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Sample records for dynamic diffusion bonding

  1. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  2. Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles.

    PubMed

    Mallik, Bhabani S; Semparithi, A; Chandra, Amalendu

    2008-06-12

    We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.

  3. Diffusion bonding aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, G. A.; Broughton, T.

    1988-10-01

    The use of diffusion bonding processes at Rolls-Royce for the manufacture of titanium-alloy aircraft engine components and structures is described. A liquid-phase diffusion bonding process called activated diffusion bonding has been developed for the manufacture of the hollow titanium wide chord fan blade. In addition, solid-state diffusion bonding is being used in the manufacture of hollow vane/blade airfoil constructions mainly in conjunction with superplastic forming and hot forming techniques.

  4. Diffusion bonding of superplastic aluminum alloys

    SciTech Connect

    Sunwoo, A.J.

    1993-12-01

    Ability to diffusion bond aluminum alloys, in particular superplastic aluminum alloys, will complete the technology-base that is strongly needed to enhance the use of superplastic forming (SPF) technology. Concurrent diffusion bonding (DB)-SPF is considered to be an energy-saving manufacturing process since it simplifies the production of complex components. Moreover, because of increased design flexibility, overall manufacturing cost and component weight are significantly reduced. Diffusion bonding is an attractive manufacturing option for applications where the preservation of the base metal microstructure and, in turn, mechanical properties is imperative in the bond area. The process utilizes either the solid state or transient liquid phase (TLP) bonding to produce a bond with microstructure continuity in the joint. In addition, there is no localized thermal gradient present to induce distortion or to create residual stresses in the component, thereby increasing structural integrity.

  5. [Diffusion bonding of hydroxyapatite ceramics and biometals].

    PubMed

    Yamane, F

    1990-03-01

    To improve the mechanical characteristics of hydroxyapatite (HAP) ceramics, a metal-ceramic composite formed by a solid state direct diffusion bonding system was studied. The joining treatment was carried out of a high vacuum and high temperature, for the bioactive ceramics (HAP) and the following biometals; platinum, gold-platinum alloy, titanium and titanium alloys, zirconium, niobium and aluminium alloy. The effects of the variations of thermal expansion mismatch and the interactive reactions at the interface were investigated by fractographic observation (SEM), X-ray diffraction method and EPMA analysis. On some of these joining combinations, the bonding strength had the same bonding strength as the adhesive materials. The results of interface observations showed that the bonding strength is affected by the interface reactions and the diffusion phenomena. PMID:2135505

  6. Interface water diffusion in silicon direct bonding

    NASA Astrophysics Data System (ADS)

    Tedjini, M.; Fournel, F.; Moriceau, H.; Larrey, V.; Landru, D.; Kononchuk, O.; Tardif, S.; Rieutord, F.

    2016-09-01

    The kinetics of water diffusion through the gap formed by the direct bonding of two silicon wafers is studied using two different techniques. X-ray reflectivity is able to monitor the interface density changes associated with the water front progression. The water intake is also revealed through the defect creation upon annealing, creating a rim-like pattern whose extent also gives the water diffusion law. At room temperature, the kinetics observed by either technique are consistent with the Lucas-Washburn law for diffusion through a gap width smaller than 1 nm, excluding any significant no-slip layer thickness.

  7. Hydrogen bond dynamics in bulk alcohols

    SciTech Connect

    Shinokita, Keisuke; Cunha, Ana V.; Jansen, Thomas L. C.; Pshenichnikov, Maxim S.

    2015-06-07

    Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics–quantum mechanical simulation have established many intriguing features of hydrogen bond dynamics in one of the fundamental solvents in nature, water. The next class of a hydrogen-bonded liquid—alcohols—has attracted much less attention. This is surprising given such important differences between water and alcohols as the imbalance between the number of hydrogen bonds, each molecule can accept (two) and donate (one) and the very presence of the hydrophobic group in alcohols. Here, we use polarization-resolved pump-probe and 2D infrared spectroscopy supported by extensive theoretical modeling to investigate hydrogen bond dynamics in methanol, ethanol, and isopropanol employing the OH stretching mode as a reporter. The sub-ps dynamics in alcohols are similar to those in water as they are determined by similar librational and hydrogen-bond stretch motions. However, lower density of hydrogen bond acceptors and donors in alcohols leads to the appearance of slow diffusion-controlled hydrogen bond exchange dynamics, which are essentially absent in water. We anticipate that the findings herein would have a potential impact on fundamental chemistry and biology as many processes in nature involve the interplay of hydrophobic and hydrophilic groups.

  8. Diffusion bonding of aluminium alloy, 8090

    SciTech Connect

    Sunwoo, A. )

    1994-08-15

    Ability to diffusion bond aluminum (Al) alloys, in particular superplastic aluminum alloys, will complete the technology-base that is strongly needed to enhance the use of superplastic forming (SPF) technology. Diffusion bonding (DB) is an attractive manufacturing option for applications where the preservation of the base metal microstructure and, in turn, mechanical properties is important in the bond area. As the technology moves from the laboratory to production, the DB process has to be production-feasible and cost-effective. At the Lawrence Livermore National Laboratory, the DB study of SPF Al alloys has been initiated. This paper describes the effect of surface chemistry on the DB properties of the Al alloy, 8090 (2.4Li-1.18Cu-0.57Mg-0.14Zr-Al). The integrity of the diffusion bonds was evaluated for both interlayered and bare surfaces. Two interlayer elements, copper (Cu) and zinc (Zn), were compared. Although the eutectic temperature of Al-Cu is 548 C, a thin Cu layer in contact with 8090 has been shown to lower its eutectic temperature to [approximately]521 C. In 8090, Cu is one of the primary alloying elements but has a limited solubility in Al at the bonding temperature. Zinc, on the other hand, forms a considerably lower eutectic (380 C) with Al and is highly soluble in Al. The diffusivity of Zn in Al is much faster than that of Cu, but Zn forms a more thermodynamically stable oxide. These subtle metallurgical differences will affect the transient liquid phase (TLP) formation at the interface, which will subsequently influence the bond quality.

  9. Hydrogen Bonding Slows Down Surface Diffusion of Molecular Glasses.

    PubMed

    Chen, Yinshan; Zhang, Wei; Yu, Lian

    2016-08-18

    Surface-grating decay has been measured for three organic glasses with extensive hydrogen bonding: sorbitol, maltitol, and maltose. For 1000 nm wavelength gratings, the decay occurs by viscous flow in the entire range of temperature studied, covering the viscosity range 10(5)-10(11) Pa s, whereas under the same conditions, the decay mechanism transitions from viscous flow to surface diffusion for organic glasses of similar molecular sizes but with no or limited hydrogen bonding. These results indicate that extensive hydrogen bonding slows down surface diffusion in organic glasses. This effect arises because molecules can preserve hydrogen bonding even near the surface so that the loss of nearest neighbors does not translate into a proportional decrease of the kinetic barrier for diffusion. This explanation is consistent with a strong correlation between liquid fragility and the surface enhancement of diffusion, both reporting resistance of a liquid to dynamic excitation. Slow surface diffusion is expected to hinder any processes that rely on surface transport, for example, surface crystal growth and formation of stable glasses by vapor deposition. PMID:27404465

  10. Photoinduced hydrogen-bonding dynamics.

    PubMed

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water. PMID:27491849

  11. Using Diffusion Bonding in Making Piezoelectric Actuators

    NASA Technical Reports Server (NTRS)

    Sager, Frank E.

    2003-01-01

    A technique for the fabrication of piezoelectric actuators that generate acceptably large forces and deflections at relatively low applied voltages involves the stacking and diffusion bonding of multiple thin piezoelectric layers coated with film electrodes. The present technique stands in contrast to an older technique in which the layers are bonded chemically, by use of urethane or epoxy agents. The older chemical-bonding technique entails several disadvantages, including the following: It is difficult to apply the bonding agents to the piezoelectric layers. It is difficult to position the layers accurately and without making mistakes. There is a problem of disposal of hazardous urethane and epoxy wastes. The urethane and epoxy agents are nonpiezoelectric materials. As such, they contribute to the thickness of a piezoelectric laminate without contributing to its performance; conversely, for a given total thickness, the performance of the laminate is below that of a unitary piezoelectric plate of the same thickness. The figure depicts some aspects of the fabrication of a laminated piezoelectric actuator by the present diffusion- bonding technique. First, stock sheets of the piezoelectric material are inspected and tested. Next, the hole pattern shown in the figure is punched into the sheets. Alternatively, if the piezoelectric material is not a polymer, then the holes are punched in thermoplastic films. Then both faces of each punched piezoelectric sheet or thermoplastic film are coated with a silver-ink electrode material by use of a silkscreen printer. The electrode and hole patterns are designed for minimal complexity and minimal waste of material. After a final electrical test, all the coated piezoelectric layers (or piezoelectric layers and coated thermoplastic films) are stacked in an alignment jig, which, in turn, is placed in a curved press for the diffusion-bonding process. In this process, the stack is pressed and heated at a specified curing temperature

  12. Thermal diffusion and colored energy dissipation in hydrogen bonded liquids

    NASA Astrophysics Data System (ADS)

    Dettori, Riccardo; Melis, Claudio; Ceriotti, Michele; Donadio, Davide; Colombo, Luciano

    H-bonded liquids show a manifold energy dissipation dynamics due to: strong directionality of H-bonds and complexity of their network. This affects both thermal diffusion and energy dissipation mechanisms in pump-probe spectroscopy experiments. By nonequilibrium molecular dynamics (MD) simulations we investigate such phenomena in liquid methanol. While heat transport is studied by approach-to-equilibrium MD, energy dissipation is investigated by making use of a novel Generalized Langevin Equation (GLE) colored noise thermostat, which can generate a non-equilibrium frequency-resolved dynamics by using a correlated noise. The colored thermostat can thermally excite a narrow range of vibrational modes, typically the stretching mode of the OH involved in H-bonding, leaving the other degrees of freedom at the equilibrium temperature. The energy dissipation is then observed as a function of time, by probing the excitation decay and the energy transfer to other modes. In particular, by monitoring in time the different contributions to the potential energy of the system, we evaluate how energy is transferred from the excited mode to other modes of the nearby molecules and provide understanding on the dynamics of H-bonded liquids, as resulting from current experimental investigations

  13. Diffusion Bonding of Silicon Carbide for MEMS-LDI Applications

    NASA Technical Reports Server (NTRS)

    Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, J. Douglas

    2007-01-01

    A robust joining approach is critically needed for a Micro-Electro-Mechanical Systems-Lean Direct Injector (MEMS-LDI) application which requires leak free joints with high temperature mechanical capability. Diffusion bonding is well suited for the MEMS-LDI application. Diffusion bonds were fabricated using titanium interlayers between silicon carbide substrates during hot pressing. The interlayers consisted of either alloyed titanium foil or physically vapor deposited (PVD) titanium coatings. Microscopy shows that well adhered, crack free diffusion bonds are formed under optimal conditions. Under less than optimal conditions, microcracks are present in the bond layer due to the formation of intermetallic phases. Electron microprobe analysis was used to identify the reaction formed phases in the diffusion bond. Various compatibility issues among the phases in the interlayer and substrate are discussed. Also, the effects of temperature, pressure, time, silicon carbide substrate type, and type of titanium interlayer and thickness on the microstructure and composition of joints are discussed.

  14. Diffusion Bonding of Silicon Carbide Ceramics using Titanium Interlayers

    NASA Technical Reports Server (NTRS)

    Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

    2006-01-01

    Robust joining approaches for silicon carbide ceramics are critically needed to fabricate leak free joints with high temperature mechanical capability. In this study, titanium foils and physical vapor deposited (PVD) titanium coatings were used to form diffusion bonds between SiC ceramics using hot pressing. Silicon carbide substrate materials used for bonding include sintered SiC and two types of CVD SiC. Microscopy results show the formation of well adhered diffusion bonds. The bond strengths as determined from pull tests are on the order of several ksi, which is much higher than required for a proposed application. Microprobe results show the distribution of silicon, carbon, titanium, and other minor elements across the diffusion bond. Compositions of several phases formed in the joint region were identified. Potential issues of material compatibility and optimal bond formation will also be discussed.

  15. Application of diffusion bonding to electronic interconnection of flatpack leads

    NASA Technical Reports Server (NTRS)

    Korb, R. W.; Lardenoit, V. F.

    1973-01-01

    Diffusion-bonded joints between gold-plated Kovar leads and indium-plated copper circuit pads offer some advantages for electronic circuit packaging. Test results show that consistent high strength bonds stronger than the copper circuit foil are achieved by parallel-gap bonding at relatively low power settings. The bonds are basically formed by the alloying of the gold, indium and copper at the bond interface. Other low melting metals such as tin can also be used; however, tin does not offer the ease of bonding that results in consistent separation of the copper foil during pull testing. The investigation was conducted in three parts consisting of: (1) an evaluation of the physical strength of resulting bonds at ambient and elevated temperature, (2) a metallurgical analysis of bonds using scanning electron microscopy and nondispersive X-ray analysis, and (3) evaluation and development of various schemes for multiple lead flatpack bonding.

  16. Diffusion-bonded-stacked gallium arsenide for mid- infrared generation

    NASA Astrophysics Data System (ADS)

    Gordon, Leslie Ann

    One of the limiting factors in mid-infrared nonlinear generation is the availability of adequate crystals. Current mid-infrared nonlinear crystals suffer from poor thermal properties and/or high absorption, minimizing their usefulness for high-peak and high-average-power conversion. While new materials are continually being explored, more than 15 years may be necessary to develop and test a new crystal, with no guarantee of final success. A new nonlinear material has been synthesized, combining the knowledge from two existing fields: quasi- phasematching (QPM) and diffusion bonding. QPM allows the use of well known semiconductors which are not birefringent, but which have good thermal properties, high damage thresholds, and high nonlinear coefficients. Diffusion bonding provides a robust monolithic structure. Prior to this work, bonded semiconductor structures were single interface, with little attention to optical losses. During this work, techniques were developed to precisely thin and clean the wafers in preparation for bonding. Two generations of bonding furnaces were designed and built to provide uniform temperatures and pressures, fully adjustable and repeatable bonding parameters, and multiple-interface capabilities. GaAs wafers were stacked with alternating crystal orientation, and annealed under compression to diffusion bond the interfaces. The quasi-phasematching was controlled by the wafer thickness. Diffusion-bonded stacks of 2 to 50-layers were bonded, and demonstrated close to theoretical conversion efficiency of second- harmonic generation of CO2 laser radiation. The quality of the bonds was affected by surface cleanliness and contact uniformity of the interfaces. Conversion efficiency was limited by fabrication techniques, chiefly accurate wafer thinning and process- induced bulk losses. Diffusion-bonded-stacked structures can be optimized for all types of nonlinear devices. This technology can be expanded to other well known semiconductors, and is

  17. Joining of Silicon Carbide: Diffusion Bond Optimization and Characterization

    NASA Technical Reports Server (NTRS)

    Halbig, Michael C.; Singh, Mrityunjay

    2008-01-01

    Joining and integration methods are critically needed as enabling technologies for the full utilization of advanced ceramic components in aerospace and aeronautics applications. One such application is a lean direct injector for a turbine engine to achieve low NOx emissions. In the application, several SiC substrates with different hole patterns to form fuel and combustion air channels are bonded to form the injector. Diffusion bonding is a joining approach that offers uniform bonds with high temperature capability, chemical stability, and high strength. Diffusion bonding was investigated with the aid of titanium foils and coatings as the interlayer between SiC substrates to aid bonding. The influence of such variables as interlayer type, interlayer thickness, substrate finish, and processing time were investigated. Optical microscopy, scanning electron microscopy, and electron microprobe analysis were used to characterize the bonds and to identify the reaction formed phases.

  18. Fabrication and Characterization of Diffusion Bonds for Silicon Carbide

    NASA Technical Reports Server (NTRS)

    Halbig, Michael; Singh, Mrityunjay; Martin, Richard E.; Cosgriff, Laura M.

    2007-01-01

    Diffusion bonds of silicon carbide (SiC) were fabricated using several different types of titanium (Ti) based interlayers between the SiC substrates. The interlayers were an alloyed Ti foil, a pure Ti foil, and a physically vapor deposited (PVD) Ti coating. Microscopy was conducted to evaluate the cross-sections of the resulting bonds. Microprobe analysis identified reaction formed phases in the diffusion bonded region. Uniform and well adhered bonds were formed between the SiC substrates. In the case where the alloyed Ti foil or a thick Ti coating (i.e. 20 micron) was used as the interlayer, microcracks and several phases were present in the diffusion bonds. When a thinner interlayer was used (i.e. 10 micron PVD Ti), no microcracks were observed and only two reaction formed phases were present. The two phases were preferred and fully reacted phases that did not introduce thermal stresses or microcracks during the cool-down stage after processing. Diffusion bonded samples were evaluated with the non-destructive evaluation (NDE) methods of pulsed thermography and immersion ultrasonic testing. Joined SiC substrates that were fully bonded and that had simulated bond flaws in the interlayer were also evaluated using immersion ultrasound. Pull testing was conducted on the bonds to determine the tensile strength. To demonstrate the joining approach for a complex multilayered component for a low NOx injector application, the diffusion bonding approach was used to join three 4" diameter SiC discs that contained complex fuel and air flow channels.

  19. Diffusion bonding of titanium-titanium aluminide-alumina sandwich

    SciTech Connect

    Wickman, H.A.; Chin, E.S.C.; Biederman, R.R.

    1995-12-31

    Diffusion bonding of a metallic-intermetallic-ceramic sandwich is of interest for potential armor applications. Low cost titanium, titanium diboride reinforced titanium aluminide (Ti-48at.%Al), and aluminum oxide are diffusion bonded in a vacuum furnace between 1,000 C and 1,400 C. Metallographic examination of the prior bonding interface showed excellent metallurgical coupling between the Ti-48at.%Al composite and the low cost Ti. A series of microstructures representative of phases consistent with a hypothetical Ti-Al-B phase diagram is visible. The alumina-Ti-48at.%Al interfacial bond is achieved through penetration of titanium-aluminum phases into the existing alumina porosity. A detailed microstructural analysis identifying mechanisms of interfacial bonding will be presented for each interfacial zone.

  20. Fast Through-Bond Diffusion of Nitrogen in Silicon

    SciTech Connect

    SCHULTZ,PETER A.; NELSON,JEFFREY S.

    2000-07-12

    The authors report first principles total energy calculations of interaction of nitrogen in silicon with silicon self-interstitials. Substitutional nitrogen captures a silicon interstitial with 3.5 eV binding energy forming a {l_angle}001{r_angle} split interstitial ground state geometry, with the nitrogen forming three bonds. The low energy migration path is through a bond bridge state having two bonds. Fast diffusion of nitrogen occurs through a pure interstitialcy mechanism; the nitrogen never has less than two bonds. Near-zero formation energy of the nitrogen interstitialcy with respect to the substitutional rationalizes the low solubility of substitutional nitrogen in silicon.

  1. Diffusion bonding of the oxide dispersion strengthened steel PM2000

    NASA Astrophysics Data System (ADS)

    Sittel, Wiebke; Basuki, Widodo W.; Aktaa, Jarir

    2013-11-01

    Ferritic oxide dispersion strengthened (ODS) steels are well suited as structural materials, e.g. for claddings in fission reactors and for plasma facing components in fusion power plants due to their high mechanical and oxidation stability at high temperatures and their high irradiation resistance. PM2000 is an iron based ODS ferritic steel with homogeneously distributed nanometric yttria particles. Melting joining techniques are not suitable for such ODS materials because of the precipitation and agglomeration of the oxide particles and hence the loss of their strengthening effect. Solid state diffusion bonding is thus chosen to join PM2000 and is investigated in this work with a focus on oxide particles. The diffusion bonding process is aided by the computational modeling, including the influence of the ODS particles. For modeling the microstructure stability and the creep behavior of PM2000 at various, diffusion bonding relevant temperatures (50-80% Tm) are investigated. Particle distribution (TEM), strength (tensile test) and toughness (Charpy impact test) obtained at temperatures relevant for bonding serve as input for the prediction of optimal diffusion bonding parameters. The optimally bonded specimens show comparable strength and toughness relative to the base material.

  2. Interface formation and strength of Be/DSCu diffusion bonding

    NASA Astrophysics Data System (ADS)

    Makino, T.; Iwadachi, T.

    1998-10-01

    Beryllium has been proposed to be used as a plasma facing material of the first wall for ITER, and will be bonded by HIP process to Dispersion Strengthened Copper (DSCu). Be/DSCu diffusion bonding tests in the range of temperature from 600°C to 850°C by hot pressing techniques have been conducted to identify the effect of bonding temperature and time on interface formation and joint strength. The bonded Be/DSCu joints were evaluated by microstructural analysis of the interface and shear strength tests at room temperature. The diffusion layer of directly bonded Be/DSCu joints and the joints with Be-Cu interlayer consisted of Be 2Cu( δ) phase on the Be side and Cu + BeCu( γ) phase on the DSCu side. Cu + BeCu( γ) phase generated remarkably fast at 800-850°C. The thickness of the diffusion layer was linear to a square root of bonding time. Shear strength of the joints bonded at 650-750°C are all around 200 MPa. Shear strength is dominated by the formation of the layer of Be 2Cu( δ) phase on the Be side.

  3. Interface nanochemistry effects on stainless steel diffusion bonding

    NASA Astrophysics Data System (ADS)

    Cox, M. J.; Carpenter, R. W.; Kim, M. J.

    2002-02-01

    The diffusion-bonding behavior of single-phase austenitic stainless steel depends strongly on the chemistry of the surfaces to be bounded. We found that very smooth (0.5 nm root-mean-square (RMS) roughness), mechanically polished and lapped substrates would bond completely in ultrahigh vacuum (UHV) in 1 hour at 1000 °C under 3.5 MPa uniaxial pressure, if the native oxide on the substrates was removed by ion-beam cleaning, as shown by in-situ Auger analysis. No voids were observed in these bonded interfaces by transmission electron microscopy (TEM), and the strength was equal to that of the unbounded bare material. No bond formed between the substrates if in-situ ion cleaning was not used. The rougher cleaned substrates partially bonded, indicating that roughness, as well as native oxides, reduced the bonding kinetics.

  4. Functional systems with orthogonal dynamic covalent bonds.

    PubMed

    Wilson, Adam; Gasparini, Giulio; Matile, Stefan

    2014-03-21

    This review summarizes the use of orthogonal dynamic covalent bonds to build functional systems. Dynamic covalent bonds are unique because of their dual nature. They can be as labile as non-covalent interactions or as permanent as covalent bonds, depending on conditions. Examples from nature, reaching from the role of disulfides in protein folding to thioester exchange in polyketide biosynthesis, indicate how dynamic covalent bonds are best used in functional systems. Several synthetic functional systems that employ a single type of dynamic covalent bonds have been reported. Considering that most functional systems make simultaneous use of several types of non-covalent interactions together, one would expect the literature to contain many examples in which different types of dynamic covalent bonds are similarly used in tandem. However, the incorporation of orthogonal dynamic covalent bonds into functional systems is a surprisingly rare and recent development. This review summarizes the available material comprehensively, covering a remarkably diverse collection of functions. However, probably more revealing than the specific functions addressed is that the questions asked are consistently quite unusual, very demanding and highly original, focusing on molecular systems that can self-sort, self-heal, adapt, exchange, replicate, transcribe, or even walk and "think" (logic gates). This focus on adventurous chemistry off the beaten track supports the promise that with orthogonal dynamic covalent bonds we can ask questions that otherwise cannot be asked. The broad range of functions and concepts covered should appeal to the supramolecular organic chemist but also to the broader community. PMID:24287608

  5. Superplastically formed diffusion bonded metallic structure

    NASA Technical Reports Server (NTRS)

    Ko, W. L. (Inventor)

    1981-01-01

    A metallic sandwich structure particularly suited for use in aerospace industries comprising a base plate, a cover plate, and an orthogonally corrugated core is described. A pair of core plates formed of a superplastic alloy are interposed between the base plate and the cover plate and bonded. Each of the core plates is characterized by a plurality of protrusions comprising square-based, truncated pyramids uniformly aligned along orthogonally related axes perpendicularly bisecting the legs of the bases of the pyramids and alternately inverted along orthogonally related planes diagonally bisecting the pyramids, whereby an orthogonally corrugated core is provided.

  6. Diffusion bonding of commercially pure Ni using Cu interlayer

    SciTech Connect

    Rahman, A.H.M.E. Cavalli, M.N.

    2012-07-15

    The concentration dependence of diffusivity in a multi-component diffusion system makes it complicated to predict the concentration profiles of diffusing species. This so called chemical diffusivity can be expressed as a function of thermodynamic and kinetic data. DICTRA software can calculate the concentration profiles using appropriate mobility and thermodynamic data. It can also optimize the diffusivity data using experimental diffusivity data. Then the optimized diffusivity data is stored as mobility data which is a linear function of temperature. In this work, diffusion bonding of commercially pure Ni using Cu interlayers is reported. The mobility parameters of Ni-Cu alloy binary systems were optimized using DICTRA/Thermocalc software from the available self-, tracer and chemical diffusion coefficients. The optimized mobility parameters were used to simulate concentration profiles of Ni-Cu diffusion joints using DICTRA/Thermocalc software. The calculated and experimental concentration profiles agreed well at 1100 Degree-Sign C. Agreement between the simulated and experimental profiles was less good at 1050 Degree-Sign C due to the grain boundary contribution to the overall diffusion. - Highlights: Black-Right-Pointing-Pointer The concentration profiles of Cu in Ni-Cu diffusion joints are modeled. Black-Right-Pointing-Pointer Interdiffusion coefficients in Ni-Cu system are optimized. Black-Right-Pointing-Pointer Optimized interdiffusion coefficients are expressed as mobility parameters. Black-Right-Pointing-Pointer Simulated profiles are comparable with experimental profiles.

  7. Evaluation of ultrasonic signals from diffusion and eutectic bond interfaces

    NASA Astrophysics Data System (ADS)

    Brown, C. M.

    1980-12-01

    A research program is in progress at Rocky Flats to determine correlations between ultrasonic signal content and diffusion or eutectic bond joint condition, and to develop a computer-controlled scanning, data acquisition and analysis system which utilizes these correlations and waveform analysis techniques. The initial efforts to determine effective ultrasonic waveform parameters to characterize the strength of bond interfaces is complete. A development version of a computer-controlled, automated scanning and data acquisition system is in operation.

  8. A local view of bonding and diffusion at metal surfaces

    SciTech Connect

    Feibelman, P.J.

    1996-09-01

    First-principles density functional calculations and corresponding experimental results underline the importance of basic chemical concepts, such as coordination, valence saturation and promotion-hybridization energetics, in understanding bonding and diffusion of atoms at and on metal surfaces. Several examples are reviewed, including outer-layer relaxations of clean hcp(0001) surfaces, liquid-metal-embrittlement energetics, separation energies of metal-adatom dimers, concerted substitutional self-diffusion on fcc(001) surfaces, and adsorption and diffusion barrier sites for adatoms near steps.

  9. Silver plating ensures reliable diffusion bonding of dissimilar metals

    NASA Technical Reports Server (NTRS)

    1967-01-01

    Dissimilar metals are reliably joined by diffusion bonding when the surfaces are electroplated with silver. The process involves cleaning and etching, anodization, silver striking, and silver plating with a conventional plating bath. It minimizes the formation of detrimental intermetallic phases and provides greater tolerance of processing parameters.

  10. Phase transformation diffusion bonding of titanium alloy with stainless steel

    SciTech Connect

    Qin, B. . E-mail: jjj-jenny@163.com; Sheng, G.M.; Huang, J.W.; Zhou, B.; Qiu, S.Y.; Li, C.

    2006-01-15

    Phase transformation diffusion bonding between a titanium alloy (TA17) and an austenitic stainless steel (0Cr18Ni9Ti) has been carried out in vacuum. Relationships between the bonding parameters and the tensile strength of the joints were investigated, and the optimum bond parameters were obtained: maximum cyclic temperature = 890 deg. C, minimum cyclic temperature = 800 deg. C, number of cycles = 10, bonding pressure = 5 MPa and heating rate = 30 deg. C/s. The maximum tensile strength of the joint was 307 MPa. The reaction products and the interface structure of the joints were investigated by light optical and scanning electron microscopy, energy dispersive spectroscopy and X-ray diffraction. The study indicated the existence of {sigma} phase, Fe{sub 2}Ti, Fe-Ti intermetallic and {beta}-Ti in the reaction zone. The presence of the brittle Fe-Ti intermetallic phase lowered both the strength and the ductility of the phase transformation diffusion-bonded joint significantly.

  11. Dynamic mismatch between bonded dissimilar materials

    NASA Astrophysics Data System (ADS)

    Li, Chou H.

    1993-06-01

    In the bonding of dissimilar materials, the coefficient of thermal expansion (CTE) relates to only the static or thermal equilibrium case, and does not represent most actual conditions (i.e., the service and processing temperatures are usually changing rather than fixed). This article outlines an approach that computes the effective, or dynamic, CTE mismatch. This dynamic mismatch varies with the bonded material shapes and sizes, surface characteristics, and heating or cooling conditions and times and may be several times greater than the corresponding static CTE mismatch. Unrelieved, the computed transient or dynamic thermal-strain mismatch may exceed the yield point of the metal, while the transient or dynamic mismatch stress often exceeds the flexural or compressive strength of the ceramic. Understanding transient mismatch phenomena has led to new, unmatched metal-ceramic joints that withstand repeated, rapid thermal shocks and subsequent severe mechanical shocks. The final forced fractures occur outside the bonded regions, indicating defect-free joints.

  12. Dynamic mismatch between bonded dissimilar materials

    NASA Astrophysics Data System (ADS)

    Li, Chou H.

    1993-06-01

    In the bonding of dissimilar materials, the coefficient of thermal expansion (CTE) relates to only the static or thermal equilibrium case, and does not represent most actual conditions (i.e., the service and processing temperatures are usually changing rather than fixed). This article outlines an approach that computes the effective, or dynamic, CTE mismatch. This dynamic mismatch varies with the bonded material shapes and sizes, surface characteristics, and heating or cooling conditions and times and may be several times greater than the corresponding static CTE mismatch. Unrelieved, the computed transient or dynamic thermal-strain mismatch may exceed the yield point of the metal, while the transient or dynamic mismatch stress often exceeds the flexural or compressive strength of the ceramic. Understanding transient mismatch phenomena has led to new, unmatched metal-ceramic joints that withstand repeated, rapid thermal shocks and subsequent severe mechanical shocks. The final forced fractures occur outside the bonded regions, indicating defect free joints.

  13. Dynamic strength of molecular adhesion bonds.

    PubMed Central

    Evans, E; Ritchie, K

    1997-01-01

    In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale

  14. Morphology, topography, and hardness of diffusion bonded sialon to AISI 420 at different bonding time

    NASA Astrophysics Data System (ADS)

    Ibrahim, Nor Nurulhuda Md.; Hussain, Patthi; Awang, Mokhtar

    2015-07-01

    Sialon and AISI 420 martensitic stainless steel were diffusion bonded in order to study the effect of bonding time on reaction layer's growth. Joining of these materials was conducted at 1200°C under a uniaxial pressure of 17 MPa in a vacuum ranging from 5.0 to 8.0×10-6 Torr with bonding time varied for 0.5, 2, and 3 h. Thicker reaction layer was formed in longer bonded sample since the elements from sialon could diffuse further into the steel. Sialon retained its microstructure but it was affected at the initial contact with the steel to form the new interface layer. Diffusion layer grew toward the steel and it was segregated with the parent steel as a result of the difference in properties between these regions. The segregation formed a stream-like structure and its depth decreased when the bonding time was increased. The microstructure of the steel transformed into large grain size with precipitates. Prolonging the bonding time produced more precipitates in the steel and reduced the steel thickness as well. Interdiffusions of elements occurred between the joined materials and the concentrations were decreasing toward the steel and vice versa. Silicon easily diffused into the steel because it possessed lower ionization potential compared to nitrogen. Formation of silicide and other compounds such as carbides were detected in the interface layer and steel grain boundary, respectively. These compounds were harmful due to silicide brittleness and precipitation of carbides in the grain boundary might cause intergranular corrosion cracking. Sialon retained its hardness but it dropped very low at the interface layer. The absence of crack at the joint in all samples could be contributed from the ductility characteristic of the reaction layer which compensated the residual stress that was formed upon the cooling process.

  15. Joining of Silicon Carbide Through the Diffusion Bonding Approach

    NASA Technical Reports Server (NTRS)

    Halbig, Michael .; Singh, Mrityunjay

    2009-01-01

    In order for ceramics to be fully utilized as components for high-temperature and structural applications, joining and integration methods are needed. Such methods will allow for the fabrication the complex shapes and also allow for insertion of the ceramic component into a system that may have different adjacent materials. Monolithic silicon carbide (SiC) is a ceramic material of focus due to its high temperature strength and stability. Titanium foils were used as an interlayer to form diffusion bonds between chemical vapor deposited (CVD) SiC ceramics with the aid of hot pressing. The influence of such variables as interlayer thickness and processing time were investigated to see which conditions contributed to bonds that were well adhered and crack free. Optical microscopy, scanning electron microscopy, and electron microprobe analysis were used to characterize the bonds and to identify the reaction formed phases.

  16. Dynamic heterogeneity in hydrogen-bonded polymers

    SciTech Connect

    Muresan, Adrian S.; Jeu, Wim H. de; Dubbeldam, Johan L. A.; Schoot, Paul van der; Kautz, Holger; Sijbesma, Rint P.; Monkenbusch, Michael

    2006-09-15

    We report on neutron spin echo experiments on hydrogen-bonded polymers and compare the experimentally found dynamical structure factor with theoretical predictions. Surprisingly, we find that in the melt phase the expected scaling of the Rouse dynamics is not satisfied. We propose an explanation based upon the large spatial volume occupied by the connecting groups. When the effects of these bulky groups on the local friction are taken into account, the usual scaling behavior is restored.

  17. Modeling the Hydrogen Bond within Molecular Dynamics

    ERIC Educational Resources Information Center

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  18. Mo/Ti Diffusion Bonding for Making Thermoelectric Devices

    NASA Technical Reports Server (NTRS)

    Sakamoto, Jeffrey; Kisor, Adam; Caillat, Thierry; Lara, Liana; Ravi, Vilupanur; Firdosy, Samad; Fleuiral, Jean-Pierre

    2007-01-01

    An all-solid-state diffusion bonding process that exploits the eutectoid reaction between molybdenum and titanium has been developed for use in fabricating thermoelectric devices based on skutterudite compounds. In essence, the process is one of heating a flat piece of pure titanium in contact with a flat piece of pure molybdenum to a temperature of about 700 C while pushing the pieces together with a slight pressure [a few psi (of the order of 10 kPa)]. The process exploits the energy of mixing of these two metals to form a strong bond between them. These two metals were selected partly because the bonds formed between them are free of brittle intermetallic phases and are mechanically and chemically stable at high temperatures. The process is a solution of the problem of bonding hot-side metallic interconnections (denoted hot shoes in thermoelectric jargon) to titanium-terminated skutterudite n and p legs during the course of fabrication of a unicouple, which is the basic unit cell of a thermoelectric device (see figure). The hot-side operating temperature required for a skutterudite thermoelectric device is 700 C. This temperature precludes the use of brazing to attach the hot shoe; because brazing compounds melt at lower temperatures, the hot shoe would become detached during operation. Moreover, the decomposition temperature of one of the skutterudite compounds is 762 C; this places an upper limit on the temperature used in bonding the hot shoe. Molybdenum was selected as the interconnection metal because the eutectoid reaction between it and the titanium at the ends of the p and n legs has characteristics that are well suited for this application. In addition to being suitable for use in the present bonding process, molybdenum has high electrical and thermal conductivity and excellent thermal stability - characteristics that are desired for hot shoes of thermoelectric devices. The process takes advantage of the chemical potential energy of mixing between

  19. Elastic constants for superplastically formed/diffusion-bonded sandwich structures

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1979-01-01

    Formulae and the associated graphs are presented for contrasting the effective elastic constants for a superplastically formed/diffusion-bonded (SPF/DB) corrugated sandwich core and a honeycomb sandwich core. The results used in the comparison of the structural properties of the two types of sandwich cores are under conditions of equal sandwich density. It was found that the stiffness in the thickness direction of the optimum SPF/DB corrugated core (i.e., triangular truss core) was lower than that of the honeycomb core, and that the former had higher transverse shear stiffness than the latter.

  20. Replicator dynamics with diffusion on multiplex networks

    NASA Astrophysics Data System (ADS)

    Requejo, R. J.; Díaz-Guilera, A.

    2016-08-01

    In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies.

  1. Replicator dynamics with diffusion on multiplex networks.

    PubMed

    Requejo, R J; Díaz-Guilera, A

    2016-08-01

    In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies. PMID:27627311

  2. The diffusion bonding of silicon carbide and boron carbide using refractory metals

    SciTech Connect

    Cockeram, B.V.

    1999-10-01

    Joining is an enabling technology for the application of structural ceramics at high temperatures. Metal foil diffusion bonding is a simple process for joining silicon carbide or boron carbide by solid-state, diffusive conversion of the metal foil into carbide and silicide compounds that produce bonding. Metal diffusion bonding trials were performed using thin foils (5 {micro}m to 100 {micro}m) of refractory metals (niobium, titanium, tungsten, and molybdenum) with plates of silicon carbide (both {alpha}-SiC and {beta}-SiC) or boron carbide that were lapped flat prior to bonding. The influence of bonding temperature, bonding pressure, and foil thickness on bond quality was determined from metallographic inspection of the bonds. The microstructure and phases in the joint region of the diffusion bonds were evaluated using SEM, microprobe, and AES analysis. The use of molybdenum foil appeared to result in the highest quality bond of the metal foils evaluated for the diffusion bonding of silicon carbide and boron carbide. Bonding pressure appeared to have little influence on bond quality. The use of a thinner metal foil improved the bond quality. The microstructure of the bond region produced with either the {alpha}-SiC and {beta}-SiC polytypes were similar.

  3. Dynamics and Diffusion Mechanism of Low-Density Liquid Silicon.

    PubMed

    Shen, B; Wang, Z Y; Dong, F; Guo, Y R; Zhang, R J; Zheng, Y X; Wang, S Y; Wang, C Z; Ho, K M; Chen, L Y

    2015-11-25

    A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid-liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using the classical Stillinger-Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid-liquid phase transition such as carbon and germanium.

  4. Dynamics and diffusion mechanism of low-density liquid silicon

    DOE PAGESBeta

    Shen, B.; Wang, Z. Y.; Dong, F.; Guo, Y. R.; Zhang, R. J.; Zheng, Y. X.; Wang, S. Y.; Wang, C. Z.; Ho, K. M.; Chen, L. Y.

    2015-11-05

    A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid–liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using themore » classical Stillinger–Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Here, our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid–liquid phase transition such as carbon and germanium.« less

  5. Dynamics and diffusion mechanism of low-density liquid silicon

    SciTech Connect

    Shen, B.; Wang, Z. Y.; Dong, F.; Guo, Y. R.; Zhang, R. J.; Zheng, Y. X.; Wang, S. Y.; Wang, C. Z.; Ho, K. M.; Chen, L. Y.

    2015-11-05

    A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid–liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using the classical Stillinger–Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Here, our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid–liquid phase transition such as carbon and germanium.

  6. Statics and dynamics of magnetocapillary bonds

    NASA Astrophysics Data System (ADS)

    Lagubeau, Guillaume; Grosjean, Galien; Darras, Alexis; Lumay, Geoffroy; Hubert, Maxime; Vandewalle, Nicolas

    2016-05-01

    When ferromagnetic particles are suspended at an interface under magnetic fields, dipole-dipole interactions compete with capillary attraction. This combination of forces has recently given promising results towards controllable self-assemblies as well as low-Reynolds-number swimming systems. The elementary unit of these assemblies is a pair of particles. Although equilibrium properties of this interaction are well described, the dynamics remain unclear. In this paper, the properties of magnetocapillary bonds are determined by probing them with magnetic perturbations. Two deformation modes are evidenced and discussed. These modes exhibit resonances whose frequencies can be detuned to generate nonreciprocal motion. A model is proposed that can become the basis for elaborate collective behaviors.

  7. Density, temperature, and bond-length dependence of dynamic friction on a molecular bond

    NASA Astrophysics Data System (ADS)

    Vergeles, Maxim; Szamel, Grzegorz

    1999-09-01

    We apply the theoretical formalism developed by us earlier [M. Vergeles and G. Szamel, J. Chem. Phys. 110, 6827 (1999)] to study density, temperature, and bond-length dependence of the dynamic friction on a molecular bond. We show that the theory reproduces all the trends seen in molecular dynamics (MD) simulations. The theoretical predictions agree reasonably well with the results of MD simulations except for very low densities or very short bond lengths.

  8. CO2 diffusion in champagne wines: a molecular dynamics study.

    PubMed

    Perret, Alexandre; Bonhommeau, David A; Liger-Belair, Gérard; Cours, Thibaud; Alijah, Alexander

    2014-02-20

    Although diffusion is considered as the main physical process responsible for the nucleation and growth of carbon dioxide bubbles in sparkling beverages, the role of each type of molecule in the diffusion process remains unclear. In the present study, we have used the TIP5P and SPC/E water models to perform force field molecular dynamics simulations of CO2 molecules in water and in a water/ethanol mixture respecting Champagne wine proportions. CO2 diffusion coefficients were computed by applying the generalized Fick's law for the determination of multicomponent diffusion coefficients, a law that simplifies to the standard Fick's law in the case of champagnes. The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 × 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. The remarkable agreement between the theoretical CO2 diffusion coefficients obtained within the TIP5P water/ethanol mixture and the experimental data specific to Champagne wines makes us infer that the diffusion coefficient in these emblematic hydroalcoholic sparkling beverages is expected to remain roughly constant whathever their proportions in sugars, glycerol, or peptides.

  9. The application of diffusion bonding in the manufacture of aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, J. A.

    Rolls-Royce has developed and optimized diffusion bonding processes for the manufacture of advanced titanium alloy aeroengine structures and components. Both categories of the joining technique - 'liquid-phase' and 'solid-state' - are being applied in the production of both static fabrications and complex rotating parts. In order to utilize diffusion bonding processes in a production environment, the process parameters which contribute to consistent formation of joints of the required strength have been critically examined. Process variables include temperature, pressure, time, surface roughness and, in the case of liquid-phase diffusion bonding, interlayer composition, density and thickness. Mechanical testing (tensile, impact and fatigue) complemented by metallography has predominantly been used to identify the permitted variations in the processes for the realistic and economical production manufacture of high quality lightweight aeroengine fabrications. The development of a high integrity bond via optimized diffusion bonding processes has been fundamental to the development of Rolls-Royce's unique wide chord fan design concept.

  10. Pressure Dependence of Hydrogen-Bond Dynamics in Liquid Water Probed by Ultrafast Infrared Spectroscopy.

    PubMed

    Lapini, Andrea; Pagliai, Marco; Fanetti, Samuele; Citroni, Margherita; Scandolo, Sandro; Bini, Roberto; Righini, Roberto

    2016-09-15

    Clarifying the structure/dynamics relation of water hydrogen-bond network has been the aim of extensive research over many decades. By joining anvil cell high-pressure technology, femtosecond 2D infrared spectroscopy, and molecular dynamics simulations, we studied, for the first time, the spectral diffusion of the stretching frequency of an HOD impurity in liquid water as a function of pressure. Our experimental and simulation results concordantly demonstrate that the rate of spectral diffusion is almost insensitive to the applied pressure. This behavior is in contrast with the previously reported pressure-induced speed up of the orientational dynamics, which can be rationalized in terms of large angular jumps involving sudden switching between two hydrogen-bonded configurations. The different trend of the spectral diffusion can be, instead, inferred considering that the first solvation shell preserves the tetrahedral structure with pressure and the OD stretching frequency is only slight perturbed. PMID:27560355

  11. Developing A Laser Shockwave Model For Characterizing Diffusion Bonded Interfaces

    SciTech Connect

    James A. Smith; Jeffrey M. Lacy; Barry H. Rabin

    2014-07-01

    12. Other advances in QNDE and related topics: Preferred Session Laser-ultrasonics Developing A Laser Shockwave Model For Characterizing Diffusion Bonded Interfaces 41st Annual Review of Progress in Quantitative Nondestructive Evaluation Conference QNDE Conference July 20-25, 2014 Boise Centre 850 West Front Street Boise, Idaho 83702 James A. Smith, Jeffrey M. Lacy, Barry H. Rabin, Idaho National Laboratory, Idaho Falls, ID ABSTRACT: The US National Nuclear Security Agency has a Global Threat Reduction Initiative (GTRI) which is assigned with reducing the worldwide use of high-enriched uranium (HEU). A salient component of that initiative is the conversion of research reactors from HEU to low enriched uranium (LEU) fuels. An innovative fuel is being developed to replace HEU. The new LEU fuel is based on a monolithic fuel made from a U-Mo alloy foil encapsulated in Al-6061 cladding. In order to complete the fuel qualification process, the laser shock technique is being developed to characterize the clad-clad and fuel-clad interface strengths in fresh and irradiated fuel plates. The Laser Shockwave Technique (LST) is being investigated to characterize interface strength in fuel plates. LST is a non-contact method that uses lasers for the generation and detection of large amplitude acoustic waves to characterize interfaces in nuclear fuel plates. However the deposition of laser energy into the containment layer on specimen’s surface is intractably complex. The shock wave energy is inferred from the velocity on the backside and the depth of the impression left on the surface from the high pressure plasma pulse created by the shock laser. To help quantify the stresses and strengths at the interface, a finite element model is being developed and validated by comparing numerical and experimental results for back face velocities and front face depressions with experimental results. This paper will report on initial efforts to develop a finite element model for laser

  12. Si-H bond dynamics in hydrogenated amorphous silicon

    NASA Astrophysics Data System (ADS)

    Scharff, R. Jason; McGrane, Shawn D.

    2007-08-01

    The ultrafast structural dynamics of the Si-H bond in the rigid solvent environment of an amorphous silicon thin film is investigated using two-dimensional infrared four-wave mixing techniques. The two-dimensional infrared (2DIR) vibrational correlation spectrum resolves the homogeneous line shapes ( <2.5cm-1 linewidth) of the 0→1 and 1→2 vibrational transitions within the extensively inhomogeneously broadened ( 78cm-1 linewidth) Si-H vibrational band. There is no spectral diffusion evident in correlation spectra obtained at 0.2, 1, and 4ps waiting times. The Si-H stretching mode anharmonic shift is determined to be 84cm-1 and decreases slightly with vibrational frequency. The 1→2 linewidth increases with vibrational frequency. Frequency dependent vibrational population times measured by transient grating spectroscopy are also reported. The narrow homogeneous line shape, large inhomogeneous broadening, and lack of spectral diffusion reported here present the ideal backdrop for using a 2DIR probe following electronic pumping to measure the transient structural dynamics implicated in the Staebler-Wronski degradation [Appl. Phys. Lett. 31, 292 (1977)] in a-Si:H based solar cells.

  13. A Batch Wafer Scale LIGA Assembly and Packaging Technique vai Diffusion Bonding

    SciTech Connect

    Christenson, T.R.; Schmale, D.T.

    1999-01-27

    A technique using diffusion bonding (or solid-state welding) has been used to achieve batch fabrication of two- level nickel LIGA structures. Interlayer alignment accuracy of less than 1 micron is achieved using press-fit gauge pins. A mini-scale torsion tester was built to measure the diffusion bond strength of LIGA formed specimens that has shown successful bonding at temperatures of 450"C at 7 ksi pressure with bond strength greater than 100 Mpa. Extensions to this basic process to allow for additional layers and thereby more complex assemblies as well as commensurate packaging are discussed.

  14. Dynamics of Hydrogen-Bonded Supramolecular Polymers

    NASA Astrophysics Data System (ADS)

    Buhler, Eric; Candau, Jean; Kolomiets, Elena; Lehn, Jean-Marie

    2010-03-01

    Supramolecular polymers formed from molecular recognition directed association between monomers bearing complementary hydrogen bonding groups were studied by rheology, small-angle neutron and light scattering experiments. The semiflexible fibers consist of few aggregated monomolecular wires. At T= 25 C the formation of branched aggregates occurs around the crossover concentration, C^*, between the dilute and semi-dilute regimes, whereas the classical behaviour of equilibrium polymers is observed at T=65 C. For semi-dilute solutions the steady-state flow curves showed a shear banding type instability, namely the occurrence of a stress plateau σp above a critical shear rate γ̂c. The values of σp and γ̂c were found to be of the same order of magnitude as those of the elastic plateau modulus and the inverse stress relaxation time, respectively. The above features are in agreement with the theoretical predictions based on the reptation model. Dynamic light scattering experiments showed the presence in the autocorrelation function of the concentration fluctuations of a slow viscoelastic relaxation process that is likely to be of Rouse type.

  15. Social coordination dynamics: Measuring human bonding

    PubMed Central

    Oullier, Olivier; de Guzman, Gonzalo C.; Jantzen, Kelly J.; Lagarde, Julien; Kelso, J.A. Scott

    2007-01-01

    Spontaneous social coordination has been extensively described in natural settings but so far no controlled methodological approaches have been employed that systematically advance investigations into the possible self-organized nature of bond formation and dissolution between humans. We hypothesized that, under certain contexts, spontaneous synchrony -a well-described phenomenon in biological and physical settings- could emerge spontaneously between humans as a result of information exchange. Here, a new way to quantify interpersonal interactions in real time is proposed. In a simple experimental paradigm, pairs of participants facing each other were required to actively produce actions, while provided (or not) with the vision of similar actions being performed by someone else. New indices of interpersonal coordination, inspired by the theoretical framework of coordination dynamics (based on relative phase and frequency overlap between movements of individuals forming a pair) were developed and used. Results revealed that spontaneous phase synchrony (i.e., unintentional in-phase coordinated behavior) between two people emerges as soon as they exchange visual information, even if they are not explicitly instructed to coordinate with each other. Using the same tools, we also quantified the degree to which the behavior of each individual remained influenced by the social encounter even after information exchange had been removed, apparently a kind of social memory. PMID:18552971

  16. Diffusion bonding and its application to manufacturing. [for joining of metal parts

    NASA Technical Reports Server (NTRS)

    Spurgeon, W. M.

    1972-01-01

    In its simplest form diffusion bonding is accomplished by placing clean metal surfaces together under a sufficient load and heating. The natural interatomic attractive force between atoms transforms the interface into a natural grain boundary. Therefore, in principle, the properties of the bond area are identical to those of the parent metal. Other advantages of diffusion bonding over conventional methods of bonding include freedom from residual stresses, excessive deformation, foreign metals, or changed crystal structures. Stainless steels, nickel-base superalloys, and aluminum alloys have all been successfully joined. Complex hardware, including integrated flueric devices, jet engine servovalves, and porous woven structures have been fabricated. The processing involved is discussed, along with such theoretical considerations as the role of metal surfaces, the formation of metal contact junctions, and the mechanisms of material transport in diffusion bonding.

  17. Diffusion bonding of IN 718 to VM 350 grade maraging steel

    NASA Technical Reports Server (NTRS)

    Crosby, S. R.; Biederman, R. R.; Reynolds, C. C.

    1972-01-01

    Diffusion bonding studies have been conducted on IN 718, VM 350 and the dissimilar alloy couple, IN 718 to maraging steel. The experimental processing parameters critical to obtaining consistently good diffusion bonds between IN 718 and VM 350 were determined. Interrelationships between temperature, pressure and surface preparation were explored for short bending intervals under vacuum conditions. Successful joining was achieved for a range of bonding cycle temperatures, pressures and surface preparations. The strength of the weaker parent material was used as a criterion for a successful tensile test of the heat treated bond. Studies of VM-350/VM-350 couples in the as-bonded condition showed a greater yielding and failure outside the bond region.

  18. The fabrication of all-silicon micro gas chromatography columns using gold diffusion eutectic bonding

    NASA Astrophysics Data System (ADS)

    Radadia, A. D.; Salehi-Khojin, A.; Masel, R. I.; Shannon, M. A.

    2010-01-01

    Temperature programming of gas chromatography (GC) separation columns accelerates the elution rate of chemical species through the column, increasing the speed of analysis, and hence making it a favorable technique to speedup separations in microfabricated GCs (micro-GC). Temperature-programmed separations would be preferred in an all-silicon micro-column compared to a silicon-Pyrex® micro-column given that the thermal conductivity and diffusivity of silicon is 2 orders of magnitude higher than Pyrex®. This paper demonstrates how to fabricate all-silicon micro-columns that can withstand the temperature cycling required for temperature-programmed separations. The columns were sealed using a novel bonding process where they were first bonded using a gold eutectic bond, then annealed at 1100 °C to allow gold diffusion into silicon and form what we call a gold diffusion eutectic bond. The gold diffusion eutectic-bonded micro-columns when examined using scanning electron microscopy (SEM), scanning acoustic microscopy (SAM) and blade insertion techniques showed bonding strength comparable to the previously reported anodic-bonded columns. Gas chromatography-based methane injections were also used as a novel way to investigate proper sealing between channels. A unique methane elution peak at various carrier gas inlet pressures demonstrated the suitability of gold diffusion eutectic-bonded channels as micro-GC columns. The application of gold diffusion eutectic-bonded all-silicon micro-columns to temperature-programmed separations (120 °C min-1) was demonstrated with the near-baseline separation of n-C6 to n-C12 alkanes in 35 s.

  19. Macromolecular Diffusion in Dynamic Polymer Nanocomposite

    NASA Astrophysics Data System (ADS)

    Lin, Chia-Chun; Cargnello, Matteo; Clarke, Nigel; Winey, Karen; Composto, Russell

    2015-03-01

    We consider diffusion of tracer polymers in the presence of mobile nanoparticles in polymer nanocomposites (PNCs). These nanoparticles are mobile on the time scale of polymer diffusion and have dimensions less than the entanglement mesh size (i.e., tube diameter). The PNC consists of titanium dioxide nanorods (NR, diameter=4.5nm; length=30.1nm) grafted with phenyl groups uniformly dispersed in a polystyrene (P=650kg/mol; tube diameter=8nm) matrix up to 10 volume percent. Three deuterated polystyrenes (dPS; M=800, 1800 and 3200 kg/mol) are chosen because their diffusion relative to NR allows for investigating fixed and mobile NR by simply changing M. For all M, the reduced tracer diffusivities are observed to decrease monotonically as NR loading increases. However, the reduced diffusivity of dPS (3200 kg/mol) is faster than expected compared to the fixed NR case. These findings suggest that mobile NR do not effectively slow down tracer diffusion relative to fixed particles. To test this hypothesis, dPS diffusion is investigated in a high molecular weight matrix PS (2000 kg/mol) in order to slow down NR diffusion relative to dPS (3200 kg/mol). New models are needed to incorporate these mobility dependent entanglements into a comprehensive understanding of dynamics in PNCs. Primary fundings: NSF/EPSRC Materials World Network DMR-1210379 (KIW, RJC) and EP/5065373/1 (NC). Support also by the NSF/MRSEC-DMR 11-20901, and Polymer Programs DMR 09-07493.

  20. Minimal model for dynamic bonding in colloidal transient networks.

    PubMed

    Krinninger, Philip; Fortini, Andrea; Schmidt, Matthias

    2016-04-01

    We investigate a model for colloidal network formation using Brownian dynamics computer simulations. Hysteretic springs establish transient bonds between particles with repulsive cores. If a bonded pair of particles is separated by a cutoff distance, the spring vanishes and reappears only if the two particles contact each other. We present results for the bond lifetime distribution and investigate the properties of the van Hove dynamical two-body correlation function. The model displays crossover from fluidlike dynamics, via transient network formation, to arrested quasistatic network behavior. PMID:27176346

  1. Minimal model for dynamic bonding in colloidal transient networks

    NASA Astrophysics Data System (ADS)

    Krinninger, Philip; Fortini, Andrea; Schmidt, Matthias

    2016-04-01

    We investigate a model for colloidal network formation using Brownian dynamics computer simulations. Hysteretic springs establish transient bonds between particles with repulsive cores. If a bonded pair of particles is separated by a cutoff distance, the spring vanishes and reappears only if the two particles contact each other. We present results for the bond lifetime distribution and investigate the properties of the van Hove dynamical two-body correlation function. The model displays crossover from fluidlike dynamics, via transient network formation, to arrested quasistatic network behavior.

  2. Dynamic fracture toughnesses of reaction-bonded silicon nitride

    NASA Technical Reports Server (NTRS)

    Kobayashi, A. S.; Emery, A. F.; Liaw, B. M.

    1983-01-01

    The room-temperature dynamic fracture response of reaction-bonded silicon nitride is investigated using a hybrid experimental-numerical procedure. In this procedure, experimentally determined crack velocities are utilized to drive a dynamic finite-element code or dynamic finite-difference code in its generation mode in order to extract numerically the dynamic stress intensity factor of the fracturing specimen. Results show that the dynamic fracture toughness vs crack velocity relations of the two reaction-bonded silicon nitrides do not follow the general trend in those relations of brittle polymers and steel. A definite slow crack velocity during the initial phase of dynamic crack propagation is observed in reaction-bonded silicon nitride, which results in a nonunique dynamic fracture toughness vs crack velocity relation. In addition, it is found that a propagating crack will continue to propagate under a static stress intensity factor substantially lower than K(IC).

  3. Diffusion bonding of 410 stainless steel to copper using a nickel interlayer

    SciTech Connect

    Sabetghadam, H.; Hanzaki, A. Zarei; Araee, A.

    2010-06-15

    In the present work, plates of stainless steel (grade 410) were joined to copper ones through a diffusion bonding process using a nickel interlayer at a temperature range of 800-950 deg. C. The bonding was performed through pressing the specimens under a 12-MPa compression load and a vacuum of 10{sup -4} torr for 60 min. The results indicated the formation of distinct diffusion zones at both Cu/Ni and Ni/SS interfaces during the diffusion bonding process. The thickness of the reaction layer in both interfaces was increased by raising the processing temperature. The phase constitutions and their related microstructure at the Cu/Ni and Ni/SS diffusion bonding interfaces were studied using optical microscopy, scanning electron microscopy, X-ray diffraction and elemental analyses through energy dispersive spectrometry. The resulted penetration profiles were examined using a calibrated electron probe micro-analyzer. The diffusion transition regions near the Cu/Ni and Ni/SS interfaces consist of a complete solid solution zone and of various phases based on (Fe, Ni), (Fe, Cr, Ni) and (Fe, Cr) chemical systems, respectively. The diffusion-bonded joint processed at 900 deg. C showed the maximum shear strength of about 145 MPa. The maximum hardness was obtained at the SS-Ni interface with a value of about 432 HV.

  4. Hydrogen peroxide diffusion dynamics in dental tissues.

    PubMed

    Ubaldini, A L M; Baesso, M L; Medina Neto, A; Sato, F; Bento, A C; Pascotto, R C

    2013-07-01

    The aim of this study was to investigate the diffusion dynamics of 25% hydrogen peroxide (H2O2) through enamel-dentin layers and to correlate it with dentin's structural alterations. Micro-Raman Spectroscopy (MRS) and Fourier Transform Infrared Photoacoustic Spectroscopy (FTIR-PAS) were used to measure the spectra of specimens before and during the bleaching procedure. H2O2 was applied to the outer surface of human enamel specimens for 60 minutes. MRS measurements were performed on the inner surface of enamel or on the subsurface dentin. In addition, H2O2 diffusion dynamics from outer enamel to dentin, passing through the dentin-enamel junction (DEJ) was obtained with Raman transverse scans. FTIR-PAS spectra were collected on the outer dentin. MRS findings revealed that H2O2 (O-O stretching µ-Raman band) crossed enamel, had a more marked concentration at DEJ, and accumulated in dentin. FTIR-PAS analysis showed that H2O2 modified dentin's organic compounds, observed by the decrease in amides I, II, and III absorption band intensities. In conclusion, H2O2 penetration was demonstrated to be not merely a physical passage through enamel interprismatic spaces into the dentinal tubules. H2O2 diffusion dynamics presented a concentration gradient determined by the chemical affinity of the H2O2 with each specific dental tissue.

  5. The effect of hydrogen bonds on diffusion mechanism of water inside single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chen, Qu; Wang, Qi; Liu, Ying-Chun; Wu, Tao

    2014-06-01

    Nanopores can serve as a molecule channel for transport of fluid, where water diffusion differs remarkably from that of simple particles. Hydrogen bonds play an essential role in the diffusion anomaly. Detailed investigations are carried out on the systems of rigid (6, 6), (7, 7), (8, 8), (9, 9), and (10, 10) armchair carbon nanotubes, solvated with Lennard-Jones water fluids. The role of hydrogen bonds is examined by diffusivity statistics and animation snapshots. It is found that in small (6,6) CNT, hydrogen bonds tend to aggregate water into a wire and lead to rapid collective drift. Confinement can stabilize the hydrogen bond of water molecules and enhance its lifetime. In relatively smaller CNTs, the diffusion mechanism could be altered by the temperature. Moreover, in larger nanotubes hydrogen bonding network allows the water to form regional concentrated clusters. This allows water fluid in extremely low density exhibit rather slow self-diffusion motion. This fundamental study attempts to provide insights in understanding nanoscale delivery system in aqueous solution.

  6. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

    In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

  7. Effect of Surface Preparation on CLAM/CLAM Hot Isostatic Pressing diffusion bonding joints

    NASA Astrophysics Data System (ADS)

    Li, C.; Huang, Q.; Zhang, P.

    2009-04-01

    Surface preparation is essential for the Hot Isostatic Pressing (HIP) diffusion bonding of RAFM steels. Hot Isostatic Pressing (HIP) diffusion bonding experiments on China Low Activation Martensitic (CLAM) steel was performed to study the effect of surface preparation. A few approaches such as hand lapping, dry-milling and grinding etc., were used to prepare the faying surfaces of the HIP joints. Different sealing techniques were used as well. The HIP parameters were 150 MPa/3 h/1150 °C. After post HIP heat treatment (PHHT), the tensile and Charpy impact tests were carried out. The results showed that hand lapping was not suitable to prepare the faying surfaces of HIP diffusion bonding specimens although the surface roughness by hand lapping was very low.

  8. Diffusion Bonding of Silicon Carbide for a Micro-Electro-Mechanical Systems Lean Direct Injector

    NASA Technical Reports Server (NTRS)

    Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

    2006-01-01

    Robust approaches for joining silicon carbide (SiC) to silicon carbide sub-elements have been developed for a micro-electro-mechanical systems lean direct injector (MEMS LDI) application. The objective is to join SiC sub-elements to form a leak-free injector that has complex internal passages for the flow and mixing of fuel and air. Previous bonding technology relied upon silicate glass interlayers that were not uniform or leak free. In a newly developed joining approach, titanium foils and physically vapor deposited titanium coatings were used to form diffusion bonds between SiC materials during hot pressing. Microscopy results show the formation of well adhered diffusion bonds. Initial tests show that the bond strength is much higher than required for the component system. Benefits of the joining technology are fabrication of leak free joints with high temperature and mechanical capability.

  9. Joint design for improved fatigue life of diffusion-bonded box-stiffened panels

    NASA Technical Reports Server (NTRS)

    Davis, R. C.; Moses, P. L.; Kanenko, R. S.

    1985-01-01

    Simple photoelastic models were used to identify a cross-section geometry that would eliminate the severe stress concentrations at the bond line between box stiffeners diffusion bonded to a panel skin. Experimental fatigue-test data from titanium test specimens quantified the allowable stress in terms of cycle life for various joint geometries. It is shown that the effect of stress concentration is reduced and an acceptable fatigue life is achieved.

  10. A link between structure, diffusion and rotations of hydrogen bonding tracers in ionic liquids

    NASA Astrophysics Data System (ADS)

    Araque, Juan C.; Daly, Ryan P.; Margulis, Claudio J.

    2016-05-01

    When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogeneities associated with charge enhanced (stiff) and charge depleted (soft) nanoenvironments are sampled. In a recent article [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015)], we explored large deviations from Stokes-Einstein translational diffusion caused by such a heterogeneity. The current article is set to explore the effect of soft and stiff solvent environments (i.e., structure) on OH-bond rotations in the case of water and small alcohols in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([" separators="Im1,2 + ][" separators="NTf2- ]). Is solute rotational dynamics heterogeneous? If so, are solute rotations and translations coupled in the sense that stiff and soft solvent environments hinder or speed up both types of dynamics? For the systems studied here, there appears to be a clear connection between translations, rotations, and stiff/soft solvent environments. We also discuss interesting asymmetries of the correlation between solutes with anions and cations.

  11. Dynamics of Bond Breaking Studied by Chemical Force Microscopy

    NASA Astrophysics Data System (ADS)

    Noy, Aleksandr; Zepeda, Salvador; Orme, Chris; Yeh, Yin; Deyoreo, Jim

    2000-03-01

    Intermolecular forces underline a variety of phenomena in chemical and in biological systems, such as cell adhesion, protein folding and molecular recognition in ligand-receptor pairs. Understanding the dynamics of these interactions is critical for modeling and controlling these processes. The advent of ultra-sensitive force measurement techniques has enabled direct measurement of the bond strength on the relevant length scales. Recent measurements have pointed out the importance of kinetic factors in bond strength and pointed out the necessity to explore the whole energy landscape of a chemical bond. Still, little is known about the response of the bond strength to the environmental variables such as temperature. The analysis of this response provides a way to determine thermodynamic characteristics of the binding interaction. We used chemical force microscopy to measure the temperature dependence of the interaction forces in a well-defined system presenting a finite number of identical bonds. The tip of the scanning probe microscope was modified with distinct chemical functionalities to give rise to the well-defined and uniform interactions with the sample surface. We will discuss the theoretical framework for interpretation of such measurements, as well as the relative importance of thermodynamic and kinetic factors affecting the bond strength in the presence of solvent medium. We also point out the differences in kinetics of bond breaking in single bond systems vs. multiple bond systems.

  12. Dynamical Crossover in Hot Dense Water: The Hydrogen Bond Role.

    PubMed

    Ranieri, Umbertoluca; Giura, Paola; Gorelli, Federico A; Santoro, Mario; Klotz, Stefan; Gillet, Philippe; Paolasini, Luigi; Koza, Michael Marek; Bove, Livia E

    2016-09-01

    We investigate the terahertz dynamics of liquid H2O as a function of pressure along the 450 K isotherm, by coupled quasielastic neutron scattering and inelastic X-ray scattering experiments. The pressure dependence of the single-molecule dynamics is anomalous in terms of both microscopic translation and rotation. In particular, the Stokes-Einstein-Debye equations are shown to be violated in hot water compressed to the GPa regime. The dynamics of the hydrogen bond network is only weakly affected by the pressure variation. The time scale of the structural relaxation driving the collective dynamics increases by a mere factor of 2 along the investigated isotherm, and the structural relaxation strength turns out to be almost pressure independent. Our results point at the persistence of the hydrogen bond network in hot dense water up to ice VII crystallization, thus questioning the long-standing perception that hydrogen bonds are broken in liquid water under the effect of compression. PMID:27479235

  13. Dynamic Ordering and Phase Segregation in Hydrogen-Bonded Polymers.

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

    Hydrogen bonds (H-bonds) constitute highly relevant structural units of molecular self-assembly. They bridge biological and synthetic sciences, implementing dynamic properties into materials and molecules, not achieved via purely covalent bonds. Phase segregation on the other hand represents another important assembly principle, responsible for, e.g., cell compartimentation, membrane-formation, and microphase segregation in polymers. Yet, despite the expanding elegant synthetic strategies of supramolecular polymers, the investigation of phase behavior of macromolecules driven by H-bonding forces still remains in its infancy. Compared to phase segregation arising from covalently linked block copolymers, the generation of phase segregated nanostructures via supramolecular polymers facilitates the design of novel functional materials, such as those with stimuli-responsive, self-healing, and erasable-material properties. We here discuss the phase segregation of H-bonding polymers in both the solution and solid state, wherein the molecular recognition elements are based on multiple H-bonding moieties, such as thymine/2,6-diamino-pyridine (THY/DAP), thymine/diamino triazine (THY/DAT), and barbiturate/Hamilton wedge (Ba/HW) elements. The specific aggregation of a series of different H-bonding polymers in solution, both linear and dendritic polymers, bearing heterocomplementary H-bonding moieties are described, in particular focusing on the issue of phase segregation. The exploitation of H-bonded supramolecular dendrons with segregating polymer chains leads to the formation of three-phase segregated hierarchical micelles in solution, purely linking the components via H-bonds, in turn displaying a versatile spectrum of segregated morphologies. We also focus on segregation effects of H-bonded amorphous and crystalline polymers: thus the formation of nanostructures, such as disordered micelles and well-ordered body centered cubic (BCC) packed spheres from telechelic polymers

  14. Dynamic Ordering and Phase Segregation in Hydrogen-Bonded Polymers.

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

    Hydrogen bonds (H-bonds) constitute highly relevant structural units of molecular self-assembly. They bridge biological and synthetic sciences, implementing dynamic properties into materials and molecules, not achieved via purely covalent bonds. Phase segregation on the other hand represents another important assembly principle, responsible for, e.g., cell compartimentation, membrane-formation, and microphase segregation in polymers. Yet, despite the expanding elegant synthetic strategies of supramolecular polymers, the investigation of phase behavior of macromolecules driven by H-bonding forces still remains in its infancy. Compared to phase segregation arising from covalently linked block copolymers, the generation of phase segregated nanostructures via supramolecular polymers facilitates the design of novel functional materials, such as those with stimuli-responsive, self-healing, and erasable-material properties. We here discuss the phase segregation of H-bonding polymers in both the solution and solid state, wherein the molecular recognition elements are based on multiple H-bonding moieties, such as thymine/2,6-diamino-pyridine (THY/DAP), thymine/diamino triazine (THY/DAT), and barbiturate/Hamilton wedge (Ba/HW) elements. The specific aggregation of a series of different H-bonding polymers in solution, both linear and dendritic polymers, bearing heterocomplementary H-bonding moieties are described, in particular focusing on the issue of phase segregation. The exploitation of H-bonded supramolecular dendrons with segregating polymer chains leads to the formation of three-phase segregated hierarchical micelles in solution, purely linking the components via H-bonds, in turn displaying a versatile spectrum of segregated morphologies. We also focus on segregation effects of H-bonded amorphous and crystalline polymers: thus the formation of nanostructures, such as disordered micelles and well-ordered body centered cubic (BCC) packed spheres from telechelic polymers

  15. Galactic civilizations - Population dynamics and interstellar diffusion

    NASA Technical Reports Server (NTRS)

    Newman, W. I.; Sagan, C.

    1981-01-01

    A model is developed of the interstellar diffusion of galactic civilizations which takes into account the population dynamics of such civilizations. The problem is formulated in terms of potential theory, with a family of nonlinear partial differential and difference equations specifying population growth and diffusion for an organism with advantageous genes that undergoes random dispersal while increasing in population locally, and a population at zero population growth. In the case of nonlinear diffusion with growth and saturation, it is found that the colonization wavefront from the nearest independently arisen galactic civilization can have reached the earth only if its lifetime exceeds 2.6 million years, or 20 million years if discretization can be neglected. For zero population growth, the corresponding lifetime is 13 billion years. It is concluded that the earth is uncolonized not because interstellar spacefaring civilizations are rare, but because there are too many worlds to be colonized in the plausible colonization lifetime of nearby civilizations, and that there exist no very old galactic civilizations with a consistent policy of the conquest of inhabited worlds.

  16. Molecular dynamics simulation of diffusion and electrical conductivity in montmorillonite interlayers

    DOE PAGESBeta

    Greathouse, Jeffery A.; Cygan, Randall T.; Fredrich, Joanne T.; Jerauld, Gary R.

    2016-01-20

    In this study, the diffusion of water and ions in the interlayer region of smectite clay minerals represents a direct probe of the type and strength of clay–fluid interactions. Interlayer diffusion also represents an important link between molecular simulation and macroscopic experiments. Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. For Na-montmorillonite, the largest increase in ion and water diffusion coefficients occurs between the one-layer and two-layer hydrates, corresponding to themore » transition from inner-sphere to outer-sphere surface complexes. Calculated activation energies for ion and water diffusion in Na-montmorillonite are similar to each other and to the water hydrogen bond energy, suggesting the breaking of water–water and water–clay hydrogen bonds as a likely mechanism for interlayer diffusion. A comparison of interlayer diffusion with that of bulk electrolyte solutions reveals a clear trend of decreasing diffusion coefficient with increasing electrolyte concentration, and in most cases the interlayer diffusion results are nearly coincident with the corresponding bulk solutions. Trends in electrical conductivities computed from the ion diffusion coefficients are also compared.« less

  17. TEM characterization of diffusion bonding of superplastic 8090 Al-Li alloy

    SciTech Connect

    Urena, A.; Gomez de Salazar, J.M.; Quinones, J.; Martin, J.J.

    1996-02-15

    In recent years there has been a growing interest in developing a joining process compatible with other fabrication technologies used in the aeronautical industry for superplastic aluminum-lithium alloys, and it is shown in numerous publications. There have been important advances in the research of the aluminum-lithium alloys diffusion bonding, and specially for the AA8090. However, joining of aluminum alloys by diffusion bonding encounters inherent problems which have not been solved yet. Most of these limitations come from the formation of protective oxide film (Al{sub 2}O{sub 3}) which covers the aluminum based materials. In spite of these unresolved difficulties, most of the investigators, among them are the present authors, have agreed that aluminum alloys which contain lithium as alloying element, present a higher weldability than Li-free aluminum ones. To explain this enhanced diffusion weldability in Li-doped alloys, it has been argued that Li favors the partial elimination of the unsoluble and tenacious alumina film, which acts as a diffusion barrier, through the formation of more soluble and brittle complex spinel (Al-Li-O). Nevertheless, the elimination of these oxides is not complete, resulting, in the most advantageous conditions, in a discontinuous distribution of oxide particles along the bonding interface which controls the final properties of the bond.

  18. Ion diffusion at the bonding interface of undoped YAG/Yb:YAG composite ceramics

    NASA Astrophysics Data System (ADS)

    Fujioka, Kana; Sugiyama, Akira; Fujimoto, Yasushi; Kawanaka, Junji; Miyanaga, Noriaki

    2015-08-01

    Cation diffusion across a boundary between ytterbium (Yb)-doped and undoped yttrium aluminum garnet (YAG) ceramics was examined by electron microprobe analysis (EPMA). Polished Yb:YAG and undoped YAG ceramics were bonded by surface treatment with argon fast atom beam, and then heat-treated at 1400 or 1600 °C for 50 h or at 1400 °C for 10 h under vacuum. We obtained EPMA mapping images of the bonded samples that clearly showed the bulk and grain-boundary diffusion of Y and Yb ions. The number density profiles showed that the total diffusion distances of Yb and Y ions were almost equal and approximately 2 and 15 μm at 1400 and 1600 °C, respectively, and the dependence of diffusion distance on heating time was weak. The diffusion curves were well modeled by Harrison type B kinetics including bulk and grain-boundary diffusion. In addition, it was found that Si ions added to the samples as a sintering aid might be segregated at the grain boundary by heat treatment, and diffused only along grain boundaries.

  19. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading.

  20. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading. PMID:27424868

  1. Clustering instability in adhesive contact between elastic solids via diffusive molecular bonds

    NASA Astrophysics Data System (ADS)

    Wang, Jizeng; Gao, Huajian

    Motivated by experimental observations that cell-cell and cell-matrix adhesion often involves formation of discrete patches of dense molecular bonds, we consider the plane strain problem of two elastic half-spaces, each covered with a layer of lipid membrane, joined together by mobile molecular bonds that diffuse along the interface under the combined action of a thin layer of glycocalyx repellers and an externally applied tensile stress. We show that, for a range of bond density values with or without the applied stress, the state of a uniform distribution of bonds is intrinsically unstable with respect to perturbations in bond density distribution. This instability is found to be primarily driven by elastic deformation energies in the bulk and the membrane. The change in free energy associated with a cosine perturbation in bond density distribution indicates that there exists a critical wavelength beyond which the perturbation becomes unstable and a fastest growing wavelength that tends to dominate as the instability grows. These length scales have typical values in the order of a micrometer, in agreement with the general characteristic size of bond clusters observed in cell adhesion.

  2. Shrinkage-Stress Assisted Diffusion Bonds Between Titanium and Stainless Steel: A Novel Technique

    NASA Astrophysics Data System (ADS)

    Mukherjee, A. B.; Laik, A.; Kain, V.; Chakravartty, J. K.

    2016-10-01

    Diffusion bonding of high-strength titanium (Ti) to stainless steel (SS) (i.e., transition joint of lap configuration) is designed and assessed for the possible high-temperature, high-pressure applications for the nuclear power plant and chemical industries. The strength of annular joint is enhanced by providing grooves at the interface ensuring strength of the joint compatible to Ti. The optimized hot forming conditions are utilized to facilitate the flow of Ti to fill the grooves located at the interface on SS sleeve resulting in strong mechanical connection. The shrinkage stress developed due to differential contraction during cooling facilitates the diffusion bonding at the interfaces inside the grooves under relatively lower temperature. The present design concept results in the formation of low level of intermetallic compounds at the interface. The bond width containing the intermetallic compounds toward Ti side has been found to be less than that of the high-strength diffusion bonds as occasionally reported in the open published literatures.

  3. Microstructural Characterization of Diffusion Bonds Assisted by Ni/Ti Nanolayers

    NASA Astrophysics Data System (ADS)

    Simões, Sónia; Viana, Filomena; Sofia Ramos, A.; Teresa Vieira, M.; Vieira, Manuel F.

    2016-08-01

    The microstructure of similar and dissimilar diffusion bonds of metallic materials using reactive Ni/Ti interlayers was studied in this investigation. The base material surfaces were modified by sputter deposition of alternated Ni and Ti nanolayers. These nanolayers increase the diffusivity at the interface, enhancing the bonding process. Bonding experiments were performed at 800 °C under a pressure of 10 MPa with a bonding time of 60 min. The reaction zone was characterized by high-resolution scanning and transmission electron microscopies. Microstructural characterization reveals that similar (NiTi to NiTi and TiAl to TiAl) and dissimilar (NiTi to Ti6Al4V and TiAl to stainless steel) joints can be obtained successfully with Ni/Ti reactive nanolayers. The interfaces are thin (<10 µm) and their microstructure (thickness and number of zones, size and shape of the grains) depends on the elements diffusing from the base materials. For all joints, the interface is mainly composed of equiaxed grains of NiTi and NiTi2.

  4. Shrinkage-Stress Assisted Diffusion Bonds Between Titanium and Stainless Steel: A Novel Technique

    NASA Astrophysics Data System (ADS)

    Mukherjee, A. B.; Laik, A.; Kain, V.; Chakravartty, J. K.

    2016-08-01

    Diffusion bonding of high-strength titanium (Ti) to stainless steel (SS) (i.e., transition joint of lap configuration) is designed and assessed for the possible high-temperature, high-pressure applications for the nuclear power plant and chemical industries. The strength of annular joint is enhanced by providing grooves at the interface ensuring strength of the joint compatible to Ti. The optimized hot forming conditions are utilized to facilitate the flow of Ti to fill the grooves located at the interface on SS sleeve resulting in strong mechanical connection. The shrinkage stress developed due to differential contraction during cooling facilitates the diffusion bonding at the interfaces inside the grooves under relatively lower temperature. The present design concept results in the formation of low level of intermetallic compounds at the interface. The bond width containing the intermetallic compounds toward Ti side has been found to be less than that of the high-strength diffusion bonds as occasionally reported in the open published literatures.

  5. Uniaxial diffusion bonding of CLAM/CLAM steels: Microstructure and mechanical performance

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaosheng; Liu, Yongchang; Yu, Liming; Liu, Chenxi; Sui, Guofa; Yang, Jianguo

    2015-06-01

    By performing a two-step uniaxial diffusion bonding, the reliable joining between CLAM/CLAM steels has been attained. The microstructures at the vicinity of the joint region and in base material were respectively investigated through OM, SEM and TEM. The joint interface was integrated, and no microstructural defects were observed. In the base material, small amount of austenite is retained as thin films between martensite laths, which was suggested to be related to the compressive deformation in diffusion bonding. As a candidate structural material for the first wall in fusion energy systems, the radiation resistance of CLAM steel would be deteriorated by the retained austenite. Tensile and impact tests were carried out to assess the reliability of the joints subjected to post bond heat treatment. All the tensile specimens fractured in the base CLAM steel, meaning the good joining between CLAM steels. However, due to the low impact absorbed energy of the joints, efforts should still be made to optimize the bonding technology and the post bond heat treatment further.

  6. Effects of interface bonding and defects on boron diffusion at Si/SiO2 interface

    NASA Astrophysics Data System (ADS)

    Kim, Geun-Myeong; Oh, Young Jun; Chang, K. J.

    2013-12-01

    We perform first-principles density functional calculations to find the migration pathway and barrier for B diffusion at the Si/SiO2 interface. For various interface models, in which crystalline α-quartz or amorphous silica (a-SiO2) is placed on Si, we examine stable and metastable configurations of B-related defects which play a role in B diffusion. While a substitutional B alone is immobile in Si, it tends to diffuse to the interface via an interstitialcy mechanism in the presence of a self-interstitial and then changes into an interstitial B in oxide via a kick-out mechanism, leaving the self-interstitial at the interface. At the defect-free interface, where bridging O atoms are inserted to remove interface dangling bonds, an interstitial B prefers to intervene between the interface Si and bridging O atoms and subsequently diffuses through the hollow space or along the network of the Si-O-Si bonds in oxide. The overall migration barriers are calculated to be 2.02-2.12 eV at the Si/α-quartz interface, while they lie in the range of 2.04 ± 0.44 eV at the Si/a-SiO2 interface, similar to that in α-quartz. The migration pathway and barrier are not significantly affected by interface defects such as suboxide bond and O protrusion, while dangling bonds in the suboxide region can increase the migration barrier by about 1.5 eV. The result that the interface generally does not hinder the B diffusion from Si to SiO2 assists in understanding the underlying mechanism for B segregation which commonly occurs at the Si/SiO2 interface.

  7. Diffusion Bonding Beryllium to Reduced Activation Ferritic Martensitic Steel: Development of Processes and Techniques

    NASA Astrophysics Data System (ADS)

    Hunt, Ryan Matthew

    Only a few materials are suitable to act as armor layers against the thermal and particle loads produced by magnetically confined fusion. These candidates include beryllium, tungsten, and carbon fiber composites. The armor layers must be joined to the plasma facing components with high strength bonds that can withstand the thermal stresses resulting from differential thermal expansion. While specific joints have been developed for use in ITER (an experimental reactor in France), including beryllium to CuCrZr as well as tungsten to stainless steel interfaces, joints specific to commercially relevant fusion reactors are not as well established. Commercial first wall components will likely be constructed front Reduced Activation Ferritic Martensitic (RAFM) steel, which will need to be coating with one of the three candidate materials. Of the candidates, beryllium is particularly difficult to bond, because it reacts during bonding with most elements to form brittle intermetallic compounds. This brittleness is unacceptable, as it can lead to interface crack propagation and delamination of the armor layer. I have attempted to overcome the brittle behavior of beryllium bonds by developing a diffusion bonding process of beryllium to RAFM steel that achieves a higher degree of ductility. This process utilized two bonding aids to achieve a robust bond: a. copper interlayer to add ductility to the joint, and a titanium interlayer to prevent beryllium from forming unwanted Be-Cu intermetallics. In addition, I conducted a series of numerical simulations to predict the effect of these bonding aids on the residual stress in the interface. Lastly, I fabricated and characterized beryllium to ferritic steel diffusion bonds using various bonding parameters and bonding aids. Through the above research, I developed a process to diffusion bond beryllium to ferritic steel with a 150 M Pa tensile strength and 168 M Pa shear strength. This strength was achieved using a Hot Isostatic

  8. Restoration of rhythmicity in diffusively coupled dynamical networks

    PubMed Central

    Zou, Wei; Senthilkumar, D. V.; Nagao, Raphael; Kiss, István Z.; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen

    2015-01-01

    Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks. PMID:26173555

  9. Restoration of rhythmicity in diffusively coupled dynamical networks.

    PubMed

    Zou, Wei; Senthilkumar, D V; Nagao, Raphael; Kiss, István Z; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen

    2015-01-01

    Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks. PMID:26173555

  10. Restoration of rhythmicity in diffusively coupled dynamical networks

    NASA Astrophysics Data System (ADS)

    Zou, Wei; Senthilkumar, D. V.; Nagao, Raphael; Kiss, István Z.; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen

    2015-07-01

    Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks.

  11. Fabrication and Design Aspects of High-Temperature Compact Diffusion Bonded Heat Exchangers

    SciTech Connect

    Mylavarapu, Sai K.; Sun, Xiaodong; Christensen, Richard N.; Glosup, Richard E.; Unocic, Raymond R

    2012-01-01

    The very high temperature reactor (VHTR), using gas-cooled reactor technology, is one of the six reactor concepts selected by the Generation IV International Forum and is anticipated to be the reactor type for the next generation nuclear plant (NGNP). In this type of reactor with an indirect power cycle system, a high-temperature and high integrity intermediate heat exchanger (IHX) with high effectiveness is required to efficiently transfer the core thermal output to secondary fluid for electricity production, process heat, or hydrogen cogeneration. The current Technology Readiness Level status issued by NGNP to all components associated with the IHX for reactor core outlet temperatures of 750-800oC is 3 on a scale of 1 to 10 with 10 being the most ready. At present, there is no proven high-temperature IHX concept for VHTRs. Amongst the various potential IHX concepts available, diffusion bonded heat exchangers (henceforth called printed circuit heat exchangers, or PCHEs) appear promising for NGNP applications. The design and fabrication of this key component of NGNP is the primary focus of this paper. In the current study, two PCHEs were fabricated using Alloy 617 plates and will be experimentally investigated for their thermal-hydraulic performance in a high-temperature helium test facility (HTHF). The HTHF was primarily designed and constructed to test the thermal-hydraulic performance of PCHEs The test facility is primarily of Alloy 800H construction and is designed to facilitate experiments at temperatures and pressures up to 800oC and 3 MPa, respectively. The PCHE fabrication related processes, i.e., photochemical machining and diffusion bonding are briefly discussed for Alloy 617 plates. Diffusion bonding of Alloy 617 plates with and without a Ni interlayer is discussed. Furthermore, preliminary microstructural and mechanical characterization studies of representative diffusion bonded Alloy 617 specimens are presented.

  12. Dynamic heterogeneity in two-dimensional supercooled liquids: comparison of bond-breaking and bond-orientational correlations

    NASA Astrophysics Data System (ADS)

    Flenner, Elijah; Szamel, Grzegorz

    2016-07-01

    We compare the spatial correlations of bond-breaking events and bond-orientational relaxation in a model two-dimensional liquid undergoing Newtonian dynamics. We find that the relaxation time of the bond-breaking correlation function is much longer than the relaxation time of the bond-orientational correlation function and self-intermediate scattering function. However, the relaxation time of the bond-orientational correlation function increases faster with decreasing temperature than the relaxation time of the bond-breaking correlation function and the self-intermediate scattering function. Moreover, the dynamic correlation length that characterizes the size of correlated bond-orientational relaxation grows faster with decreasing temperature than the dynamic correlation length that characterizes the size of correlated bond-breaking events. We also examine the ensemble-dependent and ensemble-independent dynamic susceptibilities for both bond-breaking correlations and bond-orientational correlations. We find that for both correlations, the ensemble-dependent and ensemble-independent susceptibilities exhibit a maximum at nearly the same time, and this maximum occurs at a time slightly shorter than the peak position of the dynamic correlation length.

  13. Dynamic Nuclear Polarization as Kinetically Constrained Diffusion

    NASA Astrophysics Data System (ADS)

    Karabanov, A.; Wiśniewski, D.; Lesanovsky, I.; Köckenberger, W.

    2015-07-01

    Dynamic nuclear polarization (DNP) is a promising strategy for generating a significantly increased nonthermal spin polarization in nuclear magnetic resonance (NMR) and its applications that range from medicine diagnostics to material science. Being a genuine nonequilibrium effect, DNP circumvents the need for strong magnetic fields. However, despite intense research, a detailed theoretical understanding of the precise mechanism behind DNP is currently lacking. We address this issue by focusing on a simple instance of DNP—so-called solid effect DNP—which is formulated in terms of a quantum central spin model where a single electron is coupled to an ensemble of interacting nuclei. We show analytically that the nonequilibrium buildup of polarization heavily relies on a mechanism which can be interpreted as kinetically constrained diffusion. Beyond revealing this insight, our approach furthermore permits numerical studies of ensembles containing thousands of spins that are typically intractable when formulated in terms of a quantum master equation. We believe that this represents an important step forward in the quest of harnessing nonequilibrium many-body quantum physics for technological applications.

  14. Dynamic Nuclear Polarization as Kinetically Constrained Diffusion.

    PubMed

    Karabanov, A; Wiśniewski, D; Lesanovsky, I; Köckenberger, W

    2015-07-10

    Dynamic nuclear polarization (DNP) is a promising strategy for generating a significantly increased nonthermal spin polarization in nuclear magnetic resonance (NMR) and its applications that range from medicine diagnostics to material science. Being a genuine nonequilibrium effect, DNP circumvents the need for strong magnetic fields. However, despite intense research, a detailed theoretical understanding of the precise mechanism behind DNP is currently lacking. We address this issue by focusing on a simple instance of DNP-so-called solid effect DNP-which is formulated in terms of a quantum central spin model where a single electron is coupled to an ensemble of interacting nuclei. We show analytically that the nonequilibrium buildup of polarization heavily relies on a mechanism which can be interpreted as kinetically constrained diffusion. Beyond revealing this insight, our approach furthermore permits numerical studies of ensembles containing thousands of spins that are typically intractable when formulated in terms of a quantum master equation. We believe that this represents an important step forward in the quest of harnessing nonequilibrium many-body quantum physics for technological applications. PMID:26207453

  15. Influence of silicon dangling bonds on germanium thermal diffusion within SiO{sub 2} glass

    SciTech Connect

    Barba, D.; Martin, F.; Ross, G. G.; Cai, R. S.; Wang, Y. Q.; Demarche, J.; Terwagne, G.; Rosei, F.

    2014-03-17

    We study the influence of silicon dangling bonds on germanium thermal diffusion within silicon oxide and fused silica substrates heated to high temperatures. By using scanning electron microscopy and Rutherford backscattering spectroscopy, we determine that the lower mobility of Ge found within SiO{sub 2}/Si films can be associated with the presence of unsaturated SiO{sub x} chemical bonds. Comparative measurements obtained by x-ray photoelectron spectroscopy show that 10% of silicon dangling bonds can reduce Ge desorption by 80%. Thus, the decrease of the silicon oxidation state yields a greater thermal stability of Ge inside SiO{sub 2} glass, which could enable to considerably extend the performance of Ge-based devices above 1300 K.

  16. TEM Observation of the Ti Interlayer Between SiC Substrates During Diffusion Bonding

    NASA Technical Reports Server (NTRS)

    Tsuda, Hiroshi; Mori, Shigeo; Halbig, Michael C.; Singh, Mori

    2012-01-01

    Diffusion bonding was carried out to join SiC to SiC substrates using titanium interlayers. In this study, 10 m and 20 m thick physical vapor deposited (PVD) Ti surface coatings, and 10 and 20 m thick Ti foils were used. Diffusion bonding was performed at 1250 C for PVD Ti coatings and 1200 C for Ti foil. This study investigates the microstructures of the phases formed during diffusion bonding through TEM and selected-area diffraction analysis of a sample prepared with an FIB, which allows samples to be taken from the reacted area. In all samples, Ti3SiC2, Ti5Si3Cx and TiSi2 phases were identified. In addition, TiC and unknown phases also appeared in the samples in which Ti foils were used as interlayers. Furthermore, Ti3SiC2 phases show high concentration and Ti5Si3Cx formed less when samples were processed at a higher temperature and thinner interlayer samples were used. It appears that the formation of microcracks is caused by the presence of intermediate phase Ti5Si3Cx, which has anisotropic thermal expansion, and by the presence of an unidentified Ti-Si-C ternary phase with relatively low Si content.

  17. Diffusion of two-dimensional Cu islets on Ag(111) studied with the Molecular Dynamics Method

    NASA Astrophysics Data System (ADS)

    Hayat, Sadar S.; Alcantara Ortigoza, Marisol; Rahman, Talat S.

    2009-03-01

    Our molecular dynamics simulations (at 300, 500 and 700 K) of the diffusion of two-dimensional Cun islets (1<=n<=9) on Ag(111) using many-body potentials yield an Arrhenius behavior. Concerted motion is seen to dominate the diffusion of smaller islets (2-4 atoms) whereas multiple-atom, shape-adjusting processes control the diffusion of the larger ones. Although the effective energy barrier scales with islet size, the barriers do not change considerably for islands containing 4 to 9 atoms (they are ˜ 220 ± 37 meV). While the diffusion barrier for Cu monomers on Ag(111) is higher than that on Cu(111) (both in experiment and theory), the situation reverses starting from the dimer. Our results for monomer and dimer are in excellent agreement with those extracted from experiments.^1 On comparing our results with those for Cu islets on Cu(111), we find that the comparatively large Ag-Ag bond-length sets the contrast between Cu monomer diffusion on Cu(111) and on Ag(111). The diffusivity of Cu dimer, however, is boosted on Ag(111) by the competition between optimizing the Cu-Cu and the Cu-Ag bonds. For larger islets (3-9 atoms) our results reveal several novel diffusion processes, including those in which an islet-atom climbs atop. ^1 Morgenstern et al. PRL93, 056102 (2005). Work supported by NSF-ITR 0428826.

  18. Diffusion ordered spectroscopy for resolution of double bonded cis, trans-isomers

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-06-01

    NMR spectroscopic separation of double bonded cis- and trans-isomers, that have different molecular shapes but identical mass have been carried out using Diffusion Ordered Spectroscopy (DOSY). The mixtures of fumaric acid and maleic acid, that have similar hydrodynamic radii, have resolved been 'on the basis of their diffusion coefficients arising due to their different tendencies to associate with micelles or reverse micelles. Sodium dodecyl sulfate (SDS) and Dioctyl sulfosuccinate sodium salt (AOT) have been used as the media to mimic the chromatographic conditions, modify the average mobility and to achieve differential diffusion rates. The best separation of the components has been achieved by Dioctyl sulfosuccinate sodium salt (AOT) in D2O solution.

  19. Microstructural characteristics of HIP-bonded monolithic nuclear fuels with a diffusion barrier

    NASA Astrophysics Data System (ADS)

    Jue, Jan-Fong; Keiser, Dennis D.; Breckenridge, Cynthia R.; Moore, Glenn A.; Meyer, Mitchell K.

    2014-05-01

    Due to the limitation of maximum uranium load achievable by dispersion fuel type, the Global Threat Reduction Initiative is developing an advanced monolithic fuel to convert US high-performance research reactors to low-enriched uranium. Hot-isostatic-press (HIP) bonding was the single process down-selected to bond monolithic U-Mo fuel meat to aluminum alloy cladding. A diffusion barrier was applied to the U-Mo fuel meat by roll-bonding process to prevent extensive interaction between fuel meat and aluminum-alloy cladding. Microstructural characterization was performed on fresh fuel plates fabricated at Idaho National Laboratory. Interfaces between the fuel meat, the cladding, and the diffusion barrier, as well as between the U-10Mo fuel meat and the Al-6061 cladding, were characterized by scanning electron microscopy. Preliminary results indicate that the interfaces contain many different phases while decomposition, second phases, and chemical banding were also observed in the fuel meat. The important attributes of the HIP-bonded monolithic fuel are: diffusion barrier with a thickness of 25 μm. A transverse cross section that exhibits relatively equiaxed grains with an average grain diameter of 10 μm. Chemical banding, in some areas more than 100 μm in length, that is very pronounced in longitudinal (i.e., rolling) direction with Mo concentration varying from 7-13 wt.%. Decomposed areas containing plate-shaped low-Mo phase. A typical Zr/cladding interaction layer with a thickness of 1-2 μm. A visible UZr2 bearing layer with a thickness of 1-2 μm. Mo-rich precipitates (mainly Mo2Zr, forming a layer in some areas) followed by a Mo-depleted sub-layer between the visible UZr2-bearing layer and the U-Mo matrix. No excessive interaction between cladding and the uncoated fuel edge. Cladding-to-cladding bonding that exhibits no cracks or porosity with second phases high in Mg, Si, and O decorating the bond line. Some of these attributes might be

  20. Microstructural Characteristics of HIP-bonded Monolithic Nuclear Fuels with a Diffusion Barrier

    SciTech Connect

    Jan-Fong Jue; Dennis D. Keiser, Jr.; Cynthia R. Breckenridge; Glenn A. Moore; Mitchell K. Meyer

    2014-05-01

    Due to the limitation of maximum uranium load achievable by dispersion fuel type, the Global Threat Reduction Initiative (GTRI) is developing an advanced monolithic fuel to convert US high performance research reactors to low-enriched uranium. Hot-isostatic-press bonding was the single process down-selected to bond monolithic U-Mo fuel meat to aluminum alloy cladding. A diffusion barrier was applied to the U–Mo fuel meat by roll-bonding process to prevent extensive interaction between fuel meat and aluminum-alloy cladding. Microstructural characterization was performed on fresh fuel plates fabricated at Idaho National Laboratory. Interfaces between fuel meat, cladding, and diffusion barrier, as well as U–10Mo fuel meat and Al–6061 cladding were characterized by scanning electron microscopy. Preliminary results indicate that the interfaces contain many different phases while decomposition, second phases, and chemical banding were also observed in the fuel meat. The important attributes of the HIP-bonded monolithic fuel are • A typical Zr diffusion barrier of thickness 25 µm • Transverse cross section that exhibits relatively equiaxed grains with an average grain diameter of 10 µm • Chemical banding, in some areas more than 100 µm in length, that is very pronounced in longitudinal (i.e., rolling) direction with Mo concentration varying from 7–13 wt% • Decomposed areas containing plate-shaped low-Mo phase • A typical Zr/cladding interaction layer of thickness 1-2 µm • A visible UZr2 bearing layer of thickness 1-2 µm • Mo-rich precipitates (mainly Mo2Zr, forming a layer in some areas) followed by a Mo-depleted sub-layer between the visible UZr2-bearing layer and the U–Mo matrix • No excessive interaction between cladding and the uncoated fuel edge • Cladding-to-cladding bonding that exhibits no cracks or porosity with second phases high in Mg, Si, and O decorating the bond line. • Some of these attributes might be critical to the

  1. Understanding Dynamic Competitive Technology Diffusion in Electronic Markets

    NASA Astrophysics Data System (ADS)

    Zhang, Cheng; Song, Peijian; Xu, Yunjie; Xue, Ling

    The extant literature on information technology (IT) diffusion has largely treated technology diffusion as a generic and independent process. This study, in contrast, examines the diffusion of different IT products with brand differentiation and competition. Drawing upon existing theories of product diffusion, we propose a research model to capture the dynamics of the competitive diffusion of web-based IT products and validate it with longitudinal field data of e-business platforms. Our findings suggest that IT product diffusion can be better predicted by a competitive model than by an independent-diffusion-process model. This research extends IT research to the context of competitive diffusion and provides practitioners an effective model to predict the dissemination of their products. The research also suggests the existence of asymmetric interactions among competing products, prompting scholars and practitioners to pay attention to the influence of competing products when making forecast of their product market.

  2. Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

    PubMed

    Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

    2015-03-10

    Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition. PMID:26579778

  3. Fluid dynamics of double diffusive systems

    SciTech Connect

    Koseff, J.R.

    1989-04-07

    A study of mixing processes in doubly diffusive systems is being conducted. Continuous gradients of two diffusing components (heat and salinity in our case) are being used as initial conditions, and forcing is introduced by lateral heating and surface shear. The goals of the proposed work include: (1) quantification of the effects of finite amplitude disturbances on stable, double diffusive systems, particularly with respect to lateral heating, (2) development of an improved understanding of the physical phenomena present in wind-driven shear flows in double diffusive stratified environments, (3) increasing our knowledge-base on turbulent flow in stratified environments and how to represent it, and (4) formulation of a numerical code for such flows. The work is being carried out in an experimental facility which is located in the Stanford Environmental Fluid Mechanics Laboratory, and on laboratory minicomputers and CRAY computers. In particular we are focusing on the following key issues: (1) the formation and propagation of double diffusive intrusions away from a heated wall and the effects of lateral heating on the double diffusive system; (2) the interaction between the double diffusively influenced fluxes and the turbulence induced fluxes; (3) the measurement of heat and mass fluxes; and (4) the influence of double diffusive gradients on mixed layer deepening. 1 fig.

  4. Verification of the effect of surface preparation on Hot Isostatic Pressing diffusion bonding joints of CLAM steel

    NASA Astrophysics Data System (ADS)

    Zhao, Yanyun; Li, Chunjing; Huang, Bo; Liu, Shaojun; Huang, Qunying

    2014-12-01

    Hot Isostatic Pressing (HIP) diffusion bonding with CLAM steel is the primary candidate fabrication technique for the first wall (FW) of DFLL-TBM. Surface state is one of the key factors for the joints quality. The effect of surface state prepared with grinder and miller on HIP diffusion bonding joints of CLAM steel was investigated. HIP diffusion bonding was performed at 140 MPa and 1373 K within 3 h. The mechanical properties of the joints were investigated with instrumented Charpy V-notch impact tests and the microstructures of the joints were analyzed with scanning electron microscopy (SEM). The results showed that the milled samples with fine surface roughness were more suitable for CLAM steel HIP diffusion bonding.

  5. Rumor diffusion in an interests-based dynamic social network.

    PubMed

    Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

    2013-01-01

    To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency.

  6. Rumor diffusion in an interests-based dynamic social network.

    PubMed

    Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

    2013-01-01

    To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911

  7. The dynamics of the turbopause. [variability of eddy diffusion

    NASA Technical Reports Server (NTRS)

    Roper, R. G.

    1974-01-01

    The investigation reported shows the variability of eddy diffusion at the turbopause on diurnal, seasonal, and solar cycle time scales, and also on latitude. Realistic vertical eddy diffusion profiles for the lower thermosphere are presented. The results of the studies illustrate the importance of global winds in the dynamics of the lower thermosphere. Difficulties regarding the direct measurement of eddy diffusivity in the lower thermosphere are discussed.

  8. Diffusive dynamics of nanoparticles in arrays of nanoposts.

    PubMed

    He, Kai; Babaye Khorasani, Firoozeh; Retterer, Scott T; Thomas, Darrell K; Conrad, Jacinta C; Krishnamoorti, Ramanan

    2013-06-25

    The diffusive dynamics of dilute dispersions of nanoparticles of diameter 200-400 nm were studied in microfabricated arrays of nanoposts using differential dynamic microscopy and single particle tracking. Posts of diameter 500 nm and height 10 μm were spaced by 1.2-10 μm on a square lattice. As the spacing between posts was decreased, the dynamics of the nanoparticles slowed. Moreover, the dynamics at all length scales were best represented by a stretched exponential rather than a simple exponential. Both the relative diffusivity and the stretching exponent decreased linearly with increased confinement and, equivalently, with decreased void volume. The slowing of the overall diffusive dynamics and the broadening distribution of nanoparticle displacements with increased confinement are consistent with the onset of dynamic heterogeneity and the approach to vitrification.

  9. Diffusive Dynamics of Nanoparticles in Arrays of Nanoposts

    SciTech Connect

    He, Kai; Korasani, Firoozeh; Thomas, Darrell Keith; Retterer, Scott T; Conrad, Jacinta; Krishnamoorti, Ramanan

    2013-01-01

    The diffusive dynamics of dilute dispersions of nanoparticles of diameter 200 400 nm were studied in microfabricated arrays of nanoposts using differential dynamic microscopy and single particle tracking. Posts of diameter 500 nm and height 10 m were spaced by 1.2 10 m on a square lattice. As the spacing between posts was decreased, the dynamics of the nanoparticles slowed. Moreover, the dynamics at all length scales were best represented by a stretched exponential rather than a simple exponential. Both the relative diffusivity and the stretching exponent decreased linearly with increased confinement and, equivalently, with decreased void volume. The slowing of the overall diffusive dynamics and the broadening distribution of nanoparticle displacements with increased confinement are consistent with the onset of cooperative dynamics.

  10. The use of isostatic pressing to improve the strength of TLP diffusion bonds in aluminium-based composites

    SciTech Connect

    Shirzadi, A.A.; Wallach, E.R.

    1996-12-31

    Transient Liquid Phase (TLP) diffusion bonding of aluminium-SiC composites, using copper interlayers, was carried out under low bonding pressure to minimize plastic deformation. This was followed by solid-state diffusion bonding under relatively high pressure as a complementary process to improve joint strength and reliability. In the high pressure stage, plastic deformation was avoided by lateral constraint of the sample in order to build up a hydrostatic stress state, simulating hot isostatic pressing (hipping). The bonding temperature in a TLP process is usually determined by the temperature at which the liquid phase forms, e.g., the Al-Cu eutectic formation temperature in this case. In theory, it should be possible to vary the applied pressure in order to optimize bonding. However, the superplastic behavior of the material used in this work led to excessive deformation at the bonding temperature, with consequent restrictions on the bonding pressure and on the resulting bond strengths. The subsequent use of higher bonding pressures with minimal plastic deformation in the second stage of the process resulted in considerable improvements in bond strength. Bonds with shear strengths as high as 70% and 92% respectively of the shear strengths of two aluminium composites, 8090 Al/SiC and 359 Al/SiC (given the same thermal cycles including post solution treatment and ageing), have been achieved.

  11. Elastic constants for superplastically formed/diffusion-bonded corrugated sandwich core

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1980-01-01

    Formulas and associated graphs for evaluating the effective elastic constants for a superplastically formed/diffusion bonded (SPF/DB) corrugated sandwich core, are presented. A comparison of structural stiffnesses of the sandwich core and a honeycomb core under conditions of equal sandwich core density was made. The stiffness in the thickness direction of the optimum SPF/DB corrugated core (that is, triangular truss core) is lower than that of the honeycomb core, and that the former has higher transverse shear stiffness than the latter.

  12. Diffusion Coefficients in Liquid and Grain Boundary Predicted by Ab Initio Molecular Dynamics

    SciTech Connect

    Jablonski, P.D.; Liu, Z.; Fang, H.; Wang, B.

    2011-04-01

    Molecular dynamics (MD) is a powerful tool to probe the thermodynamic and kinetic properties of solid, glass and liquid phases. In classical molecular dynamics (CMD), empirical models are used to describe the force by considering bond, bend and dihedral angle contributions with parameters fitted to experimental data or first-principles calculations of small clusters. In the ab initio molecular dynamics (AIMD), the forces are calculated on the fly using the first-principles density functional theory as discussed above. In the present work, we use AIMD simulations to follow the random walk of atoms in the liquid state. Based on the mean square displacements (MSD), the diffusion coefficients are calculated from the Einstein equation. Furthermore, we extend this approach to understand the diffusion in grain boundaries.

  13. Galactic civilizations: Population dynamics and interstellar diffusion

    NASA Technical Reports Server (NTRS)

    Newman, W. I.; Sagan, C.

    1978-01-01

    The interstellar diffusion of galactic civilizations is reexamined by potential theory; both numerical and analytical solutions are derived for the nonlinear partial differential equations which specify a range of relevant models, drawn from blast wave physics, soil science, and, especially, population biology. An essential feature of these models is that, for all civilizations, population growth must be limited by the carrying capacity of the environment. Dispersal is fundamentally a diffusion process; a density-dependent diffusivity describes interstellar emigration. Two models are considered: the first describing zero population growth (ZPG), and the second which also includes local growth and saturation of a planetary population, and for which an asymptotic traveling wave solution is found.

  14. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    SciTech Connect

    Mugnai, Mauro L.; Elber, Ron

    2015-01-07

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

  15. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

    PubMed

    Mugnai, Mauro L; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide.

  16. Diffusion bonding of iron aluminide Fe{sub 72}Al{sub 28} using a copper interlayer

    SciTech Connect

    Torun, O.; Celikyuerek, I.; Guerler, R.

    2008-07-15

    An Fe{sub 72}Al{sub 28} alloy was diffusion-bonded using a copper interlayer under vacuum at 1075 deg. C for 1 h, 2 h, 4 h and 6 h durations at 3.2 MPa applied pressure. The bond microstructure was found to be composed of the copper rich interlayer, copper rich precipitates and the base metal. SEM-EDS studies indicated major diffusion of aluminium and iron atoms from Fe{sub 72}Al{sub 28} into the copper interlayer and copper atoms from the copper interlayer into the Fe{sub 72}Al{sub 28} matrix. SEM observations of fractured surfaces of the diffusion-bonded samples showed some plastic deformation and signs of good bonding. Cu{sub 3}Al and B{sub 2}-FeAl-based phases were identified by SEM-EDS and X-ray diffraction studies at the bond and on the fracture surfaces of all samples investigated. Good bonding was achieved with a maximum shear strength of 298 MPa which is 65% of the parent material shear strength for a sample diffusion-bonded for 6 h.

  17. Dynamics and pattern formation in a cancer network with diffusion

    NASA Astrophysics Data System (ADS)

    Zheng, Qianqian; Shen, Jianwei

    2015-10-01

    Diffusion is ubiquitous inside cells, and it is capable of inducing spontaneous pattern formation in reaction-diffusion systems on a spatially homogeneous domain. In this paper, we investigate the dynamics of a diffusive cancer network regulated by microRNA and obtain the condition that the network undergoes a Hopf bifurcation and a Turing pattern bifurcation. In addition, we also develop the amplitude equation of the network model by using Taylor series expansion, multi-scaling and further expansion in powers of a small parameter. As a result of these analyses, we obtain the explicit condition on how the dynamics of the diffusive cancer network evolve. These results reveal that this system has rich dynamics, such as spotted stripe and hexagon patterns. The bifurcation diagram helps us understand the biological mechanism in the cancer network. Finally, numerical simulations confirm our analytical results.

  18. Dynamic Fracture Behavior of Plastic-Bonded Explosives

    NASA Astrophysics Data System (ADS)

    Fu, Hua; Li, Jun-Ling; Tan, Duo-Wang; Ifp, Caep Team

    2011-06-01

    Plastic-Bonded Explosives (PBX) are used as important energetic materials in nuclear or conventional weapons. Arms Warhead in the service process and the ballistic phase, may experience complex process such as long pulse and higher loading, compresson, tension and reciprocating compression - tension, friction with the projectile shell, which would lead to explosive deformation and fracture.And the dynamic deformation and fracture behavior of PBX subsequently affect reaction characteristics and initiation mechanism in explosives, then having influence on explosives safety. The dynamic fracure behavior of PBX are generally complex and not well studied or understood. In this paper, the dynamic fracture of explosives are conducted using a Kolsky bar. The Brazilian test, also known as a indirect tensile test or splitting test, is chosen as the test method. Tensile strength under different strain rates are obtained using quartz crystal embedded in rod end. The dynamic deformation and fracture process are captured in real-time by high-speed digital camera, and the displacement and strain fields distribution before specimen fracture are obtained by digital correlation method. Considering the non-uniform microstructure of explosives,the dynamic fracture behavior of explosive are simulated by discrete element method, the simulation results can reproduce the deformation and fracture process in Brazilian test using a maximum tensile strain criterion.

  19. Ultrafast internal dynamics of flexible hydrogen-bonded supramolecular complexes.

    PubMed

    Olschewski, Martin; Knop, Stephan; Seehusen, Jaane; Lindner, Jörg; Vöhringer, Peter

    2011-02-24

    Supramolecular chemistry is intimately linked to the dynamical interplay between intermolecular forces and intramolecular flexibility. Here, we studied the ultrafast equilibrium dynamics of a supramolecular hydrogen-bonded receptor-substrate complex, 18-crown-6 monohydrate, using Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy in combination with numerical simulations based on molecular mechanics, density functional theory, and transition state theory. The theoretical calculations suggest that the flexibility of the macrocyclic crown ether receptor is related to an ultrafast crankshaft isomerization occurring on a time scale of several picoseconds and that the OH stretching vibrations of the substrate can serve as internal probes for the receptor's flexibility. The importance of population transfer among the vibrational modes of a given binding motif and of chemical exchange between spectroscopically distinguishable binding motifs for shaping the two-dimensional infrared spectrum and its temporal evolution is discussed. PMID:21271721

  20. Detailed analysis of surface asperity deformation mechanism in diffusion bonding of steel hollow structural components

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Li, H.; Li, M. Q.

    2016-05-01

    This study focused on the detailed analysis of surface asperity deformation mechanism in similar diffusion bonding as well as on the fabrication of high quality martensitic stainless steel hollow structural components. A special surface with regular patterns was processed to be joined so as to observe the extent of surface asperity deformation under different bonding pressures. Results showed that an undamaged hollow structural component has been obtained with full interfacial contact and the same shear strength to that of base material. Fracture surface characteristic combined with surface roughness profiles distinctly revealed the enhanced surface asperity deformation as the applied pressure increases. The influence of surface asperity deformation mechanism on joint formation was analyzed: (a) surface asperity deformation not only directly expanded the interfacial contact areas, but also released deformation heat and caused defects, indirectly accelerating atomic diffusion, then benefits to void shrinkage; (b) surface asperity deformation readily introduced stored energy difference between two opposite sides of interface grain boundary, resulting in strain induced interface grain boundary migration. In addition, the influence of void on interface grain boundary migration was analyzed in detail.

  1. Anomalous Diffusion and Dynamical Localization in Polygonal Billiards

    SciTech Connect

    Prosen, Tomaz; Znidaric, Marko

    2001-09-10

    We study numerically classical and quantum dynamics of a piecewise parabolic area preserving map on a cylinder which emerges from the bounce map of elongated triangular billiards. The classical map exhibits anomalous diffusion. Quantization of the same map results in a system with dynamical localization and pure point spectrum.

  2. Microstructures of diffusion bonded SiC ceramics using Ti and Mo interlayers

    NASA Astrophysics Data System (ADS)

    Jung, Yang-Il; Kim, Sun-Han; Kim, Hyun-Gil; Park, Jeong-Yong; Kim, Weon-Ju

    2013-10-01

    SiC plates were diffusion bonded using metallic interlayers of Ti and Mo foils. For the joining, a uniaxial pressure of ∼7 MPa was applied at 1400 °C for 1 h in a vacuum. The interfacial microstructures along with their atomic compositions of the SiC/SiC joints were analyzed. For the Ti interlayer, Ti was converted into a Ti3SiC2 phase owing to the diffusion of silicon and carbon from the SiC part. A crystallographic orientation relationship was found between the SiC and Ti3SiC2 grains. At the middle of the Ti interlayer, a TiSi2 phase also existed, forming a dual-phase region. For the Mo interlayer, the diffusion of silicon into Mo induced the formation of the Mo5Si3C phase at the SiC/Mo interface. An unreacted metallic phase was still observed in the middle of the Mo insert. The shear strengths of the joints were 67 MPa and 76 MPa for the Ti and Mo interlayers, respectively.

  3. Multiparticle collision dynamics for diffusion-influenced signaling pathways

    NASA Astrophysics Data System (ADS)

    Strehl, R.; Rohlf, K.

    2016-08-01

    An efficient yet accurate simulation method for modeling diffusion-influenced reaction networks is presented. The method extends existing reactive multiparticle collision dynamics by incorporating species-dependent diffusion coefficients, and developing theoretical expressions for the reactant-dependent diffusion control. This off-lattice particle-based mesoscopic simulation tool is particularly suited for problems in which detailed descriptions of particle trajectories and local reactions are required. Numerical simulations of an intracellular signaling pathway for bacterial chemotaxis are carried out to validate our approach, and to demonstrate its efficiency.

  4. Diffusive dynamics of nanoparticles in ultra-confined media.

    PubMed

    Jacob, Jack Deodato C; He, Kai; Retterer, Scott T; Krishnamoorti, Ramanan; Conrad, Jacinta C

    2015-10-14

    Differential dynamic microscopy (DDM) was used to investigate the diffusive dynamics of nanoparticles of diameter 200-400 nm that were strongly confined in a periodic square array of cylindrical nanoposts. The minimum distance between posts was 1.3-5 times the diameter of the nanoparticles. The image structure functions obtained from the DDM analysis were isotropic and could be fit by a stretched exponential function. The relaxation time scaled diffusively across the range of wave vectors studied, and the corresponding scalar diffusivities decreased monotonically with increased confinement. The decrease in diffusivity could be described by models for hindered diffusion that accounted for steric restrictions and hydrodynamic interactions. The stretching exponent decreased linearly as the nanoparticles were increasingly confined by the posts. Together, these results are consistent with a picture in which strongly confined nanoparticles experience a heterogeneous spatial environment arising from hydrodynamics and volume exclusion on time scales comparable to cage escape, leading to multiple relaxation processes and Fickian but non-Gaussian diffusive dynamics.

  5. Inferring Diffusion Dynamics from FCS in Heterogeneous Nuclear Environments

    PubMed Central

    Tsekouras, Konstantinos; Siegel, Amanda P.; Day, Richard N.; Pressé, Steve

    2015-01-01

    Fluorescence correlation spectroscopy (FCS) is a noninvasive technique that probes the diffusion dynamics of proteins down to single-molecule sensitivity in living cells. Critical mechanistic insight is often drawn from FCS experiments by fitting the resulting time-intensity correlation function, G(t), to known diffusion models. When simple models fail, the complex diffusion dynamics of proteins within heterogeneous cellular environments can be fit to anomalous diffusion models with adjustable anomalous exponents. Here, we take a different approach. We use the maximum entropy method to show—first using synthetic data—that a model for proteins diffusing while stochastically binding/unbinding to various affinity sites in living cells gives rise to a G(t) that could otherwise be equally well fit using anomalous diffusion models. We explain the mechanistic insight derived from our method. In particular, using real FCS data, we describe how the effects of cell crowding and binding to affinity sites manifest themselves in the behavior of G(t). Our focus is on the diffusive behavior of an engineered protein in 1) the heterochromatin region of the cell’s nucleus as well as 2) in the cell’s cytoplasm and 3) in solution. The protein consists of the basic region-leucine zipper (BZip) domain of the CCAAT/enhancer-binding protein (C/EBP) fused to fluorescent proteins. PMID:26153697

  6. Specific Ions Modulate Diffusion Dynamics of Hydration Water on Lipid Membrane Surfaces

    PubMed Central

    2015-01-01

    Effects of specific ions on the local translational diffusion of water near large hydrophilic lipid vesicle surfaces were measured by Overhauser dynamic nuclear polarization (ODNP). ODNP relies on an unpaired electron spin-containing probe located at molecular or surface sites to report on the dynamics of water protons within ∼10 Å from the spin probe, which give rise to spectral densities for electron–proton cross-relaxation processes in the 10 GHz regime. This pushes nuclear magnetic resonance relaxometry to more than an order of magnitude higher frequencies than conventionally feasible, permitting the measurement of water moving with picosecond to subnanosecond correlation times. Diffusion of water within ∼10 Å of, i.e., up to ∼3 water layers around the spin probes located on hydrophilic lipid vesicle surfaces is ∼5 times retarded compared to the bulk water translational diffusion. This directly reflects on the activation barrier for surface water diffusion, i.e., how tightly water is bound to the hydrophilic surface and surrounding waters. We find this value to be modulated by the presence of specific ions in solution, with its order following the known Hofmeister series. While a molecular description of how ions affect the hydration structure at the hydrophilic surface remains to be answered, the finding that Hofmeister ions directly modulate the surface water diffusivity implies that the strength of the hydrogen bond network of surface hydration water is directly modulated on hydrophilic surfaces. PMID:24456096

  7. Dynamic force spectroscopy of parallel individual mucin1-antibody bonds

    SciTech Connect

    Sulchek, T A; Friddle, R W; Langry, K; Lau, E; Albrecht, H; Ratto, T; DeNardo, S; Colvin, M E; Noy, A

    2005-05-02

    We used atomic force microscopy (AFM) to measure the binding forces between Mucin1 (MUC1) peptide and a single chain antibody fragment (scFv) selected from a scFv library screened against MUC1. This binding interaction is central to the design of the molecules for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from non-specific interactions by tethering the antibody and MUC1 molecules to the AFM tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the bond rupture events corresponding to different number of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for mono-, bi-, and tri-valent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for mono and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.

  8. Towards a unified description of the hydrogen bond network of liquid water: A dynamics based approach

    SciTech Connect

    Ozkanlar, Abdullah Zhou, Tiecheng; Clark, Aurora E.

    2014-12-07

    The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.

  9. Towards a unified description of the hydrogen bond network of liquid water: a dynamics based approach.

    PubMed

    Ozkanlar, Abdullah; Zhou, Tiecheng; Clark, Aurora E

    2014-12-01

    The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.

  10. Dynamic Characterization of Crystalline Supramolecular Rotors Assembled through Halogen Bonding.

    PubMed

    Catalano, Luca; Pérez-Estrada, Salvador; Terraneo, Giancarlo; Pilati, Tullio; Resnati, Giuseppe; Metrangolo, Pierangelo; Garcia-Garibay, Miguel A

    2015-12-16

    A modular molecular kit for the preparation of crystalline molecular rotors was devised from a set of stators and rotators to gain simple access to a large number of structures with different dynamic performance and physical properties. In this work, we have accomplished this with crystalline molecular rotors self-assembled by halogen bonding of diazabicyclo[2.2.2]octane, acting as a rotator, and a set of five fluorine-substituted iodobenzenes that take the role of the stator. Using variable-temperature (1)H T1 spin-lattice relaxation measurements, we have shown that all structures display ultrafast Brownian rotation with activation energies of 2.4-4.9 kcal/mol and pre-exponential factors of the order of (1-9) × 10(12) s(-1). Line shape analysis of quadrupolar echo (2)H NMR measurements in selected examples indicated rotational trajectories consistent with the 3-fold or 6-fold symmetric potential of the rotator.

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

    SciTech Connect

    Bukkuru, S. Rao, A. D. P.; Warrier, M.

    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.

  12. Application of superplastically formed and diffusion bonded aluminum to a laminar flow control leading edge

    NASA Technical Reports Server (NTRS)

    Goodyear, M. D.

    1987-01-01

    NASA sponsored the Aircraft Energy Efficiency (ACEE) program in 1976 to develop technologies to improve fuel efficiency. Laminar flow control was one such technology. Two approaches for achieving laminar flow were designed and manufactured under NASA sponsored programs: the perforated skin concept used at McDonnell Douglas and the slotted design used at Lockheed-Georgia. Both achieved laminar flow, with the slotted design to a lesser degree (JetStar flight test program). The latter design had several fabrication problems concerning springback and adhesive flow clogging the air flow passages. The Lockheed-Georgia Company accomplishments is documented in designing and fabricating a small section of a leading edge article addressing a simpler fabrication method to overcome the previous program's manufacturing problems, i.e., design and fabrication using advanced technologies such as diffusion bonding of aluminum, which has not been used on aerospace structures to date, and the superplastic forming of aluminum.

  13. Strength and fracture behaviour of diffusion bonded joints in Al-Li (8090) alloy. III - Peel strength

    NASA Astrophysics Data System (ADS)

    Dunford, D. V.; Partridge, P. G.

    1992-11-01

    Peel strengths at room temperature and under superplastic forming conditions at 530 C were measured for diffusion-bonded joints in Al-Li 8090 alloy sheet. The bonds were made in the solid state, or via a transient liquid phase using interlayers. The effect of strain rate, sheet thickness and heat treatment were investigated. The significance of these results for the testing of DB joints and for their use in DB/SPF structures is discussed.

  14. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  15. Reactive diffusion bonding of Si3N4 to MA6000

    NASA Astrophysics Data System (ADS)

    Kaysser, W. A.; Frisch, A.; Zhang, W.; Petzow, G.

    The procedure for joining Si3N4 to the MA6000 superalloy by diffusion bonding during HIP is described. Due to the large thermal mismatch between both components, it was necessary to introduce multiphase interlayers to allow relaxation of thermal stresses. Calculations of the stress development and the results of experiments showed that stress relaxation by thin soft interlayers in Si3N4/MA6000 is very limited: during bonding of Si3N4 to metals suitable as interlayers, brittle reaction products often form at the metal/ceramic interfaces. Experiments were then performed with iron-based alloys with small thermal expansion coefficients at low temperatures, combined with V, Nb, and Hf-based layers, and the reactions at the layer interfaces and the fracture surfaces were investigated by SEM, EDX, and WDX. It was found that, in systems with low deformability of the stiff reaction layers, stress relaxation by controlled microcrack formation reduced the interfacial damage and improved the mechanical stability of the joints.

  16. Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics.

    PubMed

    Straight, Shelby C; Paesani, Francesco

    2016-08-25

    To probe the dynamic nature of the hydrogen bond network in water, linear and nonlinear infrared spectra of dilute HOD in H2O are computed from many-body molecular dynamics simulations with the MB-pol potential, which have been shown to accurately predict the properties of water from the gas to the condensed phase. The effects of various approximations to the many-body expansion of the dipole moment surface on the OD-stretch absorption line shapes are analyzed at different levels of theory. The interplay between effects associated with the variation of the HOD dipole moment and instantaneous nuclear configurations causes qualitative differences in the absorption profiles, which are traced back to how induction contributions are treated within the many-body formalism. Further analysis of the multidimensional infrared spectra demonstrates that the spectral diffusion of the OD stretching frequencies depends explicitly on the level of truncation in the many-body expansion of the dipole moment in the short-time regime that is associated with intact hydrogen-bond dynamics. In contrast, the long-time evolution of spectral diffusion, describing collective rearrangements of the hydrogen-bond network, is effectively independent of the details with which many-body contributions to the dipole moment are represented. PMID:27109247

  17. Dynamic urea bond for the design of reversible and self-healing polymers

    PubMed Central

    Ying, Hanze; Zhang, Yanfeng; Cheng, Jianjun

    2014-01-01

    Polymers bearing dynamic covalent bonds may exhibit dynamic properties, such as self-healing, shape memory and environmental adaptation. However, most dynamic covalent chemistries developed so far require either catalyst or change of environmental conditions to facilitate bond reversion and dynamic property change in bulk materials. Here we report the rational design of hindered urea bonds (urea with bulky substituent attached to its nitrogen) and the use of them to make polyureas and poly(urethane-ureas) capable of catalyst-free dynamic property change and autonomous repairing at low temperature. Given the simplicity of the hindered urea bond chemistry (reaction of a bulky amine with an isocyanate), incorporation of the catalyst-free dynamic covalent urea bonds to conventional polyurea or urea-containing polymers that typically have stable bulk properties may further broaden the scope of applications of these widely used materials. PMID:24492620

  18. FRET Fluctuation Spectroscopy of Diffusing Biopolymers: Contributions of Conformational Dynamics and Translational Diffusion

    PubMed Central

    Gurunathan, Kaushik; Levitus, Marcia

    2009-01-01

    The use of Fluorescence Correlation Spectroscopy (FCS) to study conformational dynamics in diffusing biopolymers requires that the contributions to the signal due to translational diffusion are separated from those due to conformational dynamics. A simple approach that has been proposed to achieve this goal involves the analysis of fluctuations in Fluorescence Resonance Energy Transfer (FRET) efficiency. In this work, we investigate the applicability of this methodology by combining Monte Carlo simulations and experiments. Results show that diffusion does not contribute to the measured fluctuations in FRET efficiency in conditions where the relaxation time of the kinetic process is much shorter than the mean transit time of the molecules in the optical observation volume. However, in contrast to what has been suggested in previous work, the contributions of diffusion are otherwise significant. Neglecting the contributions of diffusion can potentially lead to an erroneous interpretation of the kinetic mechanisms. As an example, we demonstrate that the analysis of FRET fluctuations in terms of a purely kinetic model would generally lead to the conclusion that the system presents complex kinetic behavior even for an idealized two-state system PMID:20030305

  19. Microstructure and mechanical properties of diffusion bonded W/steel joint using V/Ni composite interlayer

    SciTech Connect

    Liu, W.S.; Cai, Q.S. Ma, Y.Z.; Wang, Y.Y.; Liu, H.Y.; Li, D.X.

    2013-12-15

    Diffusion bonding between W and steel using V/Ni composite interlayer was carried out in vacuum at 1050 °C and 10 MPa for 1 h. The microstructural examination and mechanical property evaluation of the joints show that the bonding of W to steel was successful. No intermetallic compound was observed at the steel/Ni and V/W interfaces for the joints bonded. The electron probe microanalysis and X-ray diffraction analysis revealed that Ni{sub 3}V, Ni{sub 2}V, Ni{sub 2}V{sub 3} and NiV{sub 3} were formed at the Ni/V interface. The tensile strength of about 362 MPa was obtained for as-bonded W/steel joint and the failure occurred at W near the V/W interface. The nano-indentation test across the joining interfaces demonstrated the effect of solid solution strengthening and intermetallic compound formation in the diffusion zone. - Highlights: • Diffusion bonding of W to steel was realized using V/Ni composite interlayer. • The interfacial microstructure of the joint was clarified. • Several V–Ni intermetallic compounds were formed in the interface region. • The application of V/Ni composite interlayer improved the joining quality.

  20. The effect of the nature of H-bonding groups on diffusion through PDMS membranes saturated with octanol and toluene.

    PubMed

    Du Plessis, Jeanetta; Pugh, W John; Judefeind, Anja; Hadgraft, Jonathan

    2002-02-01

    The permeation of a series of structurally related compounds across silicone membranes (PDMS) was studied. The PDMS was saturated either with toluene, to mimic a functionally inert barrier, or octanol, to mimic the polar/hydrogen bonding environment of the stratum corneum lipid barrier. Phenol, salicylic acid, benzoic acid, anisole, phenylethanol and benzyl alcohol were chosen in an attempt to relate permeation to their different H-bonding capabilities. The flux was lower through the octanol system suggesting retardation by polar/H-bonding interactions. Separation of the permeability coefficient into its thermodynamic (partition coefficient) and kinetic (diffusion coefficient) terms suggests that the effect of altering polarity within the membrane has a greater impact on the diffusion of permeant rather than its chemical potential within the membrane.

  1. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGESBeta

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; Allendorf, M. D.

    2016-03-23

    In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

  2. Transient Liquid-Phase Diffusion Bonding of Aluminum Metal Matrix Composite Using a Mixed Cu-Ni Powder Interlayer

    NASA Astrophysics Data System (ADS)

    Maity, Joydeep; Pal, Tapan Kumar

    2012-07-01

    In the present study, the transient liquid-phase diffusion bonding of an aluminum metal matrix composite (6061-15 wt.% SiCp) has been investigated for the first time using a mixed Cu-Ni powder interlayer at 560 °C, 0.2 MPa, for different holding times up to 6 h. The microstructure of the isothermally solidified zone contains equilibrium precipitate CuAl2, metastable precipitate Al9Ni2 in the matrix of α-solid solution along with the reinforcement particles (SiC). On the other hand, the microstructure of the central bond zone consists of equilibrium phases such as NiAl3, Al7Cu4Ni and α-solid solution along with SiC particles (without any segregation) and the presence of microporosities. During shear test, the crack originates from microporosities and propagates along the interphase interfaces resulting in poor bond strength for lower holding times. As the bonding time increases, with continual diffusion, the structural heterogeneity is diminished, and the microporosities are eliminated at the central bond zone. Accordingly, after 6-h holding, the microstructure of the central bond zone mainly consists of NiAl3 without any visible microporosity. This provides a joint efficiency of 84% with failure primarily occurring through decohesion at the SiC particle/matrix interface.

  3. A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

    NASA Technical Reports Server (NTRS)

    Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

    2003-01-01

    A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

  4. Catastrophe in diffusion-controlled annihilation dynamics: general scaling properties

    NASA Astrophysics Data System (ADS)

    Shipilevsky, Boris M.

    2015-11-01

    We present a systematic analytical and numerical study of the annihilation catastrophe phenomenon which develops in an open system, where species A and B diffuse from the bulk of restricted medium and die on its surface (desorb) by the reaction A + B → 0. This phenomenon arises in the diffusion-controlled limit as a result of self-organizing explosive growth (drop) of the surface concentrations of, respectively, slow and fast particles (concentration explosion) and manifests itself in the form of an abrupt singular jump of the desorption flux relaxation rate. In the recent work [B.M. Shipilevsky, Phys. Rev. E 76, 031126 (2007)] a closed scaling theory of catastrophe development has been given for the asymptotic limit when the characteristic time scale of explosion becomes much less than the characteristic time scales of diffusion of slow and fast particles at an arbitrary ratio of their diffusivities 0 < p < 1. In this paper we consider the behavior of the system at strong difference of species diffusivities p ≪ 1 and reveal a rich general pattern of catastrophe development for an arbitrary ratio of the characteristic time scales of explosion and fast particle diffusion. As striking results we find remarkable scaling properties of catastrophe evolution at the crossover between two limiting regimes with radically different dynamics.

  5. Dynamics of double-diffusive lock-exchange gravity currents

    NASA Astrophysics Data System (ADS)

    Konopliv, Nathan; Meiburg, Eckart

    2015-11-01

    The dynamics of double-diffusive gravity currents exhibiting the fingering instability were examined using 2D simulations of a lock exchange initial configuration. Both the initial stability ratio and the diffusivity ratio were varied. It was found that although the spreading of the currents was governed by a balance of buoyancy and turbulent drag forces, currents with more intense fingering spread faster than those with less intense or no fingering. This was due to an increase in the buoyancy of the currents with stronger fingering, which had a stronger effect than the increased drag. The fingering also affected the thickness of the currents, with more fingering corresponding to thinner currents. The mechanism that caused the thinner currents was also responsible for the creation of secondary and tertiary currents after a long time in a simulation that had intense fingering. If no secondary or tertiary currents formed, the density of the current was governed by a balance of double-diffusive and diffusive fluxes. An energy budget analysis revealed that double diffusive currents released more potential energy, had more dissipation and converted a significant amount of internal energy into potential energy via the diffusion of heat and salinity.

  6. Diffusion Dynamics and Creative Destruction in a Simple Classical Model

    PubMed Central

    2015-01-01

    ABSTRACT The article explores the impact of the diffusion of new methods of production on output and employment growth and income distribution within a Classical one‐sector framework. Disequilibrium paths are studied analytically and in terms of simulations. Diffusion by differential growth affects aggregate dynamics through several channels. The analysis reveals the non‐steady nature of economic change and shows that the adaptation pattern depends both on the innovation's factor‐saving bias and on the extent of the bias, which determines the strength of the selection pressure on non‐innovators. The typology of different cases developed shows various aspects of Schumpeter's concept of creative destruction. PMID:27642192

  7. Diffuse reflectance infrared spectroscopic identification of dispersant/particle bonding mechanisms in functional inks.

    PubMed

    Deiner, L Jay; Farjami, Elaheh

    2015-05-08

    In additive manufacturing, or 3D printing, material is deposited drop by drop, to create micron to macroscale layers. A typical inkjet ink is a colloidal dispersion containing approximately ten components including solvent, the nano to micron scale particles which will comprise the printed layer, polymeric dispersants to stabilize the particles, and polymers to tune layer strength, surface tension and viscosity. To rationally and efficiently formulate such an ink, it is crucial to know how the components interact. Specifically, which polymers bond to the particle surfaces and how are they attached? Answering this question requires an experimental procedure that discriminates between polymer adsorbed on the particles and free polymer. Further, the method must provide details about how the functional groups of the polymer interact with the particle. In this protocol, we show how to employ centrifugation to separate particles with adsorbed polymer from the rest of the ink, prepare the separated samples for spectroscopic measurement, and use Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS) for accurate determination of dispersant/particle bonding mechanisms. A significant advantage of this methodology is that it provides high level mechanistic detail using only simple, commonly available laboratory equipment. This makes crucial data available to almost any formulation laboratory. The method is most useful for inks composed of metal, ceramic, and metal oxide particles in the range of 100 nm or greater. Because of the density and particle size of these inks, they are readily separable with centrifugation. Further, the spectroscopic signatures of such particles are easy to distinguish from absorbed polymer. The primary limitation of this technique is that the spectroscopy is performed ex-situ on the separated and dried particles as opposed to the particles in dispersion. However, results from attenuated total reflectance spectra of the wet separated

  8. Diffuse reflectance infrared spectroscopic identification of dispersant/particle bonding mechanisms in functional inks.

    PubMed

    Deiner, L Jay; Farjami, Elaheh

    2015-01-01

    In additive manufacturing, or 3D printing, material is deposited drop by drop, to create micron to macroscale layers. A typical inkjet ink is a colloidal dispersion containing approximately ten components including solvent, the nano to micron scale particles which will comprise the printed layer, polymeric dispersants to stabilize the particles, and polymers to tune layer strength, surface tension and viscosity. To rationally and efficiently formulate such an ink, it is crucial to know how the components interact. Specifically, which polymers bond to the particle surfaces and how are they attached? Answering this question requires an experimental procedure that discriminates between polymer adsorbed on the particles and free polymer. Further, the method must provide details about how the functional groups of the polymer interact with the particle. In this protocol, we show how to employ centrifugation to separate particles with adsorbed polymer from the rest of the ink, prepare the separated samples for spectroscopic measurement, and use Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS) for accurate determination of dispersant/particle bonding mechanisms. A significant advantage of this methodology is that it provides high level mechanistic detail using only simple, commonly available laboratory equipment. This makes crucial data available to almost any formulation laboratory. The method is most useful for inks composed of metal, ceramic, and metal oxide particles in the range of 100 nm or greater. Because of the density and particle size of these inks, they are readily separable with centrifugation. Further, the spectroscopic signatures of such particles are easy to distinguish from absorbed polymer. The primary limitation of this technique is that the spectroscopy is performed ex-situ on the separated and dried particles as opposed to the particles in dispersion. However, results from attenuated total reflectance spectra of the wet separated

  9. Diffusion bonding of CMSX-4 to UDIMET 720 using PVD-coated interfaces and HIP

    SciTech Connect

    Larker, R.; Ockborn, J.; Selling, B.

    1999-07-01

    There is an increasing interest in development of manufacturing methods for Dual Property BLISKs (BLaded dISKs), consisting of creep resistant airfoils and fatigue resistant disks bonded together by a durable joint. Optimum heat treatments are, however, very different for creep resistant single crystal CMSX-4 and fatigue resistant polycrystalline Udimet 720 selected in this study, but fortunately the first aging treatment for CMSX-4 (1140 C, 2-6h, AC) is similar to the partial solution treatment of U 720 HS2 (1115 C, 4h, OQ). Based on this, diffusion bonding was performed by HIP at 1120 C and 200 MPa argon pressure for 4 h, followed by cooling to 400 C. Subsequently, a shortened Udimet 720 HS2 two-step aging treatment was adopted by heating to 650 C for 6 h followed by cooling to 400 C, heating to 760 C for 2 h, and finally cooling to R.T. under remaining HIP pressure. Plasma etching followed by thin (80 nm) PVD coating with either nickel or titanium were used to clean and protect the polished surfaces before joining. The selection of coatings was governed by the possibility to reduce oxidized nickel by flushing with hydrogen at 330 C during evacuation of the HIP capsules, and by the large solubility of oxygen in titanium. Hot tensile testing was performed at 750 C on both joined and reference materials subjected to the modified heat treatment. Initially solution treated Udimet 720 and CMSX-4 comprised the reference materials. The testing showed that joints with Ni-PV coatings were almost as strong as Udimet 720 (although with very limited elongation), while the joints with Ti-PVD coatings were weaker.

  10. Void shrinking process and mechanisms of the diffusion bonded Ti-6Al-4V alloy with different surface roughness

    NASA Astrophysics Data System (ADS)

    Li, H.; Li, M. Q.; Kang, P. J.

    2016-01-01

    The diffusion bonding of Ti-6Al-4V alloy with different surface roughness was performed at 5 and 10 MPa. The influence of surface roughness on the void shrinking process and mechanisms was investigated. The average void size increases as the R a increases from 0.33 to 0.44 μm, while it decreases as the R a increases to 0.46 μm because of the decreasing of R λq. The void shrinking mechanisms were analyzed by using the dynamic model of void shrinking. Power-law creep is a dominant mechanism on void shrinking, of which the contribution decreases as the R a increases from 0.33 to 0.44 μm, while it increases as the R a increases to 0.46 μm. The influence of surface roughness on the contribution of plastic deformation and surface source mechanism on void shrinking is not significant while that on the contribution of interface source mechanism is dependent on the imposing pressure. The optimizing surface roughness is with a R a of 0.33 μm and R λq of 5.38 μm in this study.

  11. Dynamic Characterization of Crystalline Supramolecular Rotors Assembled through Halogen Bonding.

    PubMed

    Catalano, Luca; Pérez-Estrada, Salvador; Terraneo, Giancarlo; Pilati, Tullio; Resnati, Giuseppe; Metrangolo, Pierangelo; Garcia-Garibay, Miguel A

    2015-12-16

    A modular molecular kit for the preparation of crystalline molecular rotors was devised from a set of stators and rotators to gain simple access to a large number of structures with different dynamic performance and physical properties. In this work, we have accomplished this with crystalline molecular rotors self-assembled by halogen bonding of diazabicyclo[2.2.2]octane, acting as a rotator, and a set of five fluorine-substituted iodobenzenes that take the role of the stator. Using variable-temperature (1)H T1 spin-lattice relaxation measurements, we have shown that all structures display ultrafast Brownian rotation with activation energies of 2.4-4.9 kcal/mol and pre-exponential factors of the order of (1-9) × 10(12) s(-1). Line shape analysis of quadrupolar echo (2)H NMR measurements in selected examples indicated rotational trajectories consistent with the 3-fold or 6-fold symmetric potential of the rotator. PMID:26583701

  12. Method for producing components with internal architectures, such as micro-channel reactors, via diffusion bonding sheets

    DOEpatents

    Alman, David E.; Wilson, Rick D.; Davis, Daniel L.

    2011-03-08

    This invention relates to a method for producing components with internal architectures, and more particularly, this invention relates to a method for producing structures with microchannels via the use of diffusion bonding of stacked laminates. Specifically, the method involves weakly bonding a stack of laminates forming internal voids and channels with a first generally low uniaxial pressure and first temperature such that bonding at least between the asperites of opposing laminates occurs and pores are isolated in interfacial contact areas, followed by a second generally higher isostatic pressure and second temperature for final bonding. The method thereby allows fabrication of micro-channel devices such as heat exchangers, recuperators, heat-pumps, chemical separators, chemical reactors, fuel processing units, and combustors without limitation on the fin aspect ratio.

  13. Molecular dynamics evaluation of self-diffusion in Yukawa systems

    NASA Astrophysics Data System (ADS)

    Ohta, H.; Hamaguchi, S.

    2000-11-01

    Self-diffusion coefficients of Yukawa systems in the fluid phase are obtained from molecular dynamics simulations in a wide range of the thermodynamical parameters. The Yukawa system is a collection of particles interacting through Yukawa (i.e., screened Coulomb) potentials, which may serve as a model for charged dust particles in a plasma or colloidal particles in electrolytes. The self-diffusion coefficients are found to follow a simple scaling law with respect to the system temperature, which is consistent with the universal scaling (i.e., temperature scaling independent of the ratio of interparticle distance to screening length) observed by Robbins et al. [J. Chem. Phys. 88, 3286 (1988)] if the fluid system is near solidification. Also discussed is the velocity autocorrelation function, which is in part used to determine the self-diffusion coefficients through the Green-Kubo formula.

  14. Indirect Versus Direct Heating of Sheet Materials: Superplastic Forming and Diffusion Bonding Using Lasers

    NASA Astrophysics Data System (ADS)

    Jocelyn, Alan; Kar, Aravinda; Fanourakis, Alexander; Flower, Terence; Ackerman, Mike; Keevil, Allen; Way, Jerome

    2010-06-01

    Many from within manufacturing industry consider superplastic forming (SPF) to be ‘high tech’, but it is often criticized as too complicated, expensive, slow and, in general, an unstable process when compared to other methods of manipulating sheet materials. Perhaps, the fundamental cause of this negative perception of SPF, and also of diffusion bonding (DB), is the fact that the current process of SPF/DB relies on indirect sources of heating to produce the conditions necessary for the material to be formed. Thus, heat is usually derived from the electrically heated platens of hydraulic presses, to a lesser extent from within furnaces and, sometimes, from heaters imbedded in ceramic moulds. Recent evaluations of these isothermal methods suggest they are slow, thermally inefficient and inappropriate for the process. In contrast, direct heating of only the material to be formed by modern, electrically efficient, lasers could transform SPF/DB into the first choice of designers in aerospace, automotive, marine, medical, architecture and leisure industries. Furthermore, ‘variable temperature’ direct heating which, in theory, is possible with a laser beam(s) may provide a means to control material thickness distribution, a goal of enormous importance as fuel efficient, lightweight structures for transportation systems are universally sought. This paper compares, and contrasts, the two systems and suggests how a change to laser heating might be achieved.

  15. Evaluation of Cu as an interlayer in Be/F82H diffusion bonds for ITER TBM

    NASA Astrophysics Data System (ADS)

    Hunt, R. M.; Goods, S. H.; Ying, A.; Dorn, C. K.; Abdou, M.

    2011-10-01

    Copper has been investigated as a potential interlayer material for diffusion bonds between beryllium and Reduced Activation Ferritic/Martensitic (RAFM) steel. Utilizing Hot Isostatic Pressing (HIP), copper was directly bonded to a RAFM steel, F82H, at 650 °C, 700 °C, 750 °C, 800 °C and 850 °C, under 103 MPa for 2 h. Interdiffusion across the bonded interface was limited to 1 μm or less, even at the highest HIP'ing temperature. Through mechanical testing it was found that samples HIP'ed at 750 °C and above remain bonded up to 211 MPa under tensile loading, at which point ductile failure occurred in the bulk copper. As titanium will be used as a barrier layer to prevent the formation of brittle Be/Cu intermetallics, additional annealing studies were performed on copper samples coated with a titanium thin film to study Ti/Cu interdiffusion characteristics. Samples were heated to temperatures between 650 °C and 850 °C for 2 h in order to mimic the range of likely HIP temperatures. A correlation was drawn between HIP temperature and diffusion depth for use in determining the minimum Ti film thickness necessary to block diffusion in the Be/F82H joint.

  16. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541

  17. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  18. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  19. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    PubMed

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  20. Spatiotemporal mapping of diffusion dynamics and organization in plasma membranes

    NASA Astrophysics Data System (ADS)

    Bag, Nirmalya; Ng, Xue Wen; Sankaran, Jagadish; Wohland, Thorsten

    2016-09-01

    Imaging fluorescence correlation spectroscopy (FCS) and the related FCS diffusion law have been applied in recent years to investigate the diffusion modes of lipids and proteins in membranes. These efforts have provided new insights into the membrane structure below the optical diffraction limit, new information on the existence of lipid domains, and on the influence of the cytoskeleton on membrane dynamics. However, there has been no systematic study to evaluate how domain size, domain density, and the probe partition coefficient affect the resulting imaging FCS diffusion law parameters. Here, we characterize the effects of these factors on the FCS diffusion law through simulations and experiments on lipid bilayers and live cells. By segmenting images into smaller 7  ×  7 pixel areas, we can evaluate the FCS diffusion law on areas smaller than 2 µm and thus provide detailed maps of information on the membrane structure and heterogeneity at this length scale. We support and extend this analysis by deriving a mathematical expression to calculate the mean squared displacement (MSDACF) from the autocorrelation function of imaging FCS, and demonstrate that the MSDACF plots depend on the existence of nanoscopic domains. Based on the results, we derive limits for the detection of domains depending on their size, density, and relative viscosity in comparison to the surroundings. Finally, we apply these measurements to bilayers and live cells using imaging total internal reflection FCS and single plane illumination microscopy FCS.

  1. Collective sub-diffusive dynamics in bacterial carpet microfluidic channel

    NASA Astrophysics Data System (ADS)

    Hsiao, Yi-Teng; Wang, Jing-Hui; Hsu, Yi-Chun; Chiu, Chien-Chun; Lo, Chien-Jung; Tsao, Chia-Wen; Yen Woon, Wei

    2012-05-01

    We experimentally investigate the collective dynamics in bacterial carpet microfluidic channel. The microfluidic channel is composed of single polar flagellated Vibrio alginolyticus deposited glass substrates. The individual flagellum swimming speed is tuned by varying buffer sodium concentration. Hydrodynamic coupling strength is tuned by varying buffer viscosity. The attached bacteria constantly perform two major modes in flagellum motion, namely, the local rotation and large angle flick. Particle tracking statistics shows high flagellum rotational rate and strong hydrodynamic coupling strength lead to collective sub-diffusive dynamics. The observed effect is strongly correlated to hydrodynamic coupling of flick motions between nearby bacteria.

  2. Dynamics of Robertson–Walker spacetimes with diffusion

    SciTech Connect

    Alho, A.; Calogero, S.; Machado Ramos, M.P.; Soares, A.J.

    2015-03-15

    We study the dynamics of spatially homogeneous and isotropic spacetimes containing a fluid undergoing microscopic velocity diffusion in a cosmological scalar field. After deriving a few exact solutions of the equations, we continue by analyzing the qualitative behavior of general solutions. To this purpose we recast the equations in the form of a two dimensional dynamical system and perform a global analysis of the flow. Among the admissible behaviors, we find solutions that are asymptotically de-Sitter both in the past and future time directions and which undergo accelerated expansion at all times.

  3. Effects of interface bonding and defects on boron diffusion at Si/SiO{sub 2} interface

    SciTech Connect

    Kim, Geun-Myeong; Oh, Young Jun; Chang, K. J.

    2013-12-14

    We perform first-principles density functional calculations to find the migration pathway and barrier for B diffusion at the Si/SiO{sub 2} interface. For various interface models, in which crystalline α-quartz or amorphous silica (a-SiO{sub 2}) is placed on Si, we examine stable and metastable configurations of B-related defects which play a role in B diffusion. While a substitutional B alone is immobile in Si, it tends to diffuse to the interface via an interstitialcy mechanism in the presence of a self-interstitial and then changes into an interstitial B in oxide via a kick-out mechanism, leaving the self-interstitial at the interface. At the defect-free interface, where bridging O atoms are inserted to remove interface dangling bonds, an interstitial B prefers to intervene between the interface Si and bridging O atoms and subsequently diffuses through the hollow space or along the network of the Si-O-Si bonds in oxide. The overall migration barriers are calculated to be 2.02–2.12 eV at the Si/α-quartz interface, while they lie in the range of 2.04 ± 0.44 eV at the Si/a-SiO{sub 2} interface, similar to that in α-quartz. The migration pathway and barrier are not significantly affected by interface defects such as suboxide bond and O protrusion, while dangling bonds in the suboxide region can increase the migration barrier by about 1.5 eV. The result that the interface generally does not hinder the B diffusion from Si to SiO{sub 2} assists in understanding the underlying mechanism for B segregation which commonly occurs at the Si/SiO{sub 2} interface.

  4. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    PubMed

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  5. An investigation on microstructure evolution and mechanical properties during liquid state diffusion bonding of Al2024 to Ti–6Al–4V

    SciTech Connect

    Samavatian, Majid; Halvaee, Ayoub; Amadeh, Ahmad Ali; Khodabandeh, Alireza

    2014-12-15

    Joining mechanism of Ti/Al dissimilar alloys was studied during liquid state diffusion bonding process using Cu/Sn/Cu interlayer at 510 °C under vacuum of 7.5 × 10{sup −5} Torr for various bonding times. The microstructure and compositional changes in the joint zone were analyzed by scanning electron microscopy equipped with energy dispersive spectroscopy and X-ray diffraction. Microhardness and shear strength tests were also applied to study the mechanical properties of the joints. It was found that with an increase in bonding time, the elements of interlayer diffused into the parent metals and formed various intermetallic compounds at the interface. Diffusion process led to the isothermal solidification and the bonding evolution in the joint zone. The results from mechanical tests showed that microhardness and shear strength values have a straight relation with bonding time so that the maximum shear strength of joint was obtained for a bond made with 60 min bonding time. - Highlights: • Liquid state diffusion bonding of Al2024 to Ti–6Al–4V was performed successfully. • Diffusion of the elements caused the formation of various intermetallics at the interface. • Microhardness and shear strength values have a straight relation with bonding time. • The maximum shear strength reached to 36 MPa in 60 min bonding time.

  6. Convection-diffusion effects in marathon race dynamics

    NASA Astrophysics Data System (ADS)

    Rodriguez, E.; Espinosa-Paredes, G.; Alvarez-Ramirez, J.

    2014-01-01

    In the face of the recent terrorist attack event on the 2013 Boston Marathon, the increasing participation of recreational runners in large marathon races has imposed important logistical and safety issues for organizers and city authorities. An accurate understanding of the dynamics of the marathon pack along the race course can provide important insights for improving safety and performance of these events. On the other hand, marathon races can be seen as a model of pedestrian movement under confined conditions. This work used data of the 2011 Chicago Marathon event for modeling the dynamics of the marathon pack from the corral zone to the finish line. By considering the marathon pack as a set of particles moving along the race course, the dynamics are modeled as a convection-diffusion partial differential equation with position-dependent mean velocity and diffusion coefficient. A least-squares problem is posed and solved with optimization techniques for fitting field data from the 2011 Chicago Marathon. It was obtained that the mean pack velocity decreases while the diffusion coefficient increases with distance. This means that the dispersion rate of the initially compact marathon pack increases as the marathon race evolves along the race course.

  7. Assessment of diffusion-bonded KTP crystals for efficient, low pulse energy conversion from 1 to 2 microm.

    PubMed

    Perrett, Brian J; Mason, Paul D; Orchard, David A

    2006-06-20

    Diffusion bonded (DB) walk-off compensated KTP crystals offer an alternative nonlinear medium for efficient 1 to 2 microm conversion within optical parametric oscillators (OPOs) at low pulse energies. Spatial variations in optical absorption and transmission values measured at 2 mum are reported for two DB-KTP crystals. Finally, a comparison is made between the conversion efficiency obtained from a degenerate 1 microm pumped OPO using a single 20 mm KTP crystal and an equivalent length DB-KTP crystal consisting of two bonded 10 mm crystals. PMID:16778951

  8. The Structure and Properties of Diffusion Assisted Bonded Joints in 17-4 PH, Type 347, 15-5 PH and Nitronic 40 Stainless Steels

    NASA Technical Reports Server (NTRS)

    Wigley, D. A.

    1981-01-01

    Diffusion assisted bonds are formed in 17-4 PH, 15-5 PH, type 347 and Nitronic 40 stainless steels using electrodeposited copper as the bonding agent. The bonds are analyzed by conventional metallographic, electron microprobe analysis, and scanning electron microscopic techniques as well as Charpy V-notch impact tests at temperatures of 77 and 300 K. Results are discussed in terms of a postulated model for the bonding process.

  9. Diffusion Bonding Behavior and Characterization of Joints Made Between 316L Stainless Steel Alloy and AZ31 Magnesium Alloy

    NASA Astrophysics Data System (ADS)

    Elthalabawy, Waled Mohamed

    The 316L austenitic stainless steel and AZ31 magnesium alloy have physical and mechanical properties which makes these alloys suitable in a number of high technology based industries such as the aerospace and automotive sectors. However, for these alloys to be used in engineering applications, components must be fabricated and joined successfully. The differences in the physical and metallurgical properties between these two alloys prevents the use of conventional fusion welding processes commonly employed in aerospace and transport industry. Therefore, alternative techniques need to be developed and diffusion bonding technology is a process that has considerable potential to join these two dissimilar alloys. In this research work both solid-state and transient liquid phase (TLP) bonding processes were applied. The solid-state bonding of 316L steel to AZ31 magnesium alloy was possible at a bonding temperature of 550°C for 120 minutes using a pressure of 1.3 MPa. The interface characterization of the joint showed a thin intermetallic zone rich in Fe-Al was responsible for providing a metallurgical bond. However, low joint shear strengths were recorded and this was attributed to the poor surface to surface contact. The macro-deformation of the AZ31 alloy prevented the use of higher bonding pressures and longer bonding times. In order to overcome these problems, the TLP bonding process was implemented using pure Cu and Ni foils as interlayers which produced a eutectic phase at the bonding temperature. This research identified the bonding mechanism through microstructural and differential scanning calorimetry investigations. The microstructural characterization of the TLP joints identified intermetallics which became concentrated along the 316L steel/AZ31 bond interface due to the "pushing effect" of the solid/liquid interface during isothermal solidification stage of bonding. The size and concentration of the intermetallics had a noticeable effect on the final joint

  10. Dynamics of the diffusive DM-DE interaction – Dynamical system approach

    NASA Astrophysics Data System (ADS)

    Haba, Zbigniew; Stachowski, Aleksander; Szydłowski, Marek

    2016-07-01

    We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM) . The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initial conditions. We also fit the model parameters using astronomical observation: SNIa, H(z), BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.

  11. Dynamics of the diffusive DM-DE interaction - Dynamical system approach

    NASA Astrophysics Data System (ADS)

    Haba, Zbigniew; Stachowski, Aleksander; Szydłowski, Marek

    2016-07-01

    We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM) . The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initial conditions. We also fit the model parameters using astronomical observation: SNIa, H(z), BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.

  12. Brownian Dynamics Simulation of Macromolecule Diffusion in a Protocell

    NASA Astrophysics Data System (ADS)

    Ando, Tadashi; Skolnick, Jeffrey

    2011-01-01

    The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.

  13. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    PubMed

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  14. Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water.

    PubMed

    Henchman, Richard H; Irudayam, Sheeba Jem

    2010-12-23

    A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the

  15. Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry

    PubMed Central

    Means, Shawn; Smith, Alexander J.; Shepherd, Jason; Shadid, John; Fowler, John; Wojcikiewicz, Richard J. H.; Mazel, Tomas; Smith, Gregory D.; Wilson, Bridget S.

    2006-01-01

    We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations. PMID:16617072

  16. Molecular-dynamics simulation of hydrogen diffusion in palladium

    NASA Astrophysics Data System (ADS)

    Li, Yinggang; Wahnström, Göran

    1992-12-01

    Molecular-dynamics simulations for hydrogen diffusion in Pd are performed for a system consisting of 256 Pd atoms and 8 H atoms at the temperature T=623 K. Under these conditions detailed quasielastic-neutron-scattering (QNS) data are available. For the interatomic interactions we use the embedded-atom method (EAM), which incorporates some essential many-body effects in metals. Based on the EAM approach, the wave-vector dependence of the width of the QNS peak is investigated in detail. It is found that a single electronically adiabatic potential-energy surface cannot reproduce the observed wave-vector dependence. After incorporating the coupling of hydrogen atoms to the low-lying electron-hole pair excitations among the conduction electrons, close agreement with the experimental data is obtained. This is a strong indication that one has to go beyond the Born-Oppenheimer approximation in order to characterize correctly the diffusive motion of hydrogen in metals. To reveal the diffusive behavior in more detail, the residence time distribution and the correlation character in diffusion direction are investigated. We found that including the nonadiabatic corrections reduces the probability for the H atoms to move over several lattice sites without getting trapped in between. As a result, the motion of the H atoms becomes more similar to that assumed in the Chudley-Elliott model, which describes well the QNS data for the wave-vector dependence of the width.

  17. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

    1996-03-01

    We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

  18. Interface science of controlled metal/metal and metal/ceramic interfaces prepared using ultrahigh vacuum diffusion bonding

    SciTech Connect

    King, W.E.; Campbell, G.H.; Coombs, A.W.; Johnson, G.W.; Kelly, B.E.; Reitz, T.C.; Stoner, S.L.; Wien, W.L.; Wilson, D.M.

    1993-04-01

    We have designed, constructed, and are operating a capability for production of controlled homophase and heterophase interfaces: an ultrahigh vacuum diffusion bonding machine. This machine is based on a previous design which is operating at the Max Planck Institut fuer Metallforschung, Institut fuer Werkstoffwissenschaft, Stuttgart, FRG. In this method, flat-polished single or polycrystals of materials with controlled surfaced topography can be heat treated up to 1500C in ultrahigh vacuum. Surfaces of annealed samples can be sputter cleaned and characterized prior to bonding. Samples can then be precisely aligned crystallographically to obtain desired grain boundary misorientations. Material couples can then be bonded at temperatures up to 1500C and pressures up to 10 MPa. Results are presented from initial work on Mo grain boundaries and Cu/Al{sub 2}A{sub 3} interfaces.

  19. Superplastic forming and diffusion bonding of rapidly solidified, dispersion strengthened aluminum alloys for elevated temperature structural applications

    NASA Technical Reports Server (NTRS)

    Ting, E. Y.; Kennedy, J. R.

    1989-01-01

    Rapidly solidified alloys, based upon the Al-Fe-V-Si system and designed for elevated temperature applications, were evaluated for superplasticity and diffusion bonding behavior. Alloys with 8, 16, 27, and 36 volume percent silicide dispersoids were produced; dispersoid condition was varied by rolling at 300, 400, and 500 C (572, 752, and 932 F). Superplastic behavior was evaluated at strain rates from 1 x 10(exp -6)/s to 8.5/s at elevated temperatures. The results indicate that there was a significant increase in elongation at higher strain rates and at temperatures above 600 C (1112 F). However, the exposure of the alloys to temperatures greater than 600 C (1112 F) resulted in the coarsening of the strengthening dispersoid and the degradation of mechanical properties. Diffusion bonding was possible using low gas pressure at temperatures greater than 600 C (1112 F) which also resulted in degraded properties. The bonding of Al-Fe-V-Si alloys to 7475 aluminum alloy was performed at 516 C (960 F) without significant degradation in microstructure. Bond strengths equal to 90 percent that of the base metal shear strength were achieved. The mechanical properties and microstructural characteristics of the alloys were investigated.

  20. Thermal analysis of a diffusion bonded Er3+,Yb3+:glass/Co2+: MgAl2O4 microchip lasers

    NASA Astrophysics Data System (ADS)

    Belghachem, Nabil; Mlynczak, Jaroslaw; Kopczynski, krzysztof; Mierczyk, Zygmunt; Gawron, Michal

    2016-10-01

    The analysis of thermal effects in a diffusion bonded Er3+,Yb3+:glass/Co2+:MgAl2O4 microchip laser is presented. The analysis is performed for both wavelengths at 940 nm and at 975 nm as well as for two different sides of pumping, glass side and saturable absorber side. The heat sink effect of Co2+:MgAl2O4, as well as the impact of the thermal expansion and induced stress on the diffusion bonding are emphasised. The best configurations for reducing the temperature peaks, the Von Mises stresses on the diffusion bonding, and the thermal lensing are determined.

  1. Using the dynamic bond to access macroscopically responsive structurally dynamic polymers

    NASA Astrophysics Data System (ADS)

    Wojtecki, Rudy J.; Meador, Michael A.; Rowan, Stuart J.

    2011-01-01

    New materials that have the ability to reversibly adapt to their environment and possess a wide range of responses ranging from self-healing to mechanical work are continually emerging. These adaptive systems have the potential to revolutionize technologies such as sensors and actuators, as well as numerous biomedical applications. We will describe the emergence of a new trend in the design of adaptive materials that involves the use of reversible chemistry (both non-covalent and covalent) to programme a response that originates at the most fundamental (molecular) level. Materials that make use of this approach - structurally dynamic polymers - produce macroscopic responses from a change in the material's molecular architecture (that is, the rearrangement or reorganization of the polymer components, or polymeric aggregates). This design approach requires careful selection of the reversible/dynamic bond used in the construction of the material to control its environmental responsiveness.

  2. A Mathematical Model of Diffusion-Limited Gas Bubble Dynamics in Tissue with Varying Diffusion Region Thickness

    NASA Technical Reports Server (NTRS)

    Srinivasan, R. Srini; Gerth, Wayne A.; Powell, Michael R.; Paloski, William H. (Technical Monitor)

    2000-01-01

    A three-region mathematical model of gas bubble dynamics has been shown suitable for describing diffusion-limited dynamics of more than one bubble in a given volume of extravascular tissue. The model is based on the dynamics of gas exchange between a bubble and a well-stirred tissue region through an intervening unperfused diffusion region previously assumed to have constant thickness and uniform gas diffusivity. As a result, the gas content of the diffusion region remains constant as the volume of the region increases with bubble growth, causing dissolved gas in the region to violate Henry's law. Earlier work also neglected the relationship between the varying diffusion region volume and the fixed total tissue volume, because only cases in which the diffusion region volume is a small fraction of the overall tissue volume were considered. We herein extend the three-region model to correct these theoretical inconsistencies by allowing both the thickness and gas content of the diffusion region to vary during bubble evolution. A postulated difference in gas diffusivity between an infinitesimally thin layer at the bubble surface and the remainder of the diffusion region leads to variation in diffusion region gas content and thickness during bubble growth and resolution. This variable thickness, differential diffusivity (VTDD) model can yield bubble lifetimes considerably longer than those yielded by earlier three-region models for given model and decompression parameters, and meets a need for theoretically consistent but relatively simple bubble dynamics models for use in studies of decompression sickness (DCS) in human subjects, Keywords: decompression sickness, gas diffusion in tissue, diffusivity

  3. Dynamic hysteresis modeling including skin effect using diffusion equation model

    NASA Astrophysics Data System (ADS)

    Hamada, Souad; Louai, Fatima Zohra; Nait-Said, Nasreddine; Benabou, Abdelkader

    2016-07-01

    An improved dynamic hysteresis model is proposed for the prediction of hysteresis loop of electrical steel up to mean frequencies, taking into account the skin effect. In previous works, the analytical solution of the diffusion equation for low frequency (DELF) was coupled with the inverse static Jiles-Atherton (JA) model in order to represent the hysteresis behavior for a lamination. In the present paper, this approach is improved to ensure the reproducibility of measured hysteresis loops at mean frequency. The results of simulation are compared with the experimental ones. The selected results for frequencies 50 Hz, 100 Hz, 200 Hz and 400 Hz are presented and discussed.

  4. Effect of ultrasonic capillary dynamics on the mechanics of thermosonic ball bonding.

    PubMed

    Huang, Yan; Shah, Aashish; Mayer, Michael; Zhou, Norman Y; Persic, John

    2010-01-01

    Microelectronic wire bonding is an essential step in today's microchip production. It is used to weld (bond) microwires to metallized pads of integrated circuits using ultrasound with hundreds of thousands of vibration cycles. Thermosonic ball bonding is the most popular variant of the wire bonding process and frequently investigated using finite element (FE) models that simplify the ultrasonic dynamics of the process with static or quasistatic boundary conditions. In this study, the ultrasonic dynamics of the bonding tool (capillary), made from Al(2)O(3), is included in a FE model. For more accuracy of the FE model, the main material parameters are measured. The density of the capillary was measured to be rho(cap) = 3552 +/- 100 kg/m(3). The elastic modulus of the capillary, E(cap) = 389 +/- 11 GPa, is found by comparing an auxiliary FE model of the free vibrating capillary with measured values. A capillary "nodding effect" is identified and found to be essential when describing the ultrasonic vibration shape. A main FE model builds on these results and adds bonded ball, pad, chip, and die attach components. There is excellent agreement between the main model and the ultrasonic force measured at the interface on a test chip with stress microsensors. Bonded ball and underpad stress results are reported. When adjusted to the same ultrasonic force, a simplified model without ultrasonic dynamics and with an infinitely stiff capillary tip is substantially off target by -40% for the maximum underpad stress. The compliance of the capillary causes a substantial inclination effect at the bonding interface between wire and pad. This oscillating inclination effect massively influences the stress fields under the pad and is studied in more detail. For more accurate results, it is therefore recommended to include ultrasonic dynamics of the bonding tool in mechanical FE models of wire bonding.

  5. Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-10-01

    We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

  6. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-12-01

    Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle-particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle-particle interaction and high surface diffusion result in the formation of particle-particle bonds of 2 nm TiO2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO2 nanoparticles.

  7. An investigation on diffusion bonding of aluminum to copper using equal channel angular extrusion process.

    PubMed

    Eslami, P; Taheri, A Karimi

    2011-06-30

    A new method for production of bimetallic rods, utilizing the equal channel angular extrusion (ECAE) process has been introduced before by previous researchers, but no attempt has been made to assess the effect of different temperatures and holding times in order to achieve a diffusional bond between the mating surfaces. In present research copper sheathed aluminum rods have been ECAEed at room temperature and subsequently held at a constant ECAE pressure, at different temperatures and holding times to produce a diffusional bond between the copper sheath and the aluminum core. The bonding quality of the joints was examined by shear strength test and a sound bonding interface was achieved. Based on the results, a bonding temperature of 200 °C and holding time of 60-80 min yielded the highest shear strength value. PMID:21760654

  8. Diffusive reaction dynamics on invariant free energy profiles.

    PubMed

    Krivov, Sergei V; Karplus, Martin

    2008-09-16

    A fundamental problem in the analysis of protein folding and other complex reactions in which the entropy plays an important role is the determination of the activation free energy from experimental measurements or computer simulations. This article shows how to combine minimum-cut-based free energy profiles (F(C)), obtained from equilibrium molecular dynamics simulations, with conventional histogram-based free energy profiles (F(H)) to extract the coordinate-dependent diffusion coefficient on the F(C) (i.e., the method determines free energies and a diffusive preexponential factor along an appropriate reaction coordinate). The F(C), in contrast to the F(H), is shown to be invariant with respect to arbitrary transformations of the reaction coordinate, which makes possible partition of configuration space into basins in an invariant way. A "natural coordinate," for which F(H) and F(C) differ by a multiplicative constant (constant diffusion coefficient), is introduced. The approach is illustrated by a model one-dimensional system, the alanine dipeptide, and the folding reaction of a double beta-hairpin miniprotein. It is shown how the results can be used to test whether the putative reaction coordinate is a good reaction coordinate. PMID:18772379

  9. Development of a Low-Cost Process for Manufacturing of Ti-Metal Matrix Composite by Roll-Diffusion Bonding

    NASA Astrophysics Data System (ADS)

    Testani, C.; Ferraro, F.

    2010-06-01

    Composite materials with titanium-alloy matrix are currently the class of material with the highest specific resistance at temperatures up to 800 °C. The main hurdle to their application is their final cost. Even if it is clear that the costs of constituent materials are decreasing due to volume production effects, the production processing costs remain high due to the batch production approach. Centro Sviluppo Materiali’s (CSM) efforts have focused on the manufacturing process in order to obtain an innovative solution to reduce the manufacturing costs with respect to the hot isostatic pressing (HIP) process that represents the standard production process for this class of materials. The new approach can allow a cost reduction of about 40%; this result was obtained by developing an experimental “diffusion bonding” plant for co-rolling at high temperature in a superplastic rolling regime, sheets of titanium alloy and monofilament silicon carbide fabrics. The experimental pilot plant was proposed for patent with RM2006A000261 in May 2006. This paper describes the manufacturing phases and process results. Moreover, has been shown that the diffusion in the solid state was obtained in a process window that was at least 100 times faster than that of HIP. High-temperature tensile tests were carried out on specimens machined from metallic matrix composite materials produced with the roll-diffusion bonding (RDB) process. The samples produced were also submitted to electrochemical dissolution tests of the metallic matrix in order to verify the geometric integrity of the fibers inside the matrix after the bonding phase. The results achieved as well as the process knowledge acquired with the CSM pilot plant are the base for further development of industrial application of the titanium roll-diffusion bonding.

  10. Dynamic diffusion tensor measurements in muscle tissue using Single Line Multiple Echo Diffusion Tensor Acquisition Technique at 3T

    PubMed Central

    Baete, Steven H.; Cho, Gene; Sigmund, Eric E.

    2015-01-01

    When diffusion biomarkers display transient changes, i.e. in muscle following exercise, traditional diffusion tensor imaging (DTI) methods lack temporal resolution to resolve the dynamics. This paper presents an MRI method for dynamic diffusion tensor acquisitions on a clinical 3T scanner. This method, SL-MEDITATE (Single Line Multiple Echo Diffusion Tensor Acquisition Technique) achieves a high temporal resolution (4s) (1) by rapid diffusion encoding through the acquisition of multiple echoes with unique diffusion sensitization and (2) by limiting the readout to a single line volume. The method is demonstrated in a rotating anisotropic phantom, in a flow phantom with adjustable flow speed, and in in vivo skeletal calf muscle of healthy volunteers following a plantar flexion exercise. The rotating and flow-varying phantom experiments show that SL-MEDITATE correctly identifies the rotation of the first diffusion eigenvector and the changes in diffusion tensor parameter magnitudes, respectively. Immediately following exercise, the in vivo mean diffusivity (MD) time-courses show, before the well-known increase, an initial decrease which is not typically observed in traditional DTI. In conclusion, SL-MEDITATE can be used to capture transient changes in tissue anisotropy in a single line. Future progress might allow for dynamic DTI when combined with appropriate k-space trajectories and compressed sensing reconstruction. PMID:25900166

  11. Measurement of Adhesion Strength of Solid-State Diffusion Bonding Between Nickel and Copper by Means of Laser Shock Spallation Method

    NASA Astrophysics Data System (ADS)

    Satou, M.; Akamatsu, H.; Hasegawa, A.

    2009-12-01

    Coating and bonding techniques between different materials are essential to the field of technology. Bond mechanism is of interest from scientific point of view. A well-established method to make bonding between unalloyed nickel and copper was utilized, that was solid-state diffusion bonding at elevated temperatures. Irradiation by Nd:YAG laser with 7ns-pulse width created shock wave that caused tensile stress after reflection at free surface. The adhesion strength was determined by the critical laser power that caused exfoliation of the bonding interface.

  12. Diffusion dynamics in the disordered Bose Hubbard model

    NASA Astrophysics Data System (ADS)

    Wadleigh, Laura; Russ, Philip; Demarco, Brian

    2016-05-01

    We explore the dynamics of diffusion for out-of-equilibrium superfluid, Mott insulator, and Bose glass states using an atomic realization of the disordered Bose Hubbard (DBH) model. Dynamics in strongly correlated systems, especially far from equilibrium, are not well understood. The introduction of disorder further complicates these systems. We realize the DBH model--which has been central to our understanding of quantum phase transitions in disordered systems--using ultracold Rubidium-87 atoms trapped in a cubic disordered optical lattice. By tightly focusing a beam into the center of the gas, we create a hole in the atomic density profile. We achieve Mott insulator, superfluid, or Bose glass states by varying the interaction and disorder strength, and measure the time evolution of the density profile after removing the central barrier. This allows us to infer diffusion rates from the velocities at the edge of the hole and to look for signatures of superfluid puddles in the Bose glass state. We acknowledge funding from NSF Grant PHY 15-05468, NSF Grant DGE-1144245, and ARO Grant W911NF-12-1-0462.

  13. Dynamics of Diffusion Flames in von Karman Swirling Flows Studied

    NASA Technical Reports Server (NTRS)

    Nayagam, Vedha; Williams, Forman A.

    2002-01-01

    Von Karman swirling flow is generated by the viscous pumping action of a solid disk spinning in a quiescent fluid media. When this spinning disk is ignited in an oxidizing environment, a flat diffusion flame is established adjacent to the disk, embedded in the boundary layer (see the preceding illustration). For this geometry, the conservation equations reduce to a system of ordinary differential equations, enabling researchers to carry out detailed theoretical models to study the effects of varying strain on the dynamics of diffusion flames. Experimentally, the spinning disk burner provides an ideal configuration to precisely control the strain rates over a wide range. Our original motivation at the NASA Glenn Research Center to study these flames arose from a need to understand the flammability characteristics of solid fuels in microgravity where slow, subbuoyant flows can exist, producing very small strain rates. In a recent work (ref. 1), we showed that the flammability boundaries are wider and the minimum oxygen index (below which flames cannot be sustained) is lower for the von Karman flow configuration in comparison to a stagnation-point flow. Adding a small forced convection to the swirling flow pushes the flame into regions of higher strain and, thereby, decreases the range of flammable strain rates. Experiments using downward facing, polymethylmethacrylate (PMMA) disks spinning in air revealed that, close to the extinction boundaries, the flat diffusion flame breaks up into rotating spiral flames (refs. 2 and 3). Remarkably, the dynamics of these spiral flame edges exhibit a number of similarities to spirals observed in biological systems, such as the electric pulses in cardiac muscles and the aggregation of slime-mold amoeba. The tail of the spiral rotates rigidly while the tip executes a compound, meandering motion sometimes observed in Belousov-Zhabotinskii reactions.

  14. Beryllium dimer: a bond based on non-dynamical correlation.

    PubMed

    El Khatib, Muammar; Bendazzoli, Gian Luigi; Evangelisti, Stefano; Helal, Wissam; Leininger, Thierry; Tenti, Lorenzo; Angeli, Celestino

    2014-08-21

    The bond nature in beryllium dimer has been theoretically investigated using high-level ab initio methods. A series of ANO basis sets of increasing quality, going from sp to spdf ghi contractions, has been employed, combined with HF, CAS-SCF, CISD, and MRCI calculations with several different active spaces. The quality of these calculations has been checked by comparing the results with valence Full-CI calculations, performed with the same basis sets. It is shown that two quasi-degenerated partly occupied orbitals play a crucial role to give a qualitatively correct description of the bond. Their nature is similar to that of the edge orbitals that give rise to the quasi-degenerated singlet-triplet states in longer beryllium chains.

  15. Study of diffusion bond development in 6061 aluminum and its relationship to future high density fuels fabrication.

    SciTech Connect

    Prokofiev, I.; Wiencek, T.; McGann, D.

    1997-10-07

    Powder metallurgy dispersions of uranium alloys and silicides in an aluminum matrix have been developed by the RERTR program as a new generation of proliferation-resistant fuels. Testing is done with miniplate-type fuel plates to simulate standard fuel with cladding and matrix in plate-type configurations. In order to seal the dispersion fuel plates, a diffusion bond must exist between the aluminum coverplates surrounding the fuel meat. Four different variations in the standard method for roll-bonding 6061 aluminum were studied. They included mechanical cleaning, addition of a getter material, modifications to the standard chemical etching, and welding methods. Aluminum test pieces were subjected to a bend test after each rolling pass. Results, based on 400 samples, indicate that at least a 70% reduction in thickness is required to produce a diffusion bond using the standard rollbonding method versus a 60% reduction using the Type II method in which the assembly was welded 100% and contained open 9mm holes at frame corners.

  16. Chaotic dynamics and diffusion in a piecewise linear equation

    SciTech Connect

    Shahrear, Pabel; Glass, Leon; Edwards, Rod

    2015-03-15

    Genetic interactions are often modeled by logical networks in which time is discrete and all gene activity states update simultaneously. However, there is no synchronizing clock in organisms. An alternative model assumes that the logical network is preserved and plays a key role in driving the dynamics in piecewise nonlinear differential equations. We examine dynamics in a particular 4-dimensional equation of this class. In the equation, two of the variables form a negative feedback loop that drives a second negative feedback loop. By modifying the original equations by eliminating exponential decay, we generate a modified system that is amenable to detailed analysis. In the modified system, we can determine in detail the Poincaré (return) map on a cross section to the flow. By analyzing the eigenvalues of the map for the different trajectories, we are able to show that except for a set of measure 0, the flow must necessarily have an eigenvalue greater than 1 and hence there is sensitive dependence on initial conditions. Further, there is an irregular oscillation whose amplitude is described by a diffusive process that is well-modeled by the Irwin-Hall distribution. There is a large class of other piecewise-linear networks that might be analyzed using similar methods. The analysis gives insight into possible origins of chaotic dynamics in periodically forced dynamical systems.

  17. Chaotic dynamics and diffusion in a piecewise linear equation

    NASA Astrophysics Data System (ADS)

    Shahrear, Pabel; Glass, Leon; Edwards, Rod

    2015-03-01

    Genetic interactions are often modeled by logical networks in which time is discrete and all gene activity states update simultaneously. However, there is no synchronizing clock in organisms. An alternative model assumes that the logical network is preserved and plays a key role in driving the dynamics in piecewise nonlinear differential equations. We examine dynamics in a particular 4-dimensional equation of this class. In the equation, two of the variables form a negative feedback loop that drives a second negative feedback loop. By modifying the original equations by eliminating exponential decay, we generate a modified system that is amenable to detailed analysis. In the modified system, we can determine in detail the Poincaré (return) map on a cross section to the flow. By analyzing the eigenvalues of the map for the different trajectories, we are able to show that except for a set of measure 0, the flow must necessarily have an eigenvalue greater than 1 and hence there is sensitive dependence on initial conditions. Further, there is an irregular oscillation whose amplitude is described by a diffusive process that is well-modeled by the Irwin-Hall distribution. There is a large class of other piecewise-linear networks that might be analyzed using similar methods. The analysis gives insight into possible origins of chaotic dynamics in periodically forced dynamical systems.

  18. Femtosecond Hydrogen Bond Dynamics of Bulk-like and Bound Water at Positively and Negatively Charged Lipid Interfaces Revealed by 2D HD-VSFG Spectroscopy.

    PubMed

    Singh, Prashant Chandra; Inoue, Ken-Ichi; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Tahara, Tahei

    2016-08-26

    Interfacial water in the vicinity of lipids plays an important role in many biological processes, such as drug delivery, ion transportation, and lipid fusion. Hence, molecular-level elucidation of the properties of water at lipid interfaces is of the utmost importance. We report the two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) study of the OH stretch of HOD at charged lipid interfaces, which shows that the hydrogen bond dynamics of interfacial water differ drastically, depending on the lipids. The data indicate that the spectral diffusion of the OH stretch at a positively charged lipid interface is dominated by the ultrafast (<∼100 fs) component, followed by the minor sub-picosecond slow dynamics, while the dynamics at a negatively charged lipid interface exhibit sub-picosecond dynamics almost exclusively, implying that fast hydrogen bond fluctuation is prohibited. These results reveal that the ultrafast hydrogen bond dynamics at the positively charged lipid-water interface are attributable to the bulk-like property of interfacial water, whereas the slow dynamics at the negatively charged lipid interface are due to bound water, which is hydrogen-bonded to the hydrophilic head group. PMID:27482947

  19. Anomalously rapid hydration water diffusion dynamics near DNA surfaces

    PubMed Central

    Franck, John M.; Ding, Yuan; Stone, Katherine

    2015-01-01

    The emerging Overhauser effect Dynamic Nuclear Polarization (ODNP) technique measures the translational mobility of water within the vicinity (5-15 Å) of preselected sites. The work presented here expands the capabilities of the ODNP technique and illuminates an important, previously unseen, property of the translational diffusion dynamics of water at the surface of DNA duplexes. We attach nitroxide radicals (i.e., spin labels) to multiple phosphate backbone positions of DNA duplexes, allowing ODNP to measure the hydration dynamics at select positions along the DNA surface. With a novel approach to ODNP analysis, we isolate the contributions of water molecules at these sites that undergo free translational diffusion from water molecules that either loosely bind to or exchange protons with the DNA. The results reveal that a significant population of water in a localized volume adjacent to the DNA surface exhibits fast, bulk-like characteristics and moves unusually rapidly compared to water found in similar probe volumes near protein and membrane surfaces. Control studies show that the observation of these characteristics are upheld even when the DNA duplex is tethered to streptavidin or the mobility of the nitroxides is altered. This implies that, as compared to protein or lipid surfaces, it is an intrinsic feature of the DNA duplex surface that it interacts only weakly with a significant fraction of a network of surface hydration water. The displacement of this translationally mobile water is energetically less costly than that of more strongly bound water by up to several kBT and thus can lower the activation barrier for interactions involving the DNA surface. PMID:26256693

  20. Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.

    PubMed

    Franck, John M; Ding, Yuan; Stone, Katherine; Qin, Peter Z; Han, Songi

    2015-09-23

    The emerging Overhauser effect dynamic nuclear polarization (ODNP) technique measures the translational mobility of water within the vicinity (5-15 Å) of preselected sites. The work presented here expands the capabilities of the ODNP technique and illuminates an important, previously unseen, property of the translational diffusion dynamics of water at the surface of DNA duplexes. We attach nitroxide radicals (i.e., spin labels) to multiple phosphate backbone positions of DNA duplexes, allowing ODNP to measure the hydration dynamics at select positions along the DNA surface. With a novel approach to ODNP analysis, we isolate the contributions of water molecules at these sites that undergo free translational diffusion from water molecules that either loosely bind to or exchange protons with the DNA. The results reveal that a significant population of water in a localized volume adjacent to the DNA surface exhibits fast, bulk-like characteristics and moves unusually rapidly compared to water found in similar probe volumes near protein and membrane surfaces. Control studies show that the observation of these characteristics are upheld even when the DNA duplex is tethered to streptavidin or the mobility of the nitroxides is altered. This implies that, as compared to protein or lipid surfaces, it is an intrinsic feature of the DNA duplex surface that it interacts only weakly with a significant fraction of the surface hydration water network. The displacement of this translationally mobile water is energetically less costly than that of more strongly bound water by up to several kBT and thus can lower the activation barrier for interactions involving the DNA surface.

  1. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    PubMed

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

  2. Multicomponent diffusion in molten salt NaF-ZrF4: Dynamical correlations and Maxwell-Stefan diffusivities

    NASA Astrophysics Data System (ADS)

    Baig, Mohammad Saad; Chakraborty, Brahmananda; Ramaniah, Lavanya M.

    2016-05-01

    NaF-ZrF4 is used as a waste incinerator and as a coolant in Generation IV reactors.Structural and dynamical properties of molten NaF-ZrF4 system were studied along with Onsagercoefficients and Maxwell-Stefan (MS) Diffusivities applying Green-Kubo formalism and molecular dynamics (MD) simulations. The zirconium ions are found to be 8 fold coordinated with fluoride ions for all temperatures and concentrations. All the diffusive flux correlations show back-scattering. Even though the MS diffusivities are expected to depend very lightly on the composition because of decoupling of thermodynamic factor, the diffusivity ĐNa-F shows interesting behavior with the increase in concentration of ZrF4. This is because of network formation in NaF-ZrF4. Positive entropy constraints have been plotted to authenticate negative diffusivities observed.

  3. Molecular dynamics simulation of imidazolium-based ionic liquids. I. Dynamics and diffusion coefficient

    NASA Astrophysics Data System (ADS)

    Kowsari, M. H.; Alavi, Saman; Ashrafizaadeh, Mahmud; Najafi, Bijan

    2008-12-01

    Molecular dynamics simulations are used to study the dynamics and transport properties of 12 room-temperature ionic liquids of the 1-alkyl-3-methylimidazolium [amim]+ (alkyl=methyl, ethyl, propyl, and butyl) family with PF6-, NO3-, and Cl- counterions. The explicit atom transferable force field of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] is used in the simulations. In this first part, the dynamics of the ionic liquids are characterized by studying the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of mass of the ions at 400 K. Trajectory averaging was employed to evaluate the diffusion coefficients at two temperatures from the linear slope of MSD(t) functions in the range of 150-300 ps and from the integration of the VACF(t) functions at 400 K. Detailed comparisons are made between the diffusion results from the MSD and VACF methods. The diffusion coefficients from the integration of the VACFs are closer to experimental values than the diffusion coefficients calculated from the slope of MSDs. Both methods can show good agreement with experiment in predicting relative trends in the diffusion coefficients and determining the role of the cation and anion structures on the dynamical behavior of this family of ionic liquids. The MSD and self-diffusion of relatively heavier imidazolium cations are larger than those of the lighter anions from the Einstein results, except for the case of [bmim][Cl]. The cationic transference number generally decreases with temperature, in good agreement with experiments. For the same anion, the cationic transference numbers decrease with increasing length of the alkyl chain, and for the same cation, the trends in the cationic transference numbers are [NO3]-<[Cl]-<[PF6]-. The trends in the diffusion coefficient in the series of cations with identical anions are [emim]+>[pmim]+>[bmim]+ and those for anions with identical cations are [NO3]->[PF6]->[Cl]-. The [dmim]+ has a

  4. Interfacial Microstructure and Mechanical Strength of 93W/Ta Diffusion-Bonded Joints with Ni Interlayer

    NASA Astrophysics Data System (ADS)

    Luo, Guoqiang; Zhang, Jian; Li, Meijuan; Wei, Qinqin; Shen, Qiang; Zhang, Lianmeng

    2013-02-01

    93W alloy and Ta metal were successfully diffusion bonded using a Ni interlayer. Ni4W was found at the W-Ni interface, and Ni3Ta and Ni2Ta were formed at the Ni-Ta interface. The shear strength of the joints increases with increasing holding time, reaching a value of 202 MPa for a joint prepared using a 90-minute holding time at 1103 K (830 °C) and 20 MPa. The fracture of this joint occurred within the Ni/Ta interface.

  5. 4-D reconstruction for dynamic fluorescence diffuse optical tomography.

    PubMed

    Liu, Xin; Zhang, Bin; Luo, Jianwen; Bai, Jing

    2012-11-01

    Dynamic fluorescence diffuse optical tomography (FDOT) is important for the research of drug delivery, medical diagnosis and treatment. Conventionally, dynamic tomographic images are reconstructed frame by frame, independently. This approach fails to account for the temporal correlations in measurement data. Ideally, the entire image sequence should be considered as a whole and a four-dimensional (4-D) reconstruction should be performed. However, the fully 4-D reconstruction is computationally intensive. In this paper, we propose a new 4-D reconstruction approach for dynamic FDOT, which is achieved by applying a temporal Karhunen-Loève (KL) transformation to the imaging equation. By taking advantage of the decorrelation and compression properties of the KL transformation, the complex 4-D optical reconstruction problem is greatly simplified. To evaluate the performance of the method, simulation, phantom, and in vivo experiments (N=7) are performed on a hybrid FDOT/x-ray computed tomography imaging system. The experimental results indicate that the reconstruction images obtained by the KL method provide good reconstruction quality. Additionally, by discarding high-order KL components, the computation time involved with fully 4-D reconstruction can be greatly reduced in contrast to the conventional frame-by-frame reconstruction.

  6. Microstructure of arc brazed and diffusion bonded joints of stainless steel and SiC reinforced aluminum matrix composite

    NASA Astrophysics Data System (ADS)

    Elßner, M.; Weis, S.; Grund, T.; Wagner, G.; Habisch, S.; Mayr, P.

    2016-03-01

    Joint interfaces of aluminum and stainless steel often exhibit intermetallics of Al-Fe, which limit the joint strength. In order to reduce these brittle phases in joints of aluminum matrix composites (AMC) and stainless steel, diffusion bonding and arc brazing are used. Due to the absence of a liquid phase, diffusion welding can reduce the formation of these critical in- termetallics. For this joining technique, the influence of surface treatments and adjusted time- temperature-surface-pressure-regimes is investigated. On the other hand, arc brazing offers the advantage to combine a localized heat input with the application of a low melting filler and was conducted using the system Al-Ag-Cu. Results of the joining tests using both approaches are described and discussed with regard to the microstructure of the joints and the interfaces.

  7. Probing bonding and dynamics at heterogeneous adsorbate/graphene interfaces

    NASA Astrophysics Data System (ADS)

    Mattson, Eric

    Graphene-based materials are becoming an astoundingly promising choice for many relevant technological and environmental applications. Deriving graphene from the reduction of graphene oxide (GO) is becoming a popular and inexpensive route toward the synthesis of these materials. While the desired product from GO reduction is pristine graphene, defects and residual oxygen functional groups inherited from the parent GO render reduced graphene oxide (RGO) distinct from graphene. In this work, the structure and bonding for GO and RGO is investigated to the end of a working understanding of the composition and properties of these materials. In situ selected area electron diffraction and ex situ IR microspectroscopy are used to study, respectively, thermal and chemical reduction of GO. The residual oxygen functional groups are found to be predominantly epoxide, C-O-C, bonded oxygen. The role of these oxygen functional groups and the collective RGO in gas sensing applications is investigated by performing in situ IR spectromicroscopy studies of molecular adsorption onto RGO. NO2 and NH3 are the target molecules of interest; NH3 due to its widespread use in industry and NO2 is a a common byproducts in combustion reactions. Following adsorption of both molecules, numerous species are identified on the surface due to the heterogeneity of the substrate. Residual epoxide groups participate in reactions with the target molecules to produce additional surface species that have varying impacts on the conductivity of the substrate.

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Study of the Hydrogen Bond Network in sub-and supercritical Water by Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Krishtal, S.; Kiselev, M.; Puhovski, Y.; Kerdcharoen, T.; Hannongbua, S.; Heinzinger, K.

    2001-08-01

    For 12 points along the tangent to the saturation curve at the critical point the temperature dependen­cies of the heights of the first maximum in the 0 -0 RDF, the average number of hydrogen bonds, and the self-diffusion coefficients have been calculated from MD simulations. The curves of these three properties show an inflection near the critical point. To improve the understanding of these changes in going from subcritical to supercritical water the librational spectra and the change in the fractions of wa­ter molecules with a given number of hydrogen bonds as a function of temperature have been derived from the simulations, additionally.

  10. Transient Liquid Phase Diffusion Bonding of Magnesium Alloy (Mg-AZ31) to Titanium Alloy (Ti-6Al-4V)

    NASA Astrophysics Data System (ADS)

    Atieh, Anas Mahmoud

    The magnesium alloy Mg-AZ31 and titanium alloy Ti-6Al-4V have physical characteristics and mechanical properties that makes it attractive for a wide range of engineering applications in the aerospace and automotive industries. However, the differences in melting temperature and coefficient of thermal expansion hinder the use of traditional fusion welding techniques. Transient liquid phase (TLP) bonding of magnesium alloy Mg-AZ31 and titanium alloy Ti-6Al- 4V was performed and different interlayer types and configurations were used to facilitate joint formation. The joining of these alloys using Ni foils was successful at a bonding temperature of 515°C, bonding pressure 0.2 MPa, for bonding time of 5 minutes. At the Ni/Mg-AZ31 bond interface, the formation of a eutectic liquid between Mg and Ni was observed. The formation of Mg2Ni and Mg3AlNi2 were identified along the bond interface resulting in an isothermally solidified joint. At the Ni/Ti-6Al-4V interface, the solid-state diffusion process results in joint formation. The use of double Ni-Cu sandwich joint resulted in further enhancement in joint formation and this produced joints with greater shear strength values. The configuration of Mg-AZ31/Cu- Ni/Ti-6Al-4V or Mg-AZ31/Ni-Cu/Ti-6Al-4V influence the mechanism of bonding and the type of intermetallics formed within the joint. The application of thin Ni electrodeposited coatings resulted in further enhancements of joint quality due to better surface-to-surface contact and a reduction in the formation of intermetallics at the joint. The effect of Cu nano-particles in the coatings was found to decrease the eutectic zone width and this resulted in an increase the shear strength of the joints. The highest shear strength of 69 MPa was possible with bonds made using coatings containing Cu nano-particle dispersion.

  11. Rates of diffusion in dynamical systems with random jumps

    NASA Astrophysics Data System (ADS)

    Kobre, Elisha J.

    2005-12-01

    This dissertation explores the diffusion properties of a large class of measures under a dynamical system on bigcup i=0infinity S1i with randomly occurring jumps that behave according to a particular probability distribution. The drift rate for the center of mass of the system is then defined and is shown to be well defined Lebesgue almost everywhere. Properties of the drift rate are then explored. In particular the drift rate is shown to be continuous as a function of the probability "jump" distribution and, in a special case, it is shown that the drift rate increases with the probability of jumping. Finally, a central limit theorem for fluctuations about the drift rate is proved. The results are obtained by modeling the system as a random map on a compact space, and using the ergodic properties of the random map.

  12. Diffusion of innovations dynamics, biological growth and catenary function

    NASA Astrophysics Data System (ADS)

    Guseo, Renato

    2016-12-01

    The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.

  13. An ab initio molecular dynamics study on hydrogen bonds between water molecules.

    PubMed

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-28

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 Å and r(O···H) < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that

  14. An ab initio molecular dynamics study on hydrogen bonds between water molecules

    NASA Astrophysics Data System (ADS)

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-01

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dHṡṡṡH between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rOṡṡṡH between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dHṡṡṡH and rOṡṡṡH are small (e.g., dHṡṡṡH < 2.0 Å and rOṡṡṡH < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They

  15. The effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method

    NASA Astrophysics Data System (ADS)

    Su, Jonathan T.; Duncan, P. Brent; Momaya, Amit; Jutila, Arimatti; Needham, David

    2010-01-01

    While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5×10-5 cm2/s for water in n-pentane to 1.15×10-5 cm2/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75×10-5 cm2/s in n-methanol to 0.364×10-5 cm2/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents

  16. Separation of strong (bond-breaking) from weak (dynamical) correlation

    NASA Astrophysics Data System (ADS)

    Kutzelnigg, Werner

    2012-06-01

    A CC (coupled-cluster) ansatz based on a GVB (generalized valence bond) or an APSG (antisymmetrized product of strongly orthogonal geminals) reference function arises naturally if one tries to treat strong correlations exactly (to infinite order), and weak correlations by TCC (traditional coupled cluster) theory. This ansatz is proposed as an alternative to MC-CC (multi-configuration coupled cluster) theory. One uses especially that APSG and GVB are of CC type, but allow to combine separability with the variation principle. The energy and the stationarity conditions are formulated in terms of spinfree density cumulants. The replacement operators corresponding to the APSG ansatz generate a Lie algebra which is a subalgebra of that of all replacement operators.

  17. Mechanism for hydrogen diffusion in amorphous silicon

    SciTech Connect

    Biswas, R.; Li, Q.; Pan, B.C.; Yoon, Y.

    1998-01-01

    Tight-binding molecular-dynamics calculations reveal a mechanism for hydrogen diffusion in hydrogenated amorphous silicon. Hydrogen diffuses through the network by successively bonding with nearby silicons and breaking their Si{endash}Si bonds. The diffusing hydrogen carries with it a newly created dangling bond. These intermediate transporting states are densely populated in the network, have lower energies than H at the center of stretched Si{endash}Si bonds, and can play a crucial role in hydrogen diffusion. {copyright} {ital 1998} {ital The American Physical Society}

  18. Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix

    PubMed Central

    Gutman, M.; Nachliel, E.; Kiryati, S.

    1992-01-01

    The thin water layer, as found in chloroplast or mitochondria, is confined between low dielectric amphypathic surfaces a few nm apart. The physical properties of this mesoscopic space, and how its dimensions affect the rate of chemical reactions proceeding in it, is the subject for this study. The method selected for this purpose is time resolved fluorometry which can monitor the reversible dissociation of a proton from excited molecule of pyranine (8 hydroxy pyrene 1,3,6 tri sulfonate) trapped in thin water layers of a multilamellar vesicle made of neutral or slightly charged phospholipids. The results were analyzed by a computer program of N. Agmon (Pines, E., D. Huppert, and N. Agmon. 1988. J. Am. Chem. Soc. 88:5620-5630) that simulates the diffusion of a proton, subjected to electrostatic attraction, in a thin water layer enclosed between low affinity, proton binding surfaces. The analysis determines the diffusion coefficient of the proton, the effective dielectric constant of the water and the water accessibility of the phosphomoieties of the lipids. These parameters were measured for various lipids [egg-phosphatidylcholine (egg PC), dipalmitoyl phosphatidylcholine (DPPC), cholesterol + DPPC (1:1) and egg PC plus phosphatidyl serine (9:1)] and under varying osmotic pressure which reduces the width of the water layer down to ∼10 ∼ across. We found that: (a) The effective dielectric constant of the aqueous layer, depending on the lipid composition, is ∼40. (b) The diffusion coefficient of the proton in the thin layer (30-10 ∼ across) is that measured in bulk water D = 9.3 10-5 cm2/s, indicating that the water retains its normal liquid state even on contact with the membrane. (c) The reactivity of the phosphomoiety, quantitated by rate of its reaction with proton, diminishes under lateral pressure which reduces the surface area per lipid. We find no evidence for abnormal dynamics of proton transfer at the lipid water interface which, by any mechanism

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

    PubMed

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

    2016-07-08

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of 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.

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

    PubMed Central

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

    2016-01-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step. PMID:27388562

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

    NASA Astrophysics Data System (ADS)

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

    PubMed

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

    2016-01-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step. PMID:27388562

  3. Inertia, diffusion, and dynamics of a driven skyrmion

    NASA Astrophysics Data System (ADS)

    Schütte, Christoph; Iwasaki, Junichi; Rosch, Achim; Nagaosa, Naoto

    2014-11-01

    Skyrmions recently discovered in chiral magnets are a promising candidate for magnetic storage devices because of their topological stability, small size (˜3 -100 nm), and ultralow threshold current density (˜106 A/m 2) to drive their motion. However, the time-dependent dynamics has hitherto been largely unexplored. Here, we show, by combining the numerical solution of the Landau-Lifshitz-Gilbert equation and the analysis of a generalized Thiele's equation, that inertial effects are almost completely absent in skyrmion dynamics driven by a time-dependent current. In contrast, the response to time-dependent magnetic forces and thermal fluctuations depends strongly on frequency and is described by a large effective mass and a (anti-) damping depending on the acceleration of the skyrmion. Thermal diffusion is strongly suppressed by the cyclotron motion and is proportional to the Gilbert damping coefficient α . This indicates that the skyrmion position is stable, and its motion responds to the time-dependent current without delay or retardation even if it is fast. These findings demonstrate the advantages of skyrmions as information carriers.

  4. Multicomponent diffusion in molten salt LiF-BeF2: Dynamical correlations and Maxwell-Stefan diffusivities

    NASA Astrophysics Data System (ADS)

    Chakraborty, Brahmananda; Ramaniah, Lavanya M.

    2015-06-01

    Applying Green-Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied the dynamic correlation, Onsager coeeficients and Maxwell-Stefan (MS) Diffusivities of molten salt LiF-BeF2, which is used as coolant in high temperature reactor. All the diffusive flux correlations show back-scattering or cage dynamics which becomes pronouced at higher temperature. Although the MS diffusivities are expected to depend very lightly on the composition due to decoupling of thermodynamic factor, the diffusivity ĐLi-F and ĐBe-F decreases sharply for higher concentration of LiF and BeF2 respectively. Interestingly, all three MS diffusivities have highest magnitude for eutectic mixture at 1000K (except ĐBe-F at lower LiF mole fraction) which is desirable from coolant point of view. Although the diffusivity for positive-positive ion pair is negative it is not in violation of the second law of thermodynamics as it satisfies the non-negative entropic constraints.

  5. Multicomponent diffusion in molten salt LiF-BeF{sub 2}: Dynamical correlations and Maxwell–Stefan diffusivities

    SciTech Connect

    Chakraborty, Brahmananda Ramaniah, Lavanya M.

    2015-06-24

    Applying Green–Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied the dynamic correlation, Onsager coeeficients and Maxwell–Stefan (MS) Diffusivities of molten salt LiF-BeF{sub 2}, which is used as coolant in high temperature reactor. All the diffusive flux correlations show back-scattering or cage dynamics which becomes pronouced at higher temperature. Although the MS diffusivities are expected to depend very lightly on the composition due to decoupling of thermodynamic factor, the diffusivity Đ{sub Li-F} and Đ{sub Be-F} decreases sharply for higher concentration of LiF and BeF{sub 2} respectively. Interestingly, all three MS diffusivities have highest magnitude for eutectic mixture at 1000K (except Đ{sub Be-F} at lower LiF mole fraction) which is desirable from coolant point of view. Although the diffusivity for positive-positive ion pair is negative it is not in violation of the second law of thermodynamics as it satisfies the non-negative entropic constraints.

  6. A mathematical model of diffusion-limited gas bubble dynamics in tissue with varying diffusion region thickness.

    PubMed

    Srinivasan, R S; Gerth, W A; Powell, M R

    2000-10-01

    The three-region model of gas bubble dynamics consists of a bubble and a well-stirred tissue region with an intervening unperfused diffusion region previously assumed to have constant thickness and uniform gas diffusivity. As a result, the diffusion region gas content remains unchanged as its volume increases with bubble growth, causing dissolved gas in the region to violate Henry's law. Earlier work also neglected the relationship between the varying diffusion region volume and the fixed total tissue volume. The present work corrects these theoretical inconsistencies by postulating a difference in gas diffusivity between an infinitesimally thin layer at the bubble surface and the remainder of the diffusion region, thus allowing both thickness and gas content of the diffusion region to vary during bubble evolution. The corrected model can yield bubble lifetimes considerably longer than those yielded by earlier three-region models, and meets a need for theoretically consistent but relatively simple bubble dynamics models for use in studies of decompression sickness (DCS) in human subjects.

  7. An ab initio molecular dynamics study of the liquid-vapor interface of an aqueous NaCl solution: inhomogeneous density, polarity, hydrogen bonds, and frequency fluctuations of interfacial molecules.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-11-21

    We have presented a first principles simulation study of the structural and dynamical properties of a liquid-vapor interfacial system of a concentrated (5.3 M) aqueous NaCl solution. We have used ab initio molecular dynamics to examine the structural and dynamical properties of the bulk and interfacial regions. The structural aspects of the system that have been considered here include the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions in the bulk and interfacial regions. It is found that the sodium ions are mostly located in the interior, while the chloride anions occupy a significant portion of the interface of the slab. The water dipoles at the interface prefer to orient parallel to the surface. The dynamical aspects of the interfaces are investigated in terms of diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion. The results of the interfacial dynamics are compared with those of the corresponding bulk region. It is observed that the interfacial molecules exhibit faster diffusion and orientational relaxation with respect to the bulk. However, the interfacial molecules are found to have longer hydrogen bond lifetimes than those of the bulk. We have also investigated the correlations of hydrogen bond relaxation with the vibrational frequency fluctuations of interfacial water molecules.

  8. Dynamic covalent bond based on reversible photo [4 + 4] cycloaddition of anthracene for construction of double-dynamic polymers.

    PubMed

    Xu, Jiang-Fei; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2013-12-20

    Dynamic covalent bonds supplied by reversible anthracene dimerization were combined with pillar[5]arene/imidazole host-guest interactions to construct double-dynamic polymers. Heating such polymers (in solution or as a gel) led to depolymerization by dissociation of either the host-guest complexes alone or the complexes and the anthracene dimers, depending on the extent of heating. The polymers reformed readily upon cooling or irradiation.

  9. Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Nilsson, J. Arvid; Lyubartsev, Alexander; Eriksson, Leif A.; Laaksonen, Aatto

    Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. The main objectives have been to follow the dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ - is approximately perpendicular to the ring plane. Only weak hydrogen bonds are formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bond structure. We also conclude that anionic UQ can be accurately modelled by molecular mechanics methods, but the conformation of the methoxy groups in neutral UQ can hardly be properly modelled using a standard force field.

  10. Photoresponsive Liquid Crystalline Epoxy Networks with Shape Memory Behavior and Dynamic Ester Bonds.

    PubMed

    Li, Yuzhan; Rios, Orlando; Keum, Jong K; Chen, Jihua; Kessler, Michael R

    2016-06-22

    Functional polymers are intelligent materials that can respond to a variety of external stimuli. However, these materials have not yet found widespread real world applications because of the difficulties in fabrication and the limited number of functional building blocks that can be incorporated into a material. Here, we demonstrate a simple route to incorporate three functional building blocks (azobenzene chromophores, liquid crystals, and dynamic covalent bonds) into an epoxy-based liquid crystalline network (LCN), in which an azobenzene-based epoxy monomer is polymerized with an aliphatic dicarboxylic acid to create exchangeable ester bonds that can be thermally activated. All three functional building blocks exhibited good compatibility, and the resulting materials exhibits various photomechanical, shape memory, and self-healing properties because of the azobenzene molecules, liquid crystals, and dynamic ester bonds, respectively.

  11. On the ultrafast charge migration dynamics in isolated ionized halogen, chalcogen, pnicogen, and tetrel bonded clusters

    NASA Astrophysics Data System (ADS)

    Chandra, Sankhabrata; Rana, Bhaskar; Periyasamy, Ganga; Bhattacharya, Atanu

    2016-06-01

    Here we demonstrate, compare and contrast relaxation- and correlation-driven charge migration dynamics in halogen, chalcogen, pnicogen and tetrel bonded clusters, following their vertical ionization. For this work, we have selected different isolated A-X:NH3 clusters, where A represents F, Cl, CN and NH2 substituents and X features Cl, SH, PH2 and SiH3 to exhibit specific noncovalent bonding interaction. The charge migration dynamics in these clusters is studied using the density functional theory (DFT) with the wB97XD functional and the 6-31+G(d,p) basis set. Approximately 400-600 attosecond time scale is predicted for charge migration in (1:1) AX:NH3 complexes. Effects of basis set and intermolecular distance on the ultrafast charge migration dynamics through the halogen, chalcogen, pnicogen, and tetrel bonded clusters are also discussed. This is the first report on pure relaxation- and correlation-driven charge migration dynamics in chalcogen, pnicogen and tetrel bonded clusters.

  12. Silver and cesium diffusion dynamics at the β-SiC Σ5 grain boundary investigated with density functional theory molecular dynamics and metadynamics.

    PubMed

    Rabone, Jeremy; López-Honorato, Eddie; Van Uffelen, Paul

    2014-02-01

    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 density functional theory molecular dynamics simulations. The energy barriers extracted from the simulations give diffusion coefficients that are in reasonable agreement with experiment for silver (2.19 × 10(-19) to 1.05 × 10(-17) m(2) s(-1)), but for cesium the equivalent calculated coefficients for this mechanism are much smaller (3.85 × 10(-23) to 2.15 × 10(-21) m(2) s(-1)) than those found experimentally. Analysis of the simulated structures and electron densities and comparisons with the calculations of other researchers suggest that diffusion of silver and cesium in β-SiC proceeds via different mechanisms. The mechanisms of cesium diffusion appear to be dominated by its relatively large size and repulsive interactions with the silicon and carbon atoms; β-SiC grain boundaries still offer higher energy barriers to diffusion. Silver, on the other hand, is not only smaller in size but, as we show for the first time, can also participate in weak bonding interactions with the host atoms where favorable geometries allow, thus reducing the energy barrier and enhancing the rate of diffusion. PMID:24422635

  13. Ice crystal growth in a dynamic thermal diffusion chamber

    NASA Technical Reports Server (NTRS)

    Keller, V. W.

    1980-01-01

    Ice crystals were grown in a supersaturated environment produced by a dynamic thermal diffusion chamber, which employed two horizontal plates separated by a distance of 2.5 cm. Air was circulated between and along the 1.2 m length of the plates past ice crystals which nucleated and grew from a fiber suspended vertically between the two plates. A zoom stereo microscope with a magnification which ranged from 3X to 80X and both 35 mm still photographs and 16 mm time lapse cine films taken through the microscope were used to study the variation of the shape and linear growth rate of ice crystals as a function of the ambient temperature, the ambient supersaturation, and the forced ventilation velocity. The ambient growth conditions were varied over the range of temperature 0 to -40 C, over the range of supersaturation 4% to 50% with respect to ice, and over the range of forced ventilation velocities 0 cm/s to 20 cm/s.

  14. Stochastic fire-diffuse-fire model with realistic cluster dynamics

    NASA Astrophysics Data System (ADS)

    Calabrese, Ana; Fraiman, Daniel; Zysman, Daniel; Ponce Dawson, Silvina

    2010-09-01

    Living organisms use waves that propagate through excitable media to transport information. Ca2+ waves are a paradigmatic example of this type of processes. A large hierarchy of Ca2+ signals that range from localized release events to global waves has been observed in Xenopus laevis oocytes. In these cells, Ca2+ release occurs trough inositol 1,4,5-trisphosphate receptors (IP3Rs) which are organized in clusters of channels located on the membrane of the endoplasmic reticulum. In this article we construct a stochastic model for a cluster of IP3R ’s that replicates the experimental observations reported in [D. Fraiman , Biophys. J. 90, 3897 (2006)10.1529/biophysj.105.075911]. We then couple this phenomenological cluster model with a reaction-diffusion equation, so as to have a discrete stochastic model for calcium dynamics. The model we propose describes the transition regimes between isolated release and steadily propagating waves as the IP3 concentration is increased.

  15. Computational study on ionic diffusion and dynamic properties in silicate and bioactive glasses

    NASA Astrophysics Data System (ADS)

    Xiang, Ye; Du, Jincheng

    2011-03-01

    Ionic diffusion and dynamic properties in silicate glasses have been extensively studied experimentally due to its importance in understanding ion conduction and glass dissolution. In this study, computational study on ionic diffusion and dynamic properties was carried out using molecular dynamics simulations with effective partial charge potentials. The simulated structure models were validated by comparing with experimental data and systematic discussions on effects of system size, simulation thermal ensemble and temperature range were carried out. The dynamic properties were also related to structural changes with the glass. Finally, investigation of SrO/CaO substitution effect on the diffusion behaviors in 45S glasses is provided.

  16. M3B2 and M5B3 Formation in Diffusion-Affected Zone During Transient Liquid Phase Bonding Single-Crystal Superalloys

    NASA Astrophysics Data System (ADS)

    Sheng, Naicheng; Hu, Xiaobing; Liu, Jide; Jin, Tao; Sun, Xiaofeng; Hu, Zhuangqi

    2015-04-01

    Precipitates in the diffusion-affected zone (DAZ) during transient liquid phase bonding (TLP) single-crystal superalloys were observed and investigated. Small size and dendritic-shaped precipitates were identified to be M3B2 borides and intergrowth of M3B2/M5B3 borides. The orientation relationships among M3B2, M5B3, and matrix were determined using transmission electron microscope (TEM). Composition characteristics of these borides were also analyzed by TEM energy-dispersive spectrometer. Because this precipitating phenomenon deviates from the traditional parabolic transient liquid phase bonding model which assumed a precipitates free DAZ during TLP bonding, some correlations between the deviation of the isothermal solidification kinetics and these newly observed precipitating behaviors were discussed and rationalized when bonding the interlayer containing the high diffusivity melting point depressant elements and substrates of low solubility.

  17. Evaluation of superplastic forming and co-diffusion bonding of Ti-6Al-4V titanium alloy expanded sandwich structures

    NASA Technical Reports Server (NTRS)

    Arvin, G. H.; Israeli, L.; Stolpestad, J. H.; Stacher, G. W.

    1981-01-01

    The application of the superplastic forming/diffusion bonding (SPF/DB) process to supersonic cruise research is investigated. The capability of an SPF/DB titanium structure to meet the structural requirements of the inner wing area of the NASA arrow-wing advanced supersonic transport design is evaluated. Selection of structural concepts and their optimization for minimum weight, SPF/DB process optimization, fabrication of representative specimens, and specimen testing and evaluation are described. The structural area used includes both upper and lower wing panels, where the upper wing panel is used for static compression strength evaluation and the lower panel, in tension, is used for fracture mechanics evaluations. The individual test specimens, cut from six large panels, consist of 39 static specimens, 10 fracture mechanics specimens, and one each full size panel for compression stability and fracture mechanics testing. Tests are performed at temperatures of -54 C (-65 F), room temperature, and 260 C (500 F).

  18. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

    PubMed

    Dopieralski, Przemyslaw; Perrin, Charles L; Latajka, Zdzislaw

    2011-11-01

    The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water. PMID:26598249

  19. Moderately nonlinear diffuse-charge dynamics under an ac voltage.

    PubMed

    Stout, Robert F; Khair, Aditya S

    2015-09-01

    The response of a symmetric binary electrolyte between two parallel, blocking electrodes to a moderate amplitude ac voltage is quantified. The diffuse charge dynamics are modeled via the Poisson-Nernst-Planck equations for a dilute solution of point-like ions. The solution to these equations is expressed as a Fourier series with a voltage perturbation expansion for arbitrary Debye layer thickness and ac frequency. Here, the perturbation expansion in voltage proceeds in powers of V_{o}/(k_{B}T/e), where V_{o} is the amplitude of the driving voltage and k_{B}T/e is the thermal voltage with k_{B} as Boltzmann's constant, T as the temperature, and e as the fundamental charge. We show that the response of the electrolyte remains essentially linear in voltage amplitude at frequencies greater than the RC frequency of Debye layer charging, D/λ_{D}L, where D is the ion diffusivity, λ_{D} is the Debye layer thickness, and L is half the cell width. In contrast, nonlinear response is predicted at frequencies below the RC frequency. We find that the ion densities exhibit symmetric deviations from the (uniform) equilibrium density at even orders of the voltage amplitude. This leads to the voltage dependence of the current in the external circuit arising from the odd orders of voltage. For instance, the first nonlinear contribution to the current is O(V_{o}^{3}) which contains the expected third harmonic but also a component oscillating at the applied frequency. We use this to compute a generalized impedance for moderate voltages, the first nonlinear contribution to which is quadratic in V_{o}. This contribution predicts a decrease in the imaginary part of the impedance at low frequency, which is due to the increase in Debye layer capacitance with increasing V_{o}. In contrast, the real part of the impedance increases at low frequency, due to adsorption of neutral salt from the bulk to the Debye layer. PMID:26465471

  20. Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

    PubMed

    Mesele, Oluwaseun O; Vartia, Anthony A; Laage, Damien; Thompson, Ward H

    2016-03-01

    Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

  1. Peptaibol Zervamicin IIB Structure and Dynamics Refinement from Transhydrogen Bond J Couplings

    PubMed Central

    Shenkarev, Z. O.; Balashova, T. A.; Yakimenko, Z. A.; Ovchinnikova, T. V.; Arseniev, A. S.

    2004-01-01

    Zervamicin IIB (Zrv-IIB) is a channel-forming peptaibol antibiotic of fungal origin. The measured transhydrogen bond 3hJNC′ couplings in methanol solution heaving average value of −0.41 Hz indicate that the stability of the Zrv-IIB helix in this milieu is comparable to the stability of helices in globular proteins. The N-terminus of the peptide forms an α-helix, whereas 310-helical hydrogen bonds stabilize the C-terminus. However, two weak transhydrogen bond peaks are observed in a long-range HNCO spectrum for HN Aib12. Energy calculations using the Empirical Conformation Energy Program for Peptides (ECEPP)/2 force field and the implicit solvent model show that the middle of the peptide helix accommodates a bifurcated hydrogen bond that is simultaneously formed between HN Aib12 and CO Leu8 and CO Aib9. Several lowered 3hJNC′ on a polar face of the helix correlate with the conformational exchange process observed earlier and imply dynamic distortions of a hydrogen bond pattern with the predominant population of a properly folded helical structure. The refined structure of Zrv-IIB on the basis of the observed hydrogen bond pattern has a small (∼20°) angle of helix bending that is virtually identical to the angle of bending in dodecylphosphocholine (DPC) micelles, indicating the stability of a hinge region in different environments. NMR parameters (1HN chemical shifts and transpeptide bond 1JNC′ couplings) sensitive to hydrogen bonding along with the solvent accessible surface area of carbonyl oxygens indicate a large polar patch on the convex side of the helix formed by three exposed backbone carbonyls of Aib7, Aib9, and Hyp10 and polar side chains of Hyp10, Gln11, and Hyp13. The unique structural features, high helix stability and the enhanced polar patch, set apart Zrv-IIB from other peptaibols (for example, alamethicin) and possibly underlie its biological and physiological properties. PMID:15189865

  2. A molecular dynamics study of bond exchange reactions in covalent adaptable networks.

    PubMed

    Yang, Hua; Yu, Kai; Mu, Xiaoming; Shi, Xinghua; Wei, Yujie; Guo, Yafang; Qi, H Jerry

    2015-08-21

    Covalent adaptable networks are polymers that can alter the arrangement of network connections by bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond. When the polymer is stretched, bond exchange reactions lead to stress relaxation and plastic deformation, or the so-called reforming. In addition, two pieces of polymers can be rejoined together without introducing additional monomers or chemicals on the interface, enabling welding and reprocessing. Although covalent adaptable networks have been researched extensively in the past, knowledge about the macromolecular level network alternations is limited. In this study, molecular dynamics simulations are used to investigate the macromolecular details of bond exchange reactions in a recently reported epoxy system. An algorithm for bond exchange reactions is first developed and applied to study a crosslinking network formed by epoxy resin DGEBA with the crosslinking agent tricarballylic acid. The trace of the active units is tracked to show the migration of these units within the network. Network properties, such as the distance between two neighboring crosslink sites, the chain angle, and the initial modulus, are examined after each iteration of the bond exchange reactions to provide detailed information about how material behaviors and macromolecular structure evolve. Stress relaxation simulations are also conducted. It is found that even though bond exchange reactions change the macroscopic shape of the network, microscopic network characteristic features, such as the distance between two neighboring crosslink sites and the chain angle, relax back to the unstretched isotropic state. Comparison with a recent scaling theory also shows good agreement.

  3. Role of large-scale slip in mode II fracture of bimaterial interface produced by diffusion bonding

    NASA Astrophysics Data System (ADS)

    Fox, M. R.; Ghosh, A. K.

    2001-08-01

    Bimaterial interfaces present in diffusion-bonded (and in-situ) composites are often not flat interfaces. The unevenness of the interface can result not only from interface reaction products but also from long-range waviness associated with the surfaces of the component phases bonded together. Experimental studies aimed at determining interface mechanical properties generally ignore the departure in the local stress due to waviness and assume a theoretically flat interface. Furthermore, the commonly used testing methods involving superimposed tension often renders the interface so extremely brittle that if microplastic effects were present it becomes impossible to perceive them. This article examines the role of waviness of the interface and microplastic effects on crack initiation. To do this, a test was selected that provides significant stability against crack growth by superimposing compressive stresses. Mode II interface fracture was studied for NiAl/Mo model laminates using a recently developed asymmetrically loaded shear (ALS) interface shear test. The ALS test may be viewed as opposite of the laminate bend test. In the bend test, shear at the interface is created via tension on one surface of the bend, while in the ALS test, shear is created by compression on one side of the interface relative to the other. Normal to the interface, near the crack tip, an initially compressive state is replaced by slight tension due to Poisson’s expansion of the unbonded part of the compressed beam.

  4. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin.

    PubMed

    Jardón-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J

    2014-12-01

    Translocation of negatively charged ions across cell membranes by ion pumps raises the question as to how protein interactions control the location and dynamics of the ion. Here we address this question by performing extensive molecular dynamics simulations of wild type and mutant halorhodopsin, a seven-helical transmembrane protein that translocates chloride ions upon light absorption. We find that inter-helical hydrogen bonds mediated by a key arginine group largely govern the dynamics of the protein and water groups coordinating the chloride ion.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Diffusion in a Cu-Zr metallic glass studied by microsecond-scale molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Wang, C. Z.; Mendelev, M. I.; Zhang, F.; Kramer, M. J.; Ho, K. M.

    2015-05-01

    Icosahedral short-range order (ISRO) has been widely accepted to be dominant in Cu-Zr metallic glasses (MGs). However, the diffusion mechanism and correlation of ISRO and medium-range order (MRO) to diffusion in MGs remain largely unexplored. Here, we perform a long time annealing up to 1.8 μs in molecular dynamics simulations to study the diffusion mechanism and the relationship between atomic structures and the diffusion path in a C u64.5Z r35.5 MG. It is found that most of the diffusing events performed by the diffusing atoms are outside ISRO and the Bergman-type MRO. The long-range diffusion in MGs is highly heterogeneous, via collective diffusing events through the liquidlike channels in the glass. Our results clearly demonstrate a strong correlation between the atomic structures and transport in MGs.

  7. Effects of Pulse Current on Transient Liquid Phase (TLP) Diffusion Bonding of SiCp/2024Al Composites Sheet Using Mixed Al, Cu, and Ti Powder Interlayer

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Jiang, Shaosong; Zhang, Kaifeng

    2012-09-01

    The effects of pulse current on transient liquid phase (TLP) diffusion bonding of SiCp/2024Al composites sheet were investigated at 853 K (580 °C) using a mixed slurry of Al, Cu, and Ti powder interlayer. The process parameters were as follows: the pulse current density of 1.15 × 102 A/mm2, the original pressure of 0.5 MPa, the vacuum of 1.3 × 10-3 Pa, and the bonding time from 15 to 60 minutes. Moreover, the bonding mechanism in correlation with the microstructural and mechanical properties variation was analyzed.

  8. Fabrication and evaluation of enhanced diffusion bonded titanium honeycomb core sandwich panels with titanium aluminide face sheets

    NASA Technical Reports Server (NTRS)

    Hoffmann, E. K.; Bird, R. K.; Bales, T. T.

    1989-01-01

    A joining process was developed for fabricating lightweight, high temperature sandwich panels for aerospace applications using Ti-14Al-21Nb face sheets and Ti-3Al-2.5V honeycomb core. The process, termed Enhanced Diffusion Bonding (EDB), relies on the formation of a eutectic liquid through solid-state diffusion at elevated temperatures and isothermal solidification to produce joints in thin-gage titanium and titanium aluminide structural components. A technique employing a maskant on the honeycomb core was developed which permitted electroplating a controlled amount of EDB material only on the edges of the honeycomb core in order to minimize the structural weight and metallurgical interaction effects. Metallurgical analyses were conducted to determine the interaction effects between the EDB materials and the constituents of the sandwich structure following EDB processing. The initial mechanical evaluation was conducted with butt joint specimens tested at temperatures from 1400 - 1700 F. Further mechanical evaluation was conducted with EDB sandwich specimens using flatwise tension tests at temperatures from 70 - 1100 F and edgewise compression tests at ambient temperature.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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

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

    SciTech Connect

    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

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

    PubMed

    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

  12. Diffusion-limited aggregation as a markovian process: bond-sticking conditions

    PubMed

    Kol; Aharony

    2000-08-01

    Cylindrical lattice diffusion limited aggregation (DLA), with a narrow width N, is solved using a Markovian matrix method. This matrix contains the probabilities that the front moves from one configuration to another at each growth step, calculated exactly by solving the Laplace equation and using the proper normalization. The method is applied for a series of approximations, which include only a finite number of rows near the front. The matrix is then used to find the weights of the steady-state growing configurations and the rate of approaching this steady-state stage. The former are then used to find the average upward growth probability, the average steady-state density and the fractal dimensionality of the aggregate, which is extrapolated to a value near 1.64. PMID:11088734

  13. Effect of Bonding Temperature on Phase Transformation of Diffusion-Bonded Joints of Duplex Stainless Steel and Ti-6Al-4V Using Nickel and Copper as Composite Intermediate Metals

    NASA Astrophysics Data System (ADS)

    Kundu, Sukumar; Thirunavukarasu, Gopinath; Chatterjee, Subrata; Mishra, Brajendra

    2015-12-01

    In the present study, the effect of bonding temperature on phase transformation of diffusion-bonded joints of duplex stainless steel (DSS) and Ti-6Al-4V (Ti64) using simultaneously both nickel (Ni) and copper (Cu) interlayers was investigated in the temperature range of 1148 K to 1223 K (875 °C to 950 °C) insteps of 25 K (25 °C) for 60 minutes under 4 MPa uniaxial pressure in vacuum. Interfaces were characterized by scanning electron microscopy and interdiffusion of the chemical species across the diffusion interfaces were witnessed by electron probe microanalysis. At 1148 K (875 °C), layer-wise Cu4Ti, Cu2Ti, Cu4Ti3, CuTi, and CuTi2 phases were observed at the Cu-Ti64 interface; however, DSS-Ni and Ni-Cu interfaces were free from any intermetallic. At 1173 K and 1198 K (900 °C and 925 °C), Cu interlayer could not restrict the diffusion of atoms from Ti64 to Ni, and vice versa; and Ni-Ti-based intermetallics were formed at the Ni-Cu interface and throughout the Cu zone as well; however, at 1223 K (950 °C), both Ni and Cu interlayers could not inhibit the diffusion of atoms from Ti64 to DSS, and vice versa. The maximum shear strength of ~377 MPa was obtained for the diffusion couple processed at 1148 K (875 °C) and strength of the bonded joints gradually decreased with the increasing bonding temperature due to the widening of brittle intermetallics at the diffusion zone. Fracture path indicated that failure took place through the Cu4Ti intermetallic at the Cu-Ti64 interface when bonding was processed at 1148 K (875 °C). When bonding was processed at 1173 K and 1198 K (900 °C and 925 °C), fracture took place through the Ni3Ti intermetallic at the Ni-(Ni + Cu + Ti64 diffusion reaction) interface; however, at 1223 K (950 °C), fracture morphology indicated the brittle nature and the fracture took place apparently through the σ phase at the DSS-(DSS + Ni + Cu + Ti64 diffusion reaction) interface.

  14. Molecular dynamics of neutral polymer bonding agent (NPBA) as revealed by solid-state NMR spectroscopy.

    PubMed

    Hu, Wei; Su, Yongchao; Zhou, Lei; Pang, Aimin; Cai, Rulin; Ma, Xingang; Li, Shenhui

    2014-01-22

    Neutral polymer bonding agent (NPBA) is one of the most promising polymeric materials, widely used in nitrate ester plasticized polyether (NEPE) propellant as bonding agent. The structure and dynamics of NPBA under different conditions of temperatures and sample processing are comprehensively investigated by solid state NMR (SSNMR). The results indicate that both the main chain and side chain of NPBA are quite rigid below its glass transition temperature (Tg). In contrast, above the Tg, the main chain remains relatively immobilized, while the side chains become highly flexible, which presumably weakens the interaction between bonding agent and the binder or oxidant fillers and in turn destabilizes the high modulus layer formed around the oxidant fillers. In addition, no obvious variation is found for the microstructure of NPBA upon aging treatment or soaking with acetone. These experimental results provide useful insights for understanding the structural properties of NPBA and its interaction with other constituents of solid composite propellants under different processing and working conditions.

  15. Effect of loading rate on dynamic fracture of reaction bonded silicon nitride

    NASA Technical Reports Server (NTRS)

    Liaw, B. M.; Kobayashi, A. S.; Emery, A. F.

    1986-01-01

    Wedge-loaded, modified tapered double cantilever beam (WL-MTDCB) specimens under impact loading were used to determine the room temperature dynamic fracture response of reaction bonded silicon nitride (RBSN). The crack extension history, with the exception of the terminal phase, was similar to that obtained under static loading. Like its static counterpart, a distinct crack acceleration phase, which was not observed in dynamic fracture of steel and brittle polymers, was noted. Unlike its static counterpart, the crack continued to propagate at nearly its terminal velocity under a low dynamic stress intensity factor during the terminal phase of crack propagation. These and previously obtained results for glass and RBSN show that dynamic crack arrest under a positive dynamic stress intensity factor is unlikely in static and impact loaded structural ceramics.

  16. "Zwitterionic Proton Sponge" Hydrogen Bonding Investigations on the Basis of Car-Parrinello Molecular Dynamics.

    PubMed

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

    1,8-Bis(dimethylamino)-4,5-dihydroxynaphthalene has been investigated on the basis of static DFT computations and Car-Parrinello molecular dynamics. The simulations were performed in the gas phase and in the solid state. The studied "zwitterionic proton sponge" possesses two, short intramolecular hydrogen bonds (O-H···O and N-H···N) classified as Low Barrier Hydrogen Bonds (LBHBs); therefore, the system studied is strongly anharmonic. In addition, the compound exists as a "zwitterion" in solution and in the solid state, thus the intramolecular hydrogen bonds belong to the class of charge-assisted interactions. The applied quantum-chemical methods enabled investigations of metric and spectroscopic parameters of the molecule. The time-evolution investigations of the H-bonding showed a strong delocalization of the bridge protons and their high mobility, reflected in the low barriers on the free energy surfaces. Frequent proton transfer phenomena were noticed. The power spectra of atomic velocity were computed to analyze the vibrational features associated with O-H and N-H stretching. A broad absorption was indicated for both hydrogen bridges. For the first time, Car-Parrinello molecular dynamics results are reported for the compound, and they indicate a broad, shallow but not barrierless, potential well for each of the bridge protons. PMID:25965324

  17. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate.

    PubMed

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-14

    We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology. PMID:20550407

  18. Hydrogen Bond Dynamic Propensity Studies for Protein Binding and Drug Design

    PubMed Central

    2016-01-01

    We study the dynamic propensity of the backbone hydrogen bonds of the protein MDM2 (the natural regulator of the tumor suppressor p53) in order to determine its binding properties. This approach is fostered by the observation that certain backbone hydrogen bonds at the p53-binding site exhibit a dynamical propensity in simulations that differs markedly form their state-value (that is, formed/not formed) in the PDB structure of the apo protein. To this end, we conduct a series of hydrogen bond propensity calculations in different contexts: 1) computational alanine-scanning studies of the MDM2-p53 interface; 2) the formation of the complex of MDM2 with the disruptive small molecule Nutlin-3a (dissecting the contribution of the different molecular fragments) and 3) the binding of a series of small molecules (drugs) with different affinities for MDM2. Thus, the relevance of the hydrogen bond propensity analysis for protein binding studies and as a useful tool to complement existing methods for drug design and optimization will be made evident. PMID:27792778

  19. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate.

    PubMed

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-14

    We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.

  20. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate

    NASA Astrophysics Data System (ADS)

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-01

    We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrödinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm-1 and a half width of about 700 cm-1, which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm-1, respectively. The hydrogen probability densities obtained by solving the vibrational Schrödinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.

  1. Exploiting Dynamic Bonds in Polymer-grafted Nanoparticle Networks to Create Mechanomutable, Reconfigurable Composites

    NASA Astrophysics Data System (ADS)

    Balazs, Anna C.; Hamer, Matthew J.; Iyer, Balaji V. S.; Yashin, Victor V.

    2015-03-01

    Via a new dynamic, three-dimensional computer model, we simulate the tensile deformation of polymer-grafted nanoparticles (PGNs) that are cross-linked by labile bonds, which can readily rupture and reform. For a range of relatively high strains, the network does not fail, but rather restructures into a stable, ordered structure. Within this network, the reshuffling of the labile bonds enables the formation of this new morphology. The studies reveal that the appropriate combination of stress-responsive hybrid materials and applied stress can yield distinct opportunities to dynamically switch between different structures, and thus, the properties of the material. Thus, the results provide guidelines for designing mechano-responsive hybrid materials that undergo controllable structural transitions through the application of applied forces.

  2. Diffusion of Dissipative Correlation in the Dynamic Failure of Solids

    NASA Astrophysics Data System (ADS)

    Grady, Dennis

    A property identified as the dissipative action has found application as a unifying attribute underlying the dynamic failure of solid materials. Failure modes include tensile spall, impact-induced dynamic shear, shock compaction and steady shock-wave compression. The present work explores the possible application of Langevin dynamics and related statistical mechanical implications as underlying the extreme dynamic failure of solids.

  3. Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites.

    PubMed

    Holt, Adam P; Bocharova, Vera; Cheng, Shiwang; Kisliuk, Alexander M; White, B Tyler; Saito, Tomonori; Uhrig, David; Mahalik, J P; Kumar, Rajeev; Imel, Adam E; Etampawala, Thusitha; Martin, Halie; Sikes, Nicole; Sumpter, Bobby G; Dadmun, Mark D; Sokolov, Alexei P

    2016-07-26

    It is generally believed that the strength of the polymer-nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as low as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching-a parameter accessible from the MW or grafting density. PMID:27337392

  4. Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites

    DOE PAGESBeta

    Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang; Kisliuk, Alexander M.; White, B. Tyler; Saito, Tomonori; Uhrig, David; Mahalik, J. P.; Kumar, Rajeev; Imel, Adam E.; et al

    2016-06-23

    It is generally believed that the strength of the polymer nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as lowmore » as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching a parameter accessible from the MW or grafting density.« less

  5. Classically exact overlayer dynamics: Diffusion of rhodium clusters on Rh(100)

    SciTech Connect

    Voter, A.F.

    1986-11-15

    A new method is presented for describing the classical dynamics (e.g., diffusion, desorption) of adsorbed overlayers of atoms or molecules, starting from arbitrary interatomic potentials. Provided that a certain dynamical criterion is met, the method yields classically exact results, but with many orders of magnitude less computation than direct molecular dynamics. The approach provides, for what we believe to be the first time, a connection between stochastic lattice-gas dynamical methods and the interatomic potential function. As a sample application, the diffusion constants are computed for two-dimensional rhodium clusters of up to 75 atoms on the Rh(100) surface at T = 2000 K. For clusters larger than n = 15 atoms, the diffusion constant scales as n/sup -1.76//sup +- //sup 0.06/, and the dominant mechanism for the diffusion is found to be atoms running along the edges of the cluster blocks.

  6. Maxwell-Stefan diffusion and dynamical correlation in molten LiF-KF: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Jain, Richa Naja; Chakraborty, Brahmananda; Ramaniah, Lavanya M.

    2016-05-01

    In this work our main objective is to compute Dynamical correlations, Onsager coefficients and Maxwell-Stefan (MS) diffusivities for molten salt LiF-KF mixture at various thermodynamic states through Green-Kubo formalism for the first time. The equilibrium molecular dynamics (MD) simulations were performed using BHM potential for LiF-KF mixture. The velocity autocorrelations functions involving Li ions reflect the endurance of cage dynamics or backscattering with temperature. The magnitude of Onsager coefficients for all pairs increases with increase in temperature. Interestingly most of the Onsager coefficients has almost maximum magnitude at the eutectic composition indicating the most dynamic character of the eutectic mixture. MS diffusivity hence diffusion for all ion pairs increases in the system with increasing temperature. Smooth variation of the diffusivity values denies any network formation in the mixture. Also, the striking feature is the noticeable concentration dependence of MS diffusivity between cation-cation pair, ĐLi-K which remains negative for most of the concentration range but changes sign to become positive for higher LiF concentration. The negative MS diffusivity is acceptable as it satisfies the non-negative entropy constraint governed by 2nd law of thermodynamics. This high diffusivity also vouches the candidature of molten salt as a coolant.

  7. Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer.

    PubMed

    Chalabala, Jan; Slavíček, Petr

    2016-07-27

    In the case of the ammonia dimer, we address the following questions: how ultrafast ionization dynamics is controlled by hydrogen bonding and whether we can control the products via selective ionization of a specific electron. We use quantum chemical calculations and ab initio non-adiabatic molecular dynamics simulations to model the femtosecond dynamics of the ammonia dimer upon ionization. The role of nuclear quantum effects and thermal fluctuations in predicting the structure of the dimer is emphasized; it is shown that the minimum energy and vibrationally averaged structures are rather different. The ground state structure subsequently controls the ionization dynamics. We describe reaction pathways, electronic population transfers and reaction yields with respect to ionization from different molecular orbitals. The simulations showed that the ionized ammonia dimer is highly unstable and its decay rate is primarily driven by the position of the electron hole. In the case of ground state ionization (i.e. the HOMO electron is ionized), the decay is likely to be preceded by a proton transfer (PT) channel yielding NH4(+) and NH2˙ fragments. The PT is less intense and slower compared with the ionized water dimer. After ionizing deeper lying electrons, mainly NH3(+)˙ and NH3 fragments are formed. Overall, our results show that the ionization dynamics of the ammonia and water dimers differ due to the nature of the hydrogen bond in these systems. PMID:27402376

  8. Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network.

    PubMed

    Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

    2014-01-01

    Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions.

  9. A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates.

    PubMed

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Alavi, Saman; Yasuoka, Kenji

    2015-05-21

    Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

  10. Dynamics of information diffusion and its applications on complex networks

    NASA Astrophysics Data System (ADS)

    Zhang, Zi-Ke; Liu, Chuang; Zhan, Xiu-Xiu; Lu, Xin; Zhang, Chu-Xu; Zhang, Yi-Cheng

    2016-09-01

    The ongoing rapid expansion of the Word Wide Web (WWW) greatly increases the information of effective transmission from heterogeneous individuals to various systems. Extensive research for information diffusion is introduced by a broad range of communities including social and computer scientists, physicists, and interdisciplinary researchers. Despite substantial theoretical and empirical studies, unification and comparison of different theories and approaches are lacking, which impedes further advances. In this article, we review recent developments in information diffusion and discuss the major challenges. We compare and evaluate available models and algorithms to respectively investigate their physical roles and optimization designs. Potential impacts and future directions are discussed. We emphasize that information diffusion has great scientific depth and combines diverse research fields which makes it interesting for physicists as well as interdisciplinary researchers.

  11. Static and Dynamic Effects of Lateral Carrier Diffusion in Semiconductor Lasers

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  12. Perturbations and dynamics of reaction-diffusion systems with mass conservation.

    PubMed

    Kuwamura, Masataka; Morita, Yoshihisa

    2015-07-01

    In some reaction-diffusion systems where the total mass of their components is conserved, solutions with initial values near a homogeneous equilibrium converge to a simple localized pattern (spike) after exhibiting Turing-like patterns near the equilibrium for appropriate diffusion coefficients. In this study, we investigate the perturbed reaction-diffusion systems of such conserved systems. We show that a reaction-diffusion model with a globally stable homogeneous equilibrium can exhibit large amplitude Turing-like patterns in the transient dynamics. Moreover, we propose a three-component model, which exhibits an alternating repetition of spatially (almost) homogeneous oscillations and large amplitude Turing-like patterns.

  13. The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics.

    PubMed

    Jakse, N; Pasturel, A

    2014-09-01

    We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

  14. Neutron Crystallography, Molecular Dynamics, and Quantum Mechanics Studies of the Nature of Hydrogen Bonding in Cellulose I beta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the crystal structure of cellulose Ibeta, disordered hydrogen (H) bonding can be represented by the average of two mutually exclusive H bonding schemes that have been designated A and B. An unanswered question is whether A and B interconvert dynamically, or whether they are static but present in ...

  15. A role for disulfide bonding in keratin intermediate filament organization and dynamics in skin keratinocytes.

    PubMed

    Feng, Xia; Coulombe, Pierre A

    2015-04-13

    We recently reported that a trans-dimer, homotypic disulfide bond involving Cys367 in keratin 14 (K14) occurs in an atomic-resolution structure of the interacting K5/K14 2B domains and in keratinocyte cell lines. Here we show that a sizable fraction of the K14 and K5 protein pools participates in interkeratin disulfide bonding in primary cultures of mouse skin keratinocytes. By comparing the properties of wild-type K14 with a completely cysteine-free variant thereof, we found that K14-dependent disulfide bonding limited filament elongation during polymerization in vitro but was necessary for the genesis of a perinuclear-concentrated network of keratin filaments, normal keratin cycling, and the sessile behavior of the nucleus and whole cell in keratinocytes studied by live imaging. Many of these phenotypes were rescued when analyzing a K14 variant harboring a single Cys residue at position 367. These findings establish disulfide bonding as a novel and important mechanism regulating the assembly, intracellular organization, and dynamics of K14-containing intermediate filaments in skin keratinocytes.

  16. A role for disulfide bonding in keratin intermediate filament organization and dynamics in skin keratinocytes

    PubMed Central

    Feng, Xia

    2015-01-01

    We recently reported that a trans-dimer, homotypic disulfide bond involving Cys367 in keratin 14 (K14) occurs in an atomic-resolution structure of the interacting K5/K14 2B domains and in keratinocyte cell lines. Here we show that a sizable fraction of the K14 and K5 protein pools participates in interkeratin disulfide bonding in primary cultures of mouse skin keratinocytes. By comparing the properties of wild-type K14 with a completely cysteine-free variant thereof, we found that K14-dependent disulfide bonding limited filament elongation during polymerization in vitro but was necessary for the genesis of a perinuclear-concentrated network of keratin filaments, normal keratin cycling, and the sessile behavior of the nucleus and whole cell in keratinocytes studied by live imaging. Many of these phenotypes were rescued when analyzing a K14 variant harboring a single Cys residue at position 367. These findings establish disulfide bonding as a novel and important mechanism regulating the assembly, intracellular organization, and dynamics of K14-containing intermediate filaments in skin keratinocytes. PMID:25869667

  17. Hydrogen-bond-dynamics-based switching of conductivity and magnetism: a phase transition caused by deuterium and electron transfer in a hydrogen-bonded purely organic conductor crystal.

    PubMed

    Ueda, Akira; Yamada, Shota; Isono, Takayuki; Kamo, Hiromichi; Nakao, Akiko; Kumai, Reiji; Nakao, Hironori; Murakami, Youichi; Yamamoto, Kaoru; Nishio, Yutaka; Mori, Hatsumi

    2014-08-27

    A hydrogen bond (H-bond) is one of the most fundamental and important noncovalent interactions in chemistry, biology, physics, and all other molecular sciences. Especially, the dynamics of a proton or a hydrogen atom in the H-bond has attracted increasing attention, because it plays a crucial role in (bio)chemical reactions and some physical properties, such as dielectricity and proton conductivity. Here we report unprecedented H-bond-dynamics-based switching of electrical conductivity and magnetism in a H-bonded purely organic conductor crystal, κ-D3(Cat-EDT-TTF)2 (abbreviated as κ-D). This novel crystal κ-D, a deuterated analogue of κ-H3(Cat-EDT-TTF)2 (abbreviated as κ-H), is composed only of a H-bonded molecular unit, in which two crystallographically equivalent catechol-fused ethylenedithiotetrathiafulvalene (Cat-EDT-TTF) skeletons with a +0.5 charge are linked by a symmetric anionic [O···D···O](-1)-type strong H-bond. Although the deuterated and parent hydrogen systems, κ-D and κ-H, are isostructural paramagnetic semiconductors with a dimer-Mott-type electronic structure at room temperature (space group: C2/c), only κ-D undergoes a phase transition at 185 K, to change to a nonmagnetic insulator with a charge-ordered electronic structure (space group: P1). The X-ray crystal structure analysis demonstrates that this dramatic switching of the electronic structure and physical properties originates from deuterium transfer or displacement within the H-bond accompanied by electron transfer between the Cat-EDT-TTF π-systems, proving that the H-bonded deuterium dynamics and the conducting TTF π-electron are cooperatively coupled. Furthermore, the reason why this unique phase transition occurs only in κ-D is qualitatively discussed in terms of the H/D isotope effect on the H-bond geometry and potential energy curve.

  18. Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin.

    PubMed

    Saha, Suvrajit; Lee, Il-Hyung; Polley, Anirban; Groves, Jay T; Rao, Madan; Mayor, Satyajit

    2015-11-01

    Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24-37 °C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an "active actin-membrane composite" cell surface.

  19. Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin

    PubMed Central

    Saha, Suvrajit; Lee, Il-Hyung; Polley, Anirban; Groves, Jay T.; Rao, Madan; Mayor, Satyajit

    2015-01-01

    Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24–37°C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an “active actin-membrane composite” cell surface. PMID:26378258

  20. A scintillator fabricated by solid-state diffusion bonding for high spatial resolution x-ray imaging

    NASA Astrophysics Data System (ADS)

    Kameshima, Takashi; Sato, Takahiro; Kudo, Togo; Ono, Shun; Ozaki, Kyosuke; Katayama, Tetsuo; Hatsui, Takaki; Yabashi, Makina

    2016-07-01

    Lens-coupled two-dimensional indirect X-ray detectors with thin-film scintillators are important for high spatial resolution X-ray imaging. To achieve high quality high-resolution images, we propose a novel fabrication method for thin-film scintillators based on solid-state diffusion bonding. Scintillators were successfully produced with thicknesses of 5, 10, and 20 μm, with a surface flatness better than λ/10. X-ray imaging performance with a point spread function of 8 μm FWHM was demonstrated with a prototype X-ray detector equipped with a 20-μm-thick scintillator, at an effective spatial sampling of 4 μm/pixel and a field of view of 2.56 x 1.92 mm2. At the request of all authors of the paper and with the agreement of the proceedings editors an updated version of this article was published on 1 September 2016. An older version of the paper was inadvertently supplied to AIP Publishing and the final version is now available.

  1. Measurement of adhesion strength of solid-state diffusion bonding between nickel and copper by means of laser shock spallation method

    NASA Astrophysics Data System (ADS)

    Satou, Manabu; Akamatsu, Hitoshi; Hasegawa, Akira

    2009-06-01

    Coating and bonding techniques between different materials are essential to the field of technology. Bonding mechanism is of interest from scientific points of view. Several works concerning to the strength such bonding have been revealed that the strength depended on crystallographic orientations, differences of thermal expansion and chemical affinity and so on. The methods adopted for those measurements had uncertainties due to plastic deformation near the interface. A laser shock spallation method was utilized to measure adhesion strength of the bonding in this paper to minimize the deformation outside of the interface. A well-established method to make bonding between unalloyed nickel and copper was utilized, that was solid-state diffusion bonding at elevated temperatures. Irradiation by Nd:YAG laser with 7ns-pulse width created shock wave that caused tensile stress after reflection at free surface. The stress depended on laser power and was estimated by surface velocity profile measured by a laser interferometer. The adhesion strength was determined by the critical laser power that caused exfoliation of the bonding interface.

  2. Normal and Anomalous Diffusion: An Analytical Study Based on Quantum Collision Dynamics and Boltzmann Transport Theory.

    PubMed

    Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra

    2016-09-15

    Diffusion, an emergent nonequilibrium transport phenomenon, is a nontrivial manifestation of the correlation between the microscopic dynamics of individual molecules and their statistical behavior observed in experiments. We present a thorough investigation of this viewpoint using the mathematical tools of quantum scattering, within the framework of Boltzmann transport theory. In particular, we ask: (a) How and when does a normal diffusive transport become anomalous? (b) What physical attribute of the system is conceptually useful to faithfully rationalize large variations in the coefficient of normal diffusion, observed particularly within the dynamical environment of biological cells? To characterize the diffusive transport, we introduce, analogous to continuous phase transitions, the curvature of the mean square displacement as an order parameter and use the notion of quantum scattering length, which measures the effective interactions between the diffusing molecules and the surrounding, to define a tuning variable, η. We show that the curvature signature conveniently differentiates the normal diffusion regime from the superdiffusion and subdiffusion regimes and the critical point, η = ηc, unambiguously determines the coefficient of normal diffusion. To solve the Boltzmann equation analytically, we use a quantum mechanical expression for the scattering amplitude in the Boltzmann collision term and obtain a general expression for the effective linear collision operator, useful for a variety of transport studies. We also demonstrate that the scattering length is a useful dynamical characteristic to rationalize experimental observations on diffusive transport in complex systems. We assess the numerical accuracy of the present work with representative experimental results on diffusion processes in biological systems. Furthermore, we advance the idea of temperature-dependent effective voltage (of the order of 1 μV or less in a biological environment, for example

  3. Normal and Anomalous Diffusion: An Analytical Study Based on Quantum Collision Dynamics and Boltzmann Transport Theory.

    PubMed

    Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra

    2016-09-15

    Diffusion, an emergent nonequilibrium transport phenomenon, is a nontrivial manifestation of the correlation between the microscopic dynamics of individual molecules and their statistical behavior observed in experiments. We present a thorough investigation of this viewpoint using the mathematical tools of quantum scattering, within the framework of Boltzmann transport theory. In particular, we ask: (a) How and when does a normal diffusive transport become anomalous? (b) What physical attribute of the system is conceptually useful to faithfully rationalize large variations in the coefficient of normal diffusion, observed particularly within the dynamical environment of biological cells? To characterize the diffusive transport, we introduce, analogous to continuous phase transitions, the curvature of the mean square displacement as an order parameter and use the notion of quantum scattering length, which measures the effective interactions between the diffusing molecules and the surrounding, to define a tuning variable, η. We show that the curvature signature conveniently differentiates the normal diffusion regime from the superdiffusion and subdiffusion regimes and the critical point, η = ηc, unambiguously determines the coefficient of normal diffusion. To solve the Boltzmann equation analytically, we use a quantum mechanical expression for the scattering amplitude in the Boltzmann collision term and obtain a general expression for the effective linear collision operator, useful for a variety of transport studies. We also demonstrate that the scattering length is a useful dynamical characteristic to rationalize experimental observations on diffusive transport in complex systems. We assess the numerical accuracy of the present work with representative experimental results on diffusion processes in biological systems. Furthermore, we advance the idea of temperature-dependent effective voltage (of the order of 1 μV or less in a biological environment, for example

  4. Using multistate dynamical corrections to compute classically exact diffusion constants at arbitrary temperature

    SciTech Connect

    Voter, A.F.; Doll, J.D.; Cohen, J.M.

    1989-02-01

    A method is presented for computing the classically exact, surface or bulk diffusion constant of a point defect at arbitrary temperature. The thermal diffusion constant is expressed using the squared jump length averaged over all possible final states to which the atom can jump. The rate constants that weight this sum are computed using transition state theory and molecular dynamics within a recently developed many-state dynamical corrections formalism. While these rate constants are valid only in the rare-event regime (i.e., at low temperature), it is shown that for a periodic lattice of equivalent binding sites, the resulting diffusion contants is valid at any temperature for which the lattice sites remain well defined. It is thus possible to compute classically exact surface or bulk diffusion constant for an arbitrary interatomic potential, without the time scale limitations of direct molecular dynamics.

  5. Diffusion dynamics of small molecules from mesoporous silicon films by real-time optical interferometry

    SciTech Connect

    Mares, Jeremy W.; Weiss, Sharon M.

    2011-09-20

    Time-dependent laser reflectometry measurements are presented as a means to rigorously characterize analyte diffusion dynamics of small molecules from mesoporous silicon (PSi) films for drug delivery and membrane physics applications. Calculations based on inclusion of a spatially and temporally dependent solute concentration profile in a one-dimensional Fickian diffusion flow model are performed to determine the diffusion coefficients for the selected prototypical polar species, sucrose (340 Da), exiting from PSi films. The diffusion properties of the molecules depend on both PSi pore size and film thickness. For films with average pore diameters between 10-30 nm and film thicknesses between 300-900 nm, the sucrose diffusion coefficient can be tuned between approximately 100 and 550 {mu}m{sup 2}/s. Extensions of the real-time measurement and modeling approach for determining the diffusivity of small molecules that strongly interact with and corrode the internal surfaces of PSi films are also discussed.

  6. Molecular dynamics study of diffusion of krypton in water at different temperatures

    NASA Astrophysics Data System (ADS)

    Bhandari, Dipendra; Adhikari, N. P.

    2016-04-01

    Molecular dynamics study of diffusion of two krypton atoms in 300 SPC/E water molecules at temperatures 293, 303, 313, 323 and 333 K has been carried out. Self-diffusion coefficient of krypton and water along with their mutual diffusion coefficients are estimated. Self-diffusion coefficient for krypton is calculated by using Mean Square Displacement (MSD) method and Velocity Autocorrelation (VACF) method, while that for water is calculated by using MSD method only. The mutual diffusion coefficient is estimated by using the Darken’s relation. The diffusion coefficients are found to follow the Arrhenius behavior. The structural properties of the system have been estimated by the study of solute-solute, solvent-solvent, and solute-solvent Radial Distribution Function (RDF).

  7. Processing near gamma-based titanium-aluminum by cold roll bonding and diffusion reaction of elemental titanium and aluminum foils

    NASA Astrophysics Data System (ADS)

    Luo, Jian-Guo

    Near gamma-based TiAl alloys were successfully processed using a method developed in this study. This technique coupled cold roll bonding of elemental foils of Ti and Al with diffusion reactions. The processing method was cyclic in nature in that the foils were repeatedly cold rolled, diffusion reacted, cold rolled, diffusion reacted, etc. This processing cycle was repeated numerous times and the microstructures formed after 1--100 cycles were characterized using optical microscopy, scanning electron microscopy (SEM) equipped with energy dispersive spectroscopy, microhardness testing, x-ray diffraction (XRD), and differential thermal analysis (DTA). The effects of cold roll bonding, annealing temperature, annealing time, and number of cycles on the microstructure and microhardness of the gamma-TiAl alloys produced have been investigated. The near gamma-based TiAl alloy that was developed by the cold roll bonding/diffusion annealing process was then subjected to a subsequent thermal treatment that promotes the solid-state phase transformation of the lamellar structure (alternating platelets of alpha2 and gamma). A comparison of the near gamma-based structure to the lamellar structure was also performed. Finally, the processing method developed in the present study was compared to other processing methods that are currently used for processing gamma-based TiAl alloys.

  8. Dynamical properties of semidilute solutions of hydrogen-bonded supramolecular polymers

    NASA Astrophysics Data System (ADS)

    Buhler, Eric; Candau, Sauveur-Jean; Kolomiets, Elena; Lehn, Jean-Marie

    2007-12-01

    The dynamical properties of semidilute solutions of supramolecular polymers formed from molecular recognition directed association between monomers bearing complementary hydrogen bonding groups were investigated by rheological and dynamic light scattering experiments. The steady-state flow curves showed a shear banding type instability, namely the occurrence of a stress plateau σp above a critical shear rate γ˙c . The values of σp and γ˙c were found to be of the same order of magnitude as those of the elastic plateau modulus and the inverse stress relaxation time, respectively. The above features are in agreement with the theoretical predictions based on the reptation model. Dynamic light scattering experiments showed the presence in the autocorrelation function of the concentration fluctuations of a slow viscoelastic relaxation process that is likely to be of Rouse type.

  9. Structure, Bonding, and Dynamics of Alkanethylhiolates on Copper and Gold Clusters and Surfaces

    NASA Astrophysics Data System (ADS)

    Konopka, Martin; Rousseau, Roger; Stich, Ivan; Marx, Dominik

    2005-03-01

    The interaction of alkanethiolates with small coinage metal clusters and (111) surfaces of copper and gold was studied based on density functional theory with a focus on the metal-thiolate junction. Calculation of fragmentation energies indicate that for Cu cluster-thiolate (n=1,3,5,7, and 9) there is a progressive lowering in energy for the fragmentation of the S-C bond in the thiolate from a value of 2.9 eV for n=1 to 1.4 eV for n=9. The detailed electronic origins of this specific weakening are attributed to a polarization of electron density in the S-C bond as induced by bonding with the Cu cluster. For the gold analogues this effect is not observed and fragmentation at the S-C bond experiences only a slight 10% destabilization as n increases from 3 to 9 On the Cu(111) surface the metal to thiolate charge transfer which leads to a non-direction partially ionic bonding with a concurrent flat adsorption energy landscape, As a result, occupation of fcc-hollow, hcp-hollow and fcc-bridge sites is observed during the coarse of a short finite temperature ab-initio molecular dynamics simulation as opposed to a static model where only the hollow sites are stable minima. Comparison of our results with the available experimental evidence and consequences of the electrostatic profile of the metal-molecule interface are presented. The difference between Cu and Au are discussed in the context of relativistic effects.

  10. Diffusion dynamics of socially learned foraging techniques in squirrel monkeys.

    PubMed

    Claidière, Nicolas; Messer, Emily J E; Hoppitt, William; Whiten, Andrew

    2013-07-01

    Social network analyses and experimental studies of social learning have each become important domains of animal behavior research in recent years yet have remained largely separate. Here we bring them together, providing the first demonstration of how social networks may shape the diffusion of socially learned foraging techniques. One technique for opening an artificial fruit was seeded in the dominant male of a group of squirrel monkeys and an alternative technique in the dominant male of a second group. We show that the two techniques spread preferentially in the groups in which they were initially seeded and that this process was influenced by monkeys' association patterns. Eigenvector centrality predicted both the speed with which an individual would first succeed in opening the artificial fruit and the probability that they would acquire the cultural variant seeded in their group. These findings demonstrate a positive role of social networks in determining how a new foraging technique diffuses through a population. PMID:23810529

  11. Dynamics of Mesoscale Magnetic Field in Diffusive Shock Acceleration

    NASA Astrophysics Data System (ADS)

    Diamond, P. H.; Malkov, M. A.

    2007-01-01

    We present a theory for the generation of mesoscale (krg<<1, where rg is the cosmic-ray gyroradius) magnetic fields during diffusive shock acceleration. The decay or modulational instability of resonantly excited Alfvén waves scattering off ambient density perturbations in the shock environment naturally generates larger scale fields. For a broad spectrum of perturbations, the physical mechanism of energy transfer is random refraction, represented by the diffusion of Alfvén wave packets in k-space. The scattering field can be produced directly by the decay instability or by the Drury instability, a hydrodynamic instability driven by the cosmic-ray pressure gradient. This process is of interest to acceleration since it generates waves of longer wavelength, and so enables the confinement and acceleration of higher energy particles. This process also limits the intensity of resonantly generated turbulent magnetic fields on rg scales.

  12. Nonlinear dynamics of hydrogen-air detonations with detailed kinetics and diffusion

    NASA Astrophysics Data System (ADS)

    Powers, Joseph; Romick, Christopher; Aslam, Tariq

    2014-11-01

    We consider the calculation of unsteady detonation in a mixture of calorically imperfect ideal gases with detailed kinetics. The use of detailed kinetics introduces multiple reaction length scales, and their interaction gives rise to complex dynamics. These are predicted using a wavelet-based adaptive mesh refinement technique and includes multi-component species, momentum, and energy diffusion, as well as DuFour and Soret effects. In the one-dimensional limit, we predict a transition from stability to unstable limit cycles as a driving piston velocity is lowered. At low overdrive, energy is partitioned into a variety of high frequency oscillatory modes. For weak low frequency instabilities, the dynamics are largely explained by a competition between advection and reaction time scales, with diffusion serving to perturb the dynamics. For higher frequency instabilities, the influence of diffusion is larger. We present new extensions to two-dimensional dynamics.

  13. Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.

    PubMed

    Zheng, Wenwei; Best, Robert B

    2015-12-10

    Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics can indeed be accurately described as diffusion on just a single coordinate, the fraction of native contacts (Q). The diffusion models reproduce both folding rates, and finer details such as transition-path durations and diffusive propagators. The Q-averaged diffusion coefficients decrease with chain length, as anticipated from energy landscape theory. Although the Q-diffusion model does not capture transition-path durations for the protein NuG2, we show that this can be accomplished by designing an improved coordinate Qopt. Overall, one-dimensional diffusion on a suitable coordinate turns out to be a remarkably faithful model for the dynamics of the proteins considered.

  14. Langevin dynamics modeling of the water diffusion tensor in partially aligned collagen networks

    NASA Astrophysics Data System (ADS)

    Powell, Sean K.; Momot, Konstantin I.

    2012-09-01

    In this work, a Langevin dynamics model of the diffusion of water in articular cartilage was developed. Numerical simulations of the translational dynamics of water molecules and their interaction with collagen fibers were used to study the quantitative relationship between the organization of the collagen fiber network and the diffusion tensor of water in model cartilage. Langevin dynamics was used to simulate water diffusion in both ordered and partially disordered cartilage models. In addition, an analytical approach was developed to estimate the diffusion tensor for a network comprising a given distribution of fiber orientations. The key findings are that (1) an approximately linear relationship was observed between collagen volume fraction and the fractional anisotropy of the diffusion tensor in fiber networks of a given degree of alignment, (2) for any given fiber volume fraction, fractional anisotropy follows a fiber alignment dependency similar to the square of the second Legendre polynomial of cos(θ), with the minimum anisotropy occurring at approximately the magic angle (θMA), and (3) a decrease in the principal eigenvalue and an increase in the transverse eigenvalues is observed as the fiber orientation angle θ progresses from 0∘ to 90∘. The corresponding diffusion ellipsoids are prolate for θ<θMA, spherical for θ≈θMA, and oblate for θ>θMA. Expansion of the model to include discrimination between the combined effects of alignment disorder and collagen fiber volume fraction on the diffusion tensor is discussed.

  15. Dynamic response of a pulsed Burke-Schumann diffusion flame

    NASA Technical Reports Server (NTRS)

    Sheu, Jyh-Cherng; Stocker, Dennis P.; Chen, Lea-Der

    1995-01-01

    Turbulent flames are often envisioned as an ensemble of random vortices interacting with the combustion process. A better understanding of the vortex-flame interactions therefore would be useful in improving the modeling of turbulent diffusion flames. Substantial simplification may be made by investigating controlled interactions in a laminar flame, as opposed to random interactions in a turbulent flame. The general goals of the research project are to improve our understanding of (1) the influence of buoyancy on co-flow diffusion flames and (2) the effects of buoyancy on vortex-flame interactions in co-flow diffusion flames. As a first step toward objective (2), we conducted a joint experimental and numerical investigation of the vortex-flame interaction. Vortices were produced by mechanically pulsing the fuel flow at a low frequency, e.g., 10 Hz. Experiments were conducted using a nonflickering Burke-Schumann flame in both microgravity (mu-g) and normal gravity (1g) as a means of varying the buoyant force without modification of the pressure (i.e., density). The effects of buoyant convection may then be determined by a comparison of the mu-g and 1g results. The mu-g results may also reveal the important mechanisms which are masked or overwhelmed by buoyant convection in 1g. A numerical investigation was conducted using a validated, time-accurate numerical code to study the underlying physics during the flame interaction and to assist the interpretation of the experimental results.

  16. Hydrogen Bonding and Dielectric Spectra of Ethylene Glycol–Water Mixtures from Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083

  17. Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT): experimental validation with a dynamic phantom

    PubMed Central

    Unlu, Mehmet Burcin; Lin, Yuting; Gulsen, Gultekin

    2010-01-01

    Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT) can provide spatially resolved enhancement kinetics of an optical contrast agent. We undertook a systematic phantom study to evaluate the effects of the geometrical parameters such as the depth and size of the inclusion as well as the optical parameters of the background on the recovered enhancement kinetics of the most commonly used optical contrast agent, indocyanine green (ICG). For this purpose a computer-controlled dynamic phantom was constructed. An ICG–intralipid–water mixture was circulated through the inclusions while the DCE-DOT measurements were acquired with a temporal resolution of 16 s. The same dynamic study was repeated using inclusions of different sizes located at different depths. In addition to this, the effect of non-scattering regions was investigated by placing a second inclusion filled with water in the background. The phantom studies confirmed that although the peak enhancement varied substantially for each case, the recovered injection and dilution rates obtained from the percentage enhancement maps agreed within 15% independent of not only the depth and the size of the inclusion but also the presence of a non-scattering region in the background. Although no internal structural information was used in these phantom studies, it may be necessary to use it for small objects buried deep in tissue. However, the different contrast mechanisms of optical and other imaging modalities as well as imperfect co-registration between both modalities may lead to potential errors in the structural a priori. Therefore, the effect of erroneous selection of structural priors was investigated as the final step. Again, the injection and dilution rates obtained from the percentage enhancement maps were also immune to the systematic errors introduced by erroneous selection of the structural priors, e.g. choosing the diameter of the inclusion 20% smaller increased the peak enhancement 60% but

  18. Two competing species in super-diffusive dynamical regimes

    NASA Astrophysics Data System (ADS)

    La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.

    2010-09-01

    The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.

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

    SciTech Connect

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

    2014-12-01

    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. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

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

    DOE PAGESBeta

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

    2014-12-01

    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 calculationsmore » 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. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

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

    PubMed Central

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

    2014-01-01

    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. PMID:25453071

  2. Blogviz: mapping the dynamics of information diffusion in blogspace

    NASA Astrophysics Data System (ADS)

    Lima, Manuel S.

    2006-01-01

    Blogviz is a visualization model for mapping the transmission and internal structure of top links across the blogosphere. It explores the idea of meme propagation by assuming a parallel with the spreading of most cited URLs in daily weblog entries. The main goal of Blogviz is to unravel hidden patterns in the topics diffusion process. What's the life cycle of a topic? How does it start and how does it evolve through time? Are topics constrained to a specific community of users? Who are the most influential and innovative blogs in any topic? Are there any relationships amongst topic proliferators?

  3. Hydrogen Bond and Ligand Dissociation Dynamics in Fluoride Sensing of Re(I)-Polypyridyl Complex.

    PubMed

    Verma, Sandeep; Aute, Sunil; Das, Amitava; Ghosh, Hirendra N

    2015-11-25

    Hydrogen bonding interaction plays an essential role in the early phases of molecular recognition and colorimetric sensing of various anions in aprotic media. In this work, the host-guest interaction between fac-[Re(CO)3Cl(L)] with L = 4-([2,2'-bipyridin]-4-yl)phenol and fluoride ions is investigated for the hydrogen bond dynamics and the changing local coordination environment. The stoichiometric studies using (1)H NMR and ESI-MS spectroscopies have shown that proton transfer in the H-bonded phenol-fluoride complex activates the dissociation of the CO ligand in the Re(I) center. The phenol-to-phenolate conversion during formation of HF2(-) ion induces nucleophilic lability of the CO ligand which is probed by intraligand charge transfer (ILCT) and ligand-to-metal charge transfer (LMCT) transitions in transient absorption spectroscopy. After photoexcitation, phenol-phenoxide conversion rapidly equilibrates in 280 fs time scale and the ensuing excited state [Re(II)(bpy•(-)-phenolate¯) (CO)3Cl]* undergoes CO dissociation in the ultrafast time scale of ∼3 ps. A concerted mechanism of hydrogen cleavage and coordination change is established in anion sensing studies of the rhenium complex. PMID:26514688

  4. Discrete kink dynamics in hydrogen-bonded chains: the one-component model.

    PubMed

    Karpan, V M; Zolotaryuk, Y; Christiansen, P L; Zolotaryuk, A V

    2002-12-01

    We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on-site potential plays the role of the proton potential in the hydrogen bond. The system supports a rich variety of stationary kink solutions with different symmetry properties. We study the stability and bifurcation structure of all these stationary kink states. An exactly solvable model with a piecewise "parabola-constant" approximation of the double-Morse potential is suggested and studied analytically. The dependence of the Peierls-Nabarro potential on the system parameters is studied. Discrete traveling-wave solutions of a narrow permanent profile are shown to exist, depending on the anharmonicity of the Morse potential and the cooperativity of the hydrogen bond (the coupling constant of the interaction between nearest-neighbor protons).

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

    NASA Astrophysics Data System (ADS)

    Azhar, Mueed; Greiner, Andreas; Korvink, Jan G.; Kauzlarić, David

    2016-06-01

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

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

    PubMed

    Azhar, Mueed; Greiner, Andreas; Korvink, Jan G; Kauzlarić, David

    2016-06-28

    We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. After a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered. PMID:27369491

  7. Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

    PubMed

    Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong

    2016-05-01

    In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis.

  8. Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

    PubMed

    Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong

    2016-05-01

    In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis. PMID:26219250

  9. Dynamics of diffuse pollution from US southern watersheds

    USGS Publications Warehouse

    Schreiber, J.D.; Rebich, R.A.; Cooper, C.M.

    2001-01-01

    To understand the effects of diffuse pollution information on the source of pollutants, quantities in transport, mode of transport, transient nature of the pollution event, and most importantly, a consideration of remediation efforts need to be known. For example, water quality research in the Yazoo Basin uplands in Mississippi has shown sediment loads from a conventional-till upland soybean watershed to be about 19,000kg/ha/yr, and responsible for 77-96% of P and N in transport. In contrast, sediment loads from a comparable no-till soybean watershed were only 500kg/ha/yr, transporting about 31% of P and N in transport. Sediment loads from a nearby forested area were low, about 200kg/ha/yr, but responsible for about 47-76% of P and N in transport. Transient pollution events are responsible for the transport of large quantities of sediment, nutrients, and pesticides; in some storm events nearly the annual load. Best management practices (BMPs) must be designed to remediate diffuse pollution and the transient nature of pollution events which can have a profound effect on the ecological health of steams and reservoirs. Copyright ?? 2001 .

  10. Controlling Hydrogel Mechanics via Bio-Inspired Polymer-Nanoparticle Bond Dynamics.

    PubMed

    Li, Qiaochu; Barrett, Devin G; Messersmith, Phillip B; Holten-Andersen, Niels

    2016-01-26

    Interactions between polymer molecules and inorganic nanoparticles can play a dominant role in nanocomposite material mechanics, yet control of such interfacial interaction dynamics remains a significant challenge particularly in water. This study presents insights on how to engineer hydrogel material mechanics via nanoparticle interface-controlled cross-link dynamics. Inspired by the adhesive chemistry in mussel threads, we have incorporated iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network to obtain hydrogels cross-linked via reversible metal-coordination bonds at Fe3O4 NP surfaces. Unique material mechanics result from the supra-molecular cross-link structure dynamics in the gels; in contrast to the previously reported fluid-like dynamics of transient catechol-Fe(3+) cross-links, the catechol-Fe3O4 NP structures provide solid-like yet reversible hydrogel mechanics. The structurally controlled hierarchical mechanics presented here suggest how to develop hydrogels with remote-controlled self-healing dynamics.

  11. Controlling Hydrogel Mechanics via Bio-Inspired Polymer-Nanoparticle Bond Dynamics.

    PubMed

    Li, Qiaochu; Barrett, Devin G; Messersmith, Phillip B; Holten-Andersen, Niels

    2016-01-26

    Interactions between polymer molecules and inorganic nanoparticles can play a dominant role in nanocomposite material mechanics, yet control of such interfacial interaction dynamics remains a significant challenge particularly in water. This study presents insights on how to engineer hydrogel material mechanics via nanoparticle interface-controlled cross-link dynamics. Inspired by the adhesive chemistry in mussel threads, we have incorporated iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network to obtain hydrogels cross-linked via reversible metal-coordination bonds at Fe3O4 NP surfaces. Unique material mechanics result from the supra-molecular cross-link structure dynamics in the gels; in contrast to the previously reported fluid-like dynamics of transient catechol-Fe(3+) cross-links, the catechol-Fe3O4 NP structures provide solid-like yet reversible hydrogel mechanics. The structurally controlled hierarchical mechanics presented here suggest how to develop hydrogels with remote-controlled self-healing dynamics. PMID:26645284

  12. Microstructure and mechanical properties of AlMgB14-TiB2 associated with metals prepared by the field-assisted diffusion bonding sintering process

    NASA Astrophysics Data System (ADS)

    Zhuang, Lei; Lei, Yu; Chen, Shaoping; Hu, Lifang; Meng, Qingsen

    2015-02-01

    AlMgB14-TiB2 composites were prepared using the field-assisted diffusion bonding sintering process (FDB) at 1400 °C under a pressure of 50 MPa for 8 min, and then bonded to Nb and Mo plates. The microstructure of the bonded joints was analyzed using SEM, EDS and XRD techniques, allowing for the phase composition and elemental distribution characteristics of the joint interface to be studied. The shear strength and wear properties were also investigated. The results show that AlMgB14-30 wt.% TiB2 composites can be strongly bonded to Nb and Mo metals, forming dense uniform diffusion layers, with an average width above 200 μm. The shear strength of the Nb joints is higher than that of the Mo joints. The results from XRD analysis indicate that the main phase of the fractures of the AlMgB14-TiB2 + Nb and the AlMgB14-TiB2 + Mo is MoB4 and NbB2, respectively. The wear test results show that AlMgB14 decomposes into AlMg2O4 and Al2O3 at 600 °C, which can influence the friction and wear properties of AlMgB14-TiB2 composites.

  13. Bio-Inspired Composite Interfaces: Controlling Hydrogel Mechanics via Polymer-Nanoparticle Coordination Bond Dynamics

    NASA Astrophysics Data System (ADS)

    Holten-Andersen, Niels

    2015-03-01

    In soft nanocomposite materials, the effective interaction between polymer molecules and inorganic nanoparticle surfaces plays a critical role in bulk mechanical properties. However, controlling these interfacial interactions remains a challenge. Inspired by the adhesive chemistry in mussel threads, we present a novel approach to control composite mechanics via polymer-particle interfacial dynamics; by incorporating iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network the resulting hydrogels are crosslinked via reversible coordination bonds at Fe3O4 NP surfaces thereby providing a dynamic gel network with robust self-healing properties. By studying the thermally activated composite network relaxation processes we have found that the polymer-NP binding energy can be controlled by engineering both the organic and inorganic side of the interface.

  14. Anisotropic parallel self-diffusion coefficients near the calcite surface: A molecular dynamics study.

    PubMed

    Franco, Luís F M; Castier, Marcelo; Economou, Ioannis G

    2016-08-28

    Applying classical molecular dynamics simulations, we calculate the parallel self-diffusion coefficients of different fluids (methane, nitrogen, and carbon dioxide) confined between two {101̄4} calcite crystal planes. We have observed that the molecules close to the calcite surface diffuse differently in distinct directions. This anisotropic behavior of the self-diffusion coefficient is investigated for different temperatures and pore sizes. The ion arrangement in the calcite crystal and the strong interactions between the fluid particles and the calcite surface may explain the anisotropy in this transport property. PMID:27586936

  15. Anisotropic parallel self-diffusion coefficients near the calcite surface: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Franco, Luís F. M.; Castier, Marcelo; Economou, Ioannis G.

    2016-08-01

    Applying classical molecular dynamics simulations, we calculate the parallel self-diffusion coefficients of different fluids (methane, nitrogen, and carbon dioxide) confined between two { 10 1 ¯ 4 } calcite crystal planes. We have observed that the molecules close to the calcite surface diffuse differently in distinct directions. This anisotropic behavior of the self-diffusion coefficient is investigated for different temperatures and pore sizes. The ion arrangement in the calcite crystal and the strong interactions between the fluid particles and the calcite surface may explain the anisotropy in this transport property.

  16. Image processing analysis of vortex dynamics of lobed jets from three-dimensional diffusers

    NASA Astrophysics Data System (ADS)

    Nastase, Ilinca; Meslem, Amina; El Hassan, Mouhammad

    2011-12-01

    The passive control of jet flows with the aim to enhance mixing and entrainment is of wide practical interest. Our purpose here is to develop new air diffusers for heating ventilating air conditioning systems by using lobed geometry nozzles, in order to ameliorate the users' thermal comfort. Two turbulent six-lobed air jets, issued from a lobed tubular nozzle and an innovative hemispherical lobed nozzle, were studied experimentally. It was shown that the proposed innovative concept of a lobed jet, which can be easily integrated in air diffusion devices, is very efficient regarding induction capability. A vortical dynamics analysis for the two jets is performed using a new method of image processing, namely dynamic mode decomposition. A validation of this method is also proposed suggesting that the dynamical mode decomposition (DMD) image processing method succeeds in capturing the most dominant frequencies of the flow dynamics, which in our case are related to the quite special dynamics of the Kelvin-Helmholtz vortices.

  17. Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics

    PubMed Central

    Jakse, Noel; Pasturel, Alain

    2013-01-01

    We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311

  18. Particle Motion Analysis Reveals Nanoscale Bond Characteristics and Enhances Dynamic Range for Biosensing.

    PubMed

    Visser, Emiel W A; van IJzendoorn, Leo J; Prins, Menno W J

    2016-03-22

    Biofunctionalized colloidal particles are widely used as labels in bioanalytical assays, lab-on-chip devices, biophysical research, and in studies on live biological systems. With detection resolution going down to the level of single particles and single molecules, understanding the nature of the interaction of the particles with surfaces and substrates becomes of paramount importance. Here, we present a comprehensive study of motion patterns of colloidal particles maintained in close proximity to a substrate by short molecular tethers (40 nm). The motion of the particles (500-1000 nm) was optically tracked with a very high localization accuracy (below 3 nm). A surprisingly large variation in motion patterns was observed, which can be attributed to properties of the particle-molecule-substrate system, namely the bond number, the nature of the bond, particle protrusions, and substrate nonuniformities. Experimentally observed motion patterns were compared to numerical Monte Carlo simulations, revealing a close correspondence between the observed motion patterns and properties of the molecular system. Particles bound via single tethers show distinct disc-, ring-, and bell-shaped motion patterns, where the ring- and bell-shaped patterns are caused by protrusions on the particle in the direct vicinity of the molecular attachment point. Double and triple tethered particles exhibit stripe-shaped and triangular-shaped motion patterns, respectively. The developed motion pattern analysis allows for discrimination between particles bound by different bond types, which opens the possibility to improve the limit of detection and the dynamic range of bioanalytical assays, with a projected increase of dynamic range by nearly 2 orders of magnitude.

  19. Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Fernández, M. A.; Sabater, C.; Dednam, W.; Palacios, J. J.; Calvo, M. R.; Untiedt, C.; Caturla, M. J.

    2016-02-01

    The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as "jump to contact" (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.

  20. Probing surface hydrogen bonding and dynamics by natural abundance, multidimensional, 17O DNP-NMR spectroscopy

    DOE PAGESBeta

    Perras, Frederic A.; Chaudhary, Umesh; Slowing, Igor I.; Pruski, Marek

    2016-05-06

    Dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (SSNMR) spectroscopy is increasingly being used as a tool for the atomic-level characterization of surface sites. DNP surface-enhanced SSNMR spectroscopy of materials has, however, been limited to studying relatively receptive nuclei, and the particularly rare 17O nuclide, which is of great interest for materials science, has not been utilized. We demonstrate that advanced 17O SSNMR experiments can be performed on surface species at natural isotopic abundance using DNP. We use 17O DNP surface-enhanced 2D SSNMR to measure 17O{1H} HETCOR spectra as well as dipolar oscillations on a series of thermally treatedmore » mesoporous silica nanoparticle samples having different pore diameters. These experiments allow for a nonintrusive and unambiguous characterization of hydrogen bonding and dynamics at the surface of the material; no other single experiment can give such details about the interactions at the surface. Lastly, our data show that, upon drying, strongly hydrogen-bonded surface silanols, whose motions are greatly restricted by the interaction when compared to lone silanols, are selectively dehydroxylated.« less

  1. The role of hydrogen bonds in an aqueous solution of acetylsalicylic acid: a molecular dynamics simulation study.

    PubMed

    Donnamaria, Maria Cristina; de Xammar Oro, Juan Roberto

    2011-10-01

    This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed conformer structure in water, and playing an important role in stabilizing this conformation.

  2. Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian

    NASA Astrophysics Data System (ADS)

    Pittman, S. M.; Tannenbaum, E.; Heller, E. J.

    2016-08-01

    This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm-1 peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol'd diffusion, which connects different regions of phase-space by a resonance network known as the Arnol'd web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep. Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol'd web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.

  3. Comparison of Diffusion Coefficients of Aryl Carbonyls and Aryl Alcohols in Hydroxylic Solvents. Evidence that the Diffusion of Ketyl Radicals in Hydrogen-Bonding Solvents is Not Anomalous?

    SciTech Connect

    Autrey, S Thomas ); Camaioni, Donald M. ); Kandanarachchi, Pramod H.; Franz, James A. )

    2000-12-01

    The diffusion coefficients of a benzyl-, sec-phenethyl-, and diphenylmethyl alcohol and the corresponding aryl carbonyls (benzaldehyde, acetophenone and benzophenone) were measured by Taylor's dispersion method in both ethyl and isopropyl alcohol. The experimental values are compared to published transient grating measurements of the corresponding aryl ketyl radicals (benzyl-, sec-phenethyl-, and diphenylmethyl-ketyl radical). In general, the diffusion coefficient of the aryl alcohols and the corresponding aryl ketyl radicals are equivalent within experimental error. This work shows that the diffusion of ketyl radicals is not anomalously slow and that aryl alcohols are significantly better models than the corresponding aryl ketones for analyzing the diffusion of aryl ketyl radicals in both ethyl and isopropyl alcohol. Empirical estimates of the diffusion coefficients of aryl alcohols using the Spernol-Wirtz and Wilke-Chang modifications to the Stokes-Einstein diffusion equation do not adequately account for the interactions between the aryl ketyl radicals or aryl alcohols with the hydroxylic solvents ethyl and isopropyl alcohol. The excellent agreement between the experimental diffusion coefficients of the aryl alcohols and the corresponding ketyl radicals show that the transient grating method can provide accurate estimates for the diffusion coefficients of transient species. This is especially important when a stable model is not available, for example the pyranyl radical.

  4. Diffusion in a soft confining environment: Dynamic effects of thermal fluctuations

    NASA Astrophysics Data System (ADS)

    Palmieri, Benoit; Safran, Samuel A.

    2012-09-01

    A dynamical model of a soft, thermally fluctuating two-dimensional tube is used to study the effect of thermal fluctuations of a confining environment on diffusive transport. The tube fluctuations in both space and time are driven by Brownian motion and suppressed by surface tension and the rigidity of the surrounding environment. The dynamical fluctuations modify the concentration profile boundary condition at the tube surface. They decrease the diffusive transport rate through the tube for two important cases: uniform tube fluctuations (wave vector, q=0 mode) for finite tube lengths and fluctuations of any wave vector for infinitely long tubes.

  5. Diffusion in a soft confining environment: Dynamic effects of thermal fluctuations

    NASA Astrophysics Data System (ADS)

    Palmieri, Benoit; Safran, Samuel

    2013-03-01

    A dynamical model of a soft, thermally fluctuating two-dimensional tube is used to study the effect of thermal fluctuations of a confining environment on diffusive transport. The tube fluctuations in both space and time are driven by Brownian motion and suppressed by surface tension and the rigidity of the surrounding environment. The dynamical fluctuations modify the concentration profile boundary condition at the tube surface. They decrease the diffusive transport rate through the tube for two important cases: uniform tube fluctuations (wave vector, q = 0 mode) for finite tube lengths and fluctuations of any wave vector for infinitely long tubes.

  6. Emerging dynamics in neuronal networks of diffusively coupled hard oscillators.

    PubMed

    Ponta, L; Lanza, V; Bonnin, M; Corinto, F

    2011-06-01

    Oscillatory networks are a special class of neural networks where each neuron exhibits time periodic behavior. They represent bio-inspired architectures which can be exploited to model biological processes such as the binding problem and selective attention. In this paper we investigate the dynamics of networks whose neurons are hard oscillators, namely they exhibit the coexistence of different stable attractors. We consider a constant external stimulus applied to each neuron, which influences the neuron's own natural frequency. We show that, due to the interaction between different kinds of attractors, as well as between attractors and repellors, new interesting dynamics arises, in the form of synchronous oscillations of various amplitudes. We also show that neurons subject to different stimuli are able to synchronize if their couplings are strong enough.

  7. A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Timilsina, Rajendra; Termaath, Stephanie

    The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

  8. Dynamics of water at the interface in reverse micelles: measurements of spectral diffusion with two-dimensional infrared vibrational echoes.

    PubMed

    Fenn, Emily E; Wong, Daryl B; Giammanco, Chiara H; Fayer, M D

    2011-10-13

    Water dynamics inside of reverse micelles made from the surfactant Aerosol-OT (AOT) were investigated by observing spectral diffusion, orientational relaxation, and population relaxation using two-dimensional infrared (2D IR) vibrational echo spectroscopy and pump-probe experiments. The water pool sizes of the reverse micelles studied ranged in size from 5.8 to 1.7 nm in diameter. It is found that spectral diffusion, characterized by the frequency-frequency correlation function (FFCF), significantly changes as the water pool size decreases. For the larger reverse micelles (diameter 4.6 nm and larger), the 2D IR signal is composed of two spectral components: a signal from bulk-like core water, and a signal from water at the headgroup interface. Each of these signals (core water and interfacial water) is associated with a distinct FFCF. The FFCF of the interfacial water layer can be obtained using a modified center line slope (CLS) method that has been recently developed. The interfacial FFCFs for large reverse micelles have a single exponential decay (∼1.6 ps) to an offset plus a fast homogeneous component and are nearly identical for all large sizes. The observed ∼1.6 ps interfacial decay component is approximately the same as that found for bulk water and may reflect hydrogen bond rearrangement of bulk-like water molecules hydrogen bonded to the interfacial water molecules. The long time offset arises from dynamics that are too slow to be measured on the accessible experimental time scale. The influence of the chemical nature of the interface on spectral diffusion was explored by comparing data for water inside reverse micelles (5.8 nm water pool diameter) made from the surfactants AOT and Igepal CO-520. AOT has charged, sulfonate head groups, while Igepal CO-520 has neutral, hydroxyl head groups. It is found that spectral diffusion on the observable time scales is not overly sensitive to the chemical makeup of the interface. An intermediate-sized AOT reverse

  9. Dynamics of water at the interface in reverse micelles: measurements of spectral diffusion with two-dimensional infrared vibrational echoes.

    PubMed

    Fenn, Emily E; Wong, Daryl B; Giammanco, Chiara H; Fayer, M D

    2011-10-13

    Water dynamics inside of reverse micelles made from the surfactant Aerosol-OT (AOT) were investigated by observing spectral diffusion, orientational relaxation, and population relaxation using two-dimensional infrared (2D IR) vibrational echo spectroscopy and pump-probe experiments. The water pool sizes of the reverse micelles studied ranged in size from 5.8 to 1.7 nm in diameter. It is found that spectral diffusion, characterized by the frequency-frequency correlation function (FFCF), significantly changes as the water pool size decreases. For the larger reverse micelles (diameter 4.6 nm and larger), the 2D IR signal is composed of two spectral components: a signal from bulk-like core water, and a signal from water at the headgroup interface. Each of these signals (core water and interfacial water) is associated with a distinct FFCF. The FFCF of the interfacial water layer can be obtained using a modified center line slope (CLS) method that has been recently developed. The interfacial FFCFs for large reverse micelles have a single exponential decay (∼1.6 ps) to an offset plus a fast homogeneous component and are nearly identical for all large sizes. The observed ∼1.6 ps interfacial decay component is approximately the same as that found for bulk water and may reflect hydrogen bond rearrangement of bulk-like water molecules hydrogen bonded to the interfacial water molecules. The long time offset arises from dynamics that are too slow to be measured on the accessible experimental time scale. The influence of the chemical nature of the interface on spectral diffusion was explored by comparing data for water inside reverse micelles (5.8 nm water pool diameter) made from the surfactants AOT and Igepal CO-520. AOT has charged, sulfonate head groups, while Igepal CO-520 has neutral, hydroxyl head groups. It is found that spectral diffusion on the observable time scales is not overly sensitive to the chemical makeup of the interface. An intermediate-sized AOT reverse

  10. Dynamic control of protein diffusion within the granal thylakoid lumen

    PubMed Central

    Kirchhoff, Helmut; Hall, Chris; Wood, Magnus; Herbstová, Miroslava; Tsabari, Onie; Nevo, Reinat; Charuvi, Dana; Shimoni, Eyal; Reich, Ziv

    2011-01-01

    The machinery that conducts the light-driven reactions of oxygenic photosynthesis is hosted within specialized paired membranes called thylakoids. In higher plants, the thylakoids are segregated into two morphological and functional domains called grana and stroma lamellae. A large fraction of the luminal volume of the granal thylakoids is occupied by the oxygen-evolving complex of photosystem II. Electron microscopy data we obtained on dark- and light-adapted Arabidopsis thylakoids indicate that the granal thylakoid lumen significantly expands in the light. Models generated for the organization of the oxygen-evolving complex within the granal lumen predict that the light-induced expansion greatly alleviates restrictions imposed on protein diffusion in this compartment in the dark. Experiments monitoring the redox kinetics of the luminal electron carrier plastocyanin support this prediction. The impact of the increase in protein mobility within the granal luminal compartment in the light on photosynthetic electron transport rates and processes associated with the repair of photodamaged photosystem II complexes is discussed. PMID:22128333

  11. Quantum effects of hydrogen atoms on the dynamical rearrangement of hydrogen-bond networks in liquid water.

    PubMed

    Hyeon-Deuk, Kim; Ando, Koji

    2010-04-28

    Quantum effects such as zero-point energy and delocalization of wave packets (WPs) representing water hydrogen atoms are essential to understand anomalous energetics and dynamics in water. Since quantum calculations of many-body dynamics are highly complicated, no one has yet directly viewed the quantum WP dynamics of hydrogen atoms in liquid water. Our semiquantum molecular dynamics simulation made it possible to observe the hydrogen WP dynamics in liquid water. We demonstrate that the microscopic WP dynamics are closely correlated with and actually play key roles in the dynamical rearrangement in the hydrogen-bond network (HBN) of bulk water. We found the quantum effects of hydrogen atoms on liquid water dynamics such as the rearrangement of HBN and the concomitant fluctuation and relaxation. Our results provide new physical insights on HBN dynamics in water whose significance is not limited to pure liquid dynamics but also a greater understanding of chemical and biological reactions in liquid water.

  12. Dynamical Structure, Bonding, and Thermodynamics of the Superionic Sublattice in ∝-AgI

    SciTech Connect

    Wood, Brandon J.; Marzari, Nicola N.

    2006-10-17

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We characterize the superionic phase transition and the lattice and electronic structures of the archetypal type-I superionic conductor ∝-AgI using extensive first-principles molecular dynamics calculations. We find that superionicity is signaled by a phase transition of the silver ions alone. In the superionic phase, the first silver shell surrounding an iodine displays a distinct dynamical structure that would escape a time-averaged characterization, and we capture this structure in a set of ordering rules. The electronic structure demonstrates a unique chemical signature of the weakest-bound silver in the first shell, which in turn is most likely to diffuse. Silver diffusion decreases upon melting, pointing to an unusual entropic contribution to the stability of the superionic phase.

  13. Molecular dynamics simulation of surface segregation, diffusion and reaction phenomena in equiatomic Ni-Al systems

    NASA Astrophysics Data System (ADS)

    Evteev, A. V.; Levchenko, E. V.; Belova, I. V.; Murch, G. E.

    2012-12-01

    The molecular dynamics method is used to provide fundamental insights into surface segregation, bulk diffusion and alloying reaction phenomena in equiatomic Ni-Al systems. This knowledge can serve as a guide for the search and development of economic routes for controlling microstructure and properties of the intermetallic compound NiAl. This paper gives an overview of recent molecular dynamics simulations in the area along with other theoretical calculations and experimental measurements.

  14. Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds

    NASA Astrophysics Data System (ADS)

    Barsegov, V.; Thirumalai, D.

    2005-02-01

    The unbinding dynamics of complexes involving cell-adhesion molecules depends on the specific ligands. Atomic force microscopy measurements have shown that for the specific P-selectin-P-selectin glycoprotein ligand (sPSGL-1) the average bond lifetime t initially increases (catch bonds) at low (10 pN) constant force, f, and decreases when f > 10 pN (slip bonds). In contrast, for the complex with G1 anti-P-selectin monoclonal antibody t monotonically decreases with f. To quantitatively map the energy landscape of such complexes we use a model that considers the possibility of redistribution of population from one force-free state to another force-stabilized bound state. The excellent agreement between theory and experiments allows us to extract energy landscape parameters by fitting the calculated curves to the lifetime measurements for both sPSGL-1 and G1. Surprisingly, the unbinding transition state for P-selectin-G1 complex is close (0.32 nm) to the bound state, implying that the interaction is brittle, i.e., once deformed, the complex fractures. In contrast, the unbinding transition state of the P-selectin-sPSGL-1 complex is far ( 1.5 nm) from the bound state, indicative of a compliant structure. Constant f energy landscape parameters are used to compute the distributions of unbinding times and unbinding forces as a function of the loading rate, rf. For a given rf, unbinding of sPSGL-1 occurs over a broader range of f with the most probable f being an order of magnitude less than for G1. The theory for cell adhesion complexes can be used to predict the outcomes of unbinding of other protein-protein complexes.

  15. Effects of temperature, salt concentration, and the protonation state on the dynamics and hydrogen-bond interactions of polyelectrolyte multilayers on lipid membranes.

    PubMed

    Lee, Hwankyu

    2016-03-01

    Polyelectrolyte multilayers, which consist of poly-l-lysines (PLL) and hyaluronic acids (HA), are simulated on phospholipid membranes with explicit water at different temperatures, salt concentrations, and protonation states of PLL that correspond to pH 7 or higher. PLL and HA polymers, which are initially sequentially deposited as three HA/PLL bilayers above the membrane, partially intermix with each other within 300 ns, and with a significant amount of water at almost half of its bulk density. With reduced protonation of amine groups of PLL, the polymers diffuse faster, especially at higher temperatures, and for 0%-protonation, disperse into the water, due to the many fewer hydrogen bonds between PLL and HA polymers. When PLL is protonated, the addition of salt ions weakens electrostatic interactions between PLL and HA and, at 0.5 M NaCl, eventually reduces the number of hydrogen bonds, which in experiments leads to hole formation inside the PLL/HA film. Multilayers are stabilized by hydrogen bonds, primarily between charged groups and to a lesser extent between uncharged groups. PLL and HA also electrostatically interact with lipid head groups of membranes which reduces the lateral mobility of membrane lipids, to an extent dependent on the salt concentration. These findings help quantitate the effects of temperature, salt, and the protonation state (or pH) on the stability and dynamics of multilayers and membranes, and show trends that compare favorably with the experimental observations of the swelling of multilayers.

  16. A new method of optimal design for a two-dimensional diffuser by using dynamic programming

    NASA Technical Reports Server (NTRS)

    Gu, Chuangang; Zhang, Moujin; Chen, XI; Miao, Yongmiao

    1991-01-01

    A new method for predicting the optimal velocity distribution on the wall of a two dimensional diffuser is presented. The method uses dynamic programming to solve the optimal control problem with inequality constraints of state variables. The physical model of optimization is designed to prevent the separation of the boundary layer while approaching the maximum pressure ratio in a diffuser of a specified length. The computational results are in fair agreement with the experimental ones. Optimal velocity distribution on a diffuser wall is said to occur when the flow decelerates quickly at first and then smoothly, while the flow is near separation, but always protected from it. The optimal velocity distribution can be used to design the contour of the diffuser.

  17. Molecular dynamics simulation of helium cluster diffusion and bubble formation in bulk tungsten

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Chun; Shu, Xiaolin; Tao, Peng; Yu, Yi; Niu, Guo-Jiang; Xu, Yuping; Gao, Fei; Luo, Guang-Nan

    2014-12-01

    Molecular dynamics (MD) simulations have been performed to investigate the diffusion behavior of helium (He) clusters in tungsten (W), because their diffusion properties provide basic knowledge in understanding the He bubble formation. The binding energy between He and He cluster is shown to be positive, and thus, He is easy to form bubbles by self-trapping. The mean squared displacements (MSDs) were employed to determine the diffusivities of He clusters with different sizes at different temperatures. The He bubble formation at different temperatures with 1% He was also investigated. It is revealed that the formation of He bubbles is strongly associated with the temperature and the diffusivities of the He clusters in W. The results demonstrate the initial stage of the He bubble formation and growth in W.

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

    SciTech Connect

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; 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.

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

    NASA Astrophysics Data System (ADS)

    Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

    2015-02-01

    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.

  20. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

    NASA Astrophysics Data System (ADS)

    Naruemon, Rueangkham; Charin, Modchang

    2016-04-01

    Most biochemical processes in cells are usually modeled by reaction-diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

  1. On the dynamics of a forced reaction-diffusion model for biological pattern formation.

    PubMed Central

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1989-01-01

    Ideas from the theory of dynamical systems are applied in biological pattern formation. By considering a simple reaction-diffusion model subjected to an external excitation, we find that the system can give rise to a great variety of periodic, quasiperiodic, and chaotic evolutions. PMID:2740333

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

    SciTech Connect

    Barbante, Paolo; Frezzotti, Aldo; Gibelli, Livio

    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.

  3. Effect of gravity on the dynamics of nonequilibrium fluctuations in a free-diffusion experiment.

    PubMed

    Croccolo, Fabrizio; Brogioli, Doriano; Vailati, Alberto; Giglio, Marzio; Cannell, David S

    2006-09-01

    Diffusion is commonly believed to be a homogeneous process at the mesoscopic scale, being driven only by the random walk of fluid molecules. On the contrary, very large amplitude, long wavelength fluctuations always accompany diffusive processes. In the presence of gravity, fluctuations in a fluid containing a stabilizing gradient are affected by two different processes: diffusion, which relaxes them, and the buoyancy force, which quenches them. These phenomena affect both the overall amplitude of fluctuations and their time dependence. For the case of free diffusion, the time-correlation function of the concentration fluctuations is predicted to exhibit an exponential decay with correlation time depending on the wave vector q. For large wave vector fluctuations, diffusion dominates, and the correlation time is predicted to be 1 / (Dq2). For small wave vector fluctuations, gravitational forces have time to play a significant role, and the correlation time is predicted to be proportional to q2. The effects of gravity and diffusion are comparable for a critical wave vector q(c) determined by fluid properties and gravity. We have utilized a quantitative dynamic shadowgraph technique to obtain the temporal correlation function of a mixture of LUDOX(R) TMA and water undergoing free diffusion. This technique allows one to simultaneously measure correlation functions achieving good statistics for a number of different wave vectors in a single measurement. Wave vectors as small as 70 cm(-1) have been investigated, which is very difficult to achieve with ordinary dynamic light-scattering techniques. We present results on the transition from the diffusive decay of fluctuations to the regime in which gravity is dominant. PMID:17124135

  4. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  5. Monitoring the informational efficiency of European corporate bond markets with dynamical permutation min-entropy

    NASA Astrophysics Data System (ADS)

    Zunino, Luciano; Bariviera, Aurelio F.; Guercio, M. Belén; Martinez, Lisana B.; Rosso, Osvaldo A.

    2016-08-01

    In this paper the permutation min-entropy has been implemented to unveil the presence of temporal structures in the daily values of European corporate bond indices from April 2001 to August 2015. More precisely, the informational efficiency evolution of the prices of fifteen sectorial indices has been carefully studied by estimating this information-theory-derived symbolic tool over a sliding time window. Such a dynamical analysis makes possible to obtain relevant conclusions about the effect that the 2008 credit crisis has had on the different European corporate bond sectors. It is found that the informational efficiency of some sectors, namely banks, financial services, insurance, and basic resources, has been strongly reduced due to the financial crisis whereas another set of sectors, integrated by chemicals, automobiles, media, energy, construction, industrial goods & services, technology, and telecommunications has only suffered a transitory loss of efficiency. Last but not least, the food & beverage, healthcare, and utilities sectors show a behavior close to a random walk practically along all the period of analysis, confirming a remarkable immunity against the 2008 financial crisis.

  6. Dynamic of diffuse CO2 emission from Decepcion volcano, Antartica

    NASA Astrophysics Data System (ADS)

    Nolasco, D.; Padron, E.; Hernandez Perez, P. A.; Christian, F.; Kusakabe, M.; Wakita, H.

    2010-12-01

    Deception Island is a volcanic island located at the South Shetland Island off the Antartic Peninsula. It constitutes a back-arc stratovolcano with a basal diameter of ~ 30 Km, the volcano rises ~ 1400 m from the seafloor to the maximum height, Mt. Pond of 540 m above sea level and over half the island is covered by glaciers. This island has a horse-shoe shape with a large flooded caldera with a diameter of about 6x10 km and a maximum depth of 190 m. This caldera is open to the sea through a narrow channel of 500 m at Neptunes Bellows. Deception Island shows the most recent active volcanism, evidence of several eruptions since the late 18th century, and well-known eruptions in 1967, 1969 and 1970 caused serious damage to local scientific stations. The aim of this study is to estimate the CO2 emissions from the Deception volcano bay. In-situ measurements of CO2 efflux from the surface environment of Deception Bay were performed by means of a portable Non Dispersive Infrared spectrophotometer (NDIR) model LICOR Li800, following the accumulation chamber method coupled with a floating device. A total of 244 CO2 efflux measurements were performed in Deception bay in November and December, 2009. CO2 efflux values ranged from non-detectable up to 119,9 g m-2 d-1. To quantify the total CO2 emission from Deception Bay, a CO2 efflux map was constructed using sequential Gaussian simulations (sGs). Most of the studied area showed background levels of CO2 efflux (~4 g m-2 d-1), while peak levels (>20 g m-2 d-1) were mainly identified inside the Fumarole Bay, Telefon Bay and Pendulum Cove areas. The total CO2 emission from Deception Bay was estimated about 191 ± 9 t/d To study the temporal evolution of the CO2 efflux values at Fumarole bay, a two month time series of CO2 diffuse emission values was recorded by an automatic geochemical station, which was installed on December 8, 2009, which measured also soil temperature and humidity and meteorological parameters. CO2 values

  7. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    NASA Astrophysics Data System (ADS)

    Mori, Yukie; Masuda, Yuichi

    2015-09-01

    Hydrogen phthalate anion has a short strong O-H-O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl4, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17O and 1H nuclei monitoring the nuclear magnetic relaxation times of 1H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the

  8. Hydrogen bond dynamics of histamine monocation in aqueous solution: Car-Parrinello molecular dynamics and vibrational spectroscopy study.

    PubMed

    Stare, Jernej; Mavri, Janez; Grdadolnik, Jože; Zidar, Jernej; Maksić, Zvonimir B; Vianello, Robert

    2011-05-19

    Hydration of histamine was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. Histamine is a neurotransmitter and inflammation mediator, which at physiological pH conditions is present mainly in monocationic form. Our focus was on the part of vibrational spectra that corresponds to histamine N-H stretching, since these degrees of freedom are essential for its interactions with either water molecules or transporters and receptors. Assignment of the experimental spectra revealed a broad feature between 3350 and 2300 cm(-1), being centered at 2950 cm(-1), which includes a mixed contribution from the ring N-H and the aminoethyl N-H stretching vibrations. Computational analysis was performed in two ways: first, by making Fourier transformation on the autocorrelation function of all four N-H bond distances recorded during CPMD run, and second, and most importantly, by incorporating quantum effects through applying an a posteriori quantization of all N-H stretching motions utilizing our snapshot analysis of the fluctuating proton potential. The one-dimensional vibrational Schrödinger equation was solved numerically for each snapshot, and the N-H stretching envelopes were calculated as a superposition of the 0→1 transitions. The agreement with the experiment was much better in the case of the second approach. Our calculations clearly demonstrated that the ring amino group absorbs at higher frequencies than the remaining three amino N-H protons of the protonated aminoethyl group, implying that the chemical bonding in the former group is stronger than in the three amino N-H bonds, thus forming weaker hydrogen bonding with the surrounding solvent molecules. In this way the results of the simulation complemented the experimental spectrum that cannot distinguish between the two sets of protons. The effects of deuteration were also considered. The resulting N-D absorption is narrower and red-shifted. The presented methodology is of general

  9. Dynamics of chemical bonding mapped by energy-resolved 4D electron microscopy.

    PubMed

    Carbone, Fabrizio; Kwon, Oh-Hoon; Zewail, Ahmed H

    2009-07-10

    Chemical bonding dynamics are fundamental to the understanding of properties and behavior of materials and molecules. Here, we demonstrate the potential of time-resolved, femtosecond electron energy loss spectroscopy (EELS) for mapping electronic structural changes in the course of nuclear motions. For graphite, it is found that changes of milli-electron volts in the energy range of up to 50 electron volts reveal the compression and expansion of layers on the subpicometer scale (for surface and bulk atoms). These nonequilibrium structural features are correlated with the direction of change from sp2 [two-dimensional (2D) graphene] to sp3 (3D-diamond) electronic hybridization, and the results are compared with theoretical charge-density calculations. The reported femtosecond time resolution of four-dimensional (4D) electron microscopy represents an advance of 10 orders of magnitude over that of conventional EELS methods. PMID:19589997

  10. Reversible CO2 Capture by Conjugated Ionic Liquids through Dynamic Covalent Carbon-Oxygen Bonds.

    PubMed

    Pan, Mingguang; Cao, Ningning; Lin, Wenjun; Luo, Xiaoyan; Chen, Kaihong; Che, Siying; Li, Haoran; Wang, Congmin

    2016-09-01

    The strong chemisorption of CO2 is always accompanied by a high absorption enthalpy, and traditional methods to reduce the absorption enthalpy lead to decreased CO2 capacities. Through the introduction of a large π-conjugated structure into the anion, a dual-tuning approach for the improvement of CO2 capture by anion-functionalized ionic liquids (ILs) resulted in a high capacity of up to 0.96 molCO2  mol-1IL and excellent reversibility. The increased capacity and improved desorption were supported by quantum chemical calculations, spectroscopic investigations, and thermogravimetric analysis. The increased capacity may be a result of the strengthened dynamic covalent bonds in these π-electron-conjugated structures through anion aggregation upon the uptake of CO2 , and the improved desorption originates from the charge dispersion of interaction sites through the large π-electron delocalization. These results provide important insights into effective strategies for CO2 capture. PMID:27458723

  11. Reversible CO2 Capture by Conjugated Ionic Liquids through Dynamic Covalent Carbon-Oxygen Bonds.

    PubMed

    Pan, Mingguang; Cao, Ningning; Lin, Wenjun; Luo, Xiaoyan; Chen, Kaihong; Che, Siying; Li, Haoran; Wang, Congmin

    2016-09-01

    The strong chemisorption of CO2 is always accompanied by a high absorption enthalpy, and traditional methods to reduce the absorption enthalpy lead to decreased CO2 capacities. Through the introduction of a large π-conjugated structure into the anion, a dual-tuning approach for the improvement of CO2 capture by anion-functionalized ionic liquids (ILs) resulted in a high capacity of up to 0.96 molCO2  mol-1IL and excellent reversibility. The increased capacity and improved desorption were supported by quantum chemical calculations, spectroscopic investigations, and thermogravimetric analysis. The increased capacity may be a result of the strengthened dynamic covalent bonds in these π-electron-conjugated structures through anion aggregation upon the uptake of CO2 , and the improved desorption originates from the charge dispersion of interaction sites through the large π-electron delocalization. These results provide important insights into effective strategies for CO2 capture.

  12. Transient Liquid Phase Diffusion Bonding of 6061Al-15 wt.% SiC p Composite Using Mixed Cu-Ag Powder Interlayer

    NASA Astrophysics Data System (ADS)

    Roy, Pallab; Pal, Tapan Kumar; Maity, Joydeep

    2016-08-01

    Microstructure and shear strength of transient liquid phase diffusion bonded (560 °C, 0.2 MPa) 6061Al-15 wt.% SiCp extruded composite using a 50-µm-thick mixed Cu-Ag powder interlayer have been investigated. During isothermal solidification that took 2 h for completion, a ternary liquid phase formed due to diffusion of Cu and Ag in Al. Subsequent cooling formed a ternary phase mixture (α-Al + CuAl2 + Ag2Al) upon eutectic solidification. With mixed Cu-Ag powder interlayer, isothermal solidification was faster than for pure Al joints made using a 50-µm-thick Cu foil interlayer and for the composite joints made using a 50-µm-thick Cu foil/powder interlayer under similar conditions. The presence of brittle eutectic phase mixture (CuAl2 + Ag2Al) led to poor joint strength at short TLP bonding times. The mixture disappeared upon isothermal solidification with a 2-h hold yielding improved joint strength even with solidification shrinkage in the joint. Increased holding time (6 h) erased shrinkage via solid state diffusion and yielded the highest joint strength (87 MPa) and fair joint efficiency (83%).

  13. Transient Liquid Phase Diffusion Bonding of 6061Al-15 wt.% SiC p Composite Using Mixed Cu-Ag Powder Interlayer

    NASA Astrophysics Data System (ADS)

    Roy, Pallab; Pal, Tapan Kumar; Maity, Joydeep

    2016-06-01

    Microstructure and shear strength of transient liquid phase diffusion bonded (560 °C, 0.2 MPa) 6061Al-15 wt.% SiCp extruded composite using a 50-µm-thick mixed Cu-Ag powder interlayer have been investigated. During isothermal solidification that took 2 h for completion, a ternary liquid phase formed due to diffusion of Cu and Ag in Al. Subsequent cooling formed a ternary phase mixture (α-Al + CuAl2 + Ag2Al) upon eutectic solidification. With mixed Cu-Ag powder interlayer, isothermal solidification was faster than for pure Al joints made using a 50-µm-thick Cu foil interlayer and for the composite joints made using a 50-µm-thick Cu foil/powder interlayer under similar conditions. The presence of brittle eutectic phase mixture (CuAl2 + Ag2Al) led to poor joint strength at short TLP bonding times. The mixture disappeared upon isothermal solidification with a 2-h hold yielding improved joint strength even with solidification shrinkage in the joint. Increased holding time (6 h) erased shrinkage via solid state diffusion and yielded the highest joint strength (87 MPa) and fair joint efficiency (83%).

  14. Molecular dynamics study of C-C bond ordering in diacylglycerolipid monolayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Ripatti, Pauli O.; Balabaev, Nikolay K.

    2000-02-01

    Molecular dynamics investigation of diacyldlycerolipid (DG) monolayers was carried out. Each lipid molecule contained stearic fatty acid chain (C18:0) in position 3-D and one of the fatty acid chains C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position 2-D [for the nomenclature see M. Sundaralingam, Ann. N.Y. Acad. Sci. U.S.A., 195, 324 - 355 (1972)]. A polar head group of the lipid molecules was treated as an effective sphere. 1.5 nanosecond simulations were performed at temperature 303 K for monolayers 18:0/18:1(omega) 9cis DG, 18:0/18:2(omega) 6cis DG, 18:0/18:3(omega) 3cis DG, 18:0/20:4(omega) 6cis DG, 18:0/22:6(omega) 3cis DG and at T equals 326 K for 18:0/18:0 DG monolayer. The monolayers consisted of 48 glycerolipids of the same type arranged in a rectangular simulation cell. The average areas per lipid molecule over the simulations were 65.6 Angstrom2 in 18:0/18:0 DG monolayer, 66.2 Angstrom2 in 18:0/18:1(omega) 9cis DG, 66.1 angstrom2 in 18:0/18:2(omega) 6cis DG, 67.4 angstrom2 in 18:0/18:3(omega) 3cis DG, 70.6 angstrom2 in 18:0/20:4(omega) 6cis DG and 71.4 Angstrom2 in 18:0/22:6(omega) 3cis DG monolayer. The C-C bond orientation distributions and C-C bond order parameter profiles about the monolayer normals were calculated. The C-C bond orientation distribution function widths turned out to be depended on both bond location in the chain and chemical structure of the segment.

  15. Molecular dynamics study of C-C bond ordering in diacylglycerolipid monolayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Ripatti, Pauli O.; Balabaev, Nikolay K.

    2001-02-01

    Molecular dynamics investigation of diacyldlycerolipid (DG) monolayers was carried out. Each lipid molecule contained stearic fatty acid chain (C18:0) in position 3-D and one of the fatty acid chains C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position 2-D [for the nomenclature see M. Sundaralingam, Ann. N.Y. Acad. Sci. U.S.A., 195, 324 - 355 (1972)]. A polar head group of the lipid molecules was treated as an effective sphere. 1.5 nanosecond simulations were performed at temperature 303 K for monolayers 18:0/18:1(omega) 9cis DG, 18:0/18:2(omega) 6cis DG, 18:0/18:3(omega) 3cis DG, 18:0/20:4(omega) 6cis DG, 18:0/22:6(omega) 3cis DG and at T equals 326 K for 18:0/18:0 DG monolayer. The monolayers consisted of 48 glycerolipids of the same type arranged in a rectangular simulation cell. The average areas per lipid molecule over the simulations were 65.6 Angstrom2 in 18:0/18:0 DG monolayer, 66.2 Angstrom2 in 18:0/18:1(omega) 9cis DG, 66.1 angstrom2 in 18:0/18:2(omega) 6cis DG, 67.4 angstrom2 in 18:0/18:3(omega) 3cis DG, 70.6 angstrom2 in 18:0/20:4(omega) 6cis DG and 71.4 Angstrom2 in 18:0/22:6(omega) 3cis DG monolayer. The C-C bond orientation distributions and C-C bond order parameter profiles about the monolayer normals were calculated. The C-C bond orientation distribution function widths turned out to be depended on both bond location in the chain and chemical structure of the segment.

  16. Role of depletion on the dynamics of a diffusing forager

    NASA Astrophysics Data System (ADS)

    Bénichou, O.; Chupeau, M.; Redner, S.

    2016-09-01

    We study the dynamics of a starving random walk in general spatial dimension d. This model represents an idealized description for the fate of an unaware forager whose motion is not affected by the presence or absence of resources. The forager depletes its environment by consuming resources and dies if it wanders too long without finding food. In the exactly solvable case of one dimension, we explicitly derive the average lifetime of the walk and the distribution for the number of distinct sites visited by the walk at the instant of starvation. We also give a heuristic derivation for the averages of these two quantities. We tackle the complex but ecologically relevant case of two dimensions by an approximation in which the depleted zone is assumed to always be circular and which grows incrementally each time the walk reaches the edge of this zone. Within this framework, we derive a lower bound for the scaling of the average lifetime and number of distinct sites visited at starvation. We also determine the asymptotic distribution of the number of distinct sites visited at starvation. Finally, we solve the case of high spatial dimensions within a mean-field approach.

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

    PubMed

    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.

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

    SciTech Connect

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

    2014-03-14

    The binary infinite dilute diffusion coefficients, D{sub 12}{sup ∞}, of some alkylbenzenes (Ph-C{sub n}, from Ph-H to Ph-C{sub 12}) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO{sub 2}) 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{sub n}/CO{sub 2} fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C{sub n} in scCO{sub 2} is significantly influenced by the structure of Ph-C{sub 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{sub n} in scCO{sub 2}. 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{sub n} is the result of internal rotation of C-C single bond (σ{sub 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{sub 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{sub n} (n ≥ 4) in scCO{sub 2} are different.

  19. Chemical behavior in diffusion bonding of Si{sub 3}N{sub 4}-Ni and Si{sub 3}N{sub 4}-superalloy IN-738

    SciTech Connect

    Chen, Y.C.; Iwamoto, C.; Ishida, Y.

    1996-09-15

    The bulk chemical reactions between Si{sub 3}N{sub 4} and Ni have been investigated from a thermodynamics perspective by Klomp et al. and Heikinheimo et al., and from experiments by Suganuma et al., Schuster et al., Brito et al., Ishikawa et al., and Heikinheimo et al. The chemical interaction between Si{sub 3}N{sub 4} and Ni-based alloy was investigated by Benett et al., Mehan et al., and Peteves et al. In this work, instead of the Ni-Cr, or model Ni-based superalloy (Ni-Cr-Al alloy), the industrial superalloy, IN-738, was used. For comparing the different chemical behaviors between the pure Ni and Ni-based superalloy with Si{sub 3}N{sub 4}, solid state diffusion bonding of Ni/Si{sub 3}N{sub 4} and IN-738/Si{sub 3}N{sub 4} were bonded in the same bonding conditions, except Ni/Si{sub 3}N{sub 4} specimens whose bonding time were longer than that of IN-738/Si{sub 3}N{sub 4} specimen.

  20. Ballistic-diffusive approximation for the thermal dynamics of metallic nanoparticles in nanocomposite materials

    SciTech Connect

    Shirdel-Havar, A. H. Masoudian Saadabad, R.

    2015-03-21

    Based on ballistic-diffusive approximation, a method is presented to model heat transfer in nanocomposites containing metal nanoparticles. This method provides analytical expression for the temperature dynamics of metallic nanoparticles embedded in a dielectric medium. In this study, nanoparticles are considered as spherical shells, so that Boltzmann equation is solved using ballistic-diffusive approximation to calculate the electron and lattice thermal dynamics in gold nanoparticles, while thermal exchange between the particles is taken into account. The model was used to investigate the influence of particle size and metal concentration of the medium on the electron and lattice thermal dynamics. It is shown that these two parameters are crucial in determining the nanocomposite thermal behavior. Our results showed that the heat transfer rate from nanoparticles to the matrix decreases as the nanoparticle size increases. On the other hand, increasing the metal concentration of the medium can also decrease the heat transfer rate.

  1. Effect of Hydrogen Bonds on the Vibrational Relaxation and Orientational Relaxation Dynamics of HN3 and N3(-) in Solutions.

    PubMed

    Lee, Chiho; Son, Hyewon; Park, Sungnam

    2016-09-15

    Hydrogen bonds (H-bonds) play an important role in determining the structures and dynamics of molecular systems. In this work, we investigated the effect of H-bonds on the vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in methanol (CH3OH) and N,N-dimethyl sulfoxide (DMSO) using polarization-controlled infrared pump-probe spectroscopy and quantum chemical calculations. Our detailed analysis of experimental and computational results reveals that both vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in CH3OH and DMSO are substantially dependent on the strength of the H-bonds between the probing solute and its surrounding solvent. Especially in the case of N3(-) in CH3OH, the vibrational population relaxation of N3(-) is found to occur by a direct intermolecular vibrational energy transfer to CH3OH due to large vibrational coupling strength. The orientational relaxation dynamics of HN3 and N3(-), which are well fit by a biexponential function, are analyzed by the wobbling-in-a-cone model and extended Debye-Stokes-Einstein equation. Depending on the intermolecular interactions, the slow overall orientational relaxation occurs under slip, stick, and superstick boundary conditions. For HN3 and N3(-) in CH3OH and DMSO, the vibrational population relaxation becomes faster but the orientational relaxation becomes slower as the H-bond strength is increased. Our current results imply that H-bonds have significant effects on the vibrational population relaxation and orientational relaxation dynamics of a small solute whose size is comparable to the size of the solvent.

  2. Effect of Hydrogