we report on the numerical modeling we are carrying out to understand the physics underpinning these experiments. The models include 2 main parts: i) reliable computation of temperature variation throughout the lunar soil container during the experiment as constrained by temperature measurements; and ii) molecular diffusion of volatiles. The latter includes both Fick's (flight of the molecules in the porous) and Knudsen's (sublimation of volatile molecules at the grain surface) laws. We also mimic the soil porosity by randomly allocating 75 microns particles in the simulation volume. Our

  3. Characterization of water molecular state in in-vivo thick tissues using diffuse optical spectroscopic imaging

    Science.gov (United States)

    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 (pbreast 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.

  4. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

    Science.gov (United States)

    Preto, Jordane; Clementi, Cecilia

    2014-09-28

    The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

  5. The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas.

    Directory of Open Access Journals (Sweden)

    Lee A D Cooper

    Full Text Available The Cancer Genome Atlas Project (TCGA has produced an extensive collection of '-omic' data on glioblastoma (GBM, resulting in several key insights on expression signatures. Despite the richness of TCGA GBM data, the absence of lower grade gliomas in this data set prevents analysis genes related to progression and the uncovering of predictive signatures. A complementary dataset exists in the form of the NCI Repository for Molecular Brain Neoplasia Data (Rembrandt, which contains molecular and clinical data for diffuse gliomas across the full spectrum of histologic class and grade. Here we present an investigation of the significance of the TCGA consortium's expression classification when applied to Rembrandt gliomas. We demonstrate that the proneural signature predicts improved clinical outcome among 176 Rembrandt gliomas that includes all histologies and grades, including GBMs (log rank test p = 1.16e-6, but also among 75 grade II and grade III samples (p  =  2.65e-4. This gene expression signature was enriched in tumors with oligodendroglioma histology and also predicted improved survival in this tumor type (n =  43, p  =  1.25e-4. Thus, expression signatures identified in the TCGA analysis of GBMs also have intrinsic prognostic value for lower grade oligodendrogliomas, and likely represent important differences in tumor biology with implications for treatment and therapy. Integrated DNA and RNA analysis of low-grade and high-grade proneural gliomas identified increased expression and gene amplification of several genes including GLIS3, TGFB2, TNC, AURKA, and VEGFA in proneural GBMs, with corresponding loss of DLL3 and HEY2. Pathway analysis highlights the importance of the Notch and Hedgehog pathways in the proneural subtype. This demonstrates that the expression signatures identified in the TCGA analysis of GBMs also have intrinsic prognostic value for low-grade oligodendrogliomas, and likely represent important differences in tumor

  6. Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.

    Science.gov (United States)

    Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma

    2015-11-01

    Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time.

  7. Diffusion behavior of helium in titanium and the effect of grain boundaries revealed by molecular dynamics simulation

    Science.gov (United States)

    Gui-Jun, Cheng; Bao-Qin, Fu; Qing, Hou; Xiao-Song, Zhou; Jun, Wang

    2016-07-01

    The microstructures of titanium (Ti), an attractive tritium (T) storage material, will affect the evolution process of the retained helium (He). Understanding the diffusion behavior of He at the atomic scale is crucial for the mechanism of material degradation. The novel diffusion behavior of He has been reported by molecular dynamics (MD) simulation for the bulk hcp-Ti system and the system with grain boundary (GB). It is observed that the diffusion of He in the bulk hcp-Ti is significantly anisotropic (the diffusion coefficient of the [0001] direction is higher than that of the basal plane), as represented by the different migration energies. Different from convention, the GB accelerates the diffusion of He in one direction but not in the other. It is observed that a twin boundary (TB) can serve as an effective trapped region for He. The TB accelerates diffusion of He in the direction perpendicular to the twinning direction (TD), while it decelerates the diffusion in the TD. This finding is attributable to the change of diffusion path caused by the distortion of the local favorable site for He and the change of its number in the TB region. Project supported by the National Natural Science Foundation of China (Grant No. 51501119), the Scientific Research Starting Foundation for Younger Teachers of Sichuan University, China (Grant No. 2015SCU11058), the National Magnetic Confinement Fusion Science Program of China (Grant No. 2013GB109002), and the Cooperative Research Project “Research of Diffusion Behaviour of He in Grain Boundary of HCP-Titanium”, China.

  8. Origin of CH+ in diffuse molecular clouds. Warm H2 and ion-neutral drift

    Science.gov (United States)

    Valdivia, Valeska; Godard, Benjamin; Hennebelle, Patrick; Gerin, Maryvonne; Lesaffre, Pierre; Le Bourlot, Jacques

    2017-04-01

    Context. Molecular clouds are known to be magnetised and to display a turbulent and complex structure where warm and cold phases are interwoven. The turbulent motions within molecular clouds transport molecules, and the presence of magnetic fields induces a relative velocity between neutrals and ions known as the ion-neutral drift (vd). These effects all together can influence the chemical evolution of the clouds. Aims: This paper assesses the roles of two physical phenomena which have previously been invoked to boost the production of CH+ under realistic physical conditions: the presence of warm H2 and the increased formation rate due to the ion-neutral drift. Methods: We performed ideal magnetohydrodynamical (MHD) simulations that include the heating and cooling of the multiphase interstellar medium (ISM), and where we treat dynamically the formation of the H2 molecule. In a post-processing step we compute the abundances of species at chemical equilibrium using a solver that we developed. The solver uses the physical conditions of the gas as input parameters, and can also prescribe the H2 fraction if needed. We validate our approach by showing that the H2 molecule generally has a much longer chemical evolution timescale compared to the other species. Results: We show that CH+ is efficiently formed at the edge of clumps, in regions where the H2 fraction is low (0.3-30%) but nevertheless higher than its equilibrium value, and where the gas temperature is high (≳ 300 K). We show that warm and out of equilibrium H2 increases the integrated column densities of CH+ by one order of magnitude up to values still 3-10 times lower than those observed in the diffuse ISM. We balance the Lorentz force with the ion-neutral drag to estimate the ion-drift velocities from our ideal MHD simulations. We find that the ion-neutral drift velocity distribution peaks around 0.04 km s-1, and that high drift velocities are too rare to have a significant statistical impact on the

  9. THE INFLUENCE OF THERMO-CHEMICAL TREATMENT ON THE MOLECULAR DIFFUSION COEFFICIENT OF SUCROSE FROM SUGAR BEET

    Directory of Open Access Journals (Sweden)

    N. G. Kulneva

    2014-01-01

    Full Text Available Traditional methods of extraction do not provide the required amount of sucrose extraction from sugar beet pulp. To improve the process it is advisable to use additional methods of processing pulp, including the thermo-physical methods using various coolants. Thermal pre-treatment of sugar beet pulp can increase the period of active extraction, the recovery of sucrose from it and reduce the loss of sugar in the pulp, increase the productivity of diffusion unit. One of the most important criteria for evaluating the efficiency of the extraction process is the value of the molecular diffusion coefficient D, m2/s. The coefficient is a physical constant that characterizes the ability of a substance to penetrate by diffusion in the stationary medium. One of the most promising technological directions that increases the efficiency of the extraction process and accelerates the extraction of sugar from the pulp, is its scalding, as well as the use of different extractants for the diffusion process. The method of extraction sucrose from sugar beet with the application of preliminary scalding of sugar beet samples and the use of solutions of various salts as extractants was proposed. Positive effect of heat treatment on the molecular diffusion coefficient of sucrose from sugar beet was found experimentally. The value of the optimal duration of scalding is 30 seconds. It was found out that the heat treatment of sugar beet samples with the solutions of proposed salts leads to a gradual uniform heating of beet tissues and denaturation of proteins, which increases the diffusion coefficient of the sugar beet tissue sucrose. The maximum value of the diffusion coefficient is achieved by using as an extractant solution of ammonium sulfate (NH42SO4. The optimal value of the duration of contact of sugar beet pulp and the proposed reactant was determined and it accounted 30 seconds.

  10. Comparison of ion sites and diffusion paths in glasses obtained by molecular dynamics simulations and bond valence analysis

    OpenAIRE

    Muller, Christian; Zienicke, Egbert; Adams, Stefan; Habasaki, Junko; Maass, Philipp

    2006-01-01

    Based on molecular dynamics simulations of a lithium metasilicate glass we study the potential of bond valence sum calculations to identify sites and diffusion pathways of mobile Li ions in a glassy silicate network. We find that the bond valence method is not well suitable to locate the sites, but allows one to estimate the number of sites. Spatial regions of the glass determined as accessible for the Li ions by the bond valence method can capture up to 90% of the diffusion path. These regio...

  11. CANCELLED Molecular dynamics simulations of noble gases in liquidwater: Solvati on structure, self-diffusion, and kinetic isotopeeffect

    Energy Technology Data Exchange (ETDEWEB)

    Bourg, I.C.; Sposito, G.

    2007-05-25

    Despite their great importance in low-temperaturegeochemistry, self-diffusion coefficients of noble gas isotopes in liquidwater (D) have been measured only for the major isotopes of helium, neon,krypton and xenon. Data on the self-diffusion coefficients of minor noblegas isotopes are essentially non-existent and so typically are estimatedby a kinetic theory model in which D varies as the inverse square root ofthe isotopic mass (m): D proportional to m-0.5. To examine the validityof the kinetic theory model, we performed molecular dynamics (MD)simulations of the diffusion of noble gases in ambient liquid water withan accurate set of noble gas-water interaction potentials. Our simulationresults agree with available experimental data on the solvation structureand self-diffusion coefficients of the major noble gas isotopes in liquidwater and reveal for the first time that the isotopic mass-dependence ofall noble gas self-diffusion coefficients has the power-law form Dproportional to m-beta with 0diffusion in ambient liquid water.

  12. Molecular imaging probes spy on the body's inner workings: miniaturized microscopes, microbubbles, 7- and 15-T scanners, diffusion-tensor MRI, and other molecular-imaging technologies are pushing molecular imaging into the future.

    Science.gov (United States)

    Mertz, Leslie

    2013-01-01

    Molecular imaging is one of the hot-button areas within medical imaging. This technology employs imaging techniques in concert with molecular probes, or biomarkers, that together noninvasively spy on cellular function and molecular processes. In some cases, this technology may be able to detect the very earliest stages of diseases and eliminate them on the spot. This paper discusses how miniaturized microscopes, microbubbles, 7T and 15T scanners, diffusion-tensor MRI and other molecular imaging technologies are pushing molecular imaging into the future.

  13. DIFFUSE ATOMIC AND MOLECULAR GAS IN THE INTERSTELLAR MEDIUM OF M82 TOWARD SN 2014J

    Energy Technology Data Exchange (ETDEWEB)

    Ritchey, Adam M. [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Welty, Daniel E.; York, Donald G. [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States); Dahlstrom, Julie A., E-mail: aritchey@astro.washington.edu [Department of Physics and Astronomy, Carthage College, 2001 Alford Park Dr., Kenosha, WI 53140 (United States)

    2015-02-01

    We present a comprehensive analysis of interstellar absorption lines seen in moderately high resolution, high signal-to-noise ratio optical spectra of SN 2014J in M82. Our observations were acquired over the course of six nights, covering the period from ∼6 days before to ∼30 days after the supernova reached its maximum B-band brightness. We examine complex absorption from Na I, Ca II, K I, Ca I, CH{sup +}, CH, and CN, arising primarily from diffuse gas in the interstellar medium (ISM) of M82. We detect Li I absorption over a range in velocity consistent with that exhibited by the strongest Na I and K I components associated with M82; this is the first detection of interstellar Li in a galaxy outside of the Local Group. There are no significant temporal variations in the absorption-line profiles over the 37 days sampled by our observations. The relative abundances of the various interstellar species detected reveal that the ISM of M82 probed by SN 2014J consists of a mixture of diffuse atomic and molecular clouds characterized by a wide range of physical/environmental conditions. Decreasing N(Na I)/N(Ca II) ratios and increasing N(Ca I)/N(K I) ratios with increasing velocity are indicative of reduced depletion in the higher-velocity material. Significant component-to-component scatter in the N(Na I)/N(Ca II) and N(Ca I)/N(Ca II) ratios may be due to variations in the local ionization conditions. An apparent anti-correlation between the N(CH{sup +})/N(CH) and N(Ca I)/N(Ca II) ratios can be understood in terms of an opposite dependence on gas density and radiation field strength, while the overall high CH{sup +} abundance may be indicative of enhanced turbulence in the ISM of M82. The Li abundance also seems to be enhanced in M82, which supports the conclusions of recent gamma-ray emission studies that the cosmic-ray acceleration processes are greatly enhanced in this starburst galaxy.

  14. Diffuse Atomic and Molecular Gas in the Interstellar Medium of M82 toward SN 2014J

    Science.gov (United States)

    Ritchey, Adam M.; Welty, Daniel E.; Dahlstrom, Julie A.; York, Donald G.

    2015-02-01

    We present a comprehensive analysis of interstellar absorption lines seen in moderately high resolution, high signal-to-noise ratio optical spectra of SN 2014J in M82. Our observations were acquired over the course of six nights, covering the period from ~6 days before to ~30 days after the supernova reached its maximum B-band brightness. We examine complex absorption from Na I, Ca II, K I, Ca I, CH+, CH, and CN, arising primarily from diffuse gas in the interstellar medium (ISM) of M82. We detect Li I absorption over a range in velocity consistent with that exhibited by the strongest Na I and K I components associated with M82; this is the first detection of interstellar Li in a galaxy outside of the Local Group. There are no significant temporal variations in the absorption-line profiles over the 37 days sampled by our observations. The relative abundances of the various interstellar species detected reveal that the ISM of M82 probed by SN 2014J consists of a mixture of diffuse atomic and molecular clouds characterized by a wide range of physical/environmental conditions. Decreasing N(Na I)/N(Ca II) ratios and increasing N(Ca I)/N(K I) ratios with increasing velocity are indicative of reduced depletion in the higher-velocity material. Significant component-to-component scatter in the N(Na I)/N(Ca II) and N(Ca I)/N(Ca II) ratios may be due to variations in the local ionization conditions. An apparent anti-correlation between the N(CH+)/N(CH) and N(Ca I)/N(Ca II) ratios can be understood in terms of an opposite dependence on gas density and radiation field strength, while the overall high CH+ abundance may be indicative of enhanced turbulence in the ISM of M82. The Li abundance also seems to be enhanced in M82, which supports the conclusions of recent gamma-ray emission studies that the cosmic-ray acceleration processes are greatly enhanced in this starburst galaxy.

  15. Non-equilibrium molecular dynamics simulation of thermal conductivity and thermal diffusion of binary mixtures confined in a nanochannel

    Science.gov (United States)

    Pourali, Meisam; Maghari, Ali

    2014-11-01

    In this paper, direct non-equilibrium molecular dynamics simulation is developed to investigate thermal conductivity and thermal diffusion factors of confined binary mixtures of methane and some n-alkanes in a nanochannel. We used two thermal walls in different temperatures to impose temperature gradient in the system. The mixtures are confined between two parallel atomic walls, normal to temperature gradient. Simulation results show high inhomogeneity and layering in the mixtures. Thermal conductivity of mixtures increases with decreasing the channel width and increases in mixtures with high concentration of methane. Except for very small channels, confinement has minimal effect on thermal diffusion. In very narrow channels, thermal diffusion is small and it reaches a steady state value with increasing the channel width. Local velocity fields for two different channels also show different behaviors. In relatively large channels some convection patterns are observed in mixtures.

  16. Non-equilibrium molecular dynamics simulation of thermal conductivity and thermal diffusion of binary mixtures confined in a nanochannel

    Energy Technology Data Exchange (ETDEWEB)

    Pourali, Meisam; Maghari, Ali, E-mail: maghari@ut.ac.ir

    2014-11-24

    In this paper, direct non-equilibrium molecular dynamics simulation is developed to investigate thermal conductivity and thermal diffusion factors of confined binary mixtures of methane and some n-alkanes in a nanochannel. We used two thermal walls in different temperatures to impose temperature gradient in the system. The mixtures are confined between two parallel atomic walls, normal to temperature gradient. Simulation results show high inhomogeneity and layering in the mixtures. Thermal conductivity of mixtures increases with decreasing the channel width and increases in mixtures with high concentration of methane. Except for very small channels, confinement has minimal effect on thermal diffusion. In very narrow channels, thermal diffusion is small and it reaches a steady state value with increasing the channel width. Local velocity fields for two different channels also show different behaviors. In relatively large channels some convection patterns are observed in mixtures.

  17. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems

    Science.gov (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.

    2006-03-01

    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  18. MRI features predict survival and molecular markers in diffuse lower-grade gliomas.

    Science.gov (United States)

    Zhou, Hao; Vallières, Martin; Bai, Harrison X; Su, Chang; Tang, Haiyun; Oldridge, Derek; Zhang, Zishu; Xiao, Bo; Liao, Weihua; Tao, Yongguang; Zhou, Jianhua; Zhang, Paul; Yang, Li

    2017-06-01

    Previous studies have shown that MR imaging features can be used to predict survival and molecular profile of glioblastoma. However, no study of a similar type has been performed on lower-grade gliomas (LGGs). Presurgical MRIs of 165 patients with diffuse low- and intermediate-grade gliomas (histological grades II and III) were scored according to the Visually Accessible Rembrandt Images (VASARI) annotations. Radiomic models using automated texture analysis and VASARI features were built to predict isocitrate dehydrogenase 1 (IDH1) mutation, 1p/19q codeletion status, histological grade, and tumor progression. Interrater analysis showed significant agreement in all imaging features scored (k = 0.703-1.000). On multivariate Cox regression analysis, no enhancement and a smooth non-enhancing margin were associated with longer progression-free survival (PFS), while a smooth non-enhancing margin was associated with longer overall survival (OS) after taking into account age, grade, tumor location, histology, extent of resection, and IDH1 1p/19q subtype. Using logistic regression and bootstrap testing evaluations, texture models were found to possess higher prediction potential for IDH1 mutation, 1p/19q codeletion status, histological grade, and progression of LGGs than VASARI features, with areas under the receiver-operating characteristic curves of 0.86 ± 0.01, 0.96 ± 0.01, 0.86 ± 0.01, and 0.80 ± 0.01, respectively. No enhancement and a smooth non-enhancing margin on MRI were predictive of longer PFS, while a smooth non-enhancing margin was a significant predictor of longer OS in LGGs. Textural analyses of MR imaging data predicted IDH1 mutation, 1p/19q codeletion, histological grade, and tumor progression with high accuracy.

  19. The 9.7 and 18 um silicate absorption profiles towards diffuse and molecular cloud lines-of-sight

    CERN Document Server

    van Breemen, J M; Chiar, J E; Waters, L B F M; Kemper, F; Boogert, A C A; Cami, J; Decin, L; Knez, C; Sloan, G C; Tielens, A G G M

    2010-01-01

    Studying the composition of dust in the interstellar medium (ISM) is crucial in understanding the cycle of dust in our galaxy. The mid-infrared spectral signature of amorphous silicates, the most abundant dust species in the ISM, is studied in different lines-of-sight through the Galactic plane, thus probing different conditions in the ISM. We have analysed 10 spectra from the Spitzer archive, of which 6 lines-of-sight probe diffuse interstellar medium material and 4 probe molecular cloud material. The 9.7 um silicate absorption features in 7 of these spectra were studied in terms of their shape and strength. In addition, the shape of the 18 um silicate absorption features in 4 of the diffuse sightline spectra were analysed. The 9.7 um silicate absorption bands in the diffuse sightlines show a strikingly similar band shape. This is also the case for all but one of the 18 um silicate absorption bands observed in diffuse lines-of-sight. The 9.7 um bands in the 4 molecular sightlines show small variations in sha...

  20. Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

    Science.gov (United States)

    Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

    2012-01-01

    This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.

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

    Science.gov (United States)

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

    2015-01-01

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

  2. Molecular surface area based predictive models for the adsorption and diffusion of disperse dyes in polylactic acid matrix.

    Science.gov (United States)

    Xu, Suxin; Chen, Jiangang; Wang, Bijia; Yang, Yiqi

    2015-11-15

    Two predictive models were presented for the adsorption affinities and diffusion coefficients of disperse dyes in polylactic acid matrix. Quantitative structure-sorption behavior relationship would not only provide insights into sorption process, but also enable rational engineering for desired properties. The thermodynamic and kinetic parameters for three disperse dyes were measured. The predictive model for adsorption affinity was based on two linear relationships derived by interpreting the experimental measurements with molecular structural parameters and compensation effect: ΔH° vs. dye size and ΔS° vs. ΔH°. Similarly, the predictive model for diffusion coefficient was based on two derived linear relationships: activation energy of diffusion vs. dye size and logarithm of pre-exponential factor vs. activation energy of diffusion. The only required parameters for both models are temperature and solvent accessible surface area of the dye molecule. These two predictive models were validated by testing the adsorption and diffusion properties of new disperse dyes. The models offer fairly good predictive ability. The linkage between structural parameter of disperse dyes and sorption behaviors might be generalized and extended to other similar polymer-penetrant systems.

  3. A Process for Modelling Diffuse Scattering from Disordered Molecular Crystals, Illustrated by Application to Monoclinic 9-Chloro-10-methylanthracene

    Directory of Open Access Journals (Sweden)

    D. J. Goossens

    2015-01-01

    Full Text Available Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requires significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.

  4. Diffusion of CO{sub 2} Molecules in Polyethylene Terephthalate/Polylactide Blends Estimated by Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Liqiong; Fu, Yizheng; Liang, Ziaoyan; Mei, Linyu; Liu, Yaqing [North Univ. of China, Taiyuan (China)

    2013-03-15

    Molecular dynamics (MD) simulations have been used to study the diffusion behavior of small gas molecules (CO{sub 2}) in polyethylene terephthalate (PET)/polylactide (PLA) blends. The Flory-Huggins interaction parameters (χ) determined from the cohesive energy densities are smaller than the critical value of Flory-Huggins interaction parameters (χ{sub critical}), and that indicates the good compatibility of PET/PLA blends. The diffusion coefficients of CO{sub 2} are determined via MD simulations at 298 K. That the order of diffusion coefficients is correlated with the availably fractional free volume (FFV) of CO{sub 2} in the PET/PLA blends means that the FFV plays a vital role in the diffusion behavior of CO{sub 2} molecules in PET/PLA blends. The slopes of the log (MSD) as a function of log (t) are close to unity over the entire composition range of PET/PLA blends, which confirms the feasibility of MD approach reaches the normal diffusion regime of CO{sub 2} in PET/PLA blends.

  5. The effects of molecular diffusion in spatially encoded magnetic resonance imaging

    Science.gov (United States)

    Marhabaie, Sina; Bodenhausen, Geoffrey; Pelupessy, Philippe

    2016-12-01

    In spatially encoded MRI, the signal is acquired sequentially for different coordinates. In particular for single-scan acquisitions in inhomogeneous fields, spatially encoded methods improve the image quality compared to traditional k-space encoding. Previously, much attention has been paid in order to homogenize T2 losses across the sample. In this work, we investigate the effects of diffusion on the image quality in spatially encoded MRI. We show that losses due to diffusion are often not uniform along the spatially encoded dimension, and how to adapt spatially encoded sequences in order to obtain uniformly diffusion-weighted images.

  6. Molecular subtyping of diffuse large B-cell lymphoma: update on biology, diagnosis and emerging platforms for practising pathologists.

    Science.gov (United States)

    Gifford, Grace K; Gill, Anthony J; Stevenson, William S

    2016-01-01

    Molecular classification of diffuse large B-cell lymphoma (DLBCL) is critical. Numerous methodologies have demonstrated that DLBCL is biologically heterogeneous despite morphological similarities. This underlies the disparate outcomes of treatment response or failure in this common non-Hodgkin lymphoma. This review will summarise historical approaches to lymphoma classifications, current diagnosis of DLBCL, molecular techniques that have primarily been used in the research setting to distinguish and subclassify DLBCL, evaluate contemporary diagnostic methodologies that seek to translate lymphoma biology into clinical practice, and introduce novel diagnostic platforms that may overcome current issues. The review concludes with an overview of key molecular lesions currently identified in DLBCL, all of which are potential targets for drug treatments that may improve survival and cure.

  7. Thermal Diffusion in Liquid Mixtures and Polymer Solutions by Molecular Dynamics Simulations

    OpenAIRE

    2007-01-01

    This thesis is focused on simulating the transport processes of heat and matter under a sufficiently weak temperature gradient where the system linearly responds. The systems we are interested in are binary isotropic liquids with no convection and no viscous flows. Four related transport coefficients of the systems, the thermal conductivity of heat conduction, the diffusion coefficient of matter transfer, the Soret coefficient and the thermal diffusion coefficient of the cross effect between ...

  8. Dual coupled radiative transfer equation and diffusion approximation for the solution of the forward problem in fluorescence molecular imaging

    Science.gov (United States)

    Gorpas, Dimitris; Andersson-Engels, Stefan

    2012-03-01

    The solution of the forward problem in fluorescence molecular imaging is among the most important premises for the successful confrontation of the inverse reconstruction problem. To date, the most typical approach has been the application of the diffusion approximation as the forward model. This model is basically a first order angular approximation for the radiative transfer equation, and thus it presents certain limitations. The scope of this manuscript is to present the dual coupled radiative transfer equation and diffusion approximation model for the solution of the forward problem in fluorescence molecular imaging. The integro-differential equations of its weak formalism were solved via the finite elements method. Algorithmic blocks with cubature rules and analytical solutions of the multiple integrals have been constructed for the solution. Furthermore, specialized mapping matrices have been developed to assembly the finite elements matrix. As a radiative transfer equation based model, the integration over the angular discretization was implemented analytically, while quadrature rules were applied whenever required. Finally, this model was evaluated on numerous virtual phantoms and its relative accuracy, with respect to the radiative transfer equation, was over 95%, when the widely applied diffusion approximation presented almost 85% corresponding relative accuracy for the fluorescence emission.

  9. Classical molecular dynamics investigation of microstructure evolution and grain boundary diffusion in nano-polycrystalline UO2

    Science.gov (United States)

    Govers, K.; Verwerft, M.

    2013-07-01

    The High Burnup Structure (HBS) observed at pellet periphery in conventional Light Water Reactor nuclear fuels and around spots presenting high plutonium content in mixed (U, Pu) oxide fuel - MOX fuel - consists of a restructuration of the original grains into smaller ones. The process is often postulated to occur because of the accumulation of irradiation damage and the retention of fission products in the matrix. The computing power nowadays available enables for simulating larger systems at the atomic scale up to the point that nano-polycrystalline material can now be investigated by empirical potential molecular dynamics. Simulations of nano-polycrystalline UO2 structures have been carried out at various temperatures to investigate atom mobility close to grain boundaries. The variation of Arrhénius parameters for the diffusion coefficient of oxygen, uranium and xenon as a function of the distance from a grain boundary was studied, leading to the distinction of three zones: the grain boundary layers (up to 1 nm depth) presenting enhanced diffusion, an intermediate zone (1 to roughly 2 nm depth) with intermediate diffusion values and the bulk of the grains. The following Arrhénius relations for grain boundary diffusion were derived:

  10. Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study

    Indian Academy of Sciences (India)

    Bhabani S Mallik; Amalendu Chandra

    2012-01-01

    We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.

  11. Translational diffusion in mixtures of imidazolium ILs with polar aprotic molecular solvents.

    Science.gov (United States)

    Marekha, Bogdan A; Kalugin, Oleg N; Bria, Marc; Buchner, Richard; Idrissi, Abdenacer

    2014-05-22

    Self-diffusion coefficients of cations and solvent molecules were determined with (1)H NMR in mixtures of 1-n-butyl-3-methylimidazolium (Bmim(+)) tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethylsulfonyl)imide (TFSI(-)) with acetonitrile (AN), γ-butyrolactone (γ-BL), and propylene carbonate (PC) over the entire composition range at 300 K. The relative diffusivities of solvent molecules to cations as a function of concentration were found to depend on the solvent but not on the anion (i.e., IL). In all cases the values exhibit a plateau at low IL content (x(IL) IL concentrations. This behavior was related to the different solvation patterns in the employed solvents. In BmimPF6-based systems, anionic diffusivities were followed via (31)P nuclei and found to be higher than the corresponding cation values in IL-poor systems and lower in the IL-rich region. The inversion point of relative ionic diffusivities was found around equimolar composition and does not depend on the solvent. At this point, a distinct change in the ion-diffusion mechanism appears to take place.

  12. Molecular simulation and macroscopic modeling of the diffusion of hydrogen, carbon monoxide and water in heavy n-alkane mixtures.

    Science.gov (United States)

    Makrodimitri, Zoi A; Unruh, Dominik J M; Economou, Ioannis G

    2012-03-28

    The self-diffusion coefficient of hydrogen (H(2)), carbon monoxide (CO) and water (H(2)O) in n-alkanes was studied by molecular dynamics simulation. Diffusion in a few pure n-alkanes (namely n-C(8), n-C(20), n-C(64) and n-C(96)) was examined. In addition, binary n-C(12)-n-C(96) mixtures with various compositions as well as more realistic five- and six-n-alkane component mixtures were simulated. In all cases, the TraPPE united atom force field was used for the n-alkane molecules. The force field for the mixture of n-alkanes was initially validated against experimental density values and was shown to be accurate. Moreover, macroscopic correlations for predicting diffusion coefficient of H(2), CO and H(2)O in n-alkanes and mixtures of n-alkanes were developed. The functional form of the correlation was based on the rough hard sphere theory (RHS). The correlation was applied to simulation data and an absolute average deviation (AAD) of 5.8% for pure n-alkanes and 3.4% for n-alkane mixtures was obtained. Correlation parameters vary in a systematic way with carbon number and so they can be used to provide predictions in the absence of any experimental or molecular simulation data. Finally, in order to reduce the number of adjustable parameters, for the n-alkane mixtures the "pseudo-carbon number" approach was used. This approach resulted in relatively higher deviation from MD simulation data (AAD of 18.2%); however, it provides a convenient and fast method to predict diffusion coefficients. The correlations developed here are expected to be useful for engineering calculations related to the design of the Gas-to-Liquid process.

  13. Mutual and Self-Diffusivities in Binary Mixtures of [EMIM][B(CN)4] with Dissolved Gases by Using Dynamic Light Scattering and Molecular Dynamics Simulations.

    Science.gov (United States)

    Koller, Thomas M; Heller, Andreas; Rausch, Michael H; Wasserscheid, Peter; Economou, Ioannis G; Fröba, Andreas P

    2015-07-09

    Ionic liquids (ILs) are possible working fluids for the separation of carbon dioxide (CO2) from flue gases. For evaluating their performance in such processes, reliable mutual-diffusivity data are required for mixtures of ILs with relevant flue gas components. In the present study, dynamic light scattering (DLS) and molecular dynamics (MD) simulations were used for the investigation of the molecular diffusion in binary mixtures of the IL 1-ethyl-3-methylimidazolium tetracyanoborate ([EMIM][B(CN)4]) with the dissolved gases carbon dioxide, nitrogen, carbon monoxide, hydrogen, methane, oxygen, and hydrogen sulfide at temperatures from 298.15 to 363.15 K and pressures up to 63 bar. At conditions approaching infinite dilution of a gas, the Fick mutual diffusivity of the mixture measured by DLS and the self-diffusivity of the corresponding gas calculated by MD simulations match, which could be generally found within combined uncertainties. The obtained diffusivities are in agreement with literature data for the same or comparable systems as well as with the general trend of increasing diffusivities for decreasing IL viscosities. The DLS and MD results reveal distinctly larger molecular diffusivities for [EMIM][B(CN)4]-hydrogen mixtures compared to mixtures with all other gases. This behavior results in the failure of an empirical correlation with the molar volumes of the gases at their normal boiling points. The DLS experiments also showed that there is no noticeable influence of the dissolved gas and temperature on the thermal diffusivity of the studied systems.

  14. How Effective Are Simulated Molecular-Level Experiments for Teaching Diffusion and Osmosis?

    Science.gov (United States)

    Meir, Eli; Perry, Judith; Stal, Derek; Maruca, Susan; Klopfer, Eric

    2005-01-01

    Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger "et al.", 2001; and results herein). Students…

  15. Surface site diffusion and reaction on molecular organizates and colloidal catalysts: a geometrical perspective

    Energy Technology Data Exchange (ETDEWEB)

    Politowicz, P.A.; Kozak, J.J.

    1987-12-01

    The authors study surface-mediated, diffusion-controlled reactive processes on particles whose overall geometry is homeomorphic to a sphere. Rather than assuming that a coreactant can diffuse freely over the surface of the particle to a target site (reaction center), they consider the case where the coreactant can migrate only among N-1 satellite sites that are networked to the reaction site by means of a number of pathways or reaction channels. Five distinct lattice topologies are considered and they study the reaction efficiency both for the case where the satellite sites are passive and for the case where reaction may occur with finite probability at these sites. The results obtained for this class of surface problems are compared with those obtained by assuming that the reaction-diffusion process takes place on a planar, two-dimensional surface (lattice). The applicability of their results to surface-mediated processes on organizates (cells, vesicles, micelles) and on colloidally dispersed catalyst particles is brought out in the Introduction, and the correspondence between the lattice-based, Markovian approach developed here and Fickian models of surface diffusion, particularly with regard to the exponentiality of the decay, is discussed in the concluding section.

  16. Comprehensive Reactive Receiver Modeling for Diffusive Molecular Communication Systems: Reversible Binding, Molecule Degradation, and Finite Number of Receptors

    CERN Document Server

    Ahmadzadeh, Arman; Burkovski, Andreas; Schober, Robert

    2016-01-01

    This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nano-machine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form analytical expression for the expected received signal at the receiver, i.e., the expected number of activated receptors on the surface of the receiver. Then, in the second scenario, we consider the case where the number of receptor molecules is finite and the uniformly distributed receptor molecules cover the receiver surfa...

  17. A molecular dynamics evaluation of the effect of dopant addition on grain boundary diffusion in tin: Implication for whisker growth

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, S., E-mail: soumik.banerjee@wsu.edu [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920 (United States); Dutta, I. [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920 (United States); Majumdar, B.S. [Materials and Metallurgical Engineering Department, New Mexico Tech, Socorro, NM 87801 (United States)

    2016-06-01

    Addition of lead dopant has been known to be an effective way of mitigating whisker growth in tin. However, the toxic nature of lead has necessitated a search for alternative dopant species. Recent investigations have indicated that indium can be an effective agent in reducing whisker growth. In an effort to investigate if reduction in diffusivity of tin atoms near grain boundaries in presence of dopant atoms is the underlying mechanism that causes reduced whisker growth, we employed molecular dynamics simulations to model tin grain boundaries with lead and indium dopants. We simulated pure tin grain boundary as well as grain boundaries with 4% dopants by mole fraction. Our results indicate that the dopant atoms segregate near the grain boundary and forms clusters, which in turn leads to reduced diffusivity of tin atoms by up to a factor of three. Since such reduction in diffusivity alone cannot reduce whisker growth by several orders of magnitude, we conclude that other mechanisms might play a more dominant role in mitigating tin whisker growth.

  18. Influence of molecular lipophilicity on the diffusion of arylpropionate non-steroidal anti-inflammatory drugs into the cerebrospinal fluid.

    Science.gov (United States)

    Matoga, M; Péhourcq, F; Lagrange, F; Tramu, G; Bannwarth, B

    1999-06-01

    The diffusion of seven arylpropionic acid non-steroidal anti-inflammatory drugs (NSAIDs) into the cerebrospinal fluid (CSF) has been investigated in male Wistar rats by means of quantitative structure-activity relationship (QSAR) study. After intraperitoneal administration of each drug (5 mg/kg), blood and CSF samples were collected at different times (0.5, 1, 3, and 6 h). The fraction bound to plasma proteins (fb) was determined using ultracentrifugation. The total (CT) and free (CF) plasma concentrations and the concentrations in CSF (CCSF) were measured by a reversed-phase high performance liquid chromatographic (RP-HPLC) method. The areas under the curve of the free plasma (AUCF) and CSF (AUCCSF) concentrations were calculated according to the trapezoidal rule. The overall drug transit into CSF was estimated by the ratio RAUC (AUCCSF: AUCF). The lipophilicity of the compounds was expressed as their polycratic capacity factors (log k'w) measured in a RP-HPLC system. The RAUC ranged from 0.24 to 6.58 and fb from 91.4 to 99.8%. The compounds with an intermediate lipophilicity value (3 RAUC > 1). A parabolic relationship was found between log k'w and log RAUC, emphasizing the role of molecular lipophilicity in the diffusion into CSF. Considering the fb value of each drug in regard to this non-linear relationship, it can be hypothesized that the diffusion rate of NSAIDs into the CSF depends primarily on the lipophilicity.

  19. Molecular dynamics and analytical Langevin equation approach for the self-diffusion constant of an anisotropic fluid.

    Science.gov (United States)

    Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer

    2009-12-01

    We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.

  20. A Herschel/HIFI Legacy Survey of HF and H2O in the Galaxy: Probing Diffuse Molecular Cloud Chemistry

    CERN Document Server

    Sonnentrucker, P; Neufeld, D A; Flagey, N; Gerin, M; Goldsmith, P; Lis, D; Monje, R

    2015-01-01

    We combine Herschel observations of a total of 12 sources to construct the most uniform survey of HF and H2O in our Galactic disk. Both molecules are detected in absorption along all sight lines. The high spectral resolution of the Heterodyne Instrument for the Far-Infrared (HIFI) allows us to compare the HF and H2O distributions in 47 diffuse cloud components sampling the disk. We find that the HF and H2O velocity distributions follow each other almost perfectly and establish that HF and H2O probe the same gas-phase volume. Our observations corroborate theoretical predictions that HF is a sensitive tracer of H2 in diffuse clouds, down to molecular fractions of only a few percent. Using HF to trace H2 in our sample, we find that the N(H2O)-to-N(HF) ratio shows a narrow distribution with a median value of 1.51. Our results further suggest that H2O might be used as a tracer of H2 -within a factor 2.5- in the diffuse interstellar medium. We show that the measured factor of ~2.5 variation around the median is dri...

  1. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin.

    Science.gov (United States)

    Bancaud, Aurélien; Huet, Sébastien; Daigle, Nathalie; Mozziconacci, Julien; Beaudouin, Joël; Ellenberg, Jan

    2009-12-16

    The nucleus of eukaryotes is organized into functional compartments, the two most prominent being heterochromatin and nucleoli. These structures are highly enriched in DNA, proteins or RNA, and thus thought to be crowded. In vitro, molecular crowding induces volume exclusion, hinders diffusion and enhances association, but whether these effects are relevant in vivo remains unclear. Here, we establish that volume exclusion and diffusive hindrance occur in dense nuclear compartments by probing the diffusive behaviour of inert fluorescent tracers in living cells. We also demonstrate that chromatin-interacting proteins remain transiently trapped in heterochromatin due to crowding induced enhanced affinity. The kinetic signatures of these crowding consequences allow us to derive a fractal model of chromatin organization, which explains why the dynamics of soluble nuclear proteins are affected independently of their size. This model further shows that the fractal architecture differs between heterochromatin and euchromatin, and predicts that chromatin proteins use different target-search strategies in the two compartments. We propose that fractal crowding is a fundamental principle of nuclear organization, particularly of heterochromatin maintenance.

  2. An NMR study of molecular reorientations and diffusion in solid LiBF4

    Science.gov (United States)

    Reynhardt, E. C.; Lourens, J. A. J.

    1984-06-01

    The 19F second moment and the 19F, 11B, and 7Li spin-lattice relaxation times in a powdered sample of LiBF4 have been measured as a function of temperature. The results show that the BF-4 ion reorients isotropically while the Li+ ion remains stationary. The activation energy associated with the BF-4 motion is 8.5 kcal/mol. Above ˜385 K the BF-4 and Li+ diffuse through the lattice resulting in a 19F second moment which is almost zero. The activation energy of this process is 19.2 kcal/mol. A librational motion presumably influences the 19F T1ρ results just before diffusion sets in. The migration of Li+ around the BF-4 ion, which seems to be a strong possibility in the case of an isolated LiBF4 molecule, does not take place in the solid.

  3. Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl

    Science.gov (United States)

    Niblett, S. P.; de Souza, V. K.; Stevenson, J. D.; Wales, D. J.

    2016-07-01

    Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.

  4. Single molecule studies of molecular diffusion in cellular membranes: determining membrane structure.

    Science.gov (United States)

    Ritchie, Ken; Spector, Jeff

    Since the advent of single particle/molecule microscopies, researchers have applied these techniques to understanding the fluid membranes of cells. By observing diffusion of membrane proteins and lipids in live cell membranes of eukaryotic cells, it has been found that membranes contain a mosaic of fluid compartments. Such structure may be instrumental in understanding key characteristics of the membrane. Recent single molecule observations on prokaryotic cell membranes will also be discussed.

  5. Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution.

    Science.gov (United States)

    Wang, Jinyang; Zhong, Haimin; Feng, Huajie; Qiu, Wenda; Chen, Liuping

    2014-03-14

    The binary infinite dilute diffusion coefficients, D₁₂(∞), of some alkylbenzenes (Ph-C(n), from Ph-H to Ph-C12) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO2) have been studied by molecular dynamics (MD) simulation. The MD values agree well with the experimental ones, which indicate MD simulation technique is a powerful way to predict and obtain diffusion coefficients of solutes in supercritical fluids. Besides, the local structures of Ph-C(n)/CO2 fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C(n) in scCO2 is significantly influenced by the structure of Ph-C(n) solute. Meanwhile, the mean end-to-end distance, the mean radius of gyration and dihedral angle distribution are calculated to gain an insight into the structural properties of Ph-C(n) in scCO2. The abnormal trends of radial distribution functions and coordination numbers can be reasonably explained in term of molecular flexibility. Moreover, the computed results of dihedral angle clarify that flexibility of long-chain Ph-C(n) is the result of internal rotation of C-C single bond (σ(c-c)) in alkyl chain. It is interesting that compared with n-alkane, because of the existence of benzene ring, the flexibility of alkyl chain in Ph-C(n) with same carbon atom number is significantly reduced, as a result, the carbon chain dependence of diffusion behaviors for long-chain n-alkane (n ≥ 5) and long-chain Ph-C(n) (n ≥ 4) in scCO2 are different.

  6. Effects of the molecular diffusion on the determination of the quantum efficiencies in heterogenous photocatalysis

    Energy Technology Data Exchange (ETDEWEB)

    Corboz, M.; Alxneit, I.; Tschudi, H.-R.

    2000-07-01

    A framework to determine the quantum efficiency greek eta {eta} of a photoreaction in a porous layer of photocatalyst is presented. The procedure relies on a model of the photoproduct diffusion in the porous structure of the photocatalyst. The model incorporates a position dependent source term mirroring the light intensity profile in the layer and an effective diffusion coefficient D{sub eff}. It allows for a simultaneous determination of h as well as D{sub eff}. The method is applied to the photosynthesis of CH{sub 4} from gaseous H{sub 2}O at the solid/gas interface of a porous layer of TiO{sub 2} (Degussa P25). A value of h = (8.79 {+-} 0.79) x 10{sup -4} is found for the formation of CH{sub 4} and an effective diffusion coefficient D{sub eff} = (5.64 {+-} 2.51) x 10{sup -10} cm{sup 2}s{sup -1} is obtained. (authors)

  7. Molecular dynamics simulation of diffusion and structure of some n-alkanes in near critical and supercritical carbon dioxide at infinite dilution.

    Science.gov (United States)

    Feng, Huajie; Gao, Wei; Sun, Zhenfan; Lei, Bingxin; Li, Gaonan; Chen, Liuping

    2013-10-17

    The diffusion coefficients of n-alkanes (from CH4 to C14H30) in near critical and supercritical carbon dioxide at infinite dilution have been studied by molecular dynamics simulation. The simulation results agree well with experiment, which suggests that the simulation method is a powerful tool to obtain diffusion coefficients of solutes in fluids at high pressures. The local structures of such fluids are further investigated by calculating radial distribution functions and coordination numbers. Meanwhile, the dihedral, end-to-end distance and radius of gyration, which are calculated to characterize the flexibility of n-alkanes, are used to reasonably explain the abnormal trends on radial distribution functions and coordination numbers. Moreover, it is found that the flexibility effects on diffusion in pure n-alkanes and infinitely dilute n-alkane/CO2 system are different. The differences in MD simulation results of molecular diffusion in such systems could be qualitatively explained by the flexibility.

  8. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field

    NARCIS (Netherlands)

    García-Pérez, E.; Serra-Crespo,P.; Hamad, S.; Kapteijn, F.; Gascon, J.

    2014-01-01

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations o

  9. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field

    NARCIS (Netherlands)

    García-Pérez, E.; Serra-Crespo,P.; Hamad, S.; Kapteijn, F.; Gascon, J.

    2014-01-01

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations

  10. Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion.

    Science.gov (United States)

    Skånberg, Robin; Vázquez, Pere-Pau; Guallar, Victor; Ropinski, Timo

    2016-01-01

    Today molecular simulations produce complex data sets capturing the interactions of molecules in detail. Due to the complexity of this time-varying data, advanced visualization techniques are required to support its visual analysis. Current molecular visualization techniques utilize ambient occlusion as a global illumination approximation to improve spatial comprehension. Besides these shadow-like effects, interreflections are also known to improve the spatial comprehension of complex geometric structures. Unfortunately, the inherent computational complexity of interreflections would forbid interactive exploration, which is mandatory in many scenarios dealing with static and time-varying data. In this paper, we introduce a novel analytic approach for capturing interreflections of molecular structures in real-time. By exploiting the knowledge of the underlying space filling representations, we are able to reduce the required parameters and can thus apply symbolic regression to obtain an analytic expression for interreflections. We show how to obtain the data required for the symbolic regression analysis, and how to exploit our analytic solution to enhance interactive molecular visualizations.

  11. The 5' non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells

    NARCIS (Netherlands)

    Ongus, J.R.; Roode, E.C.; Pleij, C.W.A.; Vlak, J.M.; Oers, van M.M.

    2006-01-01

    Structure prediction of the 5' non-translated region (NTR) of four iflavirus RNAs revealed two types of potential internal ribosome entry site (IRES), which are discriminated by size and level of complexity, in this group of viruses. In contrast to the intergenic IRES of dicistroviruses, the potenti

  12. The 5' non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells

    NARCIS (Netherlands)

    Ongus, J.R.; Roode, E.C.; Pleij, C.W.A.; Vlak, J.M.; Oers, van M.M.

    2006-01-01

    Structure prediction of the 5' non-translated region (NTR) of four iflavirus RNAs revealed two types of potential internal ribosome entry site (IRES), which are discriminated by size and level of complexity, in this group of viruses. In contrast to the intergenic IRES of dicistroviruses, the potenti

  13. First-principles molecular dynamics simulations of proton diffusion in cubic BaZrO $$_3$$ 3 perovskite under strain conditions

    Directory of Open Access Journals (Sweden)

    Marco Fronzi

    2016-08-01

    Full Text Available Abstract First-principles molecular dynamics simulations have been employed to analyse the proton diffusion in cubic BaZrO $$_3$$ 3 perovskite at 1300 K. A non-linear effect on the proton diffusion coefficient arising from an applied isometric strain up to 2  $$\\%$$ % of the lattice parameter, and an evident enhancement of proton diffusion under compressive conditions have been observed. The structural and electronic properties of BaZrO $$_3$$ 3 are analysed from Density Functional Theory calculations, and after an analysis of the electronic structure, we provide a possible explanation for an enhanced ionic conductivity of this bulk structure that can be caused by the formation of a preferential path for proton diffusion under compressive strain conditions. By means of Nudged Elastic Band calculations, diffusion barriers were also computed with results supporting our conclusions.

  14. Hyper alginate gel microbead formation by molecular diffusion at the hydrogel/droplet interface.

    Science.gov (United States)

    Hirama, Hirotada; Kambe, Taisuke; Aketagawa, Kyouhei; Ota, Taku; Moriguchi, Hiroyuki; Torii, Toru

    2013-01-15

    We report a simple method for forming monodispersed, uniformly shaped gel microbeads with precisely controlled sizes. The basis of our method is the placement of monodispersed sodium alginate droplets, formed by a microfluidic device, on an agarose slab gel containing a high-osmotic-pressure gelation agent (CaCl(2) aq.): (1) the droplets are cross-linked (gelated) due to the diffusion of the gelation agent from the agarose slab gel to the sodium alginate droplets and (2) the droplets simultaneously shrink to a fraction of their original size (gel. We verified the mass transfer mechanism between the droplet and the agarose slab gel. This method circumvents the limitations of gel microbead formation, such as the need to prepare microchannels of various sizes, microchannel clogging, and the deformation of the produced gel microbeads.

  15. Control of quantum localization and classical diffusion in laser-kicked molecular rotors

    Science.gov (United States)

    Bitter, M.; Milner, V.

    2017-01-01

    We experimentally study a system of quantum kicked rotors—an ensemble of diatomic molecules exposed to a periodic sequence of ultrashort laser pulses. In the regime where the underlying classical dynamics is chaotic, we investigate the quantum phenomenon of dynamical localization by means of state-resolved coherent Raman spectroscopy. We examine the dependence of the exponentially localized angular momentum distribution and of the total rotational energy on the time period between the pulses and their amplitude. The former parameter is shown to provide control over the localization center, whereas the latter one controls the localization length. Similar control of the center and width of a nonlocalized rotational distribution is demonstrated in the limit of classical diffusion, established by adding noise to the periodic pulse sequence.

  16. Thermal Conductivity of Ultrahigh Molecular Weight Polyethylene Crystal: Defect Effect Uncovered by 0 K Limit Phonon Diffusion.

    Science.gov (United States)

    Liu, Jing; Xu, Zaoli; Cheng, Zhe; Xu, Shen; Wang, Xinwei

    2015-12-16

    Crystalline ultrahigh molecular weight polyethylene (UHMWPE) has the highest reported thermal conductivity at room temperature: 104 W/(m·K), while theoretical predictions proposed an even higher value of 300 W/(m·K). Defects and amorphous fraction in practical UHMWPE fibers significantly reduces the thermal conductivity from the ideal value. Although the amorphous effect can be readily analyzed based on the effective medium theory, the defect effects are poorly understood. This work reports on the temperature-dependent behavior (down to 22 K) of thermal diffusivity and conductivity of UHMWPE fibers in anticipation of observing the reduction in phonon density and scattering rate against temperature and of freezing out high-momentum phonons to clearly observe the defect effects. By studying the temperature-dependent behavior of thermal reffusivity (Θ, inverse of thermal diffusivity) of UHMWPE fibers, we are able to quantify the defect effects on thermal conductivity. After taking out the amorphous region's effect, the residual thermal reffusivities (Θ0) for the studied two samples at the 0 K limit are determined as 3.45 × 10(4) and 2.95 × 10(4) s/m(2), respectively. For rare-/no-defects crystalline materials, Θ0 should be close to zero at the 0 K limit. The defect-induced low-momentum phonon mean free paths are determined as 8.06 and 9.42 nm for the two samples. They are smaller than the crystallite size in the (002) direction (19.7 nm) determined by X-ray diffraction. This strongly demonstrates the diffuse phonon scattering at the grain boundaries. The grain boundary thermal conductance (G) can be evaluated as G ≈ βρc(p)v with sound accuracy. At room temperature, G is around 3.73 GW/(m(2)·K) for S2, comparable to that of interfaces with tight atomic bonding.

  17. Diffuse Alveolar Hemorrhage Associated With Low Molecular Weight Heparin and Dual Anti-platelet Therapy After Percutaneous Coronary Intervention.

    Science.gov (United States)

    Yildirim, Fatma; Kara, İskender; Okuyan, Hızır; Abaci, Adnan; Turkoglu, Melda; Aygencel, Gülbin

    2016-01-19

    A 54-year-old man had undergone to percutaneous coronary intervention (PCI) and two stents were placed to left anterior coronary artery and circumflex artery. Low molecular weight heparin (LMWH) together with ticagrelor 90 mg twice a day and acetylsalicylic acid (Aspirin) were started after PCI due to high risk of stent trombosis. On the fourth day of patient's follow-up in the intensive care unit (ICU), bloody secretion was started from endotracheal tube. Hemoglobin dropping, bilateral infiltration on the chest X-ray and bleeding from lung were diagnosed as diffuse alveolar hemorrhage (DAH). Apart from LMWH and antiplatelet therapies with aspirin and ticagrelor, there were no other identified risk factors for DAH. As far as we know, our report is the first case of DAH caused by LMWH and dual anti-platelet therapy including ticagrelor. This article is protected by copyright. All rights reserved.

  18. Photochemical Molecular Tailoring for Efficient Diffusion and Reorganization of Organic Nanocrystals for Ultra-Flexible Organic Semiconductor Arrays.

    Science.gov (United States)

    Kang, Jingu; Kim, Jaehyun; Jo, Jeong-Wan; Heo, Jae Sang; Kim, Myung-Gil; Kim, Yong-Hoon; Kim, Jaekyun; Park, Sung Kyu

    2017-01-01

    Solution-processed organic single crystals with high carrier mobility have been actively investigated for diverse applications such as displays, sensors, and next generation electronics on a flexible platform. However, the lack of precise alignment and growth control of organic single crystals impedes the widespread adoption of organic materials in an industrial perspective. Here, a photochemical modification approach is reported tailoring the solubility and molecular diffusivity of polymeric sacrificial layer and sequential batch-type vapor annealing to implement high-performance (average saturation mobility: 8.01 cm(2) V(-1) s(-1) ) organic single-crystal thin film transistors with large channel width including multiple aligned single crystals. Additionally, the mechanical properties of the organic single crystals are systematically investigated with extreme strain conditions such as bending radius of 150 μm.

  19. On the relationship between grain-boundary migration and grain-boundary diffusion by molecular-dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Schoenfelder, B. [Argonne National Lab., IL (United States). Materials Science Div.]|[RWTH Aachen (Germany). Inst. fuer Metallkunde und Metallphysik; Keblinski, P.; Wolf, D.; Phillpot, S.R. [Argonne National Lab., IL (United States). Materials Science Div.

    1998-07-01

    A molecular-dynamics method for the simulation of the intrinsic migration behavior of individual, flat grain boundaries is presented. A constant driving force for grain-boundary migration is generated by imposing an anisotropic elastic strain on a bicrystal such that the elastic-energy densities in its two halves are different. For the model case of the large-planar-unit-cell, high-angle (001) twist boundary in Cu the authors demonstrate that the drift velocity is proportional to the applied driving force, thus enabling determination of the boundary mobility. The activation energy for grain-boundary migration is found to be distinctly lower than that for grain-boundary self-diffusion. A decrease in the related activation energies with increasing temperature is shown to arise from a crossover in the underlying mechanisms, from solid-like at low temperatures to liquid-like at high-temperatures that is accompanied by an underlying grain-boundary structural transition.

  20. Diffuse low-grade glioma: a review on the new molecular classification, natural history and current management strategies.

    Science.gov (United States)

    Delgado-López, P D; Corrales-García, E M; Martino, J; Lastra-Aras, E; Dueñas-Polo, M T

    2017-03-02

    The management of diffuse supratentorial WHO grade II glioma remains a challenge because of the infiltrative nature of the tumor, which precludes curative therapy after total or even supratotal resection. When possible, functional-guided resection is the preferred initial treatment. Total and subtotal resections correlate with increased overall survival. High-risk patients (age >40, partial resection), especially IDH-mutated and 1p19q-codeleted oligodendroglial lesions, benefit from surgery plus adjuvant chemoradiation. Under the new 2016 WHO brain tumor classification, which now incorporates molecular parameters, all diffusely infiltrating gliomas are grouped together since they share specific genetic mutations and prognostic factors. Although low-grade gliomas cannot be regarded as benign tumors, large observational studies have shown that median survival can actually be doubled if an early, aggressive, multi-stage and personalized therapy is applied, as compared to prior wait-and-see policy series. Patients need an honest long-term therapeutic strategy that should ideally anticipate neurological, cognitive and histopathologic worsening.

  1. The low molecular weight DNA diffusion assay as an indicator of cytotoxicity for the in vitro comet assay.

    Science.gov (United States)

    Speit, Günter; Vesely, Alexandra; Schütz, Petra; Linsenmeyer, Regina; Bausinger, Julia

    2014-07-01

    The low molecular weight DNA diffusion assay (LMW assay) has been recommended as a measure for cytotoxicity for the in vivo comet assay. To better understand the relationship between effects in the LMW assay, DNA migration in the comet assay and effects in established cytotoxicity tests, we performed in vitro experiments with cultured human cell lines (TK6, A549) and comparatively investigated five test substances (methyl methanesulfonate, (±)-benzo[a]pyrene diol epoxide, sodium dodecyl sulphate, menthol and sodium arsenite). We measured DNA migration (tail intensity) in the comet assay and the frequency of 'hedgehogs' (cells with almost all DNA in the tail), DNA diffusion in the LMW assay, cell viability (trypan blue and fluorescein diacetate/ethidium bromide staining) and inhibition of proliferation (relative cell counts). Our in vitro experiments indicate that effects in the LMW assay occur independently from DNA effects in the comet assay and are not related to the occurrence of hedgehogs. Results from the LMW assay are in good agreement with results from viability assays and seem to allow discriminating genotoxic from non-genotoxic substances when appropriate preparation times are considered. Measurements of cytotoxicity by these methods only at an early preparation time after exposure to genotoxic substances may lead to erroneous results.

  2. First-principles path-integral molecular dynamics study of diffusion process of hydrogen in face-centered cubic metals

    Science.gov (United States)

    Kimizuka, Hajime; Ogata, Shigenobu

    We investigated the H diffusivity in face-centered cubic Pd and Al by performing path-integral molecular dynamics (PIMD) modeling in the framework of density functional theory (DFT); in our calculations, we took nuclear quantum effects into consideration. The DFT results showed that the H-migration barriers (Em) in Pd and Al exhibited similar values (approximately 0.16 eV), while the H atoms were stable at octahedral (O) sites for Pd and at tetrahedral (T) sites for Al. The PIMD-based free-energy profiles for H migration between the O-site and T-site were evaluated using the thermodynamic integration of the centroid forces at 150-600 K. We confirmed that the quantum effects significantly affected the Em and the difference between the energies of the H atom at the O-site and the T-site (EO - T); The Em and EO - T values in Pd at 300 K increased by 32% and 98%, respectively, relative to the classical limit. On the other hand, the Em and ET - O (i.e., -EO - T) values in Al at 300 K decreased by 3% and 41%, respectively. This suggested that the quantum nature of H nuclei was essential for understanding the H-diffusion kinetics in these metals even above ambient temperature.

  3. Real-time observation on surface diffusion and molecular orientations for phthalocyanine thin films at nanometer spacial resolution

    Science.gov (United States)

    Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Honda, Mitsunori; Hirao, Norie; Narita, Ayumi; Deng, Juzhi

    2009-08-01

    The morphology, electronic structure and ordering of the phthalocyanine thin films have been investigated at nanometer scale by photoelectron emission microscopy (PEEM) excited by polarized soft X-rays from synchrotron light source. The sample investigated was micropattern of silicon phthalocyanine deposited on gold surface. The incident angle dependences of the X-ray absorption near edge structure (XANES) spectra at the silicon K-edge revealed that the molecules of 5-layered films are lying nearly flat on the surface. Clear image of the micropattern was observed by PEEM, showing that the molecules are deposited via Volmer-Weber (VW) mode at room temperature. While, the surface diffusion was observed upon heating, and the micropattern image almost disappeared at 240 °C, representing the deposition mode changes from VW-mode to Frank-van der Merwe (FM)-one. On the basis of the photon-energy dependences of the brightnesses in the PEEM images, it was found that the molecules diffusing to the fresh gold surface rather stand-up at 240 °C. The observed changes in the molecular orientations at nanometer domains are discussed on the basis of the strengths of the molecule-molecule and molecule-surface interactions.

  4. Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics

    Science.gov (United States)

    Agosta, Lorenzo; Brandt, Erik G.; Lyubartsev, Alexander P.

    2017-07-01

    Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.

  5. Diffuse and multifocal nephrogenic adenoma with Familial Mediterranean Fever: a case report with molecular study.

    Science.gov (United States)

    Ishikawa, Noriyoshi; Amano, Chika; Taketani, Takeshi; Kumori, Koji; Harada, Yuji; Hiraiwa, Hisayuki; Itamura, Kayoko; Maruyama, Riruke

    2015-07-16

    Nephrogenic adenoma, also referred to nephrogenic metaplasia, is a benign proliferative lesion of urothelium, usually associated with chronic physical stimuli or inflammation. Familial Mediterranean fever is an inherited autosomal recessive disease characterized by recurrent short episodes of fever. The site of mutation is found in MEFV gene which controls inflammatory responses. We have experienced a case of nephrogenic adenoma in a 16-year-old girl with Familial Mediterranean Fever, showing proliferative lesions diffusely in the urinary bladder and multifocally in the other parts of urinary tract. These lesions disappeared after colchicine treatment. We searched for MEFV gene mutation using the specimen from the resected urinary bladder and detected heterozygous mutation of E148Q. There is a possibility that control of inflammation caused by the surgery for vesicoureteral reflux in the local site didn't work well on the background of heterozygous mutation of MEFV gene, and as a result, nephrogenic adenoma appeared. This is the first report of a combination of two rare diseases. We have to be aware that nephrogenic adenoma can occur in association with Familial Mediterranean Fever, and the former condition should be taken into consideration when rendering a correct pathological diagnosis.

  6. Immunohistochemical and molecular characteristics with prognostic significance in diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Carmen Bellas

    Full Text Available Diffuse large B-cell lymphoma (DLBCL is an aggressive non-Hodgkin lymphoma with marked biologic heterogeneity. We analyzed 100 cases of DLBCL to evaluate the prognostic value of immunohistochemical markers derived from the gene expression profiling-defined cell origin signature, including MYC, BCL2, BCL6, and FOXP1 protein expression. We also investigated genetic alterations in BCL2, BCL6, MYC and FOXP1 using fluorescence in situ hybridization and assessed their prognostic significance. BCL6 rearrangements were detected in 29% of cases, and BCL6 gene alteration (rearrangement and/or amplification was associated with the non-germinal center B subtype (non-GCB. BCL2 translocation was associated with the GCB phenotype, and BCL2 protein expression was associated with the translocation and/or amplification of 18q21. MYC rearrangements were detected in 15% of cases, and MYC protein expression was observed in 29% of cases. FOXP1 expression, mainly of the non-GCB subtype, was demonstrated in 37% of cases. Co-expression of the MYC and BCL2 proteins, with non-GCB subtype predominance, was observed in 21% of cases. We detected an association between high FOXP1 expression and a high proliferation rate as well as a significant positive correlation between MYC overexpression and FOXP1 overexpression. MYC, BCL2 and FOXP1 expression were significant predictors of overall survival. The co-expression of MYC and BCL2 confers a poorer clinical outcome than MYC or BCL2 expression alone, whereas cases negative for both markers had the best outcomes. Our study confirms that DLBCL, characterized by the co-expression of MYC and BCL2 proteins, has a poor prognosis and establishes a significant positive correlation with MYC and FOXP1 over-expression in this entity.

  7. H2 Molecular Clusters with Embedded Molecules and Atoms as the Source of the Diffuse Interstellar Bands

    Science.gov (United States)

    Bernstein, L. S.; Clark, F. O.; Lynch, D. K.

    2013-05-01

    We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ("seed"), embedded in a single-layer shell of H2 molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H2 molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H2 shell. We refer to these clusters as contaminated H2 clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectral profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from ~centimeter-sized, dirty H2 ice balls, called contaminated H2 ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H2 molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the ~10-100 GHz spectral region.

  8. Next-Generation Sequencing in Diffuse Large B-Cell Lymphoma Highlights Molecular Divergence and Therapeutic Opportunities: a LYSA Study.

    Science.gov (United States)

    Dubois, Sydney; Viailly, Pierre-Julien; Mareschal, Sylvain; Bohers, Elodie; Bertrand, Philippe; Ruminy, Philippe; Maingonnat, Catherine; Jais, Jean-Philippe; Peyrouze, Pauline; Figeac, Martin; Molina, Thierry J; Desmots, Fabienne; Fest, Thierry; Haioun, Corinne; Lamy, Thierry; Copie-Bergman, Christiane; Brière, Josette; Petrella, Tony; Canioni, Danielle; Fabiani, Bettina; Coiffier, Bertrand; Delarue, Richard; Peyrade, Frédéric; Bosly, André; André, Marc; Ketterer, Nicolas; Salles, Gilles; Tilly, Hervé; Leroy, Karen; Jardin, Fabrice

    2016-06-15

    Next-generation sequencing (NGS) has detailed the genomic characterization of diffuse large B-cell lymphoma (DLBCL) by identifying recurrent somatic mutations. We set out to design a clinically feasible NGS panel focusing on genes whose mutations hold potential therapeutic impact. Furthermore, for the first time, we evaluated the prognostic value of these mutations in prospective clinical trials. A Lymphopanel was designed to identify mutations in 34 genes, selected according to literature and a whole exome sequencing study of relapsed/refractory DLBCL patients. The tumor DNA of 215 patients with CD20(+)de novo DLBCL in the prospective, multicenter, and randomized LNH-03B LYSA clinical trials was sequenced to deep, uniform coverage with the Lymphopanel. Cell-of-origin molecular classification was obtained through gene expression profiling with HGU133+2.0 Affymetrix GeneChip arrays. The Lymphopanel was informative for 96% of patients. A clear depiction of DLBCL subtype molecular heterogeneity was uncovered with the Lymphopanel, confirming that activated B-cell-like (ABC), germinal center B-cell like (GCB), and primary mediastinal B-cell lymphoma (PMBL) are frequently affected by mutations in NF-κB, epigenetic, and JAK-STAT pathways, respectively. Novel truncating immunity pathway, ITPKB, MFHAS1, and XPO1 mutations were identified as highly enriched in PMBL. Notably, TNFAIP3 and GNA13 mutations in ABC patients treated with R-CHOP were associated with significantly less favorable prognoses. This study demonstrates the contribution of NGS with a consensus gene panel to personalized therapy in DLBCL, highlighting the molecular heterogeneity of subtypes and identifying somatic mutations with therapeutic and prognostic impact. Clin Cancer Res; 22(12); 2919-28. ©2016 AACRSee related commentary by Lim and Elenitoba-Johnson, p. 2829. ©2016 American Association for Cancer Research.

  9. Critical anomaly and finite size scaling of the self-diffusion coefficient for Lennard-Jones fluids by non-equilibrium molecular dynamic simulation

    Institute of Scientific and Technical Information of China (English)

    Ahmed Asad; Wu Jiang-Tao

    2011-01-01

    We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient,D,of a Lennard Jones fluid over a wide density and temperature range.The change in self-diffusion coefficient with temperature decreases by increasing density.For density p* =pσ3 =0.84 we observe a peak at the value of the self-diffusion coefficient and the critical temperature T* =kT/ε =1.25.The value of the self-diffusion coefficient strongly depends on system size.The data of the self-diffusion coefficient are fitted to a simple analytic relation based on hydrodynamic arguments.This correction scales as N-α,where α is an adjustable parameter and N is the number of particles.It is observed that the values of α < 1 provide quite a good correction to the simulation data.The system size dependence is very strong for lower densities,but it is not as strong for higher densities.The self-diffusion coefficient calculated with non-equilibrium molecular dynamic simulations at different temperatures and densities is in good agreement with other calculations from the literature.

  10. “Pore-Like” Effects of Super-Molecular Self-Assembly on Molecular Diffusion of Poly(Ethylene Oxide-Poly(Propylene Oxide-Poly(Ethylene Oxide in Water

    Directory of Open Access Journals (Sweden)

    Konstantin Ulrich

    2012-05-01

    Full Text Available Molecular diffusion of triblock copolymers poly(ethylene oxide-poly(propylene oxide-poly(ethylene oxide in water was studied with the help of Pulsed Field Gradient NMR in the broad range of polymer weight fractions from 0.09 to 0.8. Owing to amphiphilic nature of the molecules, these block copolymers exhibit rich self-organization properties when mixed with water. In particular, at ambient temperatures they form micelles and three liquid crystalline mesophases: cubic, hexagonal, and lamellar. The corresponding super-molecular structure formations were studied with the same block copolymer and at the same temperature. Self-assembly of molecules was shown to produce “pore-like” effects on their self-diffusion properties by imposing severe constraints on the dimensionality of propagation. Diffusion in the hexagonal phase was shown to be quasi one-dimensional in the direction parallel to the long axis of the ordered molecular rods. In the lamellar phase, diffusion was found to be quasi two-dimensional, in the plane of the lamellar structures. The observed diffusion anisotropy was attributed to the effects of the specific molecular ordering on the mesoscopic length scale.

  11. An analysis of hydrated proton diffusion in ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2015-01-07

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions

  12. An analysis of hydrated proton diffusion in ab initio molecular dynamics

    Science.gov (United States)

    Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A.

    2015-01-01

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ˜2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore

  13. Sign Crossover in All Maxwell-Stefan Diffusivities for Molten Salt LiF-BeF2: A Molecular Dynamics Study.

    Science.gov (United States)

    Chakraborty, Brahmananda

    2015-08-20

    Applying Green-Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied for the first time the dynamic correlation, Onsager coefficients, and Maxwell-Stefan (MS) diffusivities of molten salt LiF-BeF2, which is a potential candidate for a coolant in a high temperature reactor. We observe an unusual composition dependence and strikingly a crossover in sign for all the MS diffusivities at a composition of around 7% of LiF where the MS diffusivity between cation-anion pair (Đ(BeF) and Đ(LiF)) jumps from positive to negative value while the MS diffusivity between cation-cation pair (Đ(LiBe)) becomes positive from a negative value. Even though the negative MS diffusivities have been observed for electrolyte solutions between cation-cation pair, here we report negative MS diffusivity between cation-anion pair where Đ(BeF) shows a sharp rise around 66% of BeF2, reaches maximum value at 70% of BeF2, and then decreases almost exponentially with a sign change for BeF2 around 93%. For low mole fraction of LiF, Đ(BeF) follows the Debye-Huckel theory and rises with the square root of LiF mole fraction similar to the MS diffusivity between cation-anion pair in aqueous solution of electrolyte salt. Negative MS diffusivities while unusual are, however, shown to satisfy the non-negative entropy constraints at all thermodynamic states as required by the second law of thermodynamics. We have established a strong correlation between the structure and dynamics and predict that the formation of flouride polyanion network between Be and F ions and coulomb interaction is responsible for sharp variation of the MS diffusivities which controls the multicomponent diffusion phenomenon in LiF-BeF2 which has a strong impact on the performance of the reactor.

  14. Diffuse Atomic and Molecular Gas in the Interstellar Medium of M82 toward SN 2014J

    CERN Document Server

    Ritchey, Adam M; Dahlstrom, Julie A; York, Donald G

    2014-01-01

    We present a comprehensive analysis of interstellar absorption lines seen in moderately-high resolution, high S/N ratio optical spectra of SN 2014J in M82. Our observations were acquired over the course of six nights, covering the period from ~7 days before to ~29 days after the supernova reached its maximum V-band brightness. Complex interstellar absorption is observed from Na I, Ca II, K I, Ca I, CH+, CH, and CN, much of which arises from gas in the interstellar medium of M82, although absorption features associated with the Galactic disk and halo are also observed. We detect Li I absorption over a range in velocity consistent with that exhibited by the strongest Na I and K I components associated with M82; this is the first detection of interstellar Li in a galaxy outside of the Local Group. There are no significant temporal variations in the absorption-line profiles over the 37 days sampled by our observations. The relative abundances of the observed atomic and molecular species reveal that the ISM of M82...

  15. Molecular anisotropy effects in carbon K-edge scattering: depolarized diffuse scattering and optical anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Stone, Kevin H.

    2014-07-14

    Some polymer properties, such as conductivity, are very sensitive to short- and intermediate-range orientational and positional ordering of anisotropic molecular functional groups, and yet means to characterize orientational order in disordered systems are very limited. We demonstrate that resonant scattering at the carbon K-edge is uniquely sensitive to short-range orientation correlations in polymers through depolarized scattering at high momentum transfers, using atactic polystyrene as a well-characterized test system. Depolarized scattering is found to coexist with unpolarized fluorescence, and to exhibit pronounced anisotropy. We also quantify the spatially averaged optical anisotropy from low-angle reflectivity measurements, finding anisotropy consistent with prior visible, x-ray absorption, and theoretical studies. The average anisotropy is much smaller than that in the depolarized scattering and the two have different character. Both measurements exhibit clear spectral signatures from the phenyl rings and the polyethylene-like backbone. Discussion focuses on analysis considerations and prospects for using this depolarized scattering for studies of disorder in soft condensed matter.

  16. Molecular anisotropy effects in carbon K-edge scattering: Depolarized diffuse scattering and optical anisotropy

    Science.gov (United States)

    Stone, Kevin H.; Kortright, Jeffrey B.

    2014-09-01

    Some polymer properties, such as conductivity, are very sensitive to short- and intermediate-range orientational and positional ordering of anisotropic molecular functional groups, and yet means to characterize orientational order in disordered systems are very limited. We demonstrate that resonant scattering at the carbon K edge is uniquely sensitive to short-range orientation correlations in polymers through depolarized scattering at high momentum transfers, using atactic polystyrene as a well-characterized test system. Depolarized scattering is found to coexist with unpolarized fluorescence and to exhibit pronounced anisotropy. We also quantify the spatially averaged optical anisotropy from low-angle reflectivity measurements, finding anisotropy consistent with prior visible, x-ray absorption, and theoretical studies. The average anisotropy is much smaller than that in the depolarized scattering and the two have different character. Both measurements exhibit clear spectral signatures from the phenyl rings and the polyethylenelike backbone. Discussion focuses on analysis considerations and prospects for using this depolarized scattering for studies of disorder in soft condensed matter.

  17. Diffusion and molecular interactions in a methanol/polyimide system probed by coupling time-resolved FTIR spectroscopy with gravimetric measurements.

    Science.gov (United States)

    Musto, Pellegrino; Galizia, Michele; La Manna, Pietro; Pannico, Marianna; Mensitieri, Giuseppe

    2014-01-01

    In this contribution the diffusion of methanol in a commercial polyimide (PMDA-ODA) is studied by coupling gravimetric measurements with in-situ, time-resolved FTIR spectroscopy. The spectroscopic data have been treated with two complementary techniques, i.e., difference spectroscopy (DS) and least-squares curve fitting (LSCF). These approaches provided information about the overall diffusivity, the nature of the molecular interactions among the system components and the dynamics of the various molecular species. Additional spectroscopic measurements on thin film samples (about 2 μm) allowed us to identify the interaction site on the polymer backbone and to propose likely structures for the H-bonding aggregates. Molar absorptivity values from a previous literature report allowed us to estimate the population of first-shell and second-shell layers of methanol in the polymer matrix. In terms of diffusion kinetics, the gravimetric and spectroscopic estimates of the diffusion coefficients were found to be in good agreement with each other and with previous literature reports. A Fickian behavior was observed throughout, with diffusivity values markedly affected by the total concentration of sorbed methanol.

  18. Sulphur-bearing molecules in diffuse molecular clouds: new results from SOFIA/GREAT and the IRAM 30 m telescope

    CERN Document Server

    Neufeld, D A; Gerin, M; Forêts, G Pineau des; Bernier, C; Falgarone, E; Graf, U U; Güsten, R; Herbst, E; Lesaffre, P; Schilke, P; Sonnentrucker, P; Wiesemeyer, H

    2015-01-01

    We have observed five sulphur-bearing molecules in foreground diffuse molecular clouds lying along the sight-lines to five bright continuum sources. We have used the GREAT instrument on SOFIA to observe the 1383 GHz $^2\\Pi_{3/2} J=5/2-3/2$ transitions of SH towards the star-forming regions W31C, G29.96-0.02, G34.3+0.1, W49N and W51, detecting foreground absorption towards all five sources; and the EMIR receivers on the IRAM 30m telescope at Pico Veleta to detect the H$_2$S 1(10)-1(01), CS J=2-1 and SO 3(2)-2(1) transitions. In nine foreground absorption components detected towards these sources, the inferred column densities of the four detected molecules showed relatively constant ratios, with N(SH)/N(H$_2$S) in the range 1.1 - 3.0, N(CS)/N(H$_2$S) in the range 0.32 - 0.61, and N(SO)/N(H$_2$S) in the range 0.08 - 0.30. The observed SH/H$_2$ ratios - in the range (0.5-2.6) $\\times 10^{-8}$ - indicate that SH (and other sulphur-bearing molecules) account for << 1% of the gas-phase sulphur nuclei. The obs...

  19. Ultraviolet Survey of CO and H_2 in Diffuse Molecular Clouds: The Reflection of Two Photochemistry Regimes in Abundance Relationships

    CERN Document Server

    Sheffer, Y; Federman, S R; Abel, N P; Gredel, R; Lambert, D L; Shaw, G

    2008-01-01

    (Abridged) We carried out a comprehensive far-ultraviolet (UV) survey of ^12CO and H_2 column densities along diffuse molecular Galactic sight lines in order to explore in detail the relationship between CO and H_2. We measured new CO abundances from HST spectra, new H_2 abundances from FUSE data, and new CH, CH^+, and CN abundances from the McDonald and European Southern Observatories. A plot of log N(CO) versus log N(H_2) shows that two power-law relationships are needed for a good fit of the entire sample, with a break located at log N(CO, cm^-2) = 14.1 and log N(H_2) = 20.4, corresponding to a change in production route for CO in higher-density gas. Similar logarithmic plots among all five diatomic molecules allow us to probe their relationships, revealing additional examples of dual slopes in the cases of CO versus CH (break at log N = 14.1, 13.0), CH^+ versus H_2 (13.1, 20.3), and CH^+ versus CO (13.2, 14.1). These breaks are all in excellent agreement with each other, confirming the break in the CO ver...

  20. Studies of Diffuse Interstellar Bands. V. Pairwise Correlations of Eight Strong DIBs and Neutral Hydrogen, Molecular Hydrogen, and Color Excess

    CERN Document Server

    Friedman, Scott D; McCall, Benjamin J; Dahlstrom, Julie; Sonnentrucker, Paule; Welty, Daniel E; Drosback, Meredith M; Hobbs, L M; Rachford, Brian L; Snow, Theodore P

    2010-01-01

    We establish correlations between equivalent widths of eight diffuse interstellar bands (DIBs), and examine their correlations with atomic hydrogen, molecular hydrogen, and EB-V . The DIBs are centered at \\lambda\\lambda 5780.5, 6204.5, 6283.8, 6196.0, 6613.6, 5705.1, 5797.1, and 5487.7, in decreasing order of Pearson’s correlation coefficient with N(H) (here defined as the column density of neutral hydrogen), ranging from 0.96 to 0.82. We find the equivalent width of \\lambda 5780.5 is better correlated with column densities of H than with E(B-V) or H2, confirming earlier results based on smaller datasets. We show the same is true for six of the seven other DIBs presented here. Despite this similarity, the eight strong DIBs chosen are not well enough correlated with each other to suggest they come from the same carrier. We further conclude that these eight DIBs are more likely to be associated with H than with H2 , and hence are not preferentially located in the densest, most UV shielded parts of interste...

  1. Diffuse Interstellar Bands vs. Known Atomic and Molecular Species in the Interstellar Medium of M82 toward SN 2014J

    CERN Document Server

    Welty, Daniel E; Dahlstrom, Julie A; York, Donald G

    2014-01-01

    We discuss the absorption due to various constituents of the interstellar medium of M82 seen in moderately high resolution, high signal-to-noise ratio optical spectra of SN 2014J. Complex absorption from M82 is seen, at velocities 45 $\\le$ $v_{\\rm LSR}$ $\\le$ 260 km s$^{-1}$, for Na I, K I, Ca I, Ca II, CH, CH$^+$, and CN; many of the diffuse interstellar bands (DIBs) are also detected. Comparisons of the column densities of the atomic and molecular species and the equivalent widths of the DIBs reveal both similarities and differences in relative abundances, compared to trends seen in the ISM of our Galaxy and the Magellanic Clouds. Of the ten relatively strong DIBs considered here, six (including $\\lambda$5780.5) have strengths within $\\pm$20% of the mean values seen in the local Galactic ISM, for comparable N(K I); two are weaker by 20--45% and two (including $\\lambda$5797.1) are stronger by 25--40%. Weaker than "expected" DIBs [relative to N(K I), N(Na I), and E(B-V)] in some Galactic sight lines and towar...

  2. Diffuse interstellar bands versus known atomic and molecular species in the interstellar medium of M82 toward SN 2014J

    Energy Technology Data Exchange (ETDEWEB)

    Welty, Daniel E.; York, Donald G. [Department of Astronomy and Astrophysics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Ritchey, Adam M. [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Dahlstrom, Julie A., E-mail: dwelty@oddjob.uchicago.edu [Department of Physics and Astronomy, Carthage College, 2001 Alford Park Drive, Kenosha, WI 53140 (United States)

    2014-09-10

    We discuss the absorption due to various constituents of the interstellar medium (ISM) of M82 seen in moderately high-resolution, high signal-to-noise ratio optical spectra of SN 2014J. Complex absorption from M82 is seen, at velocities 45 ≲ v {sub LSR} ≲ 260 km s{sup –1}, for Na I, K I, Ca I, Ca II, CH, CH{sup +}, and CN; many of the diffuse interstellar bands (DIBs) are also detected. Comparisons of the column densities of the atomic and molecular species and the equivalent widths of the DIBs reveal both similarities and differences in relative abundances, compared to trends seen in the ISM of our Galaxy and the Magellanic Clouds. Of the 10 relatively strong DIBs considered here, 6 (including λ5780.5) have strengths within ±20% of the mean values seen in the local Galactic ISM, for comparable N(K I); 2 are weaker by 20%-45% and 2 (including λ5797.1) are stronger by 25%-40%. Weaker than 'expected' DIBs (relative to N(K I), N(Na I), and E(B – V)) in some Galactic sight lines and toward several other extragalactic supernovae appear to be associated with strong CN absorption and/or significant molecular fractions. While the N(CH)/N(K I) and N(CN)/N(CH) ratios seen toward SN 2014J are similar to those found in the local Galactic ISM, the combination of high N(CH{sup +})/N(CH) and high W(5797.1)/W(5780.5) ratios has not been seen elsewhere. The centroids of many of the M82 DIBs are shifted relative to the envelope of the K I profile—likely due to component-to-component variations in W(DIB)/N(K I) that may reflect the molecular content of the individual components. We compare estimates for the host galaxy reddening E(B – V) and visual extinction A {sub V} derived from the various interstellar species with the values estimated from optical and near-IR photometry of SN 2014J.

  3. Diffuse Interstellar Bands versus Known Atomic and Molecular Species in the Interstellar Medium of M82 toward SN 2014J

    Science.gov (United States)

    Welty, Daniel E.; Ritchey, Adam M.; Dahlstrom, Julie A.; York, Donald G.

    2014-09-01

    We discuss the absorption due to various constituents of the interstellar medium (ISM) of M82 seen in moderately high-resolution, high signal-to-noise ratio optical spectra of SN 2014J. Complex absorption from M82 is seen, at velocities 45 <~ v LSR <~ 260 km s-1, for Na I, K I, Ca I, Ca II, CH, CH+, and CN; many of the diffuse interstellar bands (DIBs) are also detected. Comparisons of the column densities of the atomic and molecular species and the equivalent widths of the DIBs reveal both similarities and differences in relative abundances, compared to trends seen in the ISM of our Galaxy and the Magellanic Clouds. Of the 10 relatively strong DIBs considered here, 6 (including λ5780.5) have strengths within ±20% of the mean values seen in the local Galactic ISM, for comparable N(K I); 2 are weaker by 20%-45% and 2 (including λ5797.1) are stronger by 25%-40%. Weaker than "expected" DIBs (relative to N(K I), N(Na I), and E(B - V)) in some Galactic sight lines and toward several other extragalactic supernovae appear to be associated with strong CN absorption and/or significant molecular fractions. While the N(CH)/N(K I) and N(CN)/N(CH) ratios seen toward SN 2014J are similar to those found in the local Galactic ISM, the combination of high N(CH+)/N(CH) and high W(5797.1)/W(5780.5) ratios has not been seen elsewhere. The centroids of many of the M82 DIBs are shifted relative to the envelope of the K I profile—likely due to component-to-component variations in W(DIB)/N(K I) that may reflect the molecular content of the individual components. We compare estimates for the host galaxy reddening E(B - V) and visual extinction A V derived from the various interstellar species with the values estimated from optical and near-IR photometry of SN 2014J.

  4. Native-oxide-based selective area growth of InP nanowires via metal-organic molecular beam epitaxy mediated by surface diffusion.

    Science.gov (United States)

    Calahorra, Yonatan; Greenberg, Yaakov; Cohen, Shimon; Ritter, Dan

    2012-06-22

    The growth of InP nanowires on an InP(111) B substrate is reported. The substrate native oxide was not removed from the surface prior to growth. Nanowires were grown at 400 °C from gold catalysts in a selective area manner, without bulk growth. Unlike SiO(2)-based metal-organic molecular beam epitaxy selective area growth, the growth reported here is mediated by surface diffusion with a characteristic diffusion length of 4 μm, about an order of magnitude larger than values for diffusion on bare substrates. A pre-growth heating treatment at 450 °C was found to increase the yield of nanowire nucleation from the gold catalysts.

  5. Diffuse sclerosing variant of papillary thyroid carcinoma--an update of its clinicopathological features and molecular biology.

    Science.gov (United States)

    Pillai, Suja; Gopalan, Vinod; Smith, Robert A; Lam, Alfred K-Y

    2015-04-01

    Diffuse sclerosing variant of papillary thyroid carcinoma (DSVPTC) is an uncommon variant of papillary thyroid carcinoma. The aim of this review is to critically analyse the features of this entity. A search of the literature revealed 25 clinicopathological studies with in-depth analysis of features of DSVPTC. Overall, the prevalence of DSVPTC varies from 0.7-6.6% of all papillary thyroid carcinoma. Higher prevalence of DSVPTC was noted in paediatric patients and in patients affected by irradiation. DSVPTC tends to occur more frequently in women and in patients in the third decade of life. Macroscopically, DSVPTC can involve the thyroid gland extensively without forming a dominant mass. Microscopic examination of DSVPTC revealed extensive fibrosis, squamous metaplasia and numerous psammoma bodies. The latter pathological feature can aid in the pre-operative diagnosis of the entity by fine needle aspiration and ultrasound. Compared to conventional papillary thyroid carcinoma, DSVPTC had a higher incidence of lymph node metastases at presentation. Distant metastases were noted in approximately 5% of the cases. Patients with DSVPTC were recommended to be managed by aggressive treatment protocols. It is likely that as a result of this, the prognosis of the patients with DSVPTC was noted to be similar to conventional papillary thyroid carcinoma. Overall, cancer recurrence and cancer related mortality have been reported in 14% and 3%, respectively, of patients with DSVPTC. In immunohistochemical studies, DSVPTC showed different expression patterns of epithelial membrane antigen, galectin 3, cell adhesion molecules, p53 and p63 when compared to conventional papillary thyroid carcinoma. On genetic analysis, the occurrence of BRAF and RAS mutations are uncommon events in DSVPTC and activation of RET/PTC rearrangements are common. To conclude, DSVPTC has different clinical, pathological and molecular profiles when compared to conventional papillary thyroid carcinoma.

  6. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations

    Science.gov (United States)

    La Rosa, Carmelo; Scalisi, Silvia; Lolicato, Fabio; Pannuzzo, Martina; Raudino, Antonio

    2016-05-01

    The protein transport inside a cell is a complex phenomenon that goes through several difficult steps. The facilitated transport requires sophisticated machineries involving protein assemblies. In this work, we developed a diffusion-reaction model to simulate co-transport kinetics of proteins and lipids. We assume the following: (a) there is always a small lipid concentration of order of the Critical Micellar Concentration (CMC) in equilibrium with the membrane; (b) the binding of lipids to proteins modulates the hydrophobicity of the complexes and, therefore, their ability to interact and merge with the bilayer; and (c) some lipids leave the bilayer to replenish those bound to proteins. The model leads to a pair of integral equations for the time-evolution of the adsorbed proteins in the lipid bilayer. Relationships between transport kinetics, CMC, and lipid-protein binding constants were found. Under particular conditions, a perturbation analysis suggests the onset of kinks in the protein adsorption kinetics. To validate our model, we performed leakage measurements of vesicles composed by either high or low CMC lipids interacting with Islet Amyloid PolyPeptide (IAPP) and Aβ (1-40) used as sample proteins. Since the lipid-protein complex stoichiometry is not easily accessible, molecular dynamics simulations were performed using monomeric IAPP interacting with an increasing number of phospholipids. Main results are the following: (a) 1:1 lipid-protein complexes generally show a faster insertion rate proportional to the complex hydrophobicity and inversely related to lipid CMC; (b) on increasing the number of bound lipids, the protein insertion rate decreases; and (c) at slow lipids desorption rate, the lipid-assisted proteins transport might exhibit a discontinuous behavior and does non-linearly depend on protein concentration.

  7. Adsorption and diffusion of benzene in the nanoporous catalysts FAU, ZSM-5 and MCM-22: a molecular dynamics study.

    Science.gov (United States)

    Rungsirisakun, Ratana; Nanok, Tanin; Probst, Michael; Limtrakul, Jumras

    2006-03-01

    Molecular dynamics (MD) simulations of benzene in siliceous zeolites (FAU, ZSM-5, and MCM-22) were performed at loadings of 1, 2, 4, 8, and 16 molecules per supercell. The potential energy functions for these simulations were constructed in a semi-empirical way from existing potentials and experimental energetic data. The MD simulations were employed to analyze the dynamic properties of the benzene-zeolite systems. The adsorption energies of benzene/siliceous zeolite complexes increase with increasing loading number, due to the intermolecular attraction between benzene molecules. The self-diffusion coefficient of benzene in siliceous zeolites decreases with increasing loading due to the steric hindrance between the sorbates passing each other. From the zeolite-benzene radial distribution functions it was found that the benzene molecules are relatively far from each other, about 5.2A for siliceous FAU, 5.2A for siliceous ZSM-5, and 4.8A for siliceous MCM-22. In the case of FAU, the benzene molecules prefer to be adsorbed parallel to the surface of the sodalite cage above the six-membered-ring. In ZSM-5, we found a T-structure of the benzene molecules at loadings 2, 4, and 8 molecules per supercell. At loadings of 16 molecules per supercell, the molecules are lined up along the straight channel and their movement is highly correlated. For MCM-22 we found adjacent benzene molecules at a loading of 4 molecules with an orientation similar to the stacked conformation of benzene dimer in the gas phase.

  8. Immunohistochemistry on IDH 1/2, ATRX, p53 and Ki-67 substitute molecular genetic testing and predict patient prognosis in grade III adult diffuse gliomas.

    Science.gov (United States)

    Takano, Shingo; Ishikawa, Eiichi; Sakamoto, Noriaki; Matsuda, Masahide; Akutsu, Hiroyoshi; Noguchi, Masayuki; Kato, Yukinari; Yamamoto, Tetsuya; Matsumura, Akira

    2016-04-01

    The molecular subgrouping of diffuse gliomas was recently found to stratify patients into prognostically distinct groups better than histological classification. Among several molecular parameters, the key molecules for the subtype diagnosis of diffuse gliomas are IDH mutation, 1p/19q co-deletion, and ATRX mutation; 1p/19q co-deletion is undetectable by immunohistochemistry, but is mutually exclusive with ATRX and p53 mutation in IDH mutant gliomas. Therefore, we applied ATRX and p53 immunohistochemistry instead of 1p/19q co-deletion analysis. The prognostic value of immunohistochemical diagnosis for Grade III gliomas was subsequently investigated. Then, the same immunohistochmical diagnostic approach was expanded for the evaluation of Grade II and IV diffuse glioma prognosis. The results indicate immunohistochemical analysis including IDH1/2, ATRX, p53, and Ki-67 index is valuable for the classification of diffuse gliomas, which is useful for the evaluation of prognosis, especially Grade III gliomas and lower-grade gliomas (i.e., Grade II and III).

  9. Molecular dynamics insights into the structural and diffusive properties of ZIF-8/PDMS mixed matrix membranes in the n-butanol/water pervaporation process

    Science.gov (United States)

    Sun, Tao; Fang, Manquan; Wu, Zhen; Yu, Lixin; Li, Jiding

    2017-04-01

    Molecular dynamics (MD) simulation was used to study the structural and diffusive properties of zeolitic imidazolate framework-8 (ZIF-8)/polydimethylsiloxane (PDMS), a novel alcohol-permselective mixed matrix membrane (MMM). Simulation models of one pure PDMS membrane and three ZIF-8/PDMS MMMs with increasing loadings were successfully constructed. Non-bond energy turned out to be a strong attractive interaction between the PDMS matrix and ZIF-8 cells. The morphology and mobility of PDMS chains were characterized by mean square displacement (MSD). The fraction of free volume (FFV) of the pure membrane and MMMs was calculated and showed declining trends with increasing ZIF-8 loadings. The diffusion coefficients of n-butanol and water molecules were calculated by the Einstein relation. {D}n-\\text{butanol} first increased then decreased, while {D}{{water}} decreased with the increasing loadings. The mechanism of selective diffusion behaviour was investigated and it was found that the inner channels of ZIF-8 provided selective pathways for n-butanol. Diffusion coefficients were correlated with FFV and the results showed that the logarithm of {D}{{water}} demonstrated a good linear relation with the inverse FFV and was in agreement with the free volume theory, while {D}n-\\text{butanol} showed a significant deviation in the case of MMM-1 due to the selective diffusion channels provided by ZIF-8.

  10. A Student Diffusion Activity

    Science.gov (United States)

    Kutzner, Mickey; Pearson, Bryan

    2017-01-01

    Diffusion is a truly interdisciplinary topic bridging all areas of STEM education. When biomolecules are not being moved through the body by fluid flow through the circulatory system or by molecular motors, diffusion is the primary mode of transport over short distances. The direction of the diffusive flow of particles is from high concentration…

  11. A Student Diffusion Activity

    Science.gov (United States)

    Kutzner, Mickey; Pearson, Bryan

    2017-02-01

    Diffusion is a truly interdisciplinary topic bridging all areas of STEM education. When biomolecules are not being moved through the body by fluid flow through the circulatory system or by molecular motors, diffusion is the primary mode of transport over short distances. The direction of the diffusive flow of particles is from high concentration toward low concentration.

  12. Diffusion and Adsorption of Benzene and Propylene in MFI, MWW and BEA Zeolites: Molecular Dynamics and Grand Canonical Monte Carlo Simulations

    Institute of Scientific and Technical Information of China (English)

    SUN Xiao-yan; JIAO Wei; XIANG Shu-guang; LI Jian-wei

    2011-01-01

    The diffusion and adsorption behaviors of benzene and propylene in zeolites MFI, MWW and BEA have been studied by molecular dynamics(MD) and grand canonical Monte Carlo(GCMC) simulations. The diffusion coefficients of benzene and propylene in MFI, MWW and BEA zeolites were calculated by simulating the mean-square displacements(MSD) at 298 and 600 K. Benzene and propylene showed the different adsorption rules in the channels of the three zeolites. For propylene, the molecular loadings decreased in the order: BEA(linear channel)〉BEA (tortuous channel)〉MFI(linear channel)〉MWW(l2-membered rings, 12MR channel)〉MFI(tortuous channel)〉MWW (10-membered rings, 10MR channel); for benzene, the molecular loadings decreased in the order: BEA(linear channel)〉BEA(tortuous channel)〉MWW(l2MR channel)〉MFI(linear channel)〉MFl(tortuous channel)〉MWW(10MR channel). Besides, the adsorption isotherms of benzene and propylene in the three zeolites at 298 and 443 K were simulated. The results show that the different factors influenced the molecular adsorption at various temperatures and pressures, leading to the different rules for the adsorption of benzene and propylene molecules in the zeolites. At a low pressure, the unfavorable energy would make the loadings of propylene lower than those of benzene. When pressure was higher than 0.25 kPa, the adsorption of benzene in MFI would nearly reach saturation.

  13. Insights into the Molecular Pathogenesis of Activated B-Cell-like Diffuse Large B-Cell Lymphoma and Its Therapeutic Implications

    Energy Technology Data Exchange (ETDEWEB)

    Lenz, Georg [Translational Oncology, Department of Medicine A, Albert-Schweitzer Campus 1, University Hospital Münster, 48149 Münster (Germany); Cluster of Excellence EXC 1003, Cells in Motion, 48149 Münster (Germany)

    2015-05-22

    Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL) has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC) DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.

  14. Insights into the Molecular Pathogenesis of Activated B-Cell-like Diffuse Large B-Cell Lymphoma and Its Therapeutic Implications

    Directory of Open Access Journals (Sweden)

    Georg Lenz

    2015-05-01

    Full Text Available Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.

  15. Inclusion compounds between α-, β- and γ-cyclodextrins: iron II lactate: a theoretical and experimental study using diffusion coefficients and molecular mechanics

    Science.gov (United States)

    Leite, Rosiley A.; Lino, Antonio C. S.; Takahata, Yuji

    2003-01-01

    The inclusion compounds between iron II lactate and three different cyclodextrins (CDs) were studied by means of experimental and theoretical data. The importance of iron II in the human metabolism effort the necessity of a minimum concentration to the human life. Malnutrition is one great problem in social politics of many countries on the world. The possibility to the development of novel medicines with the iron II species stable look for an increase on the efficiency for this kind of aid. Kinetics measurements confirm the possibility to stop the oxidation reaction. It was the first indication of efficient molecular encapsulation. Diffusion coefficient measurements were carried out by Taylor-Aris diffusion technique. The decrease of diffusion coefficients measured for iron II lactate when alone and forming the inclusion complexes was obtained for all hosts molecules used. Molecular Mechanics calculations were performed to elucidate the perfect arrange of iron II lactate inside CDs cavity. No great differences were obtained to the binding energy for the different hosts. Using the software HyperChem6.03v MM+, AMBER94 and OPLS Forced Fields for iron atom in two chemical environments (a) vacuum and (b) with addition of 250 water molecules (MM+). The solvent treatment was decisive to the order of stability. This order was β-CD>γ-CD>α-CD, the same order of solubility in water. The results contained in this work confirm the possibility to protect iron II lactate against oxidation.

  16. Multiphase chemical kinetics of OH radical uptake by molecular organic markers of biomass burning aerosols: humidity and temperature dependence, surface reaction, and bulk diffusion.

    Science.gov (United States)

    Arangio, Andrea M; Slade, Jonathan H; Berkemeier, Thomas; Pöschl, Ulrich; Knopf, Daniel A; Shiraiwa, Manabu

    2015-05-14

    Multiphase reactions of OH radicals are among the most important pathways of chemical aging of organic aerosols in the atmosphere. Reactive uptake of OH by organic compounds has been observed in a number of studies, but the kinetics of mass transport and chemical reaction are still not fully understood. Here we apply the kinetic multilayer model of gas-particle interactions (KM-GAP) to experimental data from OH exposure studies of levoglucosan and abietic acid, which serve as surrogates and molecular markers of biomass burning aerosol (BBA). The model accounts for gas-phase diffusion within a cylindrical coated-wall flow tube, reversible adsorption of OH, surface-bulk exchange, bulk diffusion, and chemical reactions at the surface and in the bulk of the condensed phase. The nonlinear dependence of OH uptake coefficients on reactant concentrations and time can be reproduced by KM-GAP. We find that the bulk diffusion coefficient of the organic molecules is approximately 10(-16) cm(2) s(-1), reflecting an amorphous semisolid state of the organic substrates. The OH uptake is governed by reaction at or near the surface and can be kinetically limited by surface-bulk exchange or bulk diffusion of the organic reactants. Estimates of the chemical half-life of levoglucosan in 200 nm particles in a biomass burning plume increase from 1 day at high relative humidity to 1 week under dry conditions. In BBA particles transported to the free troposphere, the chemical half-life of levoglucosan can exceed 1 month due to slow bulk diffusion in a glassy matrix at low temperature.

  17. Two-dimensional imaging of molecular hydrogen in H2-air diffusion flames using two-photon laser-induced fluorescence

    Science.gov (United States)

    Lempert, W.; Kumar, V.; Glesk, I.; Miles, R.; Diskin, G.

    1991-01-01

    The use of a tunable ArF laser at 193.26 nm to record simultaneous single-laser-shot, planar images of molecular hydrogen and hot oxygen in a turbulent H2-air diffusion flame. Excitation spectra of fuel and oxidant-rich flame zones confirm a partial overlap of the two-photon H2 and single-photon O2 Schumann-Runge absorption bands. UV Rayleigh scattering images of flame structure and estimated detection limits for the H2 two-photon imaging are also presented.

  18. Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma

    DEFF Research Database (Denmark)

    Visco, C; Xu-Monette, Z Y; Miranda, R N

    2012-01-01

    Gene expression profiling (GEP) has stratified diffuse large B-cell lymphoma (DLBCL) into molecular subgroups that correspond to different stages of lymphocyte development-namely germinal center B-cell like and activated B-cell like. This classification has prognostic significance, but GEP...... on formalin-fixed, paraffin-embedded tissue samples. Sections were stained with antibodies reactive with CD10, GCET1, FOXP1, MUM1 and BCL6 and cases were classified following a rationale of sequential steps of differentiation of B cells. Cutoffs for each marker were obtained using receiver...

  19. Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

    Science.gov (United States)

    Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

  20. Prader-Willi Critical Region, a Non-Translated, Imprinted Central Regulator of Bone Mass: Possible Role in Skeletal Abnormalities in Prader-Willi Syndrome.

    Directory of Open Access Journals (Sweden)

    Ee-Cheng Khor

    Full Text Available Prader-Willi Syndrome (PWS, a maternally imprinted disorder and leading cause of obesity, is characterised by insatiable appetite, poor muscle development, cognitive impairment, endocrine disturbance, short stature and osteoporosis. A number of causative loci have been located within the imprinted Prader-Willi Critical Region (PWCR, including a set of small non-translated nucleolar RNA's (snoRNA. Recently, micro-deletions in humans identified the snoRNA Snord116 as a critical contributor to the development of PWS exhibiting many of the classical symptoms of PWS. Here we show that loss of the PWCR which includes Snord116 in mice leads to a reduced bone mass phenotype, similar to that observed in humans. Consistent with reduced stature in PWS, PWCR KO mice showed delayed skeletal development, with shorter femurs and vertebrae, reduced bone size and mass in both sexes. The reduction in bone mass in PWCR KO mice was associated with deficiencies in cortical bone volume and cortical mineral apposition rate, with no change in cancellous bone. Importantly, while the length difference was corrected in aged mice, consistent with continued growth in rodents, reduced cortical bone formation was still evident, indicating continued osteoblastic suppression by loss of PWCR expression in skeletally mature mice. Interestingly, deletion of this region included deletion of the exclusively brain expressed Snord116 cluster and resulted in an upregulation in expression of both NPY and POMC mRNA in the arcuate nucleus. Importantly, the selective deletion of the PWCR only in NPY expressing neurons replicated the bone phenotype of PWCR KO mice. Taken together, PWCR deletion in mice, and specifically in NPY neurons, recapitulates the short stature and low BMD and aspects of the hormonal imbalance of PWS individuals. Moreover, it demonstrates for the first time, that a region encoding non-translated RNAs, expressed solely within the brain, can regulate bone mass in health

  1. Sampling 4-chlorophenol in water by DGT technique with molecularly imprinted polymer as binding agent and nylon membrane as diffusive layer.

    Science.gov (United States)

    Dong, Jia; Fan, Hongtao; Sui, Dianpeng; Li, Liangchen; Sun, Ting

    2014-04-25

    For the first time, a diffusive gradients in thin films (DGT) device using molecularly imprinted polymer (MIP) as the binding agent and nylon membrane (NM) as the diffusive layer (NM-MIP-DGT) has been developed for sampling 4-chlorophenol (4-CP) in water. The MIP was prepared by precipitation polymerization with methacrylic acid as monomer and ethyleneglycoldimethacrylate as cross-linker. The diffusion coefficient of 4-CP through NM was obtained to be 0.788±0.040 μ cm(2) s(-1) by diffusion cell method. The ratio was 1.01±0.05 (mean±standard deviation) for the concentration of 4-CP sampled by NM-MIP-DGT and analyzed by HPLC method to the total concentration of 4-CP in the synthetic solution where free 4-CP species dominated. The results showed that NM-MIP-DGT could sample 4-CP in synthetic solution accurately. The performance of NM-MIP-DGT for sampling 4-CP was independent of pH in the range of 3-7 and ionic strength in the range of 0.0001-0.1 mol L(-1) NaCl solution. The concentration of free form of 4-CP sampled by NM-MIP-DGT decreased with the increasing concentration of dissolved organic carbon in different water samples due to the electrostatic interaction of natural organic compounds with 4-CP. 1.8 mg L(-1) of the free form of 4-CP was determined by HPLC which was sampled by NM-MIP-DGT in an intermediate untreated industrial effluent. The NM-MIP-DGT can be a potential passive tool for sampling the free form of 4-CP in water. Copyright © 2014. Published by Elsevier B.V.

  2. Extensive Evaluation of a Diffusion Denuder Technique for the Quantification of Atmospheric Stable and Radioactive Molecular Iodine

    DEFF Research Database (Denmark)

    Huang, Ru-Jin; Hou, Xiaolin; Hoffmann, Thorsten

    2010-01-01

    In this paper we present the evaluation and optimization of a new approach for the quantification of gaseous molecular iodine (I2) for laboratory- and field-based studies and its novel application for the measurement of radioactive molecular iodine. α-Cyclodextrin (α-CD) in combination with 129I......− is shown to be an effective denuder coating for the sampling of gaseous I2 by the formation of an inclusion complex. The entrapped 127I2 together with the 129I− spike in the coating is then released and derivatized to 4-iodo-N,N-dimethylaniline (4-I-DMA) for gas chromatography−mass spectrometry (GC...

  3. Exploring Shifts in Middle School Learners' Modeling Activity While Generating Drawings, Animations, and Computational Simulations of Molecular Diffusion

    Science.gov (United States)

    Wilkerson-Jerde, Michelle H.; Gravel, Brian E.; Macrander, Christopher A.

    2015-04-01

    Modeling and using technology are two practices of particular interest to K-12 science educators. These practices are inextricably linked among professionals, who engage in modeling activity with and across a variety of representational technologies. In this paper, we explore the practices of five sixth-grade girls as they generated models of smell diffusion using drawing, stop-motion animation, and computational simulation during a multi-day workshop. We analyze video, student discourse, and artifacts to address the questions: In what ways did learners' modeling practices, reasoning about mechanism, and ideas about smell shift as they worked across this variety of representational technologies? And, what supports enabled them to persist and progress in the modeling activity? We found that the girls engaged in two distinct modeling cycles that reflected persistence and deepening engagement in the task. In the first, messing about, they focused on describing and representing many ideas related to the spread of smell at once. In the second, digging in, they focused on testing and revising specific mechanisms that underlie smell diffusion. Upon deeper analysis, we found these cycles were linked to the girls' invention of "oogtom," a representational object that encapsulated many ideas from the first cycle and allowed the girls to restart modeling with the mechanistic focus required to construct simulations. We analyze the role of activity design, facilitation, and technological infrastructure in this pattern of engagement over the course of the workshop and discuss implications for future research, curriculum design, and classroom practice.

  4. [Use of archival formalin-fixed, paraffin-embedded (FFPE) tissue samples for molecular genetic analysis in diffuse large B-cell lymphoma (DLBCL)].

    Science.gov (United States)

    Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš

    2014-04-01

    The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.

  5. Development and validation of a ReaxFF reactive force field for Fe/Al/Ni alloys: molecular dynamics study of elastic constants, diffusion, and segregation.

    Science.gov (United States)

    Shin, Yun Kyung; Kwak, Hyunwook; Zou, Chenyu; Vasenkov, Alex V; van Duin, Adri C T

    2012-12-13

    We have developed a ReaxFF force field for Fe/Al/Ni binary alloys based on quantum mechanical (QM) calculations. In addition to the various bulk phases of the binary alloys, the (100), (110) and (111) surface energies and adatom binding energies were included in the training set for the force field parametrization of the Fe/Al/Ni binary alloys. To validate these optimized force fields, we studied (i) elastic constants of the binary alloys at finite temperatures, (ii) diffusivity of alloy components in Al/Ni alloy, and (iii) segregation on the binary alloy surfaces. First, we calculated linear elastic constants of FeAl, FeNi(3), and Ni(3)Al in the temperature range 300 to 1100 K. The temperature dependences of the elastic constants of these three alloys, showing a decrease in C(11), C(12), and C(44) as temperature increases, were in good agreement with the experimental results. We also performed ReaxFF molecular dynamics (MD) simulations for Al or Ni diffusion in the system modeled as Al/Ni mixed layers with the linear composition gradients. At 1000 K, Al diffusivity at the pure Al end was 2 orders of magnitude larger than that in the Al trace layers, probably explaining the nature of different diffusion behavior between molten metals and alloys. However, the diffusivity of Ni at the pure Ni end was only slightly larger than that in the Ni trace layers at the system temperature much lower than the melting temperature of Ni. Third, we investigated the surface segregation in L1(2)-Fe(3)Al, Fe(3)Ni, and Ni(3)Al clusters at high temperature (2500 K). From the analysis of composition distribution of the alloy components from the bulk to the surface layer, it was found that the degree of segregation depended on the chemical composition of the alloy. Al surface segregation occurred most strongly in Fe(3)Al, whereas it occurred most weakly in Ni(3)Al. These results may support the segregation mechanism that surface segregation results from the interplay between the

  6. The effect of geometrical parameters, roughness and the number of nanoparticles on the self-diffusion coefficient in Couette flow in a nanochannel by using of molecular dynamics simulation

    Science.gov (United States)

    Tohidi, Masoumeh; Toghraie, Davood

    2017-08-01

    The effect of geometrical parameters, roughness and the number of nanoparticles on self-diffusion in Couette flow in a nanochannel is investigated by using of molecular dynamics simulation. Gold nanoparticles (50, 100 and 200) were also distributed randomly between the nanochannel upper and lower walls. The effect of geometrical parameters of rectangular roughness in a nanochannel and the number of Gold nanoparticles on global self-diffusion and local self-diffusion as well as the average amounts were investigated in Couette flow. The results show that by increasing the roughness height, the particles are entrapped within the roughness and hence reduce the local self-diffusion coefficient in the vicinity of the upper wall. Also, by increasing the roughness height, the roughness length has less effect on the local diffusion coefficient.

  7. Histopathological, Molecular, and Genetic Profile of Hereditary Diffuse Gastric Cancer: Current Knowledge and Challenges for the Future.

    Science.gov (United States)

    van der Post, Rachel S; Gullo, Irene; Oliveira, Carla; Tang, Laura H; Grabsch, Heike I; O'Donovan, Maria; Fitzgerald, Rebecca C; van Krieken, Han; Carneiro, Fátima

    2016-01-01

    Familial clustering is seen in 10 % of gastric cancer cases and approximately 1-3 % of gastric cancer arises in the setting of hereditary diffuse gastric cancer (HDGC). In families with HDGC, gastric cancer presents at young age. HDGC is predominantly caused by germline mutations in CDH1 and in a minority by mutations in other genes, including CTNNA1. Early stage HDGC is characterized by a few, up to dozens of intramucosal foci of signet ring cell carcinoma and its precursor lesions. These include in situ signet ring cell carcinoma and pagetoid spread of signet ring cells. Advanced HDGC presents as poorly cohesive/diffuse type carcinoma, normally with very few typical signet ring cells, and has a poor prognosis. Currently, it is unknown which factors drive the progression towards aggressive disease, but it is clear that most intramucosal lesions will not have such progression.Immunohistochemical profile of early and advanced HDGC is often characterized by abnormal E-cadherin immunoexpression, including absent or reduced membranous expression, as well as "dotted" or cytoplasmic expression. However, membranous expression of E-cadherin does not exclude HDGC. Intramucosal HDGC (pT1a) presents with an "indolent" phenotype, characterized by typical signet ring cells without immunoexpression of Ki-67 and p53, while advanced carcinomas (pT > 1) display an "aggressive" phenotype with pleomorphic cells, that are immunoreactive for Ki-67 and p53. These features show that the IHC profile is different between intramucosal and more advanced HDGC, providing evidence of phenotypic heterogeneity, and may help to define predictive biomarkers of progression from indolent to aggressive, widely invasive carcinomas.

  8. Single-crystal diffuse scattering studies on polymorphs of molecular crystals. I. The room-temperature polymorphs of the drug benzocaine.

    Science.gov (United States)

    Chan, E J; Welberry, T R; Goossens, D J; Heerdegen, A P; Beasley, A G; Chupas, P J

    2009-06-01

    The drug benzocaine (ethyl 4-aminobenzoate), commonly used as a local anaesthetic, is a bimorphic solid at room temperature. Form (I) is monoclinic P2(1)/c, while the metastable form (II) is orthorhombic P2(1)2(1)2(1). Three-dimensional diffuse X-ray scattering data have been collected for the two forms on the 11-ID-B beamline at the Advanced Photon Source (APS). Both forms show strong and highly structured diffuse scattering. The data have been interpreted and analysed using Monte Carlo (MC) modelling on the basis that the scattering is purely thermal in origin and indicates the presence of highly correlated molecular motions. In both forms (I) and (II) broad diffuse streaks are observed in the 0kl section which indicate strong longitudinal displacement correlations between molecules in the 031 directions, extending over distances of up to 50 A. Streaks extending between Bragg peaks in the hk0 section normal to [100] correspond to correlated motions of chains of molecules extending along a that are linked by N-H...O=C hydrogen bonds and which occur together as coplanar ribbon pairs. The main difference between the two forms is in the dynamical behaviour of the ribbon pairs and in particular how they are able to slide relative to each other. While for form (I) a model involving harmonic springs is able to describe the motion satisfactorily, as simple excursions away from the average structure, there is evidence in form (II) of anharmonic effects that are precursors of a phase transition to a new low-temperature phase, form (III), that was subsequently found.

  9. Temperature- and pressure-dependent densities, self-diffusion coefficients, and phase behavior of monoacid saturated triacylglycerides: toward molecular-level insights into processing.

    Science.gov (United States)

    Greiner, Maximilian; Reilly, Anthony M; Briesen, Heiko

    2012-05-23

    Using molecular-dynamics (MD) simulations the densities and self-diffusion coefficients of a range of liquid monoacid triacylglycerides (TAGs) have been studied as a function of temperature and, for the first time, pressure. While offset by their ambient properties, the response of the TAGs to temperature and pressure is qualitatively similar. Application of pressure was found to significantly increase densities and reduce diffusion of the TAG molecules, suggesting that it may have as much a role in processing and crystallizing TAGs as supercooling does. A solution of glycerol tripalmitate and glycerol trihexanoate was also studied, showing that application of pressure should lead to a significant decrease in the saturation point of the solution, which is an important consideration for processing TAGs. Different solid/liquid interfaces of glycerol tripalmitate have also been investigated. Although crystal growth could not be observed, dissolution of one interface was seen in the MD simulations. The results suggest that over moderate distances the melting of TAGs may be cooperative in nature, rather than involving dissolution of individual TAG molecules.

  10. PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex

    Institute of Scientific and Technical Information of China (English)

    Liu Chang; Li Shuai; Dai Xiaoyan; Ma Ji; Wan Junhu; Jiang Hao; Wang Peng; Liu Zhaoli; Zhang Hongquan

    2015-01-01

    Polycomb repression complex 2 ( PRC2 ) component EZH2 tri-methylates H3 K27 and exerts ep-igenetic repression on target gene expression. EZH2-mediated epigenetic control of RNA polymerase II(Pol II) transcribed coding gene transcription has been well established. However, little is known about EZH2-mediated epigenetic regulation of RNA polymerase III( Pol III) transcription. Here we present a paradigm that EZH2 is in-volved in the repression of Pol III transcription via interaction with transcriptional factor complex IIIC ( TFIIIC ) . EZH2 and H3K27 me3 cooccupy the promoter of tRNATyr, 5S rRNA and 7SL RNA genes. Depletion of EZH2 or inhibition of EZH2 methyl transferase activity led to upregulation of Pol III target gene transcription. EZH2-media-ted repression of Pol III transcribed gene expression requires presence of SUZ12 . SUZ12 was able to interact with TFIIIC complex and knockdown of SUZ12 decreased occupancy of EZH2 and H3 K27 me3 at the promoter of Pol III target genes. Our findings pointed out a previously unidentified role of PRC2 complex in suppressing transcription of Pol III transcribed non-translated RNA genes, putting Pol III on a new layer of epigenetic regulation.

  11. Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma.

    Science.gov (United States)

    Linton, Kim; Howarth, Christopher; Wappett, Mark; Newton, Gillian; Lachel, Cynthia; Iqbal, Javeed; Pepper, Stuart; Byers, Richard; Chan, Wing John; Radford, John

    2012-01-01

    Refractory/relapsed diffuse large B-cell lymphoma (DLBCL) has a poor prognosis. Novel drugs targeting the constitutively activated NF-κB pathway characteristic of ABC-DLBCL are promising, but evaluation depends on accurate activated B cell-like (ABC)/germinal center B cell-like (GCB) molecular classification. This is traditionally performed on gene microarray expression profiles of fresh biopsies, which are not routinely collected, or by immunohistochemistry on formalin-fixed, paraffin-embedded (FFPE) tissue, which lacks reproducibility and classification accuracy. We explored the possibility of using routine archival FFPE tissue for gene microarray applications. We examined Affymetrix HG U133 Plus 2.0 gene expression profiles from paired archival FFPE and fresh-frozen tissues of 40 ABC/GCB-classified DLBCL cases to compare classification accuracy and test the potential for this approach to aid the discovery of therapeutic targets and disease classifiers in DLBCL. Unsupervised hierarchical clustering of unselected present probe sets distinguished ABC/GCB in FFPE with remarkable accuracy, and a Bayesian classifier correctly assigned 32 of 36 cases with >90% probability. Enrichment for NF-κB genes was appropriately seen in ABC-DLBCL FFPE tissues. The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation. These results support a growing understanding that archival FFPE tissues can be used in microarray experiments aimed at molecular classification, prognostic biomarker discovery, and molecular exploration of rare diseases. Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  12. Molecular Simulations and Theoretical Predictions for Adsorption and Diffusion of CH{sub 4}/H{sub 2} and CO{sub 2}/CH{sub 4} Mixtures in ZIFs

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jinchen; Keskin, Seda; Sholl, David S; Johnson, J. Karl

    2011-05-01

    Adsorption and diffusion of CO{sub 2}/CH{sub 4} and CH{sub 4}/H{sub 2} mixtures were computed in zeolite imidazolate frameworks (ZIFs), ZIF-68 and ZIF-70, using atomically detailed simulations. Adsorption selectivity, diffusion selectivity, and membrane selectivity of ZIFs were calculated based on the results of atomistic simulations. Mixture adsorption isotherms predicted by the ideal adsorbed solution theory agree well with the results of molecular simulations for both ZIFs. Mixture diffusivity calculations indicate that diffusion of CH{sub 4} is increased with increasing concentration of H{sub 2} in the CH{sub 4}/H{sub 2} mixture, while the diffusivity of H{sub 2} decreases with increasing CH{sub 4} concentration. In contrast, the diffusivity of CH{sub 4} is essentially independent of the concentration of CO{sub 2} in the CO{sub 2}/CH{sub 4} mixture, while CO{sub 2} diffusivity decreases with increased CH{sub 4} loading, even though the diffusivity of CH{sub 4} is substantially larger than that of CO{sub 2}. This unusual behavior can be explained in terms of differences in adsorption site preferences due to charge–quadrupole interactions.

  13. Ubiquitous argonium (ArH$^+$) in the diffuse interstellar medium -- a molecular tracer of almost purely atomic gas

    CERN Document Server

    Schilke, Peter; Mueller, Holger S P; Comito, Claudia; Bergin, Edwin A; Lis, Dariusz C; Gerin, Maryvonne; Black, John H; Wolfit, Mark; Indriolo, Nick; Pearson, John C; Menten, Karl M; Winkel, Benjamin; Sanchez-Monge, Alvaro; Moeller, Thomas; Godard, Benjamin; Falgarone, Edith

    2014-01-01

    We describe the assignment of a previously unidentified interstellar absorption line to ArH$^+$ and discuss its relevance in the context of hydride absorption in diffuse gas with a low H$_2$ fraction. The column densities along several lines of sight are determined and discussd in the framework of chemical models. The column densities of ArH$^+$ are compared to those of other species, tracing interstellar medium (ISM) components with different H$_2$ abundances. Chemical models are constructed, taking UV radiation and cosmic ray ionization into account. Due to the detection of two isotopologues, $^{36}$ArH$^+$ and $^{38}$ArH$^+$, we are confident about the carrier assignment to ArH$^+$. NeH$^+$ is not detected with a limit of [NeH$^+$]/[ArH$^+$] $\\le$ 0.1. The derived column densities agree well with the predictions of chemical models. ArH$^+$ is a unique tracer of gas with a fractional H$_2$ abundance of $10^{-4}- 10^{-3}$ and shows little correlation with H$_2$O$^+$, which traces gas with a fractional H$_2$ ...

  14. Coding genes and molecular structures of the diffusible signalling proteins (pheromones) of the polar ciliate, Euplotes nobilii.

    Science.gov (United States)

    Vallesi, Adriana; Alimenti, Claudio; Pedrini, Bill; Di Giuseppe, Graziano; Dini, Fernando; Wüthrich, Kurt; Luporini, Pierangelo

    2012-12-01

    In protozoan ciliates, diffusible signalling proteins (pheromones) regulate the vegetative growth and mating interactions. Here, the coding genes and the structures of the encoded pheromones were studied in genetically distinct wild-type strains representing interbreeding Antarctic and Arctic populations of the marine ciliate Euplotes nobilii. Determination of seven allelic pheromone-coding DNA sequences revealed that an unusual extension and high structural conservation of the 5' non-coding region are peculiar traits of this gene family, implying that this region is directly involved in the mechanism of pheromone gene expression, possibly through phenomena of intron splicing and/or frame-shifting. For four pheromones, the three-dimensional structures were determined by nuclear magnetic resonance spectroscopy in solution. These structures show that the pheromones represent a protein family which adapts to its polar environment by combining a structurally stable core of a three-helix bundle with extended polypeptide segments that are devoid of regular secondary structures and concomitantly show enhanced structural flexibility. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Molecular epidemiological investigation of a diffuse outbreak caused by Salmonella enterica serotype Montevideo isolates in Osaka Prefecture, Japan.

    Science.gov (United States)

    Harada, Tetsuya; Sakata, Junko; Kanki, Masashi; Seto, Kazuko; Taguchi, Masumi; Kumeda, Yuko

    2011-10-01

    In Osaka Prefecture, Japan, three foodborne outbreaks were caused by Salmonella enterica serotype Montevideo in rapid succession between September 2007 and May 2008. Further, Salmonella Montevideo was also isolated from several sporadic diarrhea patients and asymptomatic carriers examined during approximately the identical period. To investigate the relatedness of the isolates, we performed antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) analysis, and multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) for 29 Salmonella Montevideo isolates obtained in this region between 1991 and 2008. Although antimicrobial susceptibility tests had low discriminatory power, PFGE patterns revealed 17 unique types with outbreaks, one sporadic patient, and three different carriers between 2007 and 2008 had nearly identical PFGE patterns and were classified into the identical MLVA type; further, the isolates with this PFGE and MLVA pattern appeared only at that time between 1991 and 2008. These data strongly suggest that genetically identical Salmonella Montevideo strains may have caused the 2007 and 2008 outbreaks in Osaka Prefecture. Our results demonstrate that PFGE using XbaI and BlnI is useful for discriminating between Salmonella Montevideo isolates, even within a limited area, and reconfirm that continuous epidemiological surveillance for bacterial intestinal infections such as salmonellosis may be useful to not only monitor changes in the genetic diversity of isolates, but to also detect diffuse outbreaks.

  16. Ethylene/ethane permeation, diffusion and gas sorption properties of carbon molecular sieve membranes derived from the prototype ladder polymer of intrinsic microporosity (PIM-1)

    KAUST Repository

    Salinas, Octavio

    2016-01-05

    Fine-tuning the microporosity of PIM-1 by heat treatment was applied to develop a suitable carbon molecular sieve membrane for ethylene/ethane separation. Pristine PIM-1 films were heated from 400 to 800 °C under inert N2 atmosphere (< 2 ppm O2). At 400 °C, PIM-1 self-cross-linked and developed polar carbonyl and hydroxyl groups due to partial dioxane splitting in the polymer backbone. Significant degradation occurred at 600 °C due to carbonization of PIM-1 and resulted in 30% increase in cumulative surface area compared to its cross-linked predecessor. In addition, PIM-1-based CMS developed smaller ultramicropores with increasing pyrolysis temperature, which enhanced their molecular sieving capability by restricted diffusion of ethylene and ethane through the matrix due to microstructural carbon densification. Consequently, the pure-gas ethylene permeability (measured at 35 °C and 2 bar) decreased from 1600 Barrer for the pristine PIM-1 to 1.3 Barrer for the amorphous carbon generated at 800 °C, whereas the ethylene/ethane pure-gas selectivity increased significantly from 1.8 to 13.

  17. The Effect of Molecular Structure and Environment on the Miscibility and Diffusivity in Polythiophene-Methanofullerene Bulk Heterojunctions: Theory and Modeling with the RISM Approach

    Directory of Open Access Journals (Sweden)

    Alexander E. Kobryn

    2016-04-01

    Full Text Available Although better means to model the properties of bulk heterojunction molecular blends are much needed in the field of organic optoelectronics, only a small subset of methods based on molecular dynamics- and Monte Carlo-based approaches have been hitherto employed to guide or replace empirical characterization and testing. Here, we present the first use of the integral equation theory of molecular liquids in modelling the structural properties of blends of phenyl-C61-butyric acid methyl ester (PCBM with poly(3-hexylthiophene (P3HT and a carboxylated poly(3-butylthiophene (P3BT, respectively. For this, we use the Reference Interaction Site Model (RISM with the Universal Force Field (UFF to compute the microscopic structure of blends and obtain insight into the miscibility of its components. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived by the Density Functional Theory (DFT methods. We also run Molecular Dynamics (MD simulation to compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively. A remarkably good agreement with available experimental data and results of alternative modelling/simulation is observed for PCBM in the P3HT system. We interpret this as a step in the validation of the use of our approach for organic photovoltaics and support of its results for new systems that do not have reference data for comparison or calibration. In particular, for the less-studied P3BT, our results show that expectations about its performance in binary blends with PCBM may be overestimated, as it does not demonstrate the required level of miscibility and short-range structural organization. In addition, the simulated mobility of PCBM in P3BT is somewhat higher than what is expected for polymer blends and falls into a range typical for fluids. The significance of our predictive multi-scale modelling lies in the insights it offers into nanoscale

  18. Adenovirus delivered short hairpin RNA targeting a conserved site in the 5' non-translated region inhibits all four serotypes of dengue viruses.

    Directory of Open Access Journals (Sweden)

    Anil Babu Korrapati

    Full Text Available BACKGROUND: Dengue is a mosquito-borne viral disease caused by four closely related serotypes of Dengue viruses (DENVs. This disease whose symptoms range from mild fever to potentially fatal haemorrhagic fever and hypovolemic shock, threatens nearly half the global population. There is neither a preventive vaccine nor an effective antiviral therapy against dengue disease. The difference between severe and mild disease appears to be dependent on the viral load. Early diagnosis may enable timely therapeutic intervention to blunt disease severity by reducing the viral load. Harnessing the therapeutic potential of RNA interference (RNAi to attenuate DENV replication may offer one approach to dengue therapy. METHODOLOGY/PRINCIPAL FINDINGS: We screened the non-translated regions (NTRs of the RNA genomes of representative members of the four DENV serotypes for putative siRNA targets mapping to known transcription/translation regulatory elements. We identified a target site in the 5' NTR that maps to the 5' upstream AUG region, a highly conserved cis-acting element essential for viral replication. We used a replication-defective human adenovirus type 5 (AdV5 vector to deliver a short-hairpin RNA (shRNA targeting this site into cells. We show that this shRNA matures to the cognate siRNA and is able to inhibit effectively antigen secretion, viral RNA replication and infectious virus production by all four DENV serotypes. CONCLUSION/SIGNIFICANCE: The data demonstrate the feasibility of using AdV5-mediated delivery of shRNAs targeting conserved sites in the viral genome to achieve inhibition of all four DENV serotypes. This paves the way towards exploration of RNAi as a possible therapeutic strategy to curtail DENV infection.

  19. Molecular simulations of adsorption and diffusion of NO and NH3 over zeolite catalysts with various structure configurations%Industrial Catalysis

    Institute of Scientific and Technical Information of China (English)

    李懿; 刘宁; 张润铎; 李英霞

    2016-01-01

    基于巨正则蒙特卡洛和分子动力学,对NH3-SCR反应体系中吸附质分子( NO与NH3)在不同拓扑结构沸石分子筛( LTL、FER、LEV、BEA、MOR、FAU、CHA和MFI)上的吸附和扩散特性进行系统研究。结果表明,对于全硅分子筛而言,其分子筛的拓扑结构影响NO与NH3在分子筛上的吸附,综合吸附量及吸附作用能发现,MFI和LEV分子筛对NO具有较优的吸附特性;MFI和BEA分子筛对NH3具有较优的吸附特性。研究了Si与Al物质的量比对BEA分子筛吸附性能影响,结果表明,随着Si与Al物质的量比降低,分子筛自由体积逐渐增加,进而有助于分子筛催化剂对NO和NH3的吸附。采用分子动力学模拟计算NO与NH3在不同构型全硅分子筛上的扩散系数,发现具有三维直通道且孔径较大的分子筛催化剂有利于NO和NH3在其孔道内部的扩散,MFI虽然具备三维孔道结构,但由于存在Z型交叉通道,一定程度阻碍了反应物分子的扩散。%The adsorption and diffusion of NO and NH3 as the reactant of NH3-SCR reaction system over various kinds of zeolite catalysts( LTL,FER,LEV,BEA,MOR,FAU,CHA,MFI)were investigated by employing molecule simulation methods of Monte Carlo and Molecular Dynamics. The results indicated that the zeolitic topology greatly influenced the adsorption of NO and NH3 molecules according to the sim-ulation results of adsorption amount and adsorption energy. Accordingly,it was found that MFI and LEV were efficient for NO adsorption,and MFI and BEA were efficient for NH3 adsorption. The effects of Si/Al molar ratio on the adsorption of NO and NH3 over BEA zeolite were also studied. The study showed that the free volume of zeolite catalysts gradually increased along with the decrease of Si/Al molar ratios, which facilitated the adsorption of NO and NH3 . The molecular dynamics was further employed for the cal-culations of diffusion coefficient of NO and NH3 on all

  20. Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

    OpenAIRE

    Shetty, Anil N.; CHIANG, SHARON; Maletic-Savatic, Mirjana; Kasprian, Gregor; Vannucci, Marina; Lee, Wesley

    2014-01-01

    In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffu...

  1. Targeted Next-Generation Sequencing in Molecular Subtyping of Lower-Grade Diffuse Gliomas: Application of the World Health Organization's 2016 Revised Criteria for Central Nervous System Tumors.

    Science.gov (United States)

    Carter, Jamal H; McNulty, Samantha N; Cimino, Patrick J; Cottrell, Catherine E; Heusel, Jonathan W; Vigh-Conrad, Katinka A; Duncavage, Eric J

    2017-03-01

    The 2007 World Health Organization Classification of Tumours of the Central Nervous System classifies lower-grade gliomas [LGGs (grades II to III diffuse gliomas)] morphologically as astrocytomas or oligodendrogliomas, and tumors with unclear ambiguous morphology as oligoastrocytomas. The World Health Organization's newly released (2016) classification incorporates molecular data. A single, targeted next-generation sequencing (NGS) panel was used for detecting single-nucleotide variation and copy number variation in 50 LGG cases originally classified using the 2007 criteria, including 36 oligoastrocytomas, 11 oligodendrogliomas, 2 astrocytomas, and 1 LGG not otherwise specified. NGS results were compared with those from IHC analysis and fluorescence in situ hybridization to assess concordance and to categorize the tumors according to the 2016 criteria. NGS results were concordant with those from IHC analysis in all cases. In 3 cases, NGS was superior to fluorescence in situ hybridization in distinguishing segmental chromosomal losses from whole-arm deletions. The NGS approach was effective in reclassifying 36 oligoastrocytomas as 30 astrocytomas (20 IDH1/2 mutant and 10 IDH1/2 wild type) and 6 oligodendrogliomas, and 1 oligodendroglioma as an astrocytoma (IDH1/2 mutant). Here we show that a single, targeted NGS assay can serve as the sole testing modality for categorizing LGG according to the World Health Organization's 2016 diagnostic scheme. This modality affords greater accuracy and efficiency while reducing specimen tissue requirements compared with multimodal approaches.

  2. Molecular Simulations of Adsorption and Diffusion Behaviors of Benzene Molecules in NaY Zeolite%NaY分子筛中苯分子吸附和扩散行为的分子模拟

    Institute of Scientific and Technical Information of China (English)

    张舟; 刘辉; 朱吉钦; 陈标华; 田辉平; 贺振富

    2009-01-01

    In the article the Grand Canonical Monte Carlo (GCMC), molecular dynamics (MD), and kinetic Monte Carlo (KMC) simulations with particular focus on ascertaining the loading dependence of benzene diffusion in the zeolite were performed. First, a realistic representation of the structure of the sorbate-sorbent system was obtained based on GCMC simulation. The simulation clearly shows the characteristics of the adsorption sites of the benzene-NaY system, from which two kinds of preferably adsorbing sites for benzene moleculcs, called SⅡ and W sites, are identified. The structure thus obtained was then used as a basis for KMC and MD simulations. A compara-tive study by introducing and comparing two different mechanisms underlying jump diffusion in the zeolite of in-terest shows that the MS diffusivity values predicted by the KMC and MD methods are fairly close to each other, leading to the conclusion that for benzene diffusion in NaY, the Su→W→SⅡ jumps of benzene molecules are dominated, while the W→W jumps do not exist in the process. These findings provide further support to our previous conclusion about the absence of the W→W jumps in the process of benzene diffusion in NaY. Finally, two relations for predicting the self-and MS diffusivities were derived and found to be in fair agreement with the KMC and MD simulations.

  3. The costimulatory molecule CD70 is regulated by distinct molecular mechanisms and is associated with overall survival in diffuse large B-cell lymphoma.

    Science.gov (United States)

    Bertrand, P; Maingonnat, C; Penther, D; Guney, S; Ruminy, P; Picquenot, J M; Mareschal, S; Alcantara, M; Bouzelfen, A; Dubois, S; Figeac, M; Bastard, C; Tilly, H; Jardin, F

    2013-08-01

    In diffuse large B-cell lymphomas (DLBCL), a recurrent deletion of the 19p13 region has recently been described. CD70 and TNFSF9 genes are suspected tumor suppressor genes, but previous studies suggest an oncogenic role for CD70. Therefore, we studied the consequences of variation in CD70 copy number and epigenetic modifications on CD70 expression. Copy-number variation was investigated in 144 de novo DLBCL tissues by comparative genomic hybridization array and quantitative multiplex PCR. Gene expression was assessed by quantitative RT-PCR, and CD70 promoter methylation was determined by pyrosequencing. The 19p13.3.2 region was deleted in 21 (14.6%) cases, which allowed the minimal commonly deleted region of 57 Kb that exclusively includes the CD70 gene to be defined. Homozygous deletions were observed in four (2.7%) cases, and acquired single-nucleotide variations of CD70 were detected in nine (6.3%) cases. CD70 was highly expressed in both germinal centre B-cell-like (GCB) and activated B-cell-like (ABC) DLBCL compared to normal tissue, with distinct molecular mechanisms of mRNA expression regulation. A gene dosage effect was observed in the GCB subtype, whereas promoter methylation was the predominant mechanism of down regulation in the ABC subtype. However, high CD70 expression levels correlated to shorter overall survival in both the GCB (P = 0.0021) and the ABC (P =0.0158) subtypes. In conclusion, CD70 is targeted by recurrent deletions, somatic mutations and promoter hypermethylation, but its high level of expression is related to an unfavorable outcome, indicating that this molecule may constitute a potential therapeutic target in selected DLBCL. Copyright © 2013 Wiley Periodicals, Inc.

  4. Diffusion MRI

    Science.gov (United States)

    Fukuyama, Hidenao

    Recent advances of magnetic resonance imaging have been described, especially stressed on the diffusion sequences. We have recently applied the diffusion sequence to functional brain imaging, and found the appropriate results. In addition to the neurosciences fields, diffusion weighted images have improved the accuracies of clinical diagnosis depending upon magnetic resonance images in stroke as well as inflammations.

  5. Silver and Cesium Diffusion Dynamics at the β‑SiC Σ5 Grain Boundary Investigated with Density Functional Theory Molecular Dynamics and Metadynamics

    OpenAIRE

    RABONE JEREMY; LOPEZ HONORATO Eddie; VAN UFFELEN Paul

    2012-01-01

    The diffusion and release of silver-110m, a strong γ-radiation emitter, through silicon carbide in coated nuclear fuel particles has remained an unsolved topic since it was first observed 40 years ago. The challenge remains to explain why, contrary to other elements, silver is capable of escaping the ceramic diffusion barriers. The current work investigates the underlying differences in the diffusion of silver and cesium along a symmetric tilt Σ5 grain boundary of β-SiC through accelerated de...

  6. System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ethers

    Science.gov (United States)

    Moultos, Othonas A.; Zhang, Yong; Tsimpanogiannis, Ioannis N.; Economou, Ioannis G.; Maginn, Edward J.

    2016-08-01

    Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO2, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH3O-(CH2CH2O)n-CH3 with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.

  7. Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description.

    Science.gov (United States)

    Shetty, Anil N; Chiang, Sharon; Maletic-Savatic, Mirjana; Kasprian, Gregor; Vannucci, Marina; Lee, Wesley

    2014-01-01

    In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal-Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain.

  8. Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

    Science.gov (United States)

    SHETTY, ANIL N.; CHIANG, SHARON; MALETIC-SAVATIC, MIRJANA; KASPRIAN, GREGOR; VANNUCCI, MARINA; LEE, WESLEY

    2016-01-01

    In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal–Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain. PMID:27441031

  9. Vaneless diffusers

    Science.gov (United States)

    Senoo, Y.

    The influence of vaneless diffusers on flow in centrifugal compressors, particularly on surge, is discussed. A vaneless diffuser can demonstrate stable operation in a wide flow range only if it is installed with a backward leaning blade impeller. The circumferential distortion of flow in the impeller disappears quickly in the vaneless diffuser. The axial distortion of flow at the diffuser inlet does not decay easily. In large specific speed compressors, flow out of the impeller is distorted axially. Pressure recovery of diffusers at distorted inlet flow is considerably improved by half guide vanes. The best height of the vanes is a little 1/2 diffuser width. In small specific speed compressors, flow out of the impeller is not much distorted and pressure recovery can be predicted with one-dimensional flow analysis. Wall friction loss is significant in narrow diffusers. The large pressure drop at a small flow rate can cause the positive gradient of the pressure-flow rate characteristic curve, which may cause surging.

  10. Diffusion of organic colloids in compacted bentonite. The influence of ionic strength on molecular size and transport capacity of the colloids

    Energy Technology Data Exchange (ETDEWEB)

    Wold, S.; Eriksen, Trygve E. [Royal Inst. of Tech., Stockholm (Sweden)

    2000-09-01

    Diffusion of radionuclides in compacted bentonite can be affected by inorganic and organic colloids if the radionuclides form complexes with the colloids. Formation and mobility of the colloid-radionuclide complexes will be governed by the properties of the colloids as well as the competition between complexation and sorption of the radionuclides on bentonite. This report presents the results of experiments with organic colloids humic acid (HA) and lignosulfonate (LS). The aim of the experiments has been to describe the HA and LS properties: size distribution, acidity, sorption on bentonite, diffusivity in compacted bentonite, complexation with strontium, and diffusion of strontium in bentonite in the presence of HA. This study indicates that the diffusion of cationic radionuclides like Sr{sup 2+} is not affected by the presence of HA in high ionic strength solution. In 0.1 M NaClO{sub 4} solution, HA is most probably not available for complexation due to coiling and shielding of the negative sites.

  11. Experiment of gas diffusion and its diffusion mechanism in coal

    Institute of Scientific and Technical Information of China (English)

    Li Xiangchun; Nie Baisheng; Zhang Ruming; Chi Leilei

    2012-01-01

    In coal,the gas mainly exists in a free or an adsorption state.When the coal containing gas is damaged,gas desorption and diffusion will occur which can result in gas disaster.This research on gas desorption and diffusion provides a theoretical basis for gas disaster mechanism and prevention.The influence of pressure and temperature on gas diffusion is studied by the experiment.And the mechanism of pressure and temperature on gas diffusion is also analysed.The research results indicate that gas diffusion capacity increases with increasing temperature under the same pressure for the same coal sample.This is mainly because the temperature increases,gas molecular hot motion is severer,kinetic energy of gas molecular increases,and gas desorption quickens,therefore gas diffusion capacity changes stronger.Under other unchanged conditions,the greater gas adsorption balance pressure,the more gas adsorption content,and the higher the initial gas concentration.When gas diffusion begins,the greater the gas concentration gradient,the faster the gas diffusion speeds.

  12. Molecular characterization of extended-spectrum beta-lactamases and its correlation with clinical laboratory standards institute interpretive criteria for disk diffusion susceptibility testing in enterobacteriaceae isolates in Thaialnd.

    Science.gov (United States)

    Tangkoskul, Teerawit; Tiengrim, Surapee; Onsomang, Supiluck; Pati, Naratchaphan; Aswapokee, Nalinee; Thamlikitkul, Visanu; Chayakulkeeree, Methee

    2012-11-01

    We performed extended-spectrum beta-lactamase (ESBL) phenotypic testing and molecular characterization of three ESBL genes (TEM, SHV and CTX-M) and susceptibility testing by Clinical Laboratory Standards Institute (CLSI) disk diffusion method against three cephalosporins (ceftriaxone, ceftazidime, cefepime) and a cephamycin (cefoxitin) among 128 Thai Escherichia coli and 84 Thai Klebsiella pneumoniae clinical isolates. ESBL production was discovered in 62% of E. coli and 43% of K. pneumoniae isolates. All isolates susceptible to ceftriaxone were ESBL-negative. Nearly all isolates non-susceptible to ceftriaxone, ceftazidime and cefepime produced ESBL; the presence of CTX-M genes in the isolates correlated with a ceftriaxone non-susceptible phenotype. Thirty-nine of 83 isolates (47%) of ceftazidime-susceptible E. coli and 50 of 99 isolates (50.5%) of cefepime-susceptible E. coli were ESBL-producing. SHV-type beta-lactamase genes were more prevalent among K. pneumoniae than E. coli isolates. CTX-M was the major ESBL gene harbored by ESBL-producers in both E. coli and K. pneumoniae isolates. Non-CTX-M ESBL-producers were found only among K. pneumoniae isolates. This study reveals an increase in ESBL-producing Enterobacteriaceae among Thai isolates and demonstrates gaps in the current CLSI disk diffusion susceptibility guidelines; it indicates the results of ceftazidime and cefepime disk diffusion susceptibility testing using CLSI criteria should be interpreted with caution.

  13. Sailing On Diffusion

    Science.gov (United States)

    Allshouse, Michael; Barad, Mike; Peacock, Thomas

    2009-11-01

    When a density-stratified fluid encounters a sloping boundary, diffusion alters the fluid density adjacent to the boundary, producing spontaneous along-slope flow. Since stratified fluids are ubiquitous in nature, this phenomenon plays a vital role in environmental transport processes, including salt transport in rock fissures and ocean-boundary mixing. Here we show that diffusion-driven flow can be harnessed as a remarkable means of propulsion, acting as a diffusion-engine that extracts energy from microscale diffusive processes to propel macroscale objects. Like a sailboat tacking into the wind, forward motion results from fluid flow around an object, creating a region of low pressure at the front relative to the rear. In this case, however, the flow is driven by molecular diffusion and the pressure variations arise due to the resulting small changes in the fluid density. This mechanism has implications for a number of important systems, including environmental and biological transport processes at locations of strong stratification, such as pycnoclines in oceans and lakes. There is also a strong connection with other prevalent buoyancy-driven flows, such as valley and glacier winds, significantly broadening the scope of these results and opening up a new avenue for propulsion research.

  14. Interacting Cosmic Rays with Molecular Clouds: A Bremsstrahlung Origin of Diffuse High Energy Emission from the Inner 2deg by 1deg of the Galactic Center

    CERN Document Server

    Yusef-Zadeh, F; Wardle, M; Tatischeff, V; Roberts, D; Cotton, W; Uchiyama, H; Nobukawa, M; Tsuru, T G; Heinke, C; Royster, M

    2012-01-01

    The high energy activity in the inner few degrees of the Galactic center is traced by diffuse radio, X-ray and gamma-ray emission. The physical relationship between different components of diffuse gas emitting at multiple wavelengths is a focus of this work. We first present radio continuum observations using Green Bank Telescope and model the nonthermal spectrum in terms of a broken power-law distribution of GeV electrons emitting synchrotron radiation. We show that the emission detected by Fermi is primarily due to nonthermal bremsstrahlung produced by the population of synchrotron emitting electrons in the GeV energy range interacting with neutral gas. The extrapolation of the electron population measured from radio data to low and high energies can also explain the origin of FeI 6.4 keV line and diffuse TeV emission, as observed with Suzaku, XMM-Newton, Chandra and the H.E.S.S. observatories. The inferred physical quantities from modeling multi-wavelength emission in the context of bremsstrahlung emission...

  15. Research progress on integrated molecular pathological classification of diffuse lower-grade gliomas%弥漫性较低级别胶质瘤的整合性分子病理分型研究进展

    Institute of Scientific and Technical Information of China (English)

    李朝晖; 郭志钢(综述); 李庆伟(审校)

    2016-01-01

    弥漫性较低级别胶质瘤包含WHOⅡ级和Ⅲ级的星形细胞瘤、少突胶质细胞瘤和少突星形细胞瘤,其临床表现具有高度可变性,目前的组织病理学无法准确地预测其预后。近年来,胶质瘤分子病理取得了重大进展,已经发现一系列与胶质瘤临床特征和预后密切相关的分子标志物如异柠檬酸脱氢酶(isocitrate dehydrogenase,IDH)突变、染色体1p/19q共缺失、ATRX基因突变、TERT启动子突变、MGMT启动子甲基化等。在此基础上,结合这些分子标志物对弥漫性较低级别胶质瘤进行整合性分子病理分型的研究相继开展,且这些研究的结果一致表明,整合性分子病理分型能够更好地预测弥漫性较低级别胶质瘤的预后和指导治疗。本研究对弥漫性较低级别胶质瘤的整合性分子病理分型研究进展进行综述。%Diffuse lower-grade glioma is a diversified group of infiltrative brain tumors comprising WHO grades II and III astrocytomas, oligodendrogliomas, and mixed oligoastrocytomas. These tumors exhibit a wide range of clinical heterogeneity;thus, histopathological classification does not adequately predict clinical outcomes. In recent years, a number of molecular markers closely related to the clini-cal features and prognosis of gliomas have been discovered. These molecular markers include isocitrate dehydrogenase (IDH) muta-tion, chromosome 1p/19q codeletion, ATRX mutation, TERT promoter mutation, and MGMT promoter methylation. Furthermore, nu-merous studies focusing on the integrated molecular classification of diffuse lower-grade gliomas combined with these molecular markers have been conducted. Results indicate that integrated molecular pathological classification can improve the diagnostic and prognostic accuracy and facilitate therapeutic formulation. This paper reviews the research progress on integrated molecular classifica-tion of diffuse lower-grade gliomas.

  16. Diffusion in membranes: Toward a two-dimensional diffusion map

    Directory of Open Access Journals (Sweden)

    Toppozini Laura

    2015-01-01

    Full Text Available For decades, quasi-elastic neutron scattering has been the prime tool for studying molecular diffusion in membranes over relevant nanometer distances. These experiments are essential to our current understanding of molecular dynamics of lipids, proteins and membrane-active molecules. Recently, we presented experimental evidence from X-ray diffraction and quasi-elastic neutron scattering demonstrating that ethanol enhances the permeability of membranes. At the QENS 2014/WINS 2014 conference we presented a novel technique to measure diffusion across membranes employing 2-dimensional quasi-elastic neutron scattering. We present results from our preliminary analysis of an experiment on the cold neutron multi-chopper spectrometer LET at ISIS, where we studied the self-diffusion of water molecules along lipid membranes and have the possibility of studying the diffusion in membranes. By preparing highly oriented membrane stacks and aligning them horizontally in the spectrometer, our aim is to distinguish between lateral and transmembrane diffusion. Diffusion may also be measured at different locations in the membranes, such as the water layer and the hydrocarbon membrane core. With a complete analysis of the data, 2-dimensional mapping will enable us to determine diffusion channels of water and ethanol molecules to quantitatively determine nanoscale membrane permeability.

  17. Diffuse scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kostorz, G. [Eidgenoessische Technische Hochschule, Angewandte Physik, Zurich (Switzerland)

    1996-12-31

    While Bragg scattering is characteristic for the average structure of crystals, static local deviations from the average lattice lead to diffuse elastic scattering around and between Bragg peaks. This scattering thus contains information on the occupation of lattice sites by different atomic species and on static local displacements, even in a macroscopically homogeneous crystalline sample. The various diffuse scattering effects, including those around the incident beam (small-angle scattering), are introduced and illustrated by typical results obtained for some Ni alloys. (author) 7 figs., 41 refs.

  18. Diffusion in porous crystalline materials.

    Science.gov (United States)

    Krishna, Rajamani

    2012-04-21

    The design and development of many separation and catalytic process technologies require a proper quantitative description of diffusion of mixtures of guest molecules within porous crystalline materials. This tutorial review presents a unified, phenomenological description of diffusion inside meso- and micro-porous structures. In meso-porous materials, with pore sizes 2 nm < d(p) < 50 nm, there is a central core region where the influence of interactions of the molecules with the pore wall is either small or negligible; meso-pore diffusion is governed by a combination of molecule-molecule and molecule-pore wall interactions. Within micro-pores, with d(p) < 2 nm, the guest molecules are always under the influence of the force field exerted with the wall and we have to reckon with the motion of adsorbed molecules, and there is no "bulk" fluid region. The characteristics and physical significance of the self-, Maxwell-Stefan, and Fick diffusivities are explained with the aid of data obtained either from experiments or molecular dynamics simulations, for a wide variety of structures with different pore sizes and topology. The influence of adsorption thermodynamics, molecular clustering, and segregation on both magnitudes and concentration dependences of the diffusivities is highlighted. In mixture diffusion, correlations in molecular hops have the effect of slowing-down the more mobile species. The need for proper modeling of correlation effects using the Maxwell-Stefan formulation is stressed with the aid of examples of membrane separations and catalytic reactors.

  19. 水化层影响酸酐酶内CO2扩散行为的分子动力学模拟%Molecular dynamics simulation for hydration effect on CO2 diffusion in carbonic anhydrase

    Institute of Scientific and Technical Information of China (English)

    陈功; 卢滇楠; 吴建中; 刘铮

    2015-01-01

    The hydration layer of the enzyme in the bulk gas phase has great effects on its catalytic performance. Molecular dynamics (MD) simulations at all-atom level was applied to investigate the effects of the hydration layer thickness on the diffusion of carbon dioxide molecules into the active site of a carbonic anhydrase enzyme from a bulk gas phase. Based on the distribution of water molecules surrounding the carbonic anhydrase enzyme, the effects of the hydration layer thickness on the protein structure and CO2 transport from the bulk gas phase to the protein active site was studied. The simulation results suggested an optimal hydration layer thickness of 0.7 nm for CO2 diffusion. The CO2 adsorption sites were identified, which compose of the diffusion channel inside the carbonic anhydrase. The MD simulation revealed the open states of these adsorption sites, which may be useful to identify the bottleneck position of the diffusion channel. The molecular insight is helpful for design and optimization of carbonic anhydrase, enabling more efficient CO2 adsorption and conversion.%气相中酶分子表面的水化层对其催化行为具有显著的影响。本文采用全原子分子动力学模拟方法考察了气相体系碳酸酐酶表面的水化层对酶结构以及CO2在酶分子中扩散行为的影响。首先展现了水分子在酶分子及其活性中心周围的分布,研究了水化层厚度对于酶结构以及CO2扩散速率的影响;发现最有利于CO2扩散进入酶分子的水化层厚度为0.7 nm。确认了碳酸酐酶内CO2的吸附位点,通过对其开合状态统计,显示出碳酸酐酶中CO2扩散通道中的瓶颈位置。上述结果对设计和优化碳酸酐酶催化气相体系中CO2的吸附和转化提供了依据和启示。

  20. Relativistic diffusion.

    Science.gov (United States)

    Haba, Z

    2009-02-01

    We discuss relativistic diffusion in proper time in the approach of Schay (Ph.D. thesis, Princeton University, Princeton, NJ, 1961) and Dudley [Ark. Mat. 6, 241 (1965)]. We derive (Langevin) stochastic differential equations in various coordinates. We show that in some coordinates the stochastic differential equations become linear. We obtain momentum probability distribution in an explicit form. We discuss a relativistic particle diffusing in an external electromagnetic field. We solve the Langevin equations in the case of parallel electric and magnetic fields. We derive a kinetic equation for the evolution of the probability distribution. We discuss drag terms leading to an equilibrium distribution. The relativistic analog of the Ornstein-Uhlenbeck process is not unique. We show that if the drag comes from a diffusion approximation to the master equation then its form is strongly restricted. The drag leading to the Tsallis equilibrium distribution satisfies this restriction whereas the one of the Jüttner distribution does not. We show that any function of the relativistic energy can be the equilibrium distribution for a particle in a static electric field. A preliminary study of the time evolution with friction is presented. It is shown that the problem is equivalent to quantum mechanics of a particle moving on a hyperboloid with a potential determined by the drag. A relation to diffusions appearing in heavy ion collisions is briefly discussed.

  1. Study on Adsorption Equilibrium and Diffusion Model of CH4 and N2 on a Carbon Molecular Sieve%CH 4/N 2在炭分子筛上的吸附平衡与扩散模型

    Institute of Scientific and Technical Information of China (English)

    王鹏; 石耀琦; 马正飞; 刘晓勤

    2014-01-01

    使用高精密质量吸附仪(IGA-100,HIDEN)测定了CH4和N2纯组分在炭分子筛上于298、313和328 K温度下的吸附等温线及吸附动力学曲线,研究了CH4和N2在炭分子上的吸附热力学及动力学性质。选择Double Langmuir模型(DL)对吸附等温线数据进行了模拟;选择Fick扩散模型进行了吸附动力学的模拟。结果表明,DL模型可以准确地描述CH4和N2在炭分子筛上的吸附,拟合相关系数都非常接近1,N2在该炭分子筛上的吸附量大于CH4的吸附量;通过Fick扩算模型计算得:24N CH/7.26D D =,N 2在该炭分子筛上的扩散速率大于CH 4,所以该炭分子筛可以实现固定床出口直接富集CH4的目的。%Adsorption isotherms and kinetic curves of pure CH4 and N2 gases absorbing onto a carbon molecular sieve were measured by an intelligent gravimetric analyzer apparatus (IGA-100, HIDEN) at 298, 313 and 328 K, respectively. Thermodynamics and diffusion behaviors of CH4 and N2 on the carbon molecular sieve were also investigated. The Double Langmuir (DL) model and the Fick model were introduced to fit the adsorption isotherm and adsorption kinetic data, respectively. The fitting correction coefficients of the DL model for CH4 and N2 are close to 1 and the adsorption capacity of N2 is higher than that of CH4 on the carbon molecular sieve. The results of the Fick model indicate that the diffusion rate of N2 is much faster than that of CH4 on the carbon molecular sieve. Therefore, it is possible to enrich CH4 through a fixed bed using the carbon molecular sieve studied.

  2. Characterizing the Transition from Diffuse Atomic to Dense Molecular Clouds in the Magellanic Clouds with [C ii], [C i], and CO

    Science.gov (United States)

    Pineda, Jorge L.; Langer, William D.; Goldsmith, Paul F.; Horiuchi, Shinji; Kuiper, Thomas B. H.; Muller, Erik; Hughes, Annie; Ott, Jürgen; Requena-Torres, Miguel A.; Velusamy, Thangasamy; Wong, Tony

    2017-04-01

    We present and analyze deep Herschel/HIFI observations of the [C ii] 158 μm, [C i] 609 μm, and [C i] 370 μm lines toward 54 lines of sight in the Large Magellanic Cloud (LMC) and Small Magellanic Cloud (SMC). These observations are used to determine the physical conditions of the line-emitting gas, which we use to study the transition from atomic to molecular gas and from C+ to C0 to CO in their low-metallicity environments. We trace gas with molecular fractions in the range 0.1UV absorption (f({{{H}}}2) 0.45 in both the LMC and the SMC. Ionized carbon is the dominant gas-phase form of this element that is associated with molecular gas, with C0 and CO representing a small fraction, implying that most (89% in the LMC and 77% in the SMC) of the molecular gas in our sample is CO-dark H2. The mean {X}{CO} conversion factors in our LMC and SMC sample are larger than the value typically found in the Milky Way. When applying a correction based on the filling factor of the CO emission, we find that the values of {X}{CO} in the LMC and SMC are closer to that in the Milky Way. The observed [C ii] intensity in our sample represents about 1% of the total far-infrared intensity from the lines of sight observed in both Magellanic clouds.

  3. Unraveling the effect of La A-site substitution on oxygen ion diffusion and oxygen catalysis in perovskite BaFeO3 by data-mining molecular dynamics and density functional theory.

    Science.gov (United States)

    Chen, Chi; Baiyee, Zarah Medina; Ciucci, Francesco

    2015-10-07

    BaFeO3 (BFO) is a promising parent material for high-temperature oxygen catalysis. The effects of La substitution on the oxygen ion diffusion and oxygen catalysis in A-site La-substituted BFO are studied by combining data-driven molecular dynamics (MD) simulations and density functional theory (DFT) calculations. The data-driven MD simulations are capable of providing atomic level information regarding oxygen jumps at different sites, bridging the resolution gap of analysis between MD and DFT. The simulations identify several effects due to the introduction of La. First, according to simple electroneutrality considerations and DFT calculations, La tends to decrease the concentration of oxygen vacancies in BFO. Second, La substitution lowers the activation energy of local oxygen migration, providing faster paths for oxygen diffusion. The MD analysis predicts a higher hopping rate through La-containing bottlenecks as well as easier oxygen jumps from the La-rich cages and lower dwell times of oxygen in those cages. DFT calculations confirm a lower migration energy through La-containing bottlenecks. Third, the electrocatalytic activity of the material decreases with La, as indicated by a lower O p-band center and higher oxygen vacancy formation energies.

  4. Coupled Diffusion Processes

    Institute of Scientific and Technical Information of China (English)

    章复熹

    2004-01-01

    @@ Coupled diffusion processes (or CDP for short) model the systems of molecular motors,which attract much interest from physicists and biologists in recent years[1,2,9,14,4,7,21]. The protein moves along a filament called the track, and it is crucial that there are several inner states of the protein and the underlying chemical reaction causes transitions among different inner states,while chemical energy can be converted to mechanical energy by rachet effects[5,3,2,14,12].

  5. Herschel/HIFI observations of interstellar OH+ and H2O+ towards W49N: a probe of diffuse clouds with a small molecular fraction

    CERN Document Server

    Neufeld, D A; Sonnentrucker, P; Black, J H; Pearson, J; Yu, S; Phillips, T G; Lis, D C; De Luca, M; Herbst, E; Rimmer, P; Gerin, M; Bell, T A; Boulanger, F; Cernicharo, J; Coutens, A; Dartois, E; Kazmierczak, M; Encrenaz, P; Falgarone, E; Geballe, T R; Giesen, T; Godard, B; Goldsmith, P F; Gry, C; Gupta, H; Hennebelle, P; Hily-Blant, P; Joblin, C; Ko\\los, R; Kre\\lowski, J; Mart\\in-Pintado, J; Menten, K M; Monje, R; Mookerjea, B; Perault, M; Persson, C; Plume, R; Salez, M; Schlemmer, S; Schmidt, M; Stutzki, J; Teyssier, D; Vastel, C; Cros, A; Klein, K; Lorenzani, A; Philipp, S; Samoska, L A; Shipman, R; Tielens, A G G M; Szczerba, R; Zmuidzinas, J

    2010-01-01

    We report the detection of absorption by interstellar hydroxyl cations and water cations, along the sight-line to the bright continuum source W49N. We have used Herschel's HIFI instrument, in dual beam switch mode, to observe the 972 GHz N = 1 - 0 transition of OH+ and the 1115 GHz 1(11) - 0(00) transition of ortho-H2O+. The resultant spectra show absorption by ortho-H2O+, and strong absorption by OH+, in foreground material at velocities in the range 0 to 70 km/s with respect to the local standard of rest. The inferred OH+/H2O+ abundance ratio ranges from ~ 3 to ~ 15, implying that the observed OH+ arises in clouds of small molecular fraction, in the 2 - 8% range. This conclusion is confirmed by the distribution of OH+ and H2O+ in Doppler velocity space, which is similar to that of atomic hydrogen, as observed by means of 21 cm absorption measurements, and dissimilar from that typical of other molecular tracers. The observed OH+/H abundance ratio of a few E-8 suggests a cosmic ray ionization rate for atomic ...

  6. Hereditary Diffuse Gastric Cancer

    Science.gov (United States)

    ... Hereditary Diffuse Gastric Cancer Request Permissions Hereditary Diffuse Gastric Cancer Approved by the Cancer.Net Editorial Board , 11/2015 What is hereditary diffuse gastric cancer? Hereditary diffuse gastric cancer (HDGC) is an inherited ...

  7. 分子动力学模拟超临界水微观结构及自扩散系数%Microstructure and self-diffusion coefficient of supercritical water by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    张乃强; 徐鸿; 白杨

    2011-01-01

    By using molecular dynamics simulation with COMPASS force field, microstructure and self-diffusion coefficient of supercritical water were researched. The results show that the effect of the hydrogen bond on supercritical water is weakened obviously, and still exist. The bond length and the bond angle of the water molecular changed rapidly in the region of 648-748 K. The bond length and the bond angle of the water molecular changed slowly in 748-973 K. The characteristic peaks of radial distribution function increased with the increase of temperature in the region of 648-748 K, and decreased with the increase of temperature in the region of 748-973 K, which indicated that short range structure orderliness of water was changing with the increase of temperature. The self-diffusion coefficients of supercritical water were two orders of magnitude higher than ambient water, and increased with the increase of temperature, decreased with the increase of pressure.%采用分子动力学模拟方法,选用COMPASS力场,对超临界水的微观结构和扩散系数进行了研究.结果表明,在超临界区水分子的氢键作用明显减弱,但是仍有氢键存在.水分子的键长和键角在温度为648~748 K时变化迅速,在温度为748~973 K时变化很小.径向分布函数特征峰值在温度为648~748 K时随温度的升高而增大,在温度为748~973K时随温度升高而减小,表明水分子近程结构有序性随温度变化.超临界水自扩散系数是常温常压水的2个数量级,随温度升高而增大,随压力的升高而减小.

  8. Fractional Chemotaxis Diffusion Equations

    CERN Document Server

    Langlands, T A M

    2010-01-01

    We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or macro-molecular crowding. The mesoscopic models are formulated using Continuous Time Random Walk master equations and the macroscopic models are formulated with fractional order differential equations. Different models are proposed depending on the timing of the chemotactic forcing. Generalizations of the models to include linear reaction dynamics are also derived. Finally a Monte Carlo method for simulating anomalous subdiffusion with chemotaxis is introduced and simulation results are compared with numerical solutions of the model equations. The model equations developed here could be used to replace Keller-Segel type equations in biological systems with transport hindered by traps, macro-molecular crowding or other obstacles.

  9. Diffusion coefficient in photon diffusion theory

    NARCIS (Netherlands)

    Graaff, R; Ten Bosch, JJ

    2000-01-01

    The choice of the diffusion coefficient to be used in photon diffusion theory has been a subject of discussion in recent publications on tissue optics. We compared several diffusion coefficients with the apparent diffusion coefficient from the more fundamental transport theory, D-app. Application to

  10. Diffusion coefficient in photon diffusion theory

    NARCIS (Netherlands)

    Graaff, R; Ten Bosch, JJ

    2000-01-01

    The choice of the diffusion coefficient to be used in photon diffusion theory has been a subject of discussion in recent publications on tissue optics. We compared several diffusion coefficients with the apparent diffusion coefficient from the more fundamental transport theory, D-app. Application to

  11. Assessment of the Molecular Classfication of Diffuse Large B-Cell Lymphoma by Immunohistochemistry Using A Tissue Microarray%组织芯片免疫组化法确定弥漫大B细胞性淋巴瘤的分子分型的评价

    Institute of Scientific and Technical Information of China (English)

    刘艳辉; 董秋美

    2007-01-01

    @@ 1 文献类型 预后. 2 证据水平 2b. 3 文献来源 Hans CP, Weisenburger DD, Greiner TC, et al. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray [J]. Blood, 2004,1 (103) :275-281.

  12. 油纸复合介质中水分子扩散行为的分子动力学模拟%Molecular Dynamics Simulation of the Diffusion Behavior of Water Molecules in Oil and Cellulose Composite Media

    Institute of Scientific and Technical Information of China (English)

    廖瑞金; 朱孟兆; 周欣; 杨丽君; 严家明; 孙才新

    2011-01-01

    The diffusion behaviors of water molecules in oil-cellulose composite media were studied at different temperatures using a molecular dynamics simulation. By analyzing the formation of hydrogen bonds between the water molecules and cellulose we found that the water molecules that were initially present in the oil gradually spread to the cellulose, and hydrogen bonds were formed between them. The water molecules that were present in the cellulose initially also formed hydrogen bonds and were bound to cellulose molecules. By analyzing the diffusion coefficients of the water molecules at different temperatures we found that the diffusion behaviors of the water molecules in the two single-media,namely oil and cellulose, were very different because of their different polarities. The diffusion coefficients of the water molecules in the composite media were influenced greatly by the ratio of water molecules present in the oil and cellulose and a strong correlation was apparent between them. The water molecule-oil interaction energy and the water molecule-cellulose interaction energy were also strongly related to the polarities of the oil and the cellulose. The interaction energies also exhibited a strong correlation to the distribution of water molecules at different temperatures. This was the reason for the weakened influence of temperature on the diffusion coefficient of the water molecules, which was due to the different distributions of water molecules at different temperatures.%对不同温度下水分子在油纸复合介质中的扩散行为进行了分子动力学模拟研究.通过分析水分子与纤维素形成的氢键发现,油中的水分子在模拟过程中会逐渐扩散到纤维素内并与之形成氢键,而纤维素内的水分子则与纤维素形成氢键后被束缚于纤维素中.通过分析水分子的扩散系数发现,由于油和纤维素的极性不同,使得水分子在油和纤维素两种单介质中的扩散行为有较大差别,而在

  13. An elastic-diffusion model for myosin VI molecular motor in a periodic potential field%肌球蛋白VI分子马达周期势场下的弹性扩散模型

    Institute of Scientific and Technical Information of China (English)

    李晨璞; 韩英荣; 展永; 胡金江; 张礼刚; 曲蛟

    2013-01-01

    Because of the special structure and intracellular functions of myosin VI molecular motor, its dynamic principle has become a research focus. Starting from its structure and experimental phenomenon, the elastic-diffusion model of myosin VI in a periodic potential field is established, and the stochastic dynamics of the molecular motors, which conform to the Langevin equation, is analyzed by Monte Carlo simulations. By means of the environmental noise, myosin VI molecular motors could take stable stepping motion and effective transport according to its elastic potential energy and periodic potential of track, and a load can weaken the transportation power of the molecular motor system. For a given elastic coefficient, the longer the elastic chain of myosin VI, the lower the average velocity of it. By selecting a reasonable size of elasticity coefficient, the average velocity can be the maximum for a given elastic chain. In addition, the load can increase exponentially the mean dwelling time of myosin VI at the connection site.%肌球蛋白VI分子马达因其特殊的结构及胞内功能,其动力学原理成为研究的热点。从肌球蛋白VI自身结构和实验现象出发,建立其弹性扩散模型,并通过Monte Carlo方法分析了肌球蛋白VI满足朗之万方程的随机动力学行为。结果表明,在环境噪声作用下,具有弹性势能和轨道周期势能的肌球蛋白VI可以进行梯跳运动和有效的输运,但负载力会减弱分子马达系统的输运能力;当弹性系数一定时,弹性链越长平均速度越小,当弹性链长度一定时,合理选择弹性系数平均速度可达到最大值;另外,负载力的存在使肌球蛋白VI在接触位点的平均驻留时间呈指数增加。

  14. Polymer and spherical nanoparticle diffusion in nanocomposites

    Science.gov (United States)

    Karatrantos, Argyrios; Composto, Russell J.; Winey, Karen I.; Clarke, Nigel

    2017-05-01

    Nanoparticle and polymer dynamics in nanocomposites containing spherical nanoparticles were investigated by means of molecular dynamics simulations. We show that the polymer diffusivity decreases with nanoparticle loading due to an increase of the interfacial area created by nanoparticles, in the polymer matrix. We show that small sized nanoparticles can diffuse much faster than that predicted from the Stokes-Einstein relation in the dilute regime. We show that the nanoparticle diffusivity decreases at higher nanoparticle loading due to nanoparticle-polymer interface. Increase of the nanoparticle radius slows the nanoparticle diffusion.

  15. Communication: Probing anomalous diffusion in frequency space

    Energy Technology Data Exchange (ETDEWEB)

    Stachura, Sławomir [Centre de Biophys. Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans (France); Synchrotron Soleil, L’Orme de Merisiers, 91192 Gif-sur-Yvette (France); Kneller, Gerald R., E-mail: gerald.kneller@cnrs-orleans.fr [Centre de Biophys. Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans (France); Synchrotron Soleil, L’Orme de Merisiers, 91192 Gif-sur-Yvette (France); Université d’Orléans, Chateau de la Source-Av. du Parc Floral, 45067 Orléans (France)

    2015-11-21

    Anomalous diffusion processes are usually detected by analyzing the time-dependent mean square displacement of the diffusing particles. The latter evolves asymptotically as W(t) ∼ 2D{sub α}t{sup α}, where D{sub α} is the fractional diffusion constant and 0 < α < 2. In this article we show that both D{sub α} and α can also be extracted from the low-frequency Fourier spectrum of the corresponding velocity autocorrelation function. This offers a simple method for the interpretation of quasielastic neutron scattering spectra from complex (bio)molecular systems, in which subdiffusive transport is frequently encountered. The approach is illustrated and validated by analyzing molecular dynamics simulations of molecular diffusion in a lipid POPC bilayer.

  16. Diffusion archeology for diffusion progression history reconstruction.

    Science.gov (United States)

    Sefer, Emre; Kingsford, Carl

    2016-11-01

    Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.

  17. Is diffusion weighted imaging adding value in diagnosis of focal ...

    African Journals Online (AJOL)

    Doaa Mokhtar Mohamed Emara

    2013-05-09

    May 9, 2013 ... Abstract Introduction: Diffusion weighted imaging (DWI) offers molecular information that ... model, the effect of the first (dephasing) gradient is cancelled ... Areas of true restricted diffusion demonstrate high signal ... A phased array surface coil was ..... signal intensity ratios with small diffusion gradients for.

  18. HD/H2 as a Probe of the Roles of Gas, Dust, Light, Metallicity, and Cosmic Rays in Promoting the Growth of Molecular Hydrogen in the Diffuse Interstellar Medium

    Science.gov (United States)

    Liszt, H. S.

    2015-01-01

    We modeled recent observations of UV absorption of HD and {H_2} in the Milky Way and toward damped/subdamped Lyα systems at z = 0.18 and z >1.7. N(HD)/N({H_2}) ratios reflect the separate self-shieldings of HD and {H_2} and the coupling introduced by deuteration chemistry. Locally, observations are explained by diffuse molecular gas with 16 cm-3 1.7, N(HD) is comparable to the Galaxy but with 10 times smaller N({H_2}) and somewhat smaller N({H_2})/N(H I). Comparison of our Galaxy with the Magellanic Clouds shows that smaller {H_2}/H is expected at subsolar metallicity, and we show by modeling that HD/{H_2} increases with density at low metallicity, opposite to the Milky Way. Observations of HD would be explained with higher n(H) at low metallicity, but high-z systems have high HD/{H_2} at metallicity 0.04 shielding effects. The abrupt {H_2} transition to {H_2}/H ≈ 1%-10% occurs mostly from self-shielding, although it is assisted by extinction for n(H) <~ 16 cm-3. Interior {H_2} fractions are substantially increased by dust extinction below <~ 32 cm-3. At smaller n(H), ζ H , small increases in {H_2} triggered by dust extinction can trigger abrupt increases in N(HD).

  19. HD/H2 as a probe of the roles of gas, dust, light, metallicity and cosmic rays in promoting the growth of molecular hydrogen in the diffuse interstellar medium

    CERN Document Server

    Liszt, H S

    2014-01-01

    We modelled recent observations of UV absorption of HD and \\HH\\ in the Milky Way and toward damped/sub-damped Lyman alpha systems at z=0.18 and z $>$ 1.7. N(HD)/N(\\HH) ratios reflect the separate self-shieldings of HD and \\HH\\ and the coupling introduced by deuteration chemistry. Locally, observations are explained by diffuse molecular gas with $ 16 \\pccc \\la$ n(H) $\\la 128 \\pccc $ if the cosmic-ray ionization rate per H-nucleus \\zetaH $= 2\\times 10^{-16}\\ps$ as inferred from \\H3\\p\\ and OH\\p. The dominant influence on N(HD)/N(\\HH) is the cosmic-ray ionization rate with a much weaker downward dependence on n(H) at Solar metallicity, but dust-extinction can drive N(HD) higher as with N(\\HH). At z $>$ 1.7, N(HD) is comparable to the Galaxy but with 10x smaller N(\\HH) and somewhat smaller N(\\HH)/N(H I). Comparison of our Galaxy and the Magellanic Clouds shows that smaller \\HH/H is expected at sub-Solar metallicity and we show by modelling that HD/\\HH\\ increases with density at low metallicity, opposite to the Mil...

  20. 碳纳米管储氢性能及H2分子扩散现象的分子动力学研究%Molecular dynamic study of hydrogen storage and diffusions in carbon nanotubes

    Institute of Scientific and Technical Information of China (English)

    刘健康; 何国柱

    2011-01-01

    By using Brenner potential for intramolecular and LJ potential for intermolecular interactions,we studied the adsorption and storage of H2 molecules in carbon nanotubes in terms of molecular dynamic simulation techniques. After the simulation,the adsorption sites of H2 molecules in nanotubes were analyzed,the pair distribution functions of C-H particals were computed,the mean square displacement of H2 were calculated,and the temperature dependence of diffusion coefficient was studied to investigate the physical absorption phenomena and the transport properties of H2 molecule in carbon nanotubes.%本文采用Brenner及LJ混合势对H2在C纳米管的吸附及H2分子在C纳米管中的扩散性质进行了分子动力学模拟.通过模拟轨迹的分析,分别计算了C-H之间的径向分布函数、H2分子在单壁C纳米管的均方位移及通过对H2分子的均方位移的分析,计算了不同温度下的H2分子在C纳米管中的扩散系数,分析了温度对扩散系数的影响.

  1. Enhancement of Ambipolar Diffusion Rates through Field Fluctuations

    CERN Document Server

    Fatuzzo, M; Fatuzzo, Marco; Adams, Fred C.

    2002-01-01

    Previous treatments of ambipolar diffusion in star-forming molecular clouds do not consider the effects of fluctuations in the fluid fields about their mean values. This paper generalizes the ambipolar diffusion problem in molecular cloud layers to include such fluctuations. Because magnetic diffusion is a nonlinear process, fluctuations can lead to an enhancement of the ambipolar diffusion rate. In addition, the stochastic nature of the process makes the ambipolar diffusion time take on a distribution of different values. In this paper, we focus on the case of long wavelength fluctuations and find that the rate of ambipolar diffusion increases by a significant factor $\\Lambda \\sim 1 - 10$. The corresponding decrease in the magnetic diffusion time helps make ambipolar diffusion more consistent with observations.

  2. Extragalactic diffuse (C II) emission

    Science.gov (United States)

    Madden, Suzanne C.; Geis, Norbert; Townes, Charles H.; Genzel, R.; Herrmann, F.; Poglitsch, Albrecht; Stacey, G. J.

    1995-01-01

    The 158 micro m (CII) line has been mapped in the galaxies Centaurus A, M83, NGC 6946, and NGC 891. The emission exists over very large scales, peaking in the nuclei and extending beyond the spiral arms and molecular disks. While most of the (CII) emission from the nuclei and spiral arms originates in photodissociated gas, the diffuse atomic gas can account for much of the (CII) emission in the extended regions.

  3. Diffusion and particle mobility in 1D system

    Energy Technology Data Exchange (ETDEWEB)

    Borman, V.D. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation); Johansson, B. [Condensed Matter Theory Group, Department of Physics, Box 530, Uppsala University, S-75121 Uppsala (Sweden); Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology (KTH), S-10044 Stockholm (Sweden); Skorodumova, N.V. [Condensed Matter Theory Group, Department of Physics, Box 530, Uppsala University, S-75121 Uppsala (Sweden); Tronin, I.V. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation)]. E-mail: ivt@rbcmail.ru; Tronin, V.N. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation); Troyan, V.I. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation)

    2006-12-04

    The transport properties of one-dimensional (1D) systems have been studied theoretically. Contradictory experimental results on molecular transport in quasi-1D systems, such as zeolite structures, when both diffusion transport acceleration and the existence of the diffusion mode with lower particle mobility (single-file diffusion ({approx}t{sup 1/2})) have been reported, are consolidated in a consistent model. Transition from the single-file diffusion mode to an Einstein-like diffusion {approx}t with diffusion coefficient increasing with the density has been predicted to occur at large observation times.

  4. Ion diffusion in compacted bentonite

    Energy Technology Data Exchange (ETDEWEB)

    Lehikoinen, J. [VTT Chemical Technology, Espoo (Finland)

    1999-03-01

    In the study, a two-dimensional molecular-level diffusion model, based on a modified form of the Gouy-Chapman (GC) theory of the electrical double layers, for hydrated ionic species in compacted bentonite was developed. The modifications to the GC theory, which forms the very kernel of the diffusion model, stem from various non-conventional features: ionic hydration, dielectric saturation, finite ion-sizes and specific adsorption. The principal objectives of the study were met. With the aid of the consistent diffusion model, it is a relatively simple matter to explain the experimentally observed macroscopic exclusion for anions as well as the postulated, but greatly controversial, surface diffusion for cations. From purely theoretical grounds, it was possible to show that the apparent diffusivities of cations, anions and neutral molecules (i) do not exhibit order-or-magnitude differences, and (ii) are practically independent of the solution ionic strength used and, consequently, of the distribution coefficient, K{sub d}, unless they experience specific binding onto the substrate surface. It was also of interest to investigate the equilibrium anionic concentration distribution in the pore geometry of the GMM model as a function of the solution ionic strength, and to briefly speculate its consequences to diffusion. An explicit account of the filter-plate effect was taken by developing a computerised macroscopic diffusion model, which is based upon the very robust and efficient Laplace Transform Finite-Difference technique. Finally, the inherent limitations as well as the potential fields of applications of the models were addressed. (orig.) 45 refs.

  5. Outcome of elderly patients with diffuse large B-cell lymphoma treated with R-CHOP: results from the UK NCRI R-CHOP14v21 trial with combined analysis of molecular characteristics with the DSHNHL RICOVER-60 trial.

    Science.gov (United States)

    Kühnl, A; Cunningham, D; Counsell, N; Hawkes, E A; Qian, W; Smith, P; Chadwick, N; Lawrie, A; Mouncey, P; Jack, A; Pocock, C; Ardeshna, K M; Radford, J; McMillan, A; Davies, J; Turner, D; Kruger, A; Johnson, P W; Gambell, J; Rosenwald, A; Ott, G; Horn, H; Ziepert, M; Pfreundschuh, M; Linch, D

    2017-07-01

    There is an on-going debate whether 2- or 3-weekly administration of R-CHOP is the preferred first-line treatment for elderly patients with diffuse large B-cell lymphoma (DLBCL). The UK NCRI R-CHOP14v21 randomized phase 3 trial did not demonstrate a difference in outcomes between R-CHOP-14 and R-CHOP-21 in newly diagnosed DLBCL patients aged 19-88 years, but data on elderly patients have not been reported in detail so far. Here, we provide a subgroup analysis of patients ≥60 years treated on the R-CHOP14v21 trial with extended follow-up. Six hundred and four R-CHOP14v21 patients ≥60 years were included in this subgroup analysis, with a median follow-up of 77.7 months. To assess the impact of MYC rearrangements (MYC-R) and double-hit-lymphoma (DHL) on outcome in elderly patients, we performed a joint analysis of cases with available molecular data from the R-CHOP14v21 (N = 217) and RICOVER-60 (N = 204) trials. Elderly DLBCL patients received high dose intensities with median total doses of ≥98% for all agents. Toxicities were similar in both arms with the exception of more grade ≥3 neutropenia (P R-CHOP-21 versus R-CHOP-14. The elderly patient population had a favorable 5-year overall survival (OS) of 69% (95% CI: 65-73). We did not identify any subgroup of patients that showed differential response to either regimen. In multivariable analysis including individual factors of the IPI, gender, bulk, B2M and albumin levels, only age and B2M were of independent prognostic significance for OS. Molecular analyses demonstrated a significant impact of MYC-R (HR = 1.96; 95% CI: 1.22-3.16; P = 0.01) and DHL (HR = 2.21; 95% CI: 1.18-4.11; P = 0.01) on OS in the combined trial cohorts, independent of other prognostic factors. Our data support equivalence of both R-CHOP application forms in elderly DLBCL patients. Elderly MYC-R and DHL patients have inferior prognosis and should be considered for alternative treatment approaches

  6. Translational diffusion of proteins in nanochannels

    Science.gov (United States)

    Kannam, Sridhar Kumar; Downton, Matthew T.

    2017-02-01

    Hydrodynamic interactions play an important role in the transport of analytes through nanoscale devices. Of particular note is the role that no-slip boundary conditions have on the drag coefficient of confined particles and molecules. In this work, we use a coarse grained molecular dynamics model to measure the diffusion coefficients of proteins confined within cylindrical nanochannels of similar dimension. Finite-size corrected bulk diffusion coefficients are found to agree with experimental data, while in channels, a good match is found between theoretical expressions based on continuum fluid mechanics and the reduction of the translational diffusion coefficient across a range of protein to channel size ratios. These results demonstrate that it is possible to directly use molecular simulation to make quantitative predictions of the effects of hydrodynamics on diffusion at length scales of order 1 nm.

  7. Can disorder enhance incoherent exciton diffusion?

    CERN Document Server

    Lee, Elizabeth M Y; Willard, Adam P

    2015-01-01

    Recent experiments aimed at probing the dynamics of excitons have revealed that semiconducting films composed of disordered molecular subunits, unlike expectations for their perfectly ordered counterparts, can exhibit a time-dependent diffusivity in which the effective early time diffusion constant is larger than that of the steady state. This observation has led to speculation about what role, if any, microscopic disorder may play in enhancing exciton transport properties. In this article, we present the results of a model study aimed at addressing this point. Specifically, we present a general model, based upon F\\"orster theory, for incoherent exciton diffusion in a material composed of independent molecular subunits with static energetic disorder. Energetic disorder leads to heterogeneity in molecule-to-molecule transition rates which we demonstrate has two important consequences related to exciton transport. First, the distribution of local site-specific diffusivity is broadened in a manner that results i...

  8. Conceptual Foundations of Diffusion in Magnetic Resonance

    CERN Document Server

    Koay, Cheng Guan

    2013-01-01

    A thorough review of the q-space technique is presented starting from a discussion of Fick's laws. The work presented here is primarily conceptual, theoretical and hopefully pedagogical. We offered the notion of molecular concentration to unify Fick's laws and diffusion MRI within a coherent conceptual framework. The fundamental relationship between diffusion MRI and the Fick's laws are carefully established. The conceptual and theoretical basis of the q-space technique is investigated from first principles.

  9. Conceptual Foundations of Diffusion in Magnetic Resonance.

    Science.gov (United States)

    Koay, Cheng Guan; Özarslan, Evren

    2013-07-01

    A thorough review of the q-space technique is presented starting from a discussion of Fick's laws. The work presented here is primarily conceptual, theoretical and hopefully pedagogical. We offered the notion of molecular concentration to unify Fick's laws and diffusion MRI within a coherent conceptual framework. The fundamental relationship between diffusion MRI and the Fick's laws are carefully established. The conceptual and theoretical basis of the q-space technique is investigated from first principles.

  10. Protein diffusion in photopolymerized poly(ethylene glycol) hydrogel networks

    Energy Technology Data Exchange (ETDEWEB)

    Engberg, Kristin; Frank, Curtis W, E-mail: curt.frank@stanford.edu [Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stauffer III, Stanford, CA 94305 (United States)

    2011-10-15

    In this study, protein diffusion through swollen hydrogel networks prepared from end-linked poly(ethylene glycol)-diacrylate (PEG-DA) was investigated. Hydrogels were prepared via photopolymerization from PEG-DA macromonomer solutions of two molecular weights, 4600 Da and 8000 Da, with three initial solid contents: 20, 33 and 50 wt/wt% PEG. Diffusion coefficients for myoglobin traveling across the hydrogel membrane were determined for all PEG network compositions. The diffusion coefficient depended on PEG molecular weight and initial solid content, with the slowest diffusion occurring through lower molecular weight, high-solid-content networks (D{sub gel} = 0.16 {+-} 0.02 x 10{sup -8} cm{sup 2} s{sup -1}) and the fastest diffusion occurring through higher molecular weight, low-solid-content networks (D{sub gel} = 11.05 {+-} 0.43 x 10{sup -8} cm{sup 2} s{sup -1}). Myoglobin diffusion coefficients increased linearly with the increase of water content within the hydrogels. The permeability of three larger model proteins (horseradish peroxidase, bovine serum albumin and immunoglobulin G) through PEG(8000) hydrogel membranes was also examined, with the observation that globular molecules as large as 10.7 nm in hydrodynamic diameter can diffuse through the PEG network. Protein diffusion coefficients within the PEG hydrogels ranged from one to two orders of magnitude lower than the diffusion coefficients in free water. Network defects were determined to be a significant contributing factor to the observed protein diffusion.

  11. Fast diffusion of water nanodroplets on graphene

    CERN Document Server

    Ma, Ming; Michaelides, Angelos; Aeppli, Gabriel

    2016-01-01

    Diffusion across surfaces generally involves motion on a vibrating but otherwise stationary substrate. Here, using molecular dynamics, we show that a layered material such as graphene opens up a new mechanism for surface diffusion whereby adsorbates are carried by propagating ripples via a motion similar to surfing. For water nanodroplets, we demonstrate that the mechanism leads to exceedingly fast diffusion that is 2-3 orders of magnitude faster than the self-diffusion of water molecules in liquid water. We also reveal the underlying principles that regulate this new mechanism for diffusion and show how it also applies to adsorbates other than water, thus opening up the prospect of achieving fast and controllable motion of adsorbates across material surfaces more generally.

  12. Solid-state diffusion in amorphous zirconolite

    Energy Technology Data Exchange (ETDEWEB)

    Yang, C.; Dove, M. T.; Trachenko, K. [School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom); Zarkadoula, E. [School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom); Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6138 (United States); Todorov, I. T. [STFC Daresbury Laboratory, Warrington WA4 1EP (United Kingdom); Geisler, T. [Steinmann-Institut für Geologie, Mineralogie und Paläontologie, University of Bonn, D-53115 Bonn (Germany); Brazhkin, V. V. [Institute for High Pressure Physics, RAS, 142190 Moscow (Russian Federation)

    2014-11-14

    We discuss how structural disorder and amorphization affect solid-state diffusion, and consider zirconolite as a currently important case study. By performing extensive molecular dynamics simulations, we disentangle the effects of amorphization and density, and show that a profound increase of solid-state diffusion takes place as a result of amorphization. Importantly, this can take place at the same density as in the crystal, representing an interesting general insight regarding solid-state diffusion. We find that decreasing the density in the amorphous system increases pre-factors of diffusion constants, but does not change the activation energy in the density range considered. We also find that atomic species in zirconolite are affected differently by amorphization and density change. Our microscopic insights are relevant for understanding how solid-state diffusion changes due to disorder and for building predictive models of operation of materials to be used to encapsulate nuclear waste.

  13. Molecular Simulation for the Diffusion Characteristics of Aromatic and Naphthenic Hydrocarbons in the Channel of MFI and FAU Zeolites%芳烃、环烷烃分子在MFI和FAU分子筛中扩散行为的分子模拟

    Institute of Scientific and Technical Information of China (English)

    袁帅; 龙军; 周涵; 田辉平; 赵毅

    2011-01-01

    Molecular simulation methods were applied to investigate the molecular dimensions (aXbXc) of different aromatic and naphthenic hydrocarbons in their minimum energy configurations and their diffusion energy barriers(ED) in MFI and FAU zeolites. According to the results, molecular diffusion energy barrier was sensitive to the minimum cross-sectional dimension (a X b) of molecule. Benzene, naphthalene, cyclopentane and cyclohexane molecules could diffuse in the channel of MFI, while other larger aromatic and naphthenic molecules could not. Hydrocarbon molecules diffused more easily in the straight channel than in the sinusoidal channel of MFI zeolite. Aromatic and naphthenic molecules diffused more easily in FAU than in MFI because of the larger pore size of FAU zeolite. The 12-ring openings between two adjacent super cages of FAU zeolite limited the diffusion of pyrene, perhydropyrene and other larger hydrocarbon molecules. It can be concluded that the heavy oil molecules could only first be cracked into small molecules on the surface of zeolites or other active materials, then diffuse into the channel of MFI and FAU zeolites for further conversion.%应用分子模拟技术计算了不同芳烃和环烷烃分子最低能量构象的分子尺寸(a×b×c),并计算了其在MFI、FAU分子筛中的扩散能垒.计算结果表明,分子的最小截面尺寸(a×b)与扩散能垒相关.苯、萘、环戊烷、环己烷分子可以在MFI分子筛中扩散,其它多环芳烃、多环环烷烃分子均很难扩散.分子在MFI直孔道中扩散比在正弦孔道中容易.FAU分子筛由于孔径尺寸较大,分子在其孔道内扩散比在MFI孔道中容易,而两超笼间的十二元环会限制芘、全氢芘及比之更大的分子在FAU孔道中扩散.从计算结果可以推断,催化裂化原料中的重油大分子只有先在分子筛或其他活性材料表面一次裂化成一定尺寸的小分子,才能扩散进入MFI、FAU分子筛晶内发生进一步反应.

  14. Diffusion on spatial network

    Science.gov (United States)

    Hui, Zi; Tang, Xiaoyue; Li, Wei; Greneche, Jean-Marc; Wang, Qiuping A.

    2015-04-01

    In this work, we study the problem of diffusing a product (idea, opinion, disease etc.) among agents on spatial network. The network is constructed by random addition of nodes on the planar. The probability for a previous node to be connected to the new one is inversely proportional to their spatial distance to the power of α. The diffusion rate between two connected nodes is inversely proportional to their spatial distance to the power of β as well. Inspired from the Fick's first law, we introduce the diffusion coefficient to measure the diffusion ability of the spatial network. Using both theoretical analysis and Monte Carlo simulation, we get the fact that the diffusion coefficient always decreases with the increasing of parameter α and β, and the diffusion sub-coefficient follows the power-law of the spatial distance with exponent equals to -α-β+2. Since both short-range diffusion and long-range diffusion exist, we use anomalous diffusion method in diffusion process. We get the fact that the slope index δ in anomalous diffusion is always smaller that 1. The diffusion process in our model is sub-diffusion.

  15. Advective-diffusive transport in microflows

    Science.gov (United States)

    Anderson, Patrick; Speetjens, Michel; Gorodetskyi, Oleksandr

    2014-11-01

    Advective-diffusive transport in microflows is studied by means of the diffusive mapping method, a recent extension of the mapping method by Gorodetskyi et al. (Phys. Fluids 24, 2012) that includes molecular diffusion. This greatly expands the application area of the mapping technique and makes the powerful concepts of eigenmode decomposition and spectral analysis of scalar transport accessible to an important class of flows: inline micromixers with diffusion. The staggered herringbone micro-mixer is adopted as a prototypical three-dimensional micro mixer. Simulations with the diffusive mapping method are in close agreement with experimental observations in literature and expose a strong impact of diffusion on the transport. Diffusion enables crossing of Lagrangian transport barriers and thus smoothens concentration gradients and accelerates homogenization. Spectral analysis of the mapping matrix reveals this already occurs on a modal level in that individual eigenmodes progressively smoothen and spread out across transport barriers with stronger diffusion. Concurrently, the corresponding eigenvalues diminish and thus fundamentally alter the mixing process by invariably causing homogenization, irrespective of the Lagrangian flow structure.

  16. Systematic study of exciton diffusion length in organic semiconductors by six experimental methods

    NARCIS (Netherlands)

    Lin, Jason D. A.; Mikhnenko, Oleksandr V.; Chen, Jingrun; Masri, Zarifi; Ruseckas, Arvydas; Mikhailovsky, Alexander; Raab, Reilly P.; Liu, Jianhua; Blom, Paul W. M.; Loi, Maria Antonietta; Garcia-Cervera, Carlos J.; Samuel, Ifor D. W.; Thuc-Quyen Nguyen, [No Value

    Six experimental methods have been used to investigate the exciton diffusion length in materials with systematic chemical modifications. We find that exciton diffusion length correlates with molecular ordering. We discuss situations in which certain experimental techniques are more appropriate.

  17. Diffusion Behavior of Gas Molecules in Oil-paper Insulation System Based on Molecular Dynamic Simulation%基于分子动力学模拟的油纸绝缘系统中气体小分子扩散行为

    Institute of Scientific and Technical Information of China (English)

    廖瑞金; 贡春艳; 周欣; 杨丽君; 段炼

    2012-01-01

    In order to reveal the diffusion mechanism of gas molecules in transformer oil paper insulation system on the micro level, diffusion behaviors of 7 kinds of gas molecules in oil and paper medium were simulated based on molecular dynamics, respectively. The gases includes H2, CO, CO2, CH4, C2H2, C2H4, and C2H6, which are commonly utilized in dissolved gas analysis of power transformer and produced during the aging process of oil paper composite insulating material. By using a molecular dynamics simulation software, 2 groups of models were set up to simulate the diffusion of the gas molecules in oil and paper. By investigating the diffusion coefficients, displacement features, free volume characteristics, and interaction energies of corresponding gas molecules, the diffusion micro-mechanism of the gas molecules was observed, the differences in diffusion features among the gas molecules were discussed, and the influences of impact factors on gas molecules' diffusion were contrasted. Simulation results indicate that the diffusion coefficients of gas molecule in cellulose is an order of magnitude lower than that in oil, and the order of the diffusion coefficients of these gas molecules in the 2 kinds of insulation media is different. It is concluded that, in oil, the main factor influencing the gas molecular diffusion behavior is the free volume of gas molecules, and in cellulose, this main factor is the intermolecular interaction.%为了从微观层次上揭示气体小分子在变压器油纸绝缘系统中的扩散机理,对变压器油纸复合绝缘材料老化过程中产生的7种常见气体小分子(包括H2、CO、CO2、CH4、C2H2、C2H4和C2H6)在油纸两相介质中的扩散行为进行了分子动力学模拟。采用分子动力学模拟软件,搭建了2组模型,以分别模拟各种气体小分子在油中和纤维素绝缘纸中的扩散。通过对气体小分子在油纸介质中扩散系数、位移特性、自由体积特性与油纸的相互

  18. Acoustic diffusers III

    Science.gov (United States)

    Bidondo, Alejandro

    2002-11-01

    This acoustic diffusion research presents a pragmatic view, based more on effects than causes and 15 very useful in the project advance control process, where the sound field's diffusion coefficient, sound field diffusivity (SFD), for its evaluation. Further research suggestions are presented to obtain an octave frequency resolution of the SFD for precise design or acoustical corrections.

  19. Diffusive dynamics on paper matrix

    Science.gov (United States)

    Chaudhury, Kaustav; Kar, Shantimoy; Chakraborty, Suman

    2016-11-01

    Writing with ink on a paper and the rapid diagnostics of diseases using paper cartridge, despite their remarkable diversities from application perspective, both involve the motion of a liquid from a source on a porous hydrophilic substrate. Here we bring out a generalization in the pertinent dynamics by appealing to the concerned ensemble-averaged transport with reference to the underlying molecular picture. Our results reveal that notwithstanding the associated complexities and diversities, the resultant liquid transport characteristics on a paper matrix, in a wide variety of applications, resemble universal diffusive dynamics. Agreement with experimental results from diversified applications is generic and validates our unified theory.

  20. Tortuosity and anomalous diffusion in the neuromuscular junction

    Science.gov (United States)

    Lacks, Daniel J.

    2008-04-01

    The signal transfer from nerve to muscle occurs by diffusion across the neuromuscular junction. The continuum level analysis of diffusion processes is based on the diffusion equation, which in one dimension is ∂c/∂t=D(∂2c/∂x2) , where c is the molecular concentration and D is the diffusivity. However, in confined systems such as the neuromuscular junction, the diffusion equation may not be valid, and even if valid the value of D may be altered by the confinement. In this paper, Monte Carlo simulations are used to probe diffusion at the molecular level in a realistic model of a neuromuscular junction. The results show that diffusion is anomalous (i.e., not described by the diffusion equation) for time scales less than ˜0.01s , which is the time scale relevant for signaling processes in the synapse. At longer time scales, the diffusion is normal (i.e., described by the diffusion equation), but with a value of D that is reduced by a factor of ˜5 times compared to the value for diffusion in open space. As the width of the synaptic cleft decreases, these effects become even more pronounced. The physical basis of these results is described in terms of the structure of the neuromuscular junction.

  1. On diffusion in narrow random channels

    CERN Document Server

    Freidlin, Mark

    2013-01-01

    We consider in this paper a solvable model for the motion of molecular motors. Based on the averaging principle, we reduce the problem to a diffusion process on a graph. We then calculate the effective speed of transportation of these motors.

  2. Genetics and pharmacogenomics of diffuse gliomas

    NARCIS (Netherlands)

    Thuijl, H.F. van; Ylstra, B.; Wurdinger, T.; Nieuwenhuizen, D. van; Heimans, J.J.; Wesseling, P.; Reijneveld, J.C.

    2013-01-01

    Rapidly evolving techniques for analysis of the genome provide new opportunities for cancer therapy. For diffuse gliomas this has resulted in molecular markers with potential for personalized therapy. Some drugs that utilize pharmacogenomics are currently being tested in clinical trials. In melanoma

  3. The CS molecule in diffuse interstellar clouds

    NARCIS (Netherlands)

    Drdla, K.; Knapp, G.R.; Dishoeck, van E.F.

    1989-01-01

    The CS J = 2-1 emission line at 98 GHz has been searched for in 10 diffuse molecular clouds. CS column densities are derived by performing statistical equilibrium calculations for the rotational population distribution which includes collisional excitation by electrons as well as by neutral species.

  4. Eigenmode analysis of advective-diffusive transport in micromixers by the diffusive mapping method

    Science.gov (United States)

    Anderson, Patrick; Speetjens, Michel; Gorodetskyi, Oleksandr; Giona, Max; Mixing Collaboration

    2013-11-01

    Advective-diffusive transport in microflows is studied by means of the diffusive map- ping method, a recent extension of the mapping method by Gorodetskyi et al. (Phys. Fluids 24, 2012) that includes molecular diffusion. This greatly expands the application area of the mapping technique and makes the powerful concepts of eigenmode decompo- sition and spectral analysis of scalar transport accessible to an important class of flows: inline micromixers with diffusion. The staggered herringbone micro-mixer is adopted as a prototypical three-dimensional micro mixer. Simulations with the diffusive mapping method are in close agreement with experimental observations in literature and expose a strong impact of diffusion on the transport. Diffusion enables crossing of Lagrangian trans- port barriers and thus smoothens concentration gradients and accelerates homogenization. Spectral analysis of the mapping matrix reveals this already occurs on a modal level in that individual eigenmodes progressively smoothen and spread out across transport bar- riers with stronger diffusion. Concurrently, the corresponding eigenvalues diminish and thus fundamentally alter the mixing process by invariably causing homogenization, irre- spective of the Lagrangian flow structure. This happens faster and exhibits an earlier emergence of the dominant eigenmode the stronger the diffusion. Lagrangian structures may still affect the spectral properties in that flows comprising both islands and chaotic seas typically result in a richer set of eigenmodes compared to cases with global chaos.

  5. How a Nanodroplet Diffuses on Smooth Surfaces

    Science.gov (United States)

    Li, Chu; Huang, Jizu; Li, Zhigang

    2016-11-01

    In this study, we investigate how nanodroplets diffuse on smooth surfaces through molecular dynamics (MD) simulations and theoretical analyses. The simulations results show that the surface diffusion of nanodroplet is different from that of single molecules and solid nanoparticles. The dependence of nanodroplet diffusion coefficient on temperature is surface wettability dependent, which undergoes a transition from linear to nonlinear as the surface wettability is weakened due to the coupling of temperature and surface energy. We also develop a simple relation for the diffusion coefficient by using the contact angle and contact radius of the droplet. It works well for different surface wettabilities and sized nanodroplets, as confirmed by MD simulations. This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region under Grant No. 615312.

  6. Cosmic ray penetration in diffuse clouds

    CERN Document Server

    Morlino, G

    2015-01-01

    Cosmic rays are a fundamental source of ionization for molecular and diffuse clouds, influencing their chemical, thermal, and dynamical evolution. The amount of cosmic rays inside a cloud also determines the $\\gamma$-ray flux produced by hadronic collisions between cosmic rays and cloud material. We study the spectrum of cosmic rays inside and outside of a diffuse cloud, by solving the stationary transport equation for cosmic rays including diffusion, advection and energy losses due to ionization of neutral hydrogen atoms. We found that the cosmic ray spectrum inside a diffuse cloud differs from the one in the interstellar medium for energies smaller than $E_{br}\\approx 100$ MeV, irrespective of the model details. Below $E_{br}$, the spectrum is harder (softer) than that in the interstellar medium if the latter is a power law $\\propto p^{-s}$ with $s$ larger (smaller) than $\\sim0.42$.

  7. Diffusion Weighted and Trace Images

    Directory of Open Access Journals (Sweden)

    Helen Nayeri

    2009-01-01

    Full Text Available   "nThe signal intensity in MRI depends on the proton density, T1, T2, and T2* relaxation processes of any ensemble of the spins within each imaging element. Another important contrast mechanism in MRI is signal loss caused by proton dephasing in the presence of coherent and incoherent flow. Diffusion refers to the dispersion of molecules from a region of high concentration to one of low concentration by random molecular or “Brownian” motion. "nDWI is based on the microscopic movement (Brownian motion of water molecules. The motion of water molecules, under the influence of diffusion-sensitizing gradient pulses, causes irreversible signal attenuation (hypointensity on DWI. In restricted diffusion (like acute infarction the signal attenuation is decreased (hyperintensity on DWI. "nIn biological tissues, water diffusion is not truly random. Structural barriers such as membranes and cellular elements, as well as chemical interactions, restrict Brownian motion in 3-D space. Additionally, disturbances associated with tissue perfusion and respiration can alter the biological environment. So it is termed “apparent” because the measured value does not indicate pure diffusion, but reflects capillary perfusion and other processes.  ADC (Apparent Diffusion Coefficient maps are typically created by combining at least two DWIs that are differently sensitized to diffusion (different b-values but which remain identical with respect to the other imaging parameters (TR and TE. Diffusion-weighted images are a combination of diffusion information and T2 signal intensity. In order to avoid the hyperintensity effect of T2 signal intensity (T2 shine-through, DW images should be compared with ADC images. ADC maps demonstrate contrast based purely on diffusion differences.   "nThe apparent diffusion in tissue is slowed if the protons are “hindered” or slowed in their random motion by the presence of cell membranes, walls, and macromolecules but are not

  8. A Simple Refraction Experiment for Probing Diffusion in Ternary Mixtures

    Science.gov (United States)

    Coutinho, Cecil A.; Mankidy, Bijith D.; Gupta, Vinay K.

    2010-01-01

    Diffusion is a fundamental phenomenon that is vital in many chemical processes such as mass transport in living cells, corrosion, and separations. We describe a simple undergraduate-level experiment based on Weiner's Method to probe diffusion in a ternary aqueous mixture of small molecular-weight molecules. As an illustration, the experiment…

  9. Onsager coefficients for binary mixture diffusion in nanopores

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2008-01-01

    This paper presents a critical appraisal of current estimation methods for the Onsager coefficients L-11, L-22, and L-12 for binary mixture diffusion inside nanopores using pure component diffusivity data inputs. The appraisal is based on extensive sets of molecular dynamics (MD) simulation data on

  10. Diffusion and particle mobility in 1D system

    NARCIS (Netherlands)

    Borman, V. D.; Johansson, B.; Skorodumova, N. V.; Tronin, I. V.; Tronin, V. N.; Troyan, V. I.

    2006-01-01

    The transport properties of one-dimensional (1D) systems have been studied theoretically. Contradictory experimental results on molecular transport in quasi-1D systems, such as zeolite structures, when both diffusion transport acceleration and the existence of the diffusion mode with lower particle

  11. Friction and diffusion dynamics of adsorbates at surfaces

    NARCIS (Netherlands)

    Fusco, C.

    2005-01-01

    A theoretical study of the motion of adsorbates (e. g. atoms, molecules or clusters) on solid surfaces is presented, with a focus on surface diffusion and atomic-scale friction. These two phenomena are inextricably linked, because when an atomic or molecular adsorbate diffuses, or is pulled, it unav

  12. Onsager coefficients for binary mixture diffusion in nanopores

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2008-01-01

    This paper presents a critical appraisal of current estimation methods for the Onsager coefficients L-11, L-22, and L-12 for binary mixture diffusion inside nanopores using pure component diffusivity data inputs. The appraisal is based on extensive sets of molecular dynamics (MD) simulation data on

  13. Configurational diffusion of coal macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Guin, J.A.; Curtis, C.W.; Tarrer, A.R.; Kim, S.; Hwang, D.; Chen, C.C.; Chiou, Z.

    1991-01-01

    The objective of our research was to obtain fundamental information regarding the functional dependence of the diffusion coefficient of coal molecules on the ratio of molecule to pore diameter. That is, the objective of our study was to examine the effect of molecule size and configuration on hindered diffusion of coal macromolecules through as porous medium. To best accomplish this task, we circumvented the complexities of an actual porous catalyst by using a well defined porous matrix with uniform capillaric pores, i.e., a track-etched membrane. In this way, useful information was obtained regarding the relationship of molecular size and configuration on the diffusion rate of coal derived macromolecules through a pore structure with known geometry. Similar studies were performed using a pellet formed of porous alumina, to provide a link between the idealized membranes and the actual complex pore structure of real catalyst extrudates. The fundamental information from our study will be useful toward the tailoring of catalysts to minimize diffusional influences and thereby increase coal conversion and selectivity for desirable products. (VC)

  14. Atomic diffusion behavior in Cu-Al explosive welding process

    Science.gov (United States)

    Chen, S. Y.; Wu, Z. W.; Liu, K. X.; Li, X. J.; Luo, N.; Lu, G. X.

    2013-01-01

    A hybrid method is proposed to study atomic diffusion behavior in Cu-Al explosive welding process. The method combines molecular dynamics simulation and classical diffusion theory. Cu-Al explosive welding and scanning electron microscope experiments are done to verify the method. Using the method, we find that the atomic diffusion mostly takes place in the unloading stage of the welding process. The diffusion coefficients are collision velocity-dependent, with higher velocities generating larger coefficients. When there is no transverse velocity, the diffusion coefficient is directly proportional to the longitudinal velocity. With the longitudinal velocity fixed, the diffusion coefficient is proportional to the square of the transverse velocity. The thickness of the diffusion layer is calculated from the simulation result, and it is in good agreement with the experiment result.

  15. Shape and scale dependent diffusivity of colloidal nanoclusters and aggregates

    Science.gov (United States)

    Alcanzare, M. M. T.; Ollila, S. T. T.; Thakore, V.; Laganapan, A. M.; Videcoq, A.; Cerbelaud, M.; Ferrando, R.; Ala-Nissila, T.

    2016-07-01

    The diffusion of colloidal nanoparticles and nanomolecular aggregates, which plays an important role in various biophysical and physicochemical phenomena, is currently under intense study. Here, we examine the shape and size dependent diffusion of colloidal nano- particles, fused nanoclusters and nanoaggregates using a hybrid fluctuating lattice Boltzmann-Molecular Dynamics method. We use physically realistic parameters characteristic of an aqueous solution, with explicitly implemented microscopic no-slip and full-slip boundary conditions. Results from nanocolloids below 10 nm in radii demonstrate how the volume fraction of the hydrodynamic boundary layer influences diffusivities. Full-slip colloids are found to diffuse faster than no-slip particles. We also characterize the shape dependent anisotropy of the diffusion coefficients of nanoclusters through the Green-Kubo relation. Finally, we study the size dependence of the diffusion of nanoaggregates comprising N ≤ 108 monomers and demonstrate that the diffusion coefficient approaches the continuum scaling limit of N-1/3.

  16. Metric diffusion along foliations

    CERN Document Server

    Walczak, Szymon M

    2017-01-01

    Up-to-date research in metric diffusion along compact foliations is presented in this book. Beginning with fundamentals from the optimal transportation theory and the theory of foliations; this book moves on to cover Wasserstein distance, Kantorovich Duality Theorem, and the metrization of the weak topology by the Wasserstein distance. Metric diffusion is defined, the topology of the metric space is studied and the limits of diffused metrics along compact foliations are discussed. Essentials on foliations, holonomy, heat diffusion, and compact foliations are detailed and vital technical lemmas are proved to aide understanding. Graduate students and researchers in geometry, topology and dynamics of foliations and laminations will find this supplement useful as it presents facts about the metric diffusion along non-compact foliation and provides a full description of the limit for metrics diffused along foliation with at least one compact leaf on the two dimensions.

  17. Diffusion of macromolecules through sclera.

    Science.gov (United States)

    Miao, Heng; Wu, Bi-Dong; Tao, Yong; Li, Xiao-Xin

    2013-02-01

    To quantify the in vitro permeability coefficient over different topographical locations of porcine sclera to macromolecules with different molecular weight. Fresh equatorial and posterior superotemporal porcine sclera was mounted in a two-chamber diffusion apparatus, and its permeability to fluorescein isothiocyanate (FITC)-conjugated dextrans ranging in molecular weight from 40 kDa to 150 kDa was determined by fluorescence spectrophotometry. The sclera was processed as frozen sections and viewed with a fluorescence microscope. The thickness of the area and the thickness that macromolecules enriched in the surface of sclera were measured. The permeability coefficient (Pc) of porcine sclera to macromolecules was significantly higher (40 kDa, p = 0.028; 70 kDa, p = 0.033; 150 kDa, p = 0.007) in equatorial region than posterior, which could be attributed to the significant difference of thickness (p macromolecules enriched in the scleral surface was thicker for those with larger MW (p macromolecules. Larger macromolecules are more likely to accumulate in scleral surface. The difference between topographical locations may have pharmacokinetic implications when considering transscleral diffusion of macromolecules. © 2012 The Authors. Acta Ophthalmologica © 2012 Acta Ophthalmologica Scandinavica Foundation.

  18. Diffusion formalism and applications

    CERN Document Server

    Dattagupta, Sushanta

    2013-01-01

    Within a unifying framework, Diffusion: Formalism and Applications covers both classical and quantum domains, along with numerous applications. The author explores the more than two centuries-old history of diffusion, expertly weaving together a variety of topics from physics, mathematics, chemistry, and biology. The book examines the two distinct paradigms of diffusion-physical and stochastic-introduced by Fourier and Laplace and later unified by Einstein in his groundbreaking work on Brownian motion. The author describes the role of diffusion in probability theory and stochastic calculus and

  19. Inpainting using airy diffusion

    Science.gov (United States)

    Lorduy Hernandez, Sara

    2015-09-01

    One inpainting procedure based on Airy diffusion is proposed, implemented via Maple and applied to some digital images. Airy diffusion is a partial differential equation with spatial derivatives of third order in contrast with the usual diffusion with spatial derivatives of second order. Airy diffusion generates the Airy semigroup in terms of the Airy functions which can be rewritten in terms of Bessel functions. The Airy diffusion can be used to smooth an image with the corresponding noise elimination via convolution. Also the Airy diffusion can be used to erase objects from an image. We build an algorithm using the Maple package ImageTools and such algorithm is tested using some images. Our results using Airy diffusion are compared with the similar results using standard diffusion. We observe that Airy diffusion generates powerful filters for image processing which could be incorporated in the usual packages for image processing such as ImageJ and Photoshop. Also is interesting to consider the possibility to incorporate the Airy filters as applications for smartphones and smart-glasses.

  20. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Olsen, Ole Fogh; Sporring, Jon

    2006-01-01

    . To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

  1. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Fogh Olsen, Ole; Sporring, Jon

    2007-01-01

    . To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

  2. Bronnen van diffuse bodembelasting

    NARCIS (Netherlands)

    Lijzen JPA; Ekelenkamp A; LBG; DGM/BO

    1995-01-01

    Ten behoeve van het preventieve bodembeleid was onvoldoende duidelijk welke bijdrage diverse bronnen leveren aan diffuse bodembelasting. Doel van deze inventarisatie was beschikbare kennis over diffuse bodembelasting te bundelen en kennis-lacunes aan te geven. Nevendoel is het beschrijven van de

  3. Distributed Control Diffusion

    DEFF Research Database (Denmark)

    Schultz, Ulrik Pagh

    2007-01-01

    , self-reconfigurable robots, we present the concept of distributed control diffusion: distributed queries are used to identify modules that play a specific role in the robot, and behaviors that implement specific control strategies are diffused throughout the robot based on these role assignments...... perform simple obstacle avoidance in a wide range of different car-like robots constructed using ATRON modules...

  4. Diffusion quantum Monte Carlo for molecules

    Energy Technology Data Exchange (ETDEWEB)

    Lester, W.A. Jr.

    1986-07-01

    A quantum mechanical Monte Carlo method has been used for the treatment of molecular problems. The imaginary-time Schroedinger equation written with a shift in zero energy (E/sub T/ - V(R)) can be interpreted as a generalized diffusion equation with a position-dependent rate or branching term. Since diffusion is the continuum limit of a random walk, one may simulate the Schroedinger equation with a function psi (note, not psi/sup 2/) as a density of ''walks.'' The walks undergo an exponential birth and death as given by the rate term. 16 refs., 2 tabs.

  5. Diffusion measurements in binary liquid mixtures by Raman spectroscopy

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Hansen, Susanne Brunsgaard; Shapiro, Alexander

    2007-01-01

    It is shown that Raman spectroscopy allows determination of the molar fractions in mixtures subjected to molecular diffusion. Spectra of three binary systems, benzene/n-hexane, benzene/cyclohexane, and benzene/ acetone, were obtained during vertical (exchange) diffusion at several different heights...... in the literature were found, even in a thermostatically controlled diffusion cell, recording spectra through circulating water. For the system benzene/acetone, the determined diffusion coefficients were in good agreement with the literature data. The limitations of the Raman method are discussed...

  6. Atomic diffusion in stars

    CERN Document Server

    Michaud, Georges; Richer, Jacques

    2015-01-01

    This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling.  In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...

  7. Predicting diffusivities in dense fluid mixtures

    Directory of Open Access Journals (Sweden)

    C. DARIVA

    1999-09-01

    Full Text Available In this work the Enskog solution of the Boltzmann equation, as corrected by Speedy, together with the Weeks-Chandler-Andersen (WCA perturbation theory of liquids is employed in correlating and predicting self-diffusivities of dense fluids. Afterwards this theory is used to estimate mutual diffusion coefficients of solutes at infinite dilution in sub and supercritical solvents. We have also investigated the behavior of Fick diffusion coefficients in the proximity of a binary vapor-liquid critical point since this subject is of great interest for extraction purposes. The approach presented here, which makes use of a density and temperature dependent hard-sphere diameter, is shown to be excellent for predicting diffusivities in dense pure fluids and fluid mixtures. The calculations involved highly nonideal mixtures as well as systems with high molecular asymmetry. The predicted diffusivities are in good agreement with the experimental data for the pure and binary systems. The methodology proposed here makes only use of pure component information and density of mixtures. The simple algebraic relations are proposed without any binary adjustable parameters and can be readily used for estimating diffusivities in multicomponent mixtures.

  8. Mechanism and kinetics of hydrated electron diffusion

    CERN Document Server

    Tay, Kafui A; Boutin, Anne; 10.1063/1.2964101

    2012-01-01

    Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that of the solvent. As previously postulated by both experimental and theoretical works, the instantaneous response of the electron to the librational motions of surrounding water molecules constitutes the principal mode of motion. The diffusive mechanism can be understood within the traditional framework of transfer diffusion processes, where the diffusive step is akin to the exchange of an extramolecular electron between neighboring water molecules. This is a second-order process with a computed rate constant of 5.0 ps^{-1} at 298 K. In agreement with experiment the electron diffusion exhibits Arrhenius behavior over the temperature range of 298-400 K. We compute an activation energy of 8.9 kJ/mol. Through analysis of Arrhenius plots and the application of a simple random walk...

  9. Resolving and measuring diffusion in complex interfaces: Exploring new capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd M. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    This exploratory LDRD targeted the use of a new high resolution spectroscopic diffusion capabilities developed at Sandia to resolve transport processes at interfaces in heterogeneous polymer materials. In particular, the combination of high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy with pulsed field gradient (PFG) diffusion experiments were used to directly explore interface diffusion within heterogeneous polymer composites, including measuring diffusion for individual chemical species in multi-component mixtures. Several different types of heterogeneous polymer systems were studied using these HRMAS NMR diffusion capabilities to probe the resolution limitations, determine the spatial length scales involved, and explore the general applicability to specific heterogeneous systems. The investigations pursued included a) the direct measurement of the diffusion for poly(dimethyl siloxane) polymer (PDMS) on nano-porous materials, b) measurement of penetrant diffusion in additive manufactures (3D printed) processed PDMS composites, and c) the measurement of diffusion in swollen polymers/penetrant mixtures within nano-confined aluminum oxide membranes. The NMR diffusion results obtained were encouraging and allowed for an improved understanding of diffusion and transport processes at the molecular level, while at the same time demonstrating that the spatial heterogeneity that can be resolved using HRMAS NMR PFG diffusion experiment must be larger than ~μm length scales, expect for polymer transport within nanoporous carbons where additional chemical resolution improves the resolvable heterogeneous length scale to hundreds of nm.

  10. Helium diffusion in carbonates

    Science.gov (United States)

    Amidon, W. H.; Cherniak, D. J.; Watson, E. B.; Hobbs, D.

    2013-12-01

    The abundance and large grain size of carbonate minerals make them a potentially attractive target for 4He thermochronology and 3He cosmogenic dating, although the diffusive properties of helium in carbonates remain poorly understood. This work characterizes helium diffusion in calcite and dolomite to better understand the crystal-chemical factors controlling He transport and retentivity. Slabs of cleaved natural calcite and dolomite, and polished sections of calcite cut parallel or normal to c, were implanted with 3He at 3 MeV with a dose of 5x1015/cm2. Implanted carbonates were heated in 1-atm furnaces, and 3He distributions following diffusion anneals were profiled with Nuclear Reaction Analysis using the reaction 3He(d,p)4He. For 3He transport normal to cleavage surfaces in calcite, we obtain the following Arrhenius relation over the temperature range 78-300°C: Dcalcite = 9.0x10-9exp(-55 × 6 kJ mol-1/RT) m2sec-1. Diffusion in calcite exhibits marked anisotropy, with diffusion parallel to c about two orders of magnitude slower than diffusion normal to cleavage faces. He diffusivities for transport normal to the c-axis are similar in value to those normal to cleavage surfaces. Our findings are broadly consistent with helium diffusivities from step-heating measurements of calcite by Copeland et al. (2007); these bulk degassing data may reflect varying effects of diffusional anisotropy. Helium diffusion normal to cleavage surfaces in dolomite is significantly slower than diffusion in calcite, and has a much higher activation energy for diffusion. For dolomite, we obtain the following Arrhenius relation for He diffusion over the temperature range 150-400°C: Ddolomite = 9.0x10-8exp(-92 × 9 kJ mol-1/RT) m2sec-1. The role of crystallographic structure in influencing these differences among diffusivities was evaluated using the maximum aperture approach of Cherniak and Watson (2011), in which crystallographic structures are sectioned along possible diffusion

  11. Tungsten diffusion in olivine

    Science.gov (United States)

    Cherniak, D. J.; Van Orman, J. A.

    2014-03-01

    Diffusion of tungsten has been characterized in synthetic forsterite and natural olivine (Fo90) under dry conditions. The source of diffusant was a mixture of magnesium tungstate and olivine powders. Experiments were prepared by sealing the source material and polished olivine under vacuum in silica glass ampoules with solid buffers to buffer at NNO or IW. Prepared capsules were annealed in 1 atm furnaces for times ranging from 45 min to several weeks, at temperatures from 1050 to 1450 °C. Tungsten distributions in the olivine were profiled by Rutherford Backscattering Spectrometry (RBS). The following Arrhenius relation is obtained for W diffusion in forsterite: D=1.0×10-8exp(-365±28 kJ mol/RT) m s Diffusivities for the synthetic forsterite and natural Fe-bearing olivine are similar, and tungsten diffusion in olivine shows little dependence on crystallographic orientation or oxygen fugacity. The slow diffusivities measured for W in olivine indicate that Hf-W ages in olivine-metal systems will close to diffusive exchange at higher temperatures than other chronometers commonly used in cosmochronology, and that tungsten isotopic signatures will be less likely to be reset by subsequent thermal events.

  12. Cosmology with matter diffusion

    CERN Document Server

    Calogero, Simone

    2013-01-01

    We construct a viable cosmological model based on velocity diffusion of matter particles. In order to ensure the conservation of the total energy-momentum tensor in the presence of diffusion, we include a cosmological scalar field $\\phi$ which we identify with the dark energy component of the Universe. The model is characterized by only one new degree of freedom, the diffusion parameter $\\sigma$. The standard $\\Lambda$CDM model can be recovered by setting $\\sigma=0$. If diffusion takes place ($\\sigma >0$) the dynamics of the matter and of the dark energy fields are coupled. We argue that the existence of a diffusion mechanism in the Universe can serve as a theoretical motivation for interacting models. We constrain the background dynamics of the diffusion model with Supernovae, H(z) and BAO data. We also perform a perturbative analysis of this model in order to understand structure formation in the Universe. We calculate the impact of diffusion both on the CMB spectrum, with particular attention to the integr...

  13. Effective diffusivity of passive scalars in rotating flow

    CERN Document Server

    Imazio, P Rodriguez

    2012-01-01

    We use direct numerical simulations to compute turbulent transport coefficients for passive scalars in turbulent rotating flows. Effective diffusion coefficients in the directions parallel and perpendicular to the rotations axis are obtained by studying the diffusion of an imposed initial profile for the passive scalar, and calculated by measuring the scalar average concentration and average spatial flux as a function of time. The Rossby and Schmidt numbers are varied to quantify their effect on the effective diffusion. It is find that rotation reduces scalar diffusivity in the perpendicular direction. The perpendicular diffusion can be estimated from mixing length arguments using the characteristic velocities and lengths perpendicular to the rotation axis. Deviations are observed for small Schmidt numbers, for which turbulent transport decreases and molecular diffusion becomes more significant.

  14. Pipe and grain boundary diffusion of He in UO2

    Science.gov (United States)

    Galvin, C. O. T.; Cooper, M. W. D.; Fossati, P. C. M.; Stanek, C. R.; Grimes, R. W.; Andersson, D. A.

    2016-10-01

    Molecular dynamics simulations have been conducted to study the effects of dislocations and grain boundaries on He diffusion in \\text{U}{{\\text{O}}2} . Calculations were carried out for the {1 0 0}, {1 1 0} and {1 1 1} edge dislocations, the screw dislocation and Σ5, Σ13, Σ19 and Σ25 tilt grain boundaries. He diffusivity as a function of distance from the dislocation core and grain boundaries was investigated for the temperature range 2300-3000 K. An enhancement in diffusivity was predicted within 20 Å of the dislocations or grain boundaries. Further investigation showed that He diffusion in the edge dislocations follows anisotropic behaviour along the dislocation core, suggesting that pipe diffusion occurs. An Arrhenius plot of He diffusivity against the inverse of temperature was also presented and the activation energy calculated for each structure, as a function of distance from the dislocation or grain boundary.

  15. Diffusion and reaction in crowded environments

    Energy Technology Data Exchange (ETDEWEB)

    EcheverIa, Carlos [Laboratorio de Fisica Aplicada y Computacional, Departamento de Matematica y Fisica, Universidad Nacional Experimental del Tachira, San Cristobal 5001 (Venezuela); Tucci, Kay [Centro de Fisica Fundamental, Universidad de Los Andes, Merida 5101 (Venezuela); Kapral, Raymond [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6 (Canada)

    2007-02-14

    The effects of molecular crowding on small molecule diffusion and chemical reaction rate coefficients are investigated. The systems considered comprise a random distribution of stationary spherical obstacles occupying a volume fraction {phi} of the system and a large number of small molecules whose dynamics are followed. Chemical reactions are studied in such crowded systems where, in addition to the obstacles, a large reactive sphere C is present that catalyses the reaction A+C {yields} B+C. Using a mesoscopic description of the dynamics employing multiparticle collisions among the small molecules, the {phi} dependence of the diffusion and reaction rate coefficients is computed. Both the diffusion and reaction rate coefficients decrease with increase of the obstacle volume fraction as expected but variations of these quantities with {phi} are not predicted by simple models of the dynamics.

  16. Theories on diffusion of technology

    DEFF Research Database (Denmark)

    Munch, Birgitte

    Tracing the body of the diffusion proces by analysing the diffusion process from historical, sociological, economic and technical approaches. Discussing central characteristics of the proces of diffusion og CAD/CAM in Denmark.......Tracing the body of the diffusion proces by analysing the diffusion process from historical, sociological, economic and technical approaches. Discussing central characteristics of the proces of diffusion og CAD/CAM in Denmark....

  17. Diffuse Ceiling Ventilation

    DEFF Research Database (Denmark)

    Zhang, Chen; Yu, Tao; Heiselberg, Per Kvols

    -cooling period and night cooling potential. The investment cost of this ventilation system is about 5-10% lower than the conventional ones, because the acoustic ceiling could be directly applied as air diffuser and the use of plenum to distribute air reduces the cost of ductwork. There is a growing interest...... is not well structured with this system. These become the motivations in developing the design guide. This design guide aims to establish a systematic understanding of diffuse ceiling ventilation and provide assistance in designing of such a system. The guide is targeted at design engineers, architects...... and manufacturers and the users of diffuse ceiling technology. The design guide introduces the principle and key characteristics of room air distribution with diffuse ceiling ventilation. It provides an overview of potential benefit and limitations of this technology. The benefits include high thermal comfort, high...

  18. Diffuse Ceiling Ventilation

    DEFF Research Database (Denmark)

    Zhang, Chen; Yu, Tao; Heiselberg, Per Kvols

    with conventional ventilation systems (mixing or displacement ventilation), diffuse ceiling ventilation can significantly reduce or even eliminate draught risk in the occupied zone. Moreover, this ventilation system presents a promising opportunity for energy saving, because of the low pressure loss, extended free......Diffuse ceiling ventilation is an innovative ventilation concept where the suspended ceiling serves as an air diffuser to supply fresh air into the room. Due to the large opening area, air is delivered to the room with very low velocity and no fixed direction, therefore the name ‘diffuse’. Compared......-cooling period and night cooling potential. The investment cost of this ventilation system is about 5-10% lower than the conventional ones, because the acoustic ceiling could be directly applied as air diffuser and the use of plenum to distribute air reduces the cost of ductwork. There is a growing interest...

  19. Seismic Fault Preserving Diffusion

    CERN Document Server

    Lavialle, Olivier; Germain, Christian; Donias, Marc; Guillon, Sebastien; Keskes, Naamen; Berthoumieu, Yannick

    2007-01-01

    This paper focuses on the denoising and enhancing of 3-D reflection seismic data. We propose a pre-processing step based on a non linear diffusion filtering leading to a better detection of seismic faults. The non linear diffusion approaches are based on the definition of a partial differential equation that allows us to simplify the images without blurring relevant details or discontinuities. Computing the structure tensor which provides information on the local orientation of the geological layers, we propose to drive the diffusion along these layers using a new approach called SFPD (Seismic Fault Preserving Diffusion). In SFPD, the eigenvalues of the tensor are fixed according to a confidence measure that takes into account the regularity of the local seismic structure. Results on both synthesized and real 3-D blocks show the efficiency of the proposed approach.

  20. Seismic fault preserving diffusion

    Science.gov (United States)

    Lavialle, Olivier; Pop, Sorin; Germain, Christian; Donias, Marc; Guillon, Sebastien; Keskes, Naamen; Berthoumieu, Yannick

    2007-02-01

    This paper focuses on the denoising and enhancing of 3-D reflection seismic data. We propose a pre-processing step based on a non-linear diffusion filtering leading to a better detection of seismic faults. The non-linear diffusion approaches are based on the definition of a partial differential equation that allows us to simplify the images without blurring relevant details or discontinuities. Computing the structure tensor which provides information on the local orientation of the geological layers, we propose to drive the diffusion along these layers using a new approach called SFPD (Seismic Fault Preserving Diffusion). In SFPD, the eigenvalues of the tensor are fixed according to a confidence measure that takes into account the regularity of the local seismic structure. Results on both synthesized and real 3-D blocks show the efficiency of the proposed approach.

  1. Isomorphism, Diffusion and Decoupling

    DEFF Research Database (Denmark)

    Boxenbaum, Eva; Jonsson, Stefan

    2017-01-01

    This chapter traces the evolution of the core theoretical constructs of isomorphism, decoupling and diffusion in organizational institutionalism. We first review the original theoretical formulations of these constructs and then examine their evolution in empirical research conducted over the past...

  2. Diffusing Best Practices

    DEFF Research Database (Denmark)

    Pries-Heje, Jan; Baskerville, Richard

    2014-01-01

    approach. The study context is a design case in which an organization desires to diffuse its best practices across different groups. The design goal is embodied in organizational mechanisms to achieve this diffusion. The study used Theory of Planned Behavior (TPB) as a kernel theory. The artifacts...... resulting from the design were two-day training workshops conceptually anchored to TBP. The design theory was evaluated through execution of eight diffusion workshops involving three different groups in the same company. The findings indicate that the match between the practice and the context materialized...... that the behavior will be effective). These two factors were especially critical if the source context of the best practice is qualitatively different from the target context into which the organization is seeking to diffuse the best practice....

  3. On Diffusion and Permeation

    KAUST Repository

    Peppin, Stephen S. L.

    2009-01-01

    Diffusion and permeation are discussed within the context of irreversible thermodynamics. A new expression for the generalized Stokes-Einstein equation is obtained which links the permeability to the diffusivity of a two-component solution and contains the poroelastic Biot-Willis coefficient. The theory is illustrated by predicting the concentration and pressure profiles during the filtration of a protein solution. At low concentrations the proteins diffuse independently while at higher concentrations they form a nearly rigid porous glass through which the fluid permeates. The theoretically determined pressure drop is nonlinear in the diffusion regime and linear in the permeation regime, in quantitative agreement with experimental measurements. © 2009 Walter de Gruyter, Berlin, New York.

  4. Diffusion of Wilson Loops

    CERN Document Server

    Brzoska, A M; Negele, J W; Thies, M

    2004-01-01

    A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory.

  5. Super-Diffusive Gas Recovery from Nanopores

    CERN Document Server

    Wu, Haiyi; Qiao, Rui

    2016-01-01

    Understanding the recovery of gas from reservoirs featuring pervasive nanopores is essential for effective shale gas extraction. Classical theories cannot accurately predict such gas recovery and many experimental observations are not well understood. Here we report molecular simulations of the recovery of gas from single nanopores, explicitly taking into account molecular gas-wall interactions. We show that, in very narrow pores, the strong gas-wall interactions are essential in determining the gas recovery behavior both quantitatively and qualitatively. These interactions cause the total diffusion coefficients of the gas molecules in nanopores to be smaller than those predicted by kinetic theories, hence slowing down the rate of gas recovery. These interactions also lead to significant adsorption of gas molecules on the pore walls. Because of the desorption of these gas molecules during gas recovery, the gas recovery from the nanopore does not exhibit the usual diffusive scaling law (i.e., the accumulative ...

  6. Heteronuclear diatomics in diffuse and translucent clouds

    CERN Document Server

    Weselak, T

    2013-01-01

    Diffuse and translucent molecular clouds fill a vast majority of the interstellar space in the galactic disk being thus the most typical objects of the Interstellar Medium (ISM). Recent advances in observational techniques of modern optical and ultraviolet spectroscopy led to detection of many features of atomic and molecular origin in spectra of such clouds. Molecular spectra of heteronuclear diatomic molecules, ie. OH, OH+, CH CH+, CN, NH, CO play an important role in understanding chemistry and physical conditions in environments they do populate. A historical review of astronomical observations of interstellar molecules is presented. Recent results based on visual and ultraviolet observations of molecular features in spectra of reddened, early type OB-stars are presented and discussed. Appearance of vibrational-rotational spectra with observed transitions based on high-quality spectra, are also presented. Relations between column densities of heteronuclear diatomics (based on the recommended oscillator st...

  7. Drift-Diffusion Equation

    Directory of Open Access Journals (Sweden)

    K. Banoo

    1998-01-01

    equation in the discrete momentum space. This is shown to be similar to the conventional drift-diffusion equation except that it is a more rigorous solution to the Boltzmann equation because the current and carrier densities are resolved into M×1 vectors, where M is the number of modes in the discrete momentum space. The mobility and diffusion coefficient become M×M matrices which connect the M momentum space modes. This approach is demonstrated by simulating electron transport in bulk silicon.

  8. CO diffusion capacity

    Energy Technology Data Exchange (ETDEWEB)

    Mielke, U.

    1979-01-01

    We measured in 287 persons the pulmonary CO diffusion capacity with the steady-state and the single breath methods, applying apnoeic periods of 4 and 10 seconds duration. The aspects methodical significance, polyclinical applicability and pathognostic relevance with respect to other approved pulmonary functional tests are discussed. Differing pulmonary diffusion capacity values found in normal persons or in patients suffering from silicosis, pulmonary fibrosis, Boeck's disease or rheumatoid arthritis, were investigated and critically evaluated.

  9. Diffusion in nanocrystalline solids

    OpenAIRE

    Chadwick, Alan V.

    2016-01-01

    Enhanced atomic migration was an early observation from experimental studies into nanocrystalline solids. This contribution presents an overview of the available diffusion data for simple metals and ionic materials in nanocrystalline form. It will be shown that enhanced diffusion can be interpreted in terms of atomic transport along the interfaces, which are comparable to grain boundaries in coarse-grained analogues. However, the method of sample preparation is seen to play a major role in...

  10. Diffuse Large B-Cell Lymphoma

    Science.gov (United States)

    Friedberg, Jonathan W.

    2008-01-01

    Synopsis Diffuse Large B-Cell Lymphoma (DLBCL) remains a curable lymphoma, with improved outcome due in large part to incorporation of rituximab in standard regimens. The disease is heterogeneous clinically, morphologically, and molecularly. Recent insights into the molecular heterogeneity of DLBCL are beginning to yield novel therapeutics with significant promise for key subsets of patients. Although CHOP chemotherapy with rituximab remains a standard therapeutic approach for most patients with DLBCL, we anticipate that novel agents will be included in treatment regimens for many patients in the near future. PMID:18954744

  11. Advanced manufacturing: Technology diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Tesar, A.

    1995-12-01

    In this paper we examine how manufacturing technology diffuses rom the developers of technology across national borders to those who do not have the capability or resources to develop advanced technology on their own. None of the wide variety of technology diffusion mechanisms discussed in this paper are new, yet the opportunities to apply these mechanisms are growing. A dramatic increase in technology diffusion occurred over the last decade. The two major trends which probably drive this increase are a worldwide inclination towards ``freer`` markets and diminishing isolation. Technology is most rapidly diffusing from the US In fact, the US is supplying technology for the rest of the world. The value of the technology supplied by the US more than doubled from 1985 to 1992 (see the Introduction for details). History shows us that technology diffusion is inevitable. It is the rates at which technologies diffuse to other countries which can vary considerably. Manufacturers in these countries are increasingly able to absorb technology. Their manufacturing efficiency is expected to progress as technology becomes increasingly available and utilized.

  12. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering; Caracterisation de la liaison hydrogene dans des systemes moleculaires d'interet biologique par diffusion de neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Cavillon, F

    2004-10-15

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.

  13. Diffusion in natural ilmenite

    Science.gov (United States)

    Stenhouse, Iona; O'Neill, Hugh; Lister, Gordon

    2010-05-01

    Diffusion rates in natural ilmenite of composition Fe0.842+ Fe0.163+Mn0.07Mg0.01Ti 0.92O3 from the Vishnevye Mountains (Urals, Russia) have been measured at 1000° C. Experiments were carried out in a one atmosphere furnace with oxygen fugacity controlled by flow of a CO-CO2 gas mixture, over a period of four hours. The diffusant source was a synthetic ilmenite (FeTiO3) powder doped with trace amounts of Mg, Co, Ni, Zr, Hf, V, Nb, Ta, Al, Cr, Ga and Y. Since, the natural ilmenite crystal contained Mn it was also possible to study diffusion of Mn from the ilmenite crystal. The experiments were analysed using the electron microprobe and scanning laser ablation ICP-MS. Diffusion profiles were measured for Al, Mg, Mn, Co, Ni, Ga, and Y. Diffusion of Cr, Hf, Zr, V, Nb and Ta was too slow to allow diffusion profiles to be accurately measured for the times and temperatures studied so far. The preliminary results show that diffusion in ilmenite is fast, with the diffusivity determined in this study on the order of 10-13 to 10-16 m2s-1. For comparison, Chakraborty (1997) found interdiffusion of Fe and Mg in olivine at 1000° C on the order of 10-17 to 10-18m2s-1 and Dieckmann (1998) found diffusivity of Fe, Mg, Co in magnetite at 1200° C to be on the order of 10-13 to 10-14 m2s-1. The order in which the diffusivity of the elements decreases is Mn > Co > Mg ≥ Ni > Al ≥ Y ≥ Ga, that is to say that Mn diffuses the fastest and Ga the slowest. Overall, this study intends to determine diffusion parameters such as frequency factor, activation energy and activation volume as a function of temperature and oxygen fugacity. This research is taking place in the context of a larger study focusing on the use of the garnet-ilmenite system as a geospeedometer. Examination of the consequences of simultaneous diffusion of multiple elements is a necessity if we are to develop an understanding of the crystal-chemical controls on diffusion (cf Spandler & O'Neill, in press). Chakraborty

  14. Contribution to the study of the molecular scattering of light. Use of a laser as light source (1963); Contribution a l'etude de la diffusion moleculaire de la lumiere. Utilisation d'un laser comme source lumineuse (1963)

    Energy Technology Data Exchange (ETDEWEB)

    Slama, L. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1963-07-01

    The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [French] Les experiences sur la diffusion moleculaire de la lumiere ont ete reprises en utilisant un laser a rubis comme source lumineuse. La distribution angulaire de l'intensite diffusee a ete mesuree dans le cas ou le vecteur electrique de l'onde lumineuse incidente est soit dans le plan, soit perpendiculaire a ce plan. Dans le premier cas un bon accord est observe avec la theorie de Rayleigh, ce qui n'est plus vrai dans le second cas. Des sections efficaces differentielles de diffusion ont ete mesurees pour differents gaz. Les valeurs trouvees sont 2 a 3 fois plus grandes que celles prevues par la theorie classique. On a recherche enfin l'effet d'une variation d'intensite du faisceau du laser sur la linearite du phenomene de diffusion. (auteur)

  15. Multidimensional diffusion MRI

    Science.gov (United States)

    Topgaard, Daniel

    2017-02-01

    Principles from multidimensional NMR spectroscopy, and in particular solid-state NMR, have recently been transferred to the field of diffusion MRI, offering non-invasive characterization of heterogeneous anisotropic materials, such as the human brain, at an unprecedented level of detail. Here we revisit the basic physics of solid-state NMR and diffusion MRI to pinpoint the origin of the somewhat unexpected analogy between the two fields, and provide an overview of current diffusion MRI acquisition protocols and data analysis methods to quantify the composition of heterogeneous materials in terms of diffusion tensor distributions with size, shape, and orientation dimensions. While the most advanced methods allow estimation of the complete multidimensional distributions, simpler methods focus on various projections onto lower-dimensional spaces as well as determination of means and variances rather than actual distributions. Even the less advanced methods provide simple and intuitive scalar parameters that are directly related to microstructural features that can be observed in optical microscopy images, e.g. average cell eccentricity, variance of cell density, and orientational order - properties that are inextricably entangled in conventional diffusion MRI. Key to disentangling all these microstructural features is MRI signal acquisition combining isotropic and directional dimensions, just as in the field of multidimensional solid-state NMR from which most of the ideas for the new methods are derived.

  16. Primary diffuse leptomeningeal gliosarcomatosis.

    Science.gov (United States)

    Moon, Ju Hyung; Kim, Se Hoon; Kim, Eui Hyun; Kang, Seok-Gu; Chang, Jong Hee

    2015-04-01

    Primary diffuse leptomeningeal gliomatosis (PDLG) is a rare condition with a fatal outcome, characterized by diffuse infiltration of the leptomeninges by neoplastic glial cells without evidence of primary tumor in the brain or spinal cord parenchyma. In particular, PDLG histologically diagnosed as gliosarcoma is extremely rare, with only 2 cases reported to date. We report a case of primary diffuse leptomeningeal gliosarcomatosis. A 68-year-old man presented with fever, chilling, headache, and a brief episode of mental deterioration. Initial T1-weighted post-contrast brain magnetic resonance imaging (MRI) showed diffuse leptomeningeal enhancement without a definite intraparenchymal lesion. Based on clinical and imaging findings, antiviral treatment was initiated. Despite the treatment, the patient's neurologic symptoms and mental status progressively deteriorated and follow-up MRI showed rapid progression of the disease. A meningeal biopsy revealed gliosarcoma and was conclusive for the diagnosis of primary diffuse leptomeningeal gliosarcomatosis. We suggest the inclusion of PDLG in the potential differential diagnosis of patients who present with nonspecific neurologic symptoms in the presence of leptomeningeal involvement on MRI.

  17. Cesium diffusion in graphite

    Energy Technology Data Exchange (ETDEWEB)

    Evans, R.B. III; Davis, W. Jr.; Sutton, A.L. Jr.

    1980-05-01

    Experiments on diffusion of /sup 137/Cs in five types of graphite were performed. The document provides a completion of the report that was started and includes a presentation of all of the diffusion data, previously unpublished. Except for data on mass transfer of /sup 137/Cs in the Hawker-Siddeley graphite, analyses of experimental results were initiated but not completed. The mass transfer process of cesium in HS-1-1 graphite at 600 to 1000/sup 0/C in a helium atmosphere is essentially pure diffusion wherein values of (E/epsilon) and ..delta..E of the equation D/epsilon = (D/epsilon)/sub 0/ exp (-..delta..E/RT) are about 4 x 10/sup -2/ cm/sup 2//s and 30 kcal/mole, respectively.

  18. Diffusion and mass transfer

    CERN Document Server

    Vrentas, James S

    2013-01-01

    The book first covers the five elements necessary to formulate and solve mass transfer problems, that is, conservation laws and field equations, boundary conditions, constitutive equations, parameters in constitutive equations, and mathematical methods that can be used to solve the partial differential equations commonly encountered in mass transfer problems. Jump balances, Green’s function solution methods, and the free-volume theory for the prediction of self-diffusion coefficients for polymer–solvent systems are among the topics covered. The authors then use those elements to analyze a wide variety of mass transfer problems, including bubble dissolution, polymer sorption and desorption, dispersion, impurity migration in plastic containers, and utilization of polymers in drug delivery. The text offers detailed solutions, along with some theoretical aspects, for numerous processes including viscoelastic diffusion, moving boundary problems, diffusion and reaction, membrane transport, wave behavior, sedime...

  19. GRAI N-BOUNDARY DIFFUSION

    OpenAIRE

    Peterson, N.

    1982-01-01

    The more useful experimental techniques for determining grain-boundary diffusion are briefly described followed by a presentation of results that shed light on the models and mechanisms of grain-boundary and dislocation diffusion. Studies of the following grain-boundary diffusion phenomena will be considered ; anisotropy in grain-boundary diffusion, effect of orientation relationship on grain-boundary diffusion, effect of boundary type and dislocation dissociation, lattice structure, correlat...

  20. Viscosity and mutual diffusion in strongly asymmetric binary ionic mixtures

    CERN Document Server

    Bastea, S

    2005-01-01

    We present molecular dynamics simulation results for the viscosity and mutual diffusion constant of a strongly asymmetric binary ionic mixture (BIM). We compare the results with available theoretical models previously tested for much smaller asymmetries. For the case of viscosity we propose a new predictive framework based on the linear mixing rule, while for mutual diffusion we discuss some consistency problems of widely used Boltzmann equation based models.

  1. Viscosity and mutual diffusion in strongly asymmetric plasma mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Bastea, S

    2004-09-07

    The authors present molecular dynamics simulation results for the viscosity and mutual diffusion constant of a strongly asymmetric two-component plasma (TCP). They compare the results with available theoretical models previously tested for much smaller asymmetries. for the case of viscosity they propose a new predictive framework based on the linear mixing rule, while for mutual diffusion they point out some consistency problems of widely used Boltzmann equation based models.

  2. Controllable Detemplation of Nanozeolites and Research of Molecular Diffusing Limitation%纳米沸石的模板可控去除及分子扩散限制

    Institute of Scientific and Technical Information of China (English)

    郭肖; 林少颖; 秦恺; 张亚红; 唐颐

    2015-01-01

    采用微波水热合成纳米茁沸石,并利用微波辅助的类芬顿法可控去除纳米茁沸石孔道中的模板剂,使其具备一定的孔道深度、比表面积以及可接近酸性位。以果糖酸催化转化为5-羟甲基糠醛(5-HMF)为探针反应,探索了果糖分子在不同孔道深度和活性位的纳米茁沸石中的扩散行为对催化效果的影响。研究发现,酸性位相同的条件下,纳米沸石孔道深度越深扩散限制越显著,反应选择性越差。即使在催化剂加入量相同即可接近酸性位不同时,果糖分子在孔道中的扩散限制对催化反应的影响也显著于酸量的影响,充分说明了微孔催化剂中反应物/产物分子扩散限制对于催化反应影响的重要性,使得所制备催化剂的表面酸性位和适宜的孔道深度共同对反应产生有利的影响。%Zeolites are microporous crystalline materials with large surface area and high hydrothermal stabili-ty, which have been widely applied in areas like petrochemical industry, fine chemistry and environmental protection. However, their small and long micropore channels result in larger diffusion resistance in catalytic reaction and consequent coke deposition and fast deactivation of catalysts. Here, β nanozeolites were hydro-thermally synthesized under microwave irradiation, followed with a microwave-assisted Fenton-like oxidation step to rapidly and controllably remove the template of as-preparedβnanozeolites. Consequently, a series ofβnanozeolites with different pore depths and available acid sites was obtained. Still, dehydration of fructose into 5-HMF(5-hydroxymethylfurfural) catalyzed by acid catalyst was used to study the influence of different pore depths and acid sites of β nanozeolites on their catalytic performances. It is found that diffusing limitation displays more important effects than those of the active sites numbers in the reactions catalyzed by microporous zeolites, which

  3. Nonlocal electrical diffusion equation

    Science.gov (United States)

    Gómez-Aguilar, J. F.; Escobar-Jiménez, R. F.; Olivares-Peregrino, V. H.; Benavides-Cruz, M.; Calderón-Ramón, C.

    2016-07-01

    In this paper, we present an analysis and modeling of the electrical diffusion equation using the fractional calculus approach. This alternative representation for the current density is expressed in terms of the Caputo derivatives, the order for the space domain is 0numerical methods based on Fourier variable separation. The case with spatial fractional derivatives leads to Levy flight type phenomena, while the time fractional equation is related to sub- or super diffusion. We show that the mathematical concept of fractional derivatives can be useful to understand the behavior of semiconductors, the design of solar panels, electrochemical phenomena and the description of anomalous complex processes.

  4. Phase transformation and diffusion

    CERN Document Server

    Kale, G B; Dey, G K

    2008-01-01

    Given that the basic purpose of all research in materials science and technology is to tailor the properties of materials to suit specific applications, phase transformations are the natural key to the fine-tuning of the structural, mechanical and corrosion properties. A basic understanding of the kinetics and mechanisms of phase transformation is therefore of vital importance. Apart from a few cases involving crystallographic martensitic transformations, all phase transformations are mediated by diffusion. Thus, proper control and understanding of the process of diffusion during nucleation, g

  5. Hydrogen diffusion in Zircon

    Science.gov (United States)

    Ingrin, Jannick; Zhang, Peipei

    2016-04-01

    Hydrogen mobility in gem quality zircon single crystals from Madagascar was investigated through H-D exchange experiments. Thin slices were annealed in a horizontal furnace flushed with a gas mixture of Ar/D2(10%) under ambient pressure between 900 ° C to 1150 ° C. FTIR analyses were performed on oriented slices before and after each annealing run. H diffusion along [100] and [010] follow the same diffusion law D = D0exp[-E /RT], with log D0 = 2.24 ± 1.57 (in m2/s) and E = 374 ± 39 kJ/mol. H diffusion along [001] follows a slightly more rapid diffusion law, with log D0 = 1.11 ± 0.22 (in m2/s) and E = 334 ± 49 kJ/mol. H diffusion in zircon has much higher activation energy and slower diffusivity than other NAMs below 1150 ° C even iron-poor garnets which are known to be among the slowest (Blanchard and Ingrin, 2004; Kurka et al. 2005). During H-D exchange zircon incorporates also deuterium. This hydration reaction involves uranium reduction as it is shown from the exchange of U5+ and U4+ characteristic bands in the near infrared region during annealing. It is the first time that a hydration reaction U5+ + OH- = U4+ + O2- + 1/2H2, is experimentally reported. The kinetics of deuterium incorporation is slightly slower than hydrogen diffusion, suggesting that the reaction is limited by hydrogen mobility. Hydrogen isotopic memory of zircon is higher than other NAMs. Zircons will be moderately retentive of H signatures at mid-crustal metamorphic temperatures. At 500 ° C, a zircon with a radius of 300 μm would retain its H isotopic signature over more than a million years. However, a zircon is unable to retain this information for geologically significant times under high-grade metamorphism unless the grain size is large enough. Refrences Blanchard, M. and Ingrin, J. (2004) Hydrogen diffusion in Dora Maira pyrope. Physics and Chemistry of Minerals, 31, 593-605. Kurka, A., Blanchard, M. and Ingrin, J. (2005) Kinetics of hydrogen extraction and deuteration in

  6. Nonlinear diffusion equations

    CERN Document Server

    Wu Zhuo Qun; Li Hui Lai; Zhao Jun Ning

    2001-01-01

    Nonlinear diffusion equations, an important class of parabolic equations, come from a variety of diffusion phenomena which appear widely in nature. They are suggested as mathematical models of physical problems in many fields, such as filtration, phase transition, biochemistry and dynamics of biological groups. In many cases, the equations possess degeneracy or singularity. The appearance of degeneracy or singularity makes the study more involved and challenging. Many new ideas and methods have been developed to overcome the special difficulties caused by the degeneracy and singularity, which

  7. The Trouble with Diffusion

    Directory of Open Access Journals (Sweden)

    R.T. DeHoff

    2002-09-01

    Full Text Available The phenomenological formalism, which yields Fick's Laws for diffusion in single phase multicomponent systems, is widely accepted as the basis for the mathematical description of diffusion. This paper focuses on problems associated with this formalism. This mode of description of the process is cumbersome, defining as it does matrices of interdiffusion coefficients (the central material properties that require a large experimental investment for their evaluation in three component systems, and, indeed cannot be evaluated for systems with more than three components. It is also argued that the physical meaning of the numerical values of these properties with respect to the atom motions in the system remains unknown. The attempt to understand the physical content of the diffusion coefficients in the phenomenological formalism has been the central fundamental problem in the theory of diffusion in crystalline alloys. The observation by Kirkendall that the crystal lattice moves during diffusion led Darken to develop the concept of intrinsic diffusion, i.e., atom motion relative to the crystal lattice. Darken and his successors sought to relate the diffusion coefficients computed for intrinsic fluxes to those obtained from the motion of radioactive tracers in chemically homogeneous samples which directly report the jump frequencies of the atoms as a function of composition and temperature. This theoretical connection between tracer, intrinsic and interdiffusion behavior would provide the basis for understanding the physical content of interdiffusion coefficients. Definitive tests of the resulting theoretical connection have been carried out for a number of binary systems for which all three kinds of observations are available. In a number of systems predictions of intrinsic coefficients from tracer data do not agree with measured values although predictions of interdiffusion coefficients appear to give reasonable agreement. Thus, the complete

  8. Diffusion in advanced materials

    CERN Document Server

    Murch, Graeme; Belova, Irina

    2014-01-01

    In the first chapter Prof. Kozubski and colleagues present atomisticsimulations of superstructure transformations of intermetallic nanolayers.In Chapter 2, Prof. Danielewski and colleagues discuss a formalism for themorphology of the diffusion zone in ternary alloys. In Chapter 3, ProfessorsSprengel and Koiwa discuss the classical contributions of Boltzmann andMatano for the analysis of concentration-dependent diffusion. This isfollowed by Chapter 4 by Professor Cserháti and colleagues on the use of Kirkendall porosity for fabricating hollow hemispheres. In Chapter 5,Professor Morton-Blake rep

  9. Drift in Diffusion Gradients

    Directory of Open Access Journals (Sweden)

    Fabio Marchesoni

    2013-08-01

    Full Text Available The longstanding problem of Brownian transport in a heterogeneous quasi one-dimensional medium with space-dependent self-diffusion coefficient is addressed in the overdamped (zero mass limit. A satisfactory mesoscopic description is obtained in the Langevin equation formalism by introducing an appropriate drift term, which depends on the system macroscopic observables, namely the diffuser concentration and current. The drift term is related to the microscopic properties of the medium. The paradoxical existence of a finite drift at zero current suggests the possibility of designing a Maxwell demon operating between two equilibrium reservoirs at the same temperature.

  10. Brownian yet non-Gaussian diffusion: from superstatistics to subordination of diffusing diffusivities

    CERN Document Server

    Chechkin, A V; Metzler, R; Sokolov, I M

    2016-01-01

    A growing number of biological, soft, and active matter systems are observed to exhibit normal diffusive dynamics with a linear growth of the mean squared displacement, yet with a non-Gaussian distribution of increments. Based on the Chubinsky-Slater idea of a diffusing diffusivity we here establish and analyse a complete minimal model framework of diffusion processes with fluctuating diffusivity. In particular, we demonstrate the equivalence of the diffusing diffusivity process in the short time limit with a superstatistical approach based on a distribution of diffusivities. Moreover, we establish a subordination picture of Brownian but non-Gaussian diffusion processes, that can be used for a wide class of diffusivity fluctuation statistics. Our results are shown to be in excellent agreement with simulations and numerical evaluations.

  11. Diffusion Dynamics of Cux Cluster on Cu(111) Surface

    Institute of Scientific and Technical Information of China (English)

    Jian-feng Tang; Mai-chang Xu; Xue-song Li; Wo-yun Long

    2008-01-01

    The diffusion dynamics of small two-dimensional atomic clusters Cux(1≤x≤8) on Cu(111) surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K.The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented.Our simulations show that the diffusion migration energy of the Cu7 cluster is the highest and the prefactor for the CuT cluster is almost three orders of magnitude larger than that for single atom diffusion.This conclusion is consistent with the experimental results for similar metals.In addition,the dependence of cluster diffusion on film growth is also discussed.

  12. A transformation approach to modelling multi-modal diffusions

    DEFF Research Database (Denmark)

    Forman, Julie Lyng; Sørensen, Michael

    2014-01-01

    when the diffusion is observed with additional measurement error. The new approach is applied to molecular dynamics data in the form of a reaction coordinate of the small Trp-zipper protein, from which the folding and unfolding rates of the protein are estimated. Because the diffusion coefficient...... is state-dependent, the new models provide a better fit to this type of protein folding data than the previous models with a constant diffusion coefficient, particularly when the effect of errors with a short time-scale is taken into account....

  13. Experimental Investigation of Radio-Turbulence Induced Diffusion -- Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Spitz, H. B.; Usman, S.

    2005-07-07

    The outcome of this research project suggests that the transport of radon in water is significantly greater than that predicted solely by molecular diffusion. The original study was related to the long term storage of {sup 226}Ra-bearing sand at the DOE Fernald site and determining whether a barrier of water covering the sand would be effective in reducing the emanation of {sup 222}Rn from the sand. Initial observations before this study found the transport of radon in water to be greater than that predicted solely by molecular diffusion. Fick's law on diffusion was used to model the transport of radon in water including the impact associated with radioactive decay. Initial measurements suggested that the deposition of energy in water associated with the radioactive decay process influences diffusion and enhances transport of radon. A multi-region, one-dimensional, steady-state transport model was used to analyze the movement of radon through a sequential column of air, water and air. An effective diffusion coefficient was determined by varying the thickness of the water column and measuring the time for transport of {sup 222}Rn through of the water barrier. A one-region, one-dimensional transient diffusion equation was developed to investigate the build up of radon at the end of the water column to the time when a steady-state, equilibrium condition was achieved. This build up with time is characteristic of the transport rate of radon in water and established the basis for estimating the effective diffusion coefficient for {sup 222}Rn in water. Several experiments were conducted using different types and physical arrangements of water barriers to examine how radon transport is influenced by the water barrier. Results of our measurements confirm our theoretical analyses which suggest that convective forces other than pure molecular diffusion impact the transport of {sup 222}Rn through the water barrier. An effective diffusion coefficient is defined that

  14. Low temperature diffusivity of self-interstitial defects in tungsten

    Science.gov (United States)

    Swinburne, Thomas D.; Ma, Pui-Wai; Dudarev, Sergei L.

    2017-07-01

    The low temperature diffusivity of nanoscale crystal defects, where quantum mechanical fluctuations are known to play a crucial role, are essential to interpret observations of irradiated microstructures conducted at cryogenic temperatures. Using density functional theory calculations, quantum heat bath molecular dynamics and open quantum systems theory, we evaluate the low temperature diffusivity of self-interstitial atom clusters in tungsten valid down to temperatures of 1 K. Due to an exceptionally low defect migration barrier, our results show that interstitial defects exhibit very high diffusivity of order {10}3 μ {{{m}}}2 {{{s}}}-1 over the entire range of temperatures investigated.

  15. Low barriers for hydrogen diffusion in sII clathrate.

    Science.gov (United States)

    Trinh, Thuat T; Waage, Magnus H; van Erp, Titus S; Kjelstrup, Signe

    2015-06-01

    The transport of gas molecules in hydrates is presently poorly understood. In sII structured hydrates with hydrogen guests there is, for instance, a mismatch between experimental and computed values for diffusion constants. We provide an explanation for the experimentally observed diffusion rates, using DFT-based molecular dynamics simulations at 100 K. By considering the effect of cage occupancy, as well as the flexibility of the water lattice, we show that barriers for hydrogen diffusing between cages, can approach values as low as 5 kJ mol(-1), which is very close to experimental values.

  16. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Sporring, Jon; Fogh Olsen, Ole

    2008-01-01

    . To address this problem, we introduce a photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way, we preserve important illumination features, while...

  17. Diffusing Best Practices

    DEFF Research Database (Denmark)

    Pries-Heje, Jan; Baskerville, Richard

    2014-01-01

    Both the practice and the research literature on information systems attach great value to the identification and dissemination of information on “best practices”. In the philosophy of science, this type of knowledge is regarded as technological knowledge because it becomes manifest in the succes......Both the practice and the research literature on information systems attach great value to the identification and dissemination of information on “best practices”. In the philosophy of science, this type of knowledge is regarded as technological knowledge because it becomes manifest...... in the successful techniques in one context. While the value for other contexts is unproven, knowledge of best practices circulates under an assumption that the practices will usefully self-diffuse through innovation and adoption in other contexts. We study diffusion of best practices using a design science...... approach. The study context is a design case in which an organization desires to diffuse its best practices across different groups. The design goal is embodied in organizational mechanisms to achieve this diffusion. The study used Theory of Planned Behavior (TPB) as a kernel theory. The artifacts...

  18. Model of information diffusion

    CERN Document Server

    Lande, D V

    2008-01-01

    The system of cellular automata, which expresses the process of dissemination and publication of the news among separate information resources, has been described. A bell-shaped dependence of news diffusion on internet-sources (web-sites) coheres well with a real behavior of thematic data flows, and at local time spans - with noted models, e.g., exponential and logistic ones.

  19. DEVELOPMENT, DIFFUSION, AND EVALUATION.

    Science.gov (United States)

    GUBA, EGON G.

    THE KNOWLEDGE GAP BETWEEN INITIAL RESEARCH AND FINAL USE IS DISCUSSED IN TERMS OF THE FOUR STATES OF THE THEORY-PRACTICE CONTINUUM (RESEARCH, DEVELOPMENT, DIFFUSION, AND ADOPTION). THE TWO MIDDLE STAGES ARE EMPHASIZED. RESEARCH AND DEVELOPMENT CENTERS, REGIONAL EDUCATIONAL LABORATORIES, AND TITLE III PROJECTS ARE SUGGESTED AS AGENCIES RESPONSIBLE…

  20. Osmosis and Diffusion

    Science.gov (United States)

    Sack, Jeff

    2005-01-01

    OsmoBeaker is a CD-ROM designed to enhance the learning of diffusion and osmosis by presenting interactive experimentation to the student. The software provides several computer simulations that take the student through different scenarios with cells, having different concentrations of solutes in them.

  1. Diffusion in ceramics

    CERN Document Server

    Pelleg, Joshua

    2016-01-01

    This textbook provides an introduction to changes that occur in solids such as ceramics, mainly at high temperatures, which are diffusion controlled, as well as presenting research data. Such changes are related to the kinetics of various reactions such as precipitation, oxidation and phase transformations, but are also related to some mechanical changes, such as creep. The book is composed of two parts, beginning with a look at the basics of diffusion according to Fick's Laws. Solutions of Fick’s second law for constant D, diffusion in grain boundaries and dislocations are presented along with a look at the atomistic approach for the random motion of atoms. In the second part, the author discusses diffusion in several technologically important ceramics. The ceramics selected are monolithic single phase ones, including: A12O3, SiC, MgO, ZrO2 and Si3N4. Of these, three refer to oxide ceramics (alumina, magnesia and zirconia). Carbide based ceramics are represented by the technologically very important Si-ca...

  2. Nanocrystal diffusion doping.

    Science.gov (United States)

    Vlaskin, Vladimir A; Barrows, Charles J; Erickson, Christian S; Gamelin, Daniel R

    2013-09-25

    A diffusion-based synthesis of doped colloidal semiconductor nanocrystals is demonstrated. This approach involves thermodynamically controlled addition of both impurity cations and host anions to preformed seed nanocrystals under equilibrium conditions, rather than kinetically controlled doping during growth. This chemistry allows thermodynamic crystal compositions to be prepared without sacrificing other kinetically trapped properties such as shape, size, or crystallographic phase. This doping chemistry thus shares some similarities with cation-exchange reactions, but proceeds without the loss of host cations and excels at the introduction of relatively unreactive impurity ions that have not been previously accessible using cation exchange. Specifically, we demonstrate the preparation of Cd(1-x)Mn(x)Se (0 ≤ x ≤ ∼0.2) nanocrystals with narrow size distribution, unprecedentedly high Mn(2+) content, and very large magneto-optical effects by diffusion of Mn(2+) into seed CdSe nanocrystals grown by hot injection. Controlling the solution and lattice chemical potentials of Cd(2+) and Mn(2+) allows Mn(2+) diffusion into the internal volumes of the CdSe nanocrystals with negligible Ostwald ripening, while retaining the crystallographic phase (wurtzite or zinc blende), shape anisotropy, and ensemble size uniformity of the seed nanocrystals. Experimental results for diffusion doping of other nanocrystals with other cations are also presented that indicate this method may be generalized, providing access to a variety of new doped semiconductor nanostructures not previously attainable by kinetic routes or cation exchange.

  3. Diffuse ceiling ventilation

    DEFF Research Database (Denmark)

    Zhang, Chen

    both thermal comfort and energy efficient aspects. The present study aims to characterize the air distribution and thermal comfort in the rooms with diffuse ceiling ventilation. Both the stand-alone ventilation system and its integration with a radiant ceiling system are investigated. This study also...

  4. Diffusion in aggregated soil.

    NARCIS (Netherlands)

    Rappoldt, C.

    1992-01-01

    The structure of an aggregated soil is characterized by the distribution of the distance from an arbitrary point in the soil to the nearest macropore or crack. From this distribution an equivalent model system is derived to which a diffusion model can be more easily applied. The model system consist

  5. Simulations of (an)isotropic diffusion on curved biological surfaces.

    Science.gov (United States)

    Sbalzarini, Ivo F; Hayer, Arnold; Helenius, Ari; Koumoutsakos, Petros

    2006-02-01

    We present a computational particle method for the simulation of isotropic and anisotropic diffusion on curved biological surfaces that have been reconstructed from image data. The method is capable of handling surfaces of high curvature and complex shape, which are often encountered in biology. The method is validated on simple benchmark problems and is shown to be second-order accurate in space and time and of high parallel efficiency. It is applied to simulations of diffusion on the membrane of endoplasmic reticula (ER) in live cells. Diffusion simulations are conducted on geometries reconstructed from real ER samples and are compared to fluorescence recovery after photobleaching experiments in the same ER samples using the transmembrane protein tsO45-VSV-G, C-terminally tagged with green fluorescent protein. Such comparisons allow derivation of geometry-corrected molecular diffusion constants for membrane components from fluorescence recovery after photobleaching data. The results of the simulations indicate that the diffusion behavior of molecules in the ER membrane differs significantly from the volumetric diffusion of soluble molecules in the lumen of the same ER. The apparent speed of recovery differs by a factor of approximately 4, even when the molecular diffusion constants of the two molecules are identical. In addition, the specific shape of the membrane affects the recovery half-time, which is found to vary by a factor of approximately 2 in different ER samples.

  6. Reaction-diffusion basis of retroviral infectivity

    Science.gov (United States)

    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'.

  7. Fluctuations in diffusion processes in microgravity.

    Science.gov (United States)

    Mazzoni, Stefano; Cerbino, Roberto; Vailati, Alberto; Giglio, Marzio

    2006-09-01

    It has been shown recently that diffusion processes exhibit giant nonequilibrium fluctuations (NEFs). That is, the diffusing fronts display corrugations whose length scale ranges from the molecular to the macroscopic one. The amplitude of the NEF diverges following a power law behavior proportional to q(-4) (where q is the wave vector). However, fluctuations of wave number smaller than a critical "rolloff" wave vector are quenched by the presence of gravity. It is therefore expected that in microgravity conditions, the amplitude of the NEF should be boosted by the absence of the buoyancy-driven restoring force. This may affect any diffusion process performed in microgravity, such as the crystallization of a protein solution induced by the diffusion of a salt buffer. The aim of GRADFLEX (GRAdient-Driven FLuctuation EXperiment), a joint project of ESA and NASA, is to investigate the presence of NEFs arising in a diffusion process under microgravity conditions. The project consists of two experiments. One is carried out by UNIMI (University of Milan) and INFM (Istituto Nazionale per la Fisica della Materia) and is focused on NEF in a concentration diffusion process. The other experiment is performed by UCSB (University of California at Santa Barbara) concerning temperature NEF in a simple fluid. In the UNIMI part of the GRADFLEX experimental setup, NEFs are induced in a binary mixture by means of the Soret effect. The diagnostic method is an all-optical quantitative shadowgraph technique. The power spectrum of the induced NEFs is obtained by the processing of the shadowgraph images. A detailed description of the experimental apparatus as well as the ground-based experimental results is presented here for the UNIMI-INFM experiment. The GRADFLEX payload is scheduled to fly on the FOTON M3 capsule in April 2007.

  8. Diffusive retention of atmospheric gases in chert

    Science.gov (United States)

    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

  9. Nonmonotonic diffusion in crowded environments

    Science.gov (United States)

    Putzel, Gregory Garbès; Tagliazucchi, Mario; Szleifer, Igal

    2015-01-01

    We study the diffusive motion of particles among fixed spherical crowders. The diffusers interact with the crowders through a combination of a hard-core repulsion and a short-range attraction. The long-time effective diffusion coefficient of the diffusers is found to depend non-monotonically on the strength of their attraction to the crowders. That is, for a given concentration of crowders, a weak attraction to the crowders enhances diffusion. We show that this counterintuitive fact can be understood in terms of the mesoscopic excess chemical potential landscape experienced by the diffuser. The roughness of this excess chemical potential landscape quantitatively captures the nonmonotonic dependence of the diffusion rate on the strength of crowder-diffuser attraction; thus it is a purely static predictor of dynamic behavior. The mesoscopic view given here provides a unified explanation for enhanced diffusion effects that have been found in various systems of technological and biological interest. PMID:25302920

  10. Effective Potential Theory for Diffusion in Binary Ionic Mixtures

    CERN Document Server

    Shaffer, Nathaniel R; Daligault, Jérôme

    2016-01-01

    Self-diffusion and interdiffusion coefficients of binary ionic mixtures are evaluated using the Effective Potential Theory (EPT), and the predictions are compared with the results of molecular dynamics simulations. We find that EPT agrees with molecular dynamics from weak coupling well into the strong coupling regime, which is a similar range of coupling strengths as previously observed in comparisons with the one-component plasma. Within this range, typical relative errors of approximately 20% and worst-case relative errors of approximately 40% are observed. We also examine the Darken model, which approximates the interdiffusion coefficients based on the self-diffusion coefficients.

  11. Axial dispersion via shear-enhanced diffusion in colloidal suspensions

    KAUST Repository

    Griffiths, I. M.

    2012-03-01

    The familiar example of Taylor dispersion of molecular solutes is extended to describe colloidal suspensions, where the fluctuations that contribute to dispersion arise from hydrodynamic interactions. The generic scheme is illustrated for a suspension of particles in a pressure-driven pipe flow, with a concentration-dependent diffusivity that captures both the shear-induced and Brownian contributions. The effect of the cross-stream migration via shear-induced diffusion is shown to dramatically reduce the axial dispersion predicted by classical Taylor dispersion for a molecular solute. Analytic and numerical solutions are presented that illustrate the effect of the concentration dependence of this nonlinear hydrodynamic mechanism. Copyright © EPLA, 2012.

  12. Long-Range Effects on Polymer Diffusion Induced by a Bounding Interface

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, X.; Rafailovich, M.H.; Sokolov, J. [Department of Materials Science and Engineering, State University of New York at Stony Brook, Stony Brook, New York 11794-2275 (United States); Strzhemechny, Y.; Schwarz, S.A. [Physics Department, Queens College of The City University of New York, Flushing, New York 11376 (United States); Sauer, B.B. [E.I. DuPont de Nemours Company, Inc., Experimental Station, Wilmington, Delaware 19880 (United States); Rubinstein, M. [Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 (United States)

    1997-07-01

    We have measured the diffusion of deuterated polystyrene of molecular weight 90{times}10{sup 3} in various matrices of hydrogenated polystyrene as a function of distance from an attractive interface, oxide-covered silicon. Surprisingly long-range effects are observed. Diffusion rates an order of magnitude slower than bulk persist up to 10R{sub g} (radius of gyration) from the interface of either the diffusant or matrix polymers. The slowdown is independent of matrix molecular weight over a broad range. However, mixing of polymers within the matrix strongly influences the rates of diffusion. {copyright} {ital 1997} {ital The American Physical Society}

  13. Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

    Indian Academy of Sciences (India)

    Manish Agrawal; S B Santra; Rajat Anand; Rajaram Swaminathan

    2008-08-01

    The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.

  14. Substrate catalysis enhances single-enzyme diffusion.

    Science.gov (United States)

    Muddana, Hari S; Sengupta, Samudra; Mallouk, Thomas E; Sen, Ayusman; Butler, Peter J

    2010-02-24

    We show that diffusion of single urease enzyme molecules increases in the presence of urea in a concentration-dependent manner and calculate the force responsible for this increase. Urease diffusion measured using fluorescence correlation spectroscopy increased by 16-28% over buffer controls at urea concentrations ranging from 0.001 to 1 M. This increase was significantly attenuated when urease was inhibited with pyrocatechol, demonstrating that the increase in diffusion was the result of enzyme catalysis of urea. Local molecular pH changes as measured using the pH-dependent fluorescence lifetime of SNARF-1 conjugated to urease were not sufficient to explain the increase in diffusion. Thus, a force generated by self-electrophoresis remains the most plausible explanation. This force, evaluated using Brownian dynamics simulations, was 12 pN per reaction turnover. These measurements demonstrate force generation by a single enzyme molecule and lay the foundation for a further understanding of biological force generation and the development of enzyme-driven nanomotors.

  15. Diffusion-weighted imaging of pancreatic cancer

    Institute of Scientific and Technical Information of China (English)

    Riccardo; De; Robertis; Paolo; Tinazzi; Martini; Emanuele; Demozzi; Flavia; Dal; Corso; Claudio; Bassi; Paolo; Pederzoli; Mirko; D’Onofrio

    2015-01-01

    Magnetic resonance imaging(MRI) is a reliable and accurate imaging method for the evaluation of patients with pancreatic ductal adenocarcinoma(PDAC). Diffusion-weighted imaging(DWI) is a relatively recent technological improvement that expanded MRI capabilities, having brought functional aspects into conventional morphologic MRI evaluation. DWI can depict the random diffusion of water molecules within tissues(the so-called Brownian motions). Modifications of water diffusion induced by different factors acting on the extracellular and intracellular spaces, as increased cell density, edema, fibrosis, or altered functionality of cell membranes, can be detected using this MR sequence. The intravoxel incoherent motion(IVIM) model is an advanced DWI technique that consent a separate quantitative evaluation of all the microscopic random motions that contribute to DWI, which are essentially represented by molecular diffusion and blood microcirculation(perfusion). Technological improvements have made possible the routine use of DWI during abdominal MRI study. Several authors have reported that the addition of DWI sequence can be of value for the evaluation of patients with PDAC, especially improving the staging; nevertheless, it is still unclear whether and how DWI could be helpful for identification, characterization, prognostic stratification and follow-up during treatment. The aim of this paper is to review up-to-date literature data regarding the applications of DWI and IVIM to PDACs.

  16. Concentration dependent hydrogen diffusion in tungsten

    Science.gov (United States)

    Ahlgren, T.; Bukonte, L.

    2016-10-01

    The diffusion of hydrogen in tungsten is studied as a function of temperature, hydrogen concentration and pressure using Molecular Dynamics technique. A new analysis method to determine diffusion coefficients that accounts for the random oscillation of atoms around the equilibrium position is presented. The results indicate that the hydrogen migration barrier of 0.25 eV should be used instead of the presently recommended value of 0.39 eV. This conclusion is supported by both experiments and density functional theory calculations. Moreover, the migration volume at the saddle point for H in W is found to be positive: ΔVm ≈ 0.488 Å3, leading to a decrease in the diffusivity at high pressures. At high H concentrations, a dramatic reduction in the diffusion coefficient is observed, due to site blocking and the repulsive H-H interaction. The results of this study indicates that high flux hydrogen irradiation leads to much higher H concentrations in tungsten than expected.

  17. Cosmic ray penetration in diffuse clouds

    CERN Document Server

    Morlino, G; Krause, J

    2015-01-01

    Cosmic rays are a fundamental source of ionization for molecular and diffuse clouds, influencing their chemical, thermal, and dynamical evolution. The amount of cosmic rays inside a cloud also determines the $\\gamma$-ray flux produced by hadronic collisions between cosmic rays and cloud material. We study the spectrum of cosmic rays inside and outside of a diffuse cloud, by solving the stationary transport equation for cosmic rays including diffusion, advection and energy losses due to ionization of neutral hydrogen atoms. We found that the cosmic ray spectrum inside a diffuse cloud differs from the one in the interstellar medium (ISM) for energies smaller than $E_{br}\\approx 100$ MeV, irrespective of the model details. Below $E_{br}$, the spectrum is harder (softer) than that in the ISM if the latter is a power law $\\propto p^{-s}$ with $s$ larger (smaller) than $\\sim0.42$. As a consequence also the ionization rate due to CRs is strongly affected. Assuming an average Galactic spectrum similar to the one infe...

  18. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  19. Molecular machines open cell membranes

    Science.gov (United States)

    García-López, Víctor; Chen, Fang; Nilewski, Lizanne G.; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B.; Robinson, Jacob T.; Wang, Gufeng; Pal, Robert; Tour, James M.

    2017-08-01

    Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.

  20. NMR relaxation and water self-diffusion studies in whey protein solutions and gels.

    Science.gov (United States)

    Colsenet, Roxane; Mariette, François; Cambert, Mireille

    2005-08-24

    The changes in water proton transverse relaxation behavior induced by aggregation of whey proteins are explained in terms of the simple molecular processes of diffusion and chemical exchange. The water self-diffusion coefficient was measured in whey protein solutions and gels by the pulsed field gradient NMR method. As expected, water self-diffusion was reduced with increased protein concentrations. Whatever the concentration, the water molecules were free to diffuse over distances varying from 15 to 47 mum. Water diffusion was constant over these distances, demonstrating that no restrictions were found to explain the water hindrance. The modification in protein structure by gelation induced a decrease in water diffusion. The effects of protein concentration on water diffusion are discussed and modeled. Two approaches were compared, the obstruction effect induced by a spherical particle and the cell model, which considered two water compartments with specific self-diffusion coefficients.

  1. Fractal model of anomalous diffusion.

    Science.gov (United States)

    Gmachowski, Lech

    2015-12-01

    An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.

  2. Diffusion in porous crystalline materials

    NARCIS (Netherlands)

    Krishna, R.

    2012-01-01

    The design and development of many separation and catalytic process technologies require a proper quantitative description of diffusion of mixtures of guest molecules within porous crystalline materials. This tutorial review presents a unified, phenomenological description of diffusion inside meso-

  3. Reflective Inverse Diffusion

    Directory of Open Access Journals (Sweden)

    Kenneth Burgi

    2016-11-01

    Full Text Available Phase front modulation was previously used to refocus light after transmission through scattering media. This process has been adapted here to work in reflection. A liquid crystal spatial light modulator is used to conjugate the phase scattering properties of diffuse reflectors to produce a converging phase front just after reflection. The resultant focused spot had intensity enhancement values between 13 and 122 depending on the type of reflector. The intensity enhancement of more specular materials was greater in the specular region, while diffuse reflector materials achieved a greater enhancement in non-specular regions, facilitating non-mechanical steering of the focused spot. Scalar wave optics modeling corroborates the experimental results.

  4. Diffused Religion and Prayer

    Directory of Open Access Journals (Sweden)

    Roberto Cipriani

    2011-06-01

    Full Text Available It is quite likely that the origins of prayer are to be found in ancient mourning and bereavement rites. Primeval ritual prayer was codified and handed down socially to become a deep-rooted feature of people’s cultural behavior, so much so, that it may surface again several years later, in the face of death, danger, need, even in the case of relapse from faith and religious practice. Modes of prayer depend on religious experience, on relations between personal prayer and political action, between prayer and forgiveness, and between prayer and approaches to religions. Various forms of prayer exist, from the covert-hidden to the overt-manifest kind. How can they be investigated? How can one, for instance, explore mental prayer? These issues regard the canon of diffused religion and, therefore, of diffused prayer.

  5. Galactic Diffuse Polarized Emission

    Indian Academy of Sciences (India)

    Ettore Carretti

    2011-12-01

    Diffuse polarized emission by synchrotron is a key tool to investigate magnetic fields in the Milky Way, particularly the ordered component of the large scale structure. Key observables are the synchrotron emission itself and the RM is by Faraday rotation. In this paper the main properties of the radio polarized diffuse emission and its use to investigate magnetic fields will be reviewed along with our current understanding of the galactic magnetic field and the data sets available. We will then focus on the future perspective discussing RM-synthesis – the new powerful instrument devised to unlock the information encoded in such an emission – and the surveys currently in progress like S-PASS and GMIMS.

  6. Enhancing Cation Diffusion and Suppressing Anion Diffusion via Lewis-Acidic Polymer Electrolytes

    CERN Document Server

    Savoie, Brett M; Miller, Thomas F

    2016-01-01

    Solid polymer electrolytes (SPE) have the potential to increase both the energy density and stability of lithium-based batteries, but low Li-ion conductivity remains a barrier to technological viability. SPEs are designed to maximize Li-ion diffusivity relative to the anion, while maintaining sufficient salt solubility. It is thus remarkable that polyethylene oxide (PEO), the most widely used SPE, exhibits Li-ion diffusivity that is an order of magnitude smaller than that of typical counter-ions, such as TFSI, at moderate salt concentrations. Here, we show that Lewis-basic polymers like PEO intrinsically favor slow cation and rapid anion diffusion while this relationship can be reversed in Lewis-acidic polymers. Using molecular dynamics (MD) simulations, Lewis-acidic polyboranes are identified that achieve up to a ten-fold increase in Li-ion diffusivity and a significant decrease in anion diffusivity, relative to PEO. The results for this new class of Lewis-acidic SPEs illustrate a general principle for incre...

  7. Anomalous diffusion of epicentres

    CERN Document Server

    Sotolongo-Costa, Oscar; Posadas, A; Luzon, F

    2007-01-01

    The classification of earthquakes in main shocks and aftershocks by a method recently proposed by M. Baiesi and M. Paczuski allows to the generation of a complex network composed of clusters that group the most correlated events. The spatial distribution of epicentres inside these structures corresponding to the catalogue of earthquakes in the eastern region of Cuba shows anomalous anti-diffusive behaviour evidencing the attractive nature of the main shock and the possible description in terms of fractional kinetics.

  8. [The diffusion of knowledge].

    Science.gov (United States)

    Ramiro-H, Manuel; Cruz-A, Enrique

    2016-01-01

    Between August 19 and 21, the Feria del Libro de las Ciencias de la Salud (Healthcare Book Fair) took place in the Palacio de Medicina in Mexico City. Archives of Medical Research, Revista Médica del IMSS, and Saber IMSS, three of the main instruments of knowledge diffusion of the Instituto Mexicano del Seguro Social, assisted to this book fair, which was organized by the Facultad de Medicina of UNAM.

  9. Diffusing Best Practices

    DEFF Research Database (Denmark)

    Pries-Heje, Jan; Baskerville, Richard

    2014-01-01

    Both the practice and the research literature on information systems attach great value to the identification and dissemination of information on “best practices”. In the philosophy of science, this type of knowledge is regarded as technological knowledge because it becomes manifest in the succes...... that the behavior will be effective). These two factors were especially critical if the source context of the best practice is qualitatively different from the target context into which the organization is seeking to diffuse the best practice.......Both the practice and the research literature on information systems attach great value to the identification and dissemination of information on “best practices”. In the philosophy of science, this type of knowledge is regarded as technological knowledge because it becomes manifest...... approach. The study context is a design case in which an organization desires to diffuse its best practices across different groups. The design goal is embodied in organizational mechanisms to achieve this diffusion. The study used Theory of Planned Behavior (TPB) as a kernel theory. The artifacts...

  10. Turbulent diffusion of chemically reacting gaseous admixtures

    Science.gov (United States)

    Elperin, T.; Kleeorin, N.; Liberman, M.; Rogachevskii, I.

    2014-11-01

    We study turbulent diffusion of chemically reacting gaseous admixtures in a developed turbulence. In our previous study [Phys. Rev. Lett. 80, 69 (1998), 10.1103/PhysRevLett.80.69] using a path-integral approach for a delta-correlated in a time random velocity field, we demonstrated a strong modification of turbulent transport in fluid flows with chemical reactions or phase transitions. In the present study we use the spectral τ approximation that is valid for large Reynolds and Peclet numbers and show that turbulent diffusion of the reacting species can be strongly depleted by a large factor that is the ratio of turbulent and chemical times (turbulent Damköhler number). We have demonstrated that the derived theoretical dependence of a turbulent diffusion coefficient versus the turbulent Damköhler number is in good agreement with that obtained previously in the numerical modeling of a reactive front propagating in a turbulent flow and described by the Kolmogorov-Petrovskii-Piskunov-Fisher equation. We have found that turbulent cross-effects, e.g., turbulent mutual diffusion of gaseous admixtures and turbulent Dufour effect of the chemically reacting gaseous admixtures, are less sensitive to the values of stoichiometric coefficients. The mechanisms of the turbulent cross-effects differ from the molecular cross-effects known in irreversible thermodynamics. In a fully developed turbulence and at large Peclet numbers the turbulent cross-effects are much larger than the molecular ones. The obtained results are applicable also to heterogeneous phase transitions.

  11. Sodium diffusion in boroaluminosilicate glasses

    DEFF Research Database (Denmark)

    Smedskjaer, Morten M.; Zheng, Qiuju; Mauro, John C.

    2011-01-01

    diffusivity are explored in terms of the structural role of ferric and ferrous ions. By comparing the results obtained by the three approaches, we observe that both the tracer Na diffusion and the Na-K interdiffusion are significantly faster than the Na inward diffusion. The origin of this discrepancy could...

  12. Epidemic Diffusion on Complex Networks

    Institute of Scientific and Technical Information of China (English)

    WU Xiao-Yan; LIU Zong-Hua

    2007-01-01

    Boyh diffusion and epidemic are well studied in the stochastic systems and complex networks,respetively.Here we combine these two fields and study epidemic diffusion in complex networks.Instead of studying the threshold of infection,which was focused on in previous works,we focus on the diffusion.behaviour.We find that the epidemic diffusion in a complex network is an anomalous superdiffusion with varyingg diffusion exponext γand that γ is influenced seriously by the network structure,such as the clustering coefficient and the degree distribution.Numerical simulations have confirmed the theoretical predictions.

  13. Advanced diffusion processes and phenomena

    CERN Document Server

    Öchsner, Andreas; Belova, Irina

    2014-01-01

    This topical volume on Advanced Diffusion Processes and Phenomena addresses diffusion in a wider sense of not only mass diffusion but also heat diffusion in fluids and solids. Both diffusion phenomena play an important role in the characterization of engineering materials and corresponding structures. Understanding these different transport phenomena at many levels, from atomistic to macro, has therefore long attracted the attention of many researchers in materials science and engineering and related disciplines. The present topical volume captures a representative cross-section of some of the

  14. Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia

    Science.gov (United States)

    Good, Brian

    2011-01-01

    Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.

  15. The mathematical model of dye diffusion and adsorption on modified cellulose with triazine derivatives containing cationic and anionic groups

    Science.gov (United States)

    Xie, K.; Hou, A.; Chen, Y.

    2008-02-01

    Cellulose fabric is chemically modified with the compounds containing cationic and anionic groups. The molecular chains of modified cellulose have both cationic and anionic groups. Dye diffusion properties on modified cellulose are discussed. The dye adsorption and diffusion on modified cellulose are higher than those on unmodified cellulose. The diffusion properties of dyes at different temperature are discussed. Compared with unmodified cellulose, the diffusion processing of dyes in the modified cotton cellulose shows significant change.

  16. Characterizing microstructure of living tissues with time-dependent diffusion

    CERN Document Server

    Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A

    2012-01-01

    Molecular diffusion measurements are widely used to probe microstructure in materials and living organisms noninvasively. The precise relation of diffusion metrics to microstructure remains a major challenge: In complex samples, it is often unclear which structural features are most relevant and can be quantified. Here we classify the structural complexity in terms of the long time tail exponent in the molecular velocity autocorrelation function. The specific values of the dynamical exponent let us identify the relevant tissue microanatomy affecting water diffusion measured with MRI in muscles and in brain, and the microstructural changes in ischemic stroke. Our framework presents a systematic way to identify the most relevant part of structural complexity using transport measured with a variety of techniques.

  17. Mitosis, diffusible crosslinkers, and the ideal gas law.

    Science.gov (United States)

    Odde, David J

    2015-03-12

    During mitosis, molecular motors hydrolyze ATP to generate sliding forces between adjacent microtubules and form the bipolar mitotic spindle. Lansky et al. now show that the diffusible microtubule crosslinker Ase1p can generate sliding forces between adjacent microtubules, and it does so without ATP hydrolysis. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Profiling of diffuse large B-cell lymphoma by immunohistochemistry

    DEFF Research Database (Denmark)

    Sjö, Lene Dissing; Poulsen, Christian Bjørn; Hansen, Mads;

    2007-01-01

    Diffuse large B-cell lymphoma (DLBCL) is a frequent lymphoma subtype with a heterogeneous behavior and a variable response to conventional chemotherapy. This clinical diversity is believed to reflect differences in the molecular pathways leading to lymphomagenesis. In this study, we have analyzed...

  19. A practical guide to stochastic simulations of reaction-diffusion processes

    OpenAIRE

    Erban, Radek; Chapman, Jonathan; Maini, Philip

    2007-01-01

    A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the classical Gillespie algorithm for the stochastic modelling of chemical reactions. Then stochastic algorithms for modelling molecular diffusion are given. Finally, basic stochastic reaction-diffusion methods are presented. The connections between stochastic simul...

  20. Thermodynamic properties and diffusion of water + methane binary mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au [Centre for Molecular Simulation, Swinburne University of Technology, PO Box 218 Hawthorn, Victoria 3122 (Australia)

    2014-03-14

    Thermodynamic and diffusion properties of water + methane mixtures in a single liquid phase are studied using NVT molecular dynamics. An extensive comparison is reported for the thermal pressure coefficient, compressibilities, expansion coefficients, heat capacities, Joule-Thomson coefficient, zero frequency speed of sound, and diffusion coefficient at methane concentrations up to 15% in the temperature range of 298–650 K. The simulations reveal a complex concentration dependence of the thermodynamic properties of water + methane mixtures. The compressibilities, heat capacities, and diffusion coefficients decrease with increasing methane concentration, whereas values of the thermal expansion coefficients and speed of sound increase. Increasing methane concentration considerably retards the self-diffusion of both water and methane in the mixture. These effects are caused by changes in hydrogen bond network, solvation shell structure, and dynamics of water molecules induced by the solvation of methane at constant volume conditions.

  1. Diffusion of Small Molecules in Metal Organic Framework Materials

    Science.gov (United States)

    Canepa, Pieremanuele; Nijem, Nour; Chabal, Yves J.; Thonhauser, T.

    2013-01-01

    Ab initio simulations are combined with in situ infrared spectroscopy to unveil the molecular transport of H2, CO2, and H2O in the metal organic framework MOF-74-Mg. Our study uncovers—at the atomistic level—the major factors governing the transport mechanism of these small molecules. In particular, we identify four key diffusion mechanisms and calculate the corresponding diffusion barriers, which are nicely confirmed by time-resolved infrared experiments. We also answer a long-standing question about the existence of secondary adsorption sites for the guest molecules, and we show how those sites affect the macroscopic diffusion properties. Our findings are important to gain a fundamental understanding of the diffusion processes in these nanoporous materials, with direct implications for the usability of MOFs in gas sequestration and storage applications.

  2. Influence of adsorption thermodynamics on guest diffusivities in nanoporous crystalline materials

    NARCIS (Netherlands)

    R. Krishna; J.M. van Baten

    2013-01-01

    Published experimental data, underpinned by molecular simulations, are used to highlight the strong influence of adsorption thermodynamics on diffusivities of guest molecules inside ordered nanoporous crystalline materials such as zeolites, metal-organic frameworks (MOFs), and zeolitic imidazolate f

  3. Atomic diffusion across Ni50Ti50—Cu explosive welding interface: Diffusion layer thickness and atomic concentration distribution

    Science.gov (United States)

    Chen, Shi-Yang; Wu, Zhen-Wei; Liu, Kai-Xin

    2014-06-01

    Molecular dynamics simulations are carried out to study atomic diffusion in the explosive welding process of Ni50Ti50—Cu (at.%). By using a hybrid method which combines molecular dynamics simulation and classical diffusion theory, the thickness of the diffusion layer and the atomic concentration distribution across the welding interface are obtained. The results indicate that the concentration distribution curves at different times have a geometric similarity. According to the geometric similarity, the atomic concentration distribution at any time in explosive welding can be calculated. Ni50Ti50—Cu explosive welding and scanning electron microscope experiments are done to verify the results. The simulation results and the experimental results are in good agreement.

  4. Magnetic resonance diffusion-weighted imaging in the diagnosis of diffuse liver diseases in rats

    Institute of Scientific and Technical Information of China (English)

    GUAN Sheng; ZHOU Kang-rong; ZHAO Wei-dong; PENG Wei-jun; TANG Feng; MAO Jian

    2005-01-01

    Background The diagnosis of diffuse hepatic lesions in early stage is a tough task at any time for clinical conventional imaging Magnetic resonance diffusion-weighted imaging (MR DWI) can detect the changes of tissue structure at molecular level This study was designed to determine the value of DWI in the diagnosis of diffuse liver lesions in early stage.Methods Diffuse liver lesions were induced by diethylnitrosamine in 42 rats of test group. Fourteen rats in control group were fed with pure water. Dynamic changes of MR DWI were observed every week in both groups during the early stage of diffuse liver lesions (1 to 12 weeks after drug administration in the test group). Apparent diffusion coefficient (ADC) values of liver parenchyma in different stages and pathologic changes were analyzed.Results The process of diffuse hepatic lesions in the test group was classified into three stages according to pathological changes, namely hepatitis, hepatic fibrosis and cirrhosis. No obvious morphological changes were shown by conventional imaging in both groups during this stage. But MR DWI demonstrated heterogeneous signal changes in early stage of hepatic cirrhosis in the test group. No significant change of ADC values was found in the control group between different weeks (P>0.05). The ADC values of the test group declined from the fifth week, and after the tenth week the ADC values were significantly different between the test and control groups at gradient factor (b) value 300 sec/mm2 (P<0.05). At b value 600 and 1000 sec/mm2, significant difference was seen between the two groups from the sixth week onward. The range of ADC value of the groups was (1.7-0.9)±(0.40-0.04) mm2/sec (b=600) and (1.38-0.75)±(0.07-0.35) mm2/sec (b=1000), respectively. Dominant pathological changes included swelled hepatocytes within 1 to 4 weeks after the administration of diethylnitrosamine in the test group, hyperplasia of fibrous tissues in 5-8 weeks and formation of cirrhotic nodules in 9

  5. Diffusion in Solids Fundamentals, Methods, Materials, Diffusion-Controlled Processes

    CERN Document Server

    Mehrer, Helmut

    2007-01-01

    Diffusion is a vital topic in solid-state physics and chemistry, physical metallurgy and materials science. Diffusion processes are ubiquitous in solids at elevated temperatures. A thorough understanding of diffusion in materials is crucial for materials development and engineering. This book first gives an account of the central aspects of diffusion in solids, for which the necessary background is a course in solid state physics. It then provides easy access to important information about diffuson in metals, alloys, semiconductors, ion-conducting materials, glasses and nanomaterials. Several diffusion-controlled phenomena, including ionic conduction, grain-boundary and dislocation pipe diffusion, are considered as well. Graduate students in solid-state physics, physical metallurgy, materials science, physical and inorganic chemistry or geophysics will benefit from this book as will physicists, chemists, metallurgists, materials engineers in academic and industrial research laboratories.

  6. Diffusion and association processes in biological systems: theory, computation and experiment

    Directory of Open Access Journals (Sweden)

    Mereghetti Paolo

    2011-03-01

    Full Text Available Abstract Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.

  7. Diffusion and association processes in biological systems: theory, computation and experiment.

    Science.gov (United States)

    Mereghetti, Paolo; Kokh, Daria; McCammon, J Andrew; Wade, Rebecca C

    2011-03-02

    Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.

  8. Impacts of Water Within Transformer Oil on the Diffusion and Distribution Characteristics of Furfural by Molecular Dynamics%变压器油中水分对糠醛扩散及分布影响的分子动力学研究

    Institute of Scientific and Technical Information of China (English)

    廖瑞金; 周欣; 杨丽君; 朱孟兆; 贡春艳; 李伟

    2011-01-01

    Furfural is an aging by-product of power transformer insulation paper.The concentration of furfural can be directly used as a tool to evaluate the aging extent of insulation paper.However,no universally acknowledged production mechanisms and distribution laws of furfural in oil-paper system have been obtained.Among various influential factors,water is considered to play an important but ambiguous role in effecting furfural's production rate and distribution.Therefore,four naphthenic mineral oil models,of which the water contents were set to 0%,1%,3% and 5% respectively,were constructed by means of molecular modeling.Molecular dynamics were performed on the models subsequently.By investigating interactions between furfural and ambient media,hydrogen bonding and diffusion phenomenon of furfural in oil,the microscopic mechanism of water influencing the diffusion and distribution characteristics of furfural in oil-paper composite system was revealed.Research results show water in transformer oil would significantly enhance oil's ability in absorbing furfural and improve solubility of furfural in oil as well.Moreover,water in transformer oil suppresses the free diffusion of furfural in oil which will exert native influence on furfural's homogeneous distribution in oil.%糠醛是电力变压器绝缘纸的老化产物,通过监测油中糠醛质量浓度可以直接评估绝缘纸的老化程度,但关于糠醛的生成机制及在油纸复合绝缘系统的分布规律至今没有形成统一的认识。在众多的因素中,水分被认为在影响糠醛的生成速率及其在油纸复合绝缘系统分布的过程中具有重要作用,但其作用机制却不够明晰。为此,利用分子模拟手段分别构建出糠醛分子在无水、水与油之质量比分别为1%、3%和5%的环烷基矿物绝缘油中的扩散模型并进行动力学仿真和分析。通过考察糠醛与含水油介质的相互作用、氢键成键特性以及糠醛的扩散现象,

  9. Anode characterisation and gas diffusion behaviour in aluminium smelting

    Science.gov (United States)

    Putri, Epma; Brooks, Geoffrey; Snook, Graeme; Eick, Ingo

    2017-01-01

    Over the past century, significant research on different aspects of the Hall-Héroult process has been conducted to increase energy efficiency. Bubble generation at the anode reaction and its contribution to the overall voltage drop in aluminium production holds significant potential for energy saving, yet the details of the gas transport mechanism for bubble nucleation behaviour are not completely understood. The multi-step electrochemical reaction releases predominantly CO2 gas along with CO gas, which is a reduction product formed by reaction of CO2 with the anode carbon. Complicating the reaction is the multiple paths by which the gas can diffuse (either through the porous anode or the electrolyte bath). There has been no detailed investigation of the correlation between gas diffusion as a function of anode and bath properties. In the present study, the porosity measurement techniques in the anode will be used to understand the relation of gas diffusion and anode properties. A porosimetric study was conducted for two different anode samples using mercury intrusion porosimetry (MIP) and hydrostatic method. The MIP method provides important anode properties information such as density, percent porosity, pore size distribution, permeability, and tortuosity factor which affect gas diffusion and anode performance. The Knudsen number obtained from MIP data shows both Knudsen diffusion and molecular diffusion need to be considered when predicting the effective diffusion.

  10. Enhanced diffusion of tracer particles in dilute bacterial suspensions.

    Science.gov (United States)

    Morozov, Alexander; Marenduzzo, Davide

    2014-04-28

    Swimming bacteria create long-range velocity fields that stir a large volume of fluid and move around passive particles dispersed in the fluid. Recent experiments and simulations have shown that long-time mean-squared displacement of passive particles in a bath of swimming bacteria exhibits diffusive behaviour with an effective diffusion coefficient significantly larger than its thermal counterpart. A comprehensive theoretical prediction of this effective diffusion coefficient and the understanding of the enhancement mechanism remain a challenge. Here, we adapt the kinetic theory by Lin et al., J. Fluid Mech., 2011, 669, 167 developed for 'squirmers' to the bacterial case to quantitatively predict enhanced diffusivity of tracer particles in dilute two- and three-dimensional suspensions of swimming bacteria. We demonstrate that the effective diffusion coefficient is a product of the bacterial number density, their swimming speed, a geometric factor characterising the velocity field created by a single bacterium, and a numerical factor. We show that the numerical factor is, in fact, a rather strong function of the system parameters, most notably the run length of the bacteria, and that these dependencies have to be taken into account to quantitatively predict the enhanced diffusivity. We perform molecular-dynamics-type simulations to confirm the conclusions of the kinetic theory. Our results are in good agreement with the values of enhanced diffusivity measured in recent two- and three-dimensional experiments.

  11. Why does hydronium diffuse faster than hydroxide in liquid water?

    Science.gov (United States)

    Zheng, Lixin; Santra, Biswajit; Distasio, Robert; Klein, Michael; Car, Roberto; Wu, Xifan

    Experiments show that the hydronium ion (H3O+) diffuses much faster than the hydroxide ion (OH-) in liquid water. ab initio molecular dynamics (AIMD) simulations correctly associated the diffusion mechanism to proton transfer (PT) but have been unable so far to clearly identify the reason for the faster diffusion of hydronium compared to hydroxide, as the diffusion rate was found to depend sensitively on the adopted functional approximation. We carried out AIMD simulations of the solvated water ions using a van der Waals (vdW) inclusive PBE0 hybrid density functional. It is found that not only hydronium diffuses faster than hydroxide but also the absolute rates agree with experiment. The fast diffusion of H3O+ occurs via concerted PT that enables the ion to jump across several H-bonded molecules in successful transfer events; in contrast, such concerted motion is significantly hindered in OH- where the ion is easily trapped in a hyper-coordination configuration (a local solvation structure that forbids PT). As a result multiple PT events are rare and the diffusion of OH- is significantly slowed down. Such a clear difference between the two ions results from the combined effect of vdW interactions and self-interaction correction. Doe SciDac: DE-SC0008626 and DE-SC0008726.

  12. The diffusion of microfinance.

    Science.gov (United States)

    Banerjee, Abhijit; Chandrasekhar, Arun G; Duflo, Esther; Jackson, Matthew O

    2013-07-26

    To study the impact of the choice of injection points in the diffusion of a new product in a society, we developed a model of word-of-mouth diffusion and then applied it to data on social networks and participation in a newly available microfinance loan program in 43 Indian villages. Our model allows us to distinguish information passing among neighbors from direct influence of neighbors' participation decisions, as well as information passing by participants versus nonparticipants. The model estimates suggest that participants are seven times as likely to pass information compared to informed nonparticipants, but information passed by nonparticipants still accounts for roughly one-third of eventual participation. An informed household is not more likely to participate if its informed friends participate. We then propose two new measures of how effective a given household would be as an injection point. We show that the centrality of the injection points according to these measures constitutes a strong and significant predictor of eventual village-level participation.

  13. Anisotropic Thermal Diffusion

    Science.gov (United States)

    Gardiner, Thomas

    2013-10-01

    Anisotropic thermal diffusion in magnetized plasmas is an important physical phenomena for a diverse set of physical conditions ranging from astrophysical plasmas to MFE and ICF. Yet numerically simulating this phenomenon accurately poses significant challenges when the computational mesh is misaligned with respect to the magnetic field. Particularly when the temperature gradients are unresolved, one frequently finds entropy violating solutions with heat flowing from cold to hot zones for χ∥ /χ⊥ >=102 which is substantially smaller than the range of interest which can reach 1010 or higher. In this talk we present a new implicit algorithm for solving the anisotropic thermal diffusion equations and demonstrate its characteristics on what has become a fairly standard set of test problems in the literature. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. SAND2013-5687A.

  14. Cross-diffusion effects in isothermal double diffusive

    Energy Technology Data Exchange (ETDEWEB)

    Becerril, R. [Michoacan Univ. Michoacana de San Nicolas de Hidalgo, Michoacan (Mexico). Inst. de Fisica y Mathematicas

    2000-11-01

    The nonlinear coefficients of the amplitude equations for the stationary, oscillatory and codimension-2 point bifurcations are calculated for isothermal double diffusive convection with cross-diffusion. The locations of the tricritical point for the stationary instability and the codimension-2 point are also found. Thereby the separation between these points in parameter space can be calculated as a function of rescaled cross-diffusion constants.

  15. The Pearson diffusions: A class of statistically tractable diffusion processes

    DEFF Research Database (Denmark)

    Forman, Julie Lyng; Sørensen, Michael

    The Pearson diffusions is a flexible class of diffusions defined by having linear drift and quadratic squared diffusion coefficient. It is demonstrated that for this class explicit statistical inference is feasible. Explicit optimal martingale estimating func- tions are found, and the corresponding...... volatility models with Pearson volatility process. For the non-Markov models explicit optimal prediction based estimating functions are found and shown to yield consistent and asymptotically normal estimators...

  16. The Pearson diffusions: A class of statistically tractable diffusion processes

    DEFF Research Database (Denmark)

    Forman, Julie Lyng; Sørensen, Michael

    estimators are shown to be consistent and asymptotically normal. The discussion covers GMM, quasi-likelihood, and non- linear weighted least squares estimation too, and it is discussed how explicit likeli- hood or approximate likelihood inference is possible for the Pearson diffusions. A complete model....... Special attention is given to a skew t-type distribution. Explicit formulae for the conditional moments and the polynomial eigenfunctions are derived. The analyti- cal tractability is inherited by transformed Pearson diffusions, integrated Pearson diffusions, sums of Pearson diffusions, and stochastic...

  17. Diffusion and perfusion imaging of bone marrow

    Energy Technology Data Exchange (ETDEWEB)

    Biffar, Andreas; Dietrich, Olaf [Josef Lissner Laboratory for Biomedical Imaging, Department of Clinical Radiology, LMU University Hospitals, Grosshadern-Munich (Germany); Sourbron, Steven [Josef Lissner Laboratory for Biomedical Imaging, Department of Clinical Radiology, LMU University Hospitals, Grosshadern-Munich (Germany); Division of Medical Physics, University of Leeds, Leeds (United Kingdom); Duerr, Hans-Roland [Department of Orthopedic Surgery, LMU University Hospitals, Grosshadern-Munich (Germany); Reiser, Maximilian F. [Josef Lissner Laboratory for Biomedical Imaging, Department of Clinical Radiology, LMU University Hospitals, Grosshadern-Munich (Germany); Department of Clinical Radiology, LMU University Hospitals, Grosshadern-Munich (Germany); Baur-Melnyk, Andrea, E-mail: andrea.baur@med.uni-muenchen.de [Department of Clinical Radiology, LMU University Hospitals, Grosshadern-Munich (Germany)

    2010-12-15

    In diffusion-weighted magnetic resonance imaging (DWI), the observed MRI signal intensity is attenuated by the self-diffusion of water molecules. DWI provides information about the microscopic structure and organization of a biological tissue, since the extent and orientation of molecular motion is influenced by these tissue properties. The most common method to measure perfusion in the body using MRI is T1-weighted dynamic contrast enhancement (DCE-MRI). The analysis of DCE-MRI data allows determining the perfusion and permeability of a biological tissue. DWI as well as DCE-MRI are established techniques in MRI of the brain, while significantly fewer studies have been published in body imaging. In recent years, both techniques have been applied successfully in healthy bone marrow as well as for the characterization of bone marrow alterations or lesions; e.g., DWI has been used in particular for the differentiation of benign and malignant vertebral compression fractures. In this review article, firstly a short introduction to diffusion-weighted and dynamic contrast-enhanced MRI is given. Non-quantitative and quantitative approaches for the analysis of DWI and semiquantitative and quantitative approaches for the analysis of DCE-MRI are introduced. Afterwards a detailed overview of the results of both techniques in healthy bone marrow and their applications for the diagnosis of various bone-marrow pathologies, like osteoporosis, bone tumors, and vertebral compression fractures are described.

  18. Low Molecular Weight Heparin in the Treatment of Neonatal Sepsis with Diffuse effect Analysis of Intravascular Coagulation%低分子肝素治疗新生儿脓毒症合并弥散性血管内凝血的临床疗效

    Institute of Scientific and Technical Information of China (English)

    刘莲香; 王健; 李燕芳

    2015-01-01

    目的:探讨低分子肝素治疗新生儿脓毒症合并弥散性血管内凝血的临床疗效。方法收集我院2012年3月至2014年6月收治的66例脓毒症合并弥散性血管内凝血患儿资料,随机将其分为两组,均接受抗感染、对症处理等基础治疗,对照组患儿给予普通肝素治疗,观察组患儿则采取低分子肝素治疗,比较两组患者的临床疗效、不良反应及治疗前后凝血功能指标。结果观察组患儿总有效率为93.9%,对照组患儿总有效率为72.7%;观察组患儿治疗后凝血酶原时间(PT)、部分凝血酶原时间(APTT)、D-二聚体(D-D)及纤维蛋白原(FIB)均较对照组明显改善,差异均有统计学意义(均P<0.05);治疗期间均未发生明显不良反应。结论低分子肝素治疗新生儿脓毒症并弥散性血管内凝血安全有效,能明显改善患儿凝血功能。%Objective To investigate the efficacy of combined with diffuse intravascular coagulation in sepsis newborn babies with low molecular weight heparin treatment.Methods In 66 cases of sepsis in our hospital from 2012 March to 2014 June were children with diffuse intravascular coagulation as the object of study,and randomly divided into two groups,were treated with basic anti infection,symptomatic treatment and so on,in addition,the control group were given ordinary heparin therapy,the observation group with low molecular weight heparin treatment is taken,the adverse reactions were compared between the two groups before and after treatment,the clinical curative effect and the function indexes of blood coagulation.Results Observation group with total efficiency is 93.9%,control group the total effective rate was 72.7%;the observation group after treatment PT,APTT,D-D and FIB were significantly improved than control group,the difference was statistical y significant(P<0.05);during the treatment had no obvious adverse reaction.Conclusion Low molecular weight

  19. Reaction and diffusion in turbulent combustion

    Energy Technology Data Exchange (ETDEWEB)

    Pope, S.B. [Mechanical and Aerospace Engineering, Ithaca, NY (United States)

    1993-12-01

    The motivation for this project is the need to obtain a better quantitative understanding of the technologically-important phenomenon of turbulent combustion. In nearly all applications in which fuel is burned-for example, fossil-fuel power plants, furnaces, gas-turbines and internal-combustion engines-the combustion takes place in a turbulent flow. Designers continually demand more quantitative information about this phenomenon-in the form of turbulent combustion models-so that they can design equipment with increased efficiency and decreased environmental impact. For some time the PI has been developing a class of turbulent combustion models known as PDF methods. These methods have the important virtue that both convection and reaction can be treated without turbulence-modelling assumptions. However, a mixing model is required to account for the effects of molecular diffusion. Currently, the available mixing models are known to have some significant defects. The major motivation of the project is to seek a better understanding of molecular diffusion in turbulent reactive flows, and hence to develop a better mixing model.

  20. Osmosis and Diffusion Conceptual Assessment

    OpenAIRE

    Fisher, Kathleen M.; Williams, Kathy S.; Lineback, Jennifer Evarts

    2011-01-01

    Biology student mastery regarding the mechanisms of diffusion and osmosis is difficult to achieve. To monitor comprehension of these processes among students at a large public university, we developed and validated an 18-item Osmosis and Diffusion Conceptual Assessment (ODCA). This assessment includes two-tiered items, some adopted or modified from the previously published Diffusion and Osmosis Diagnostic Test (DODT) and some newly developed items. The ODCA, a validated instrument containing ...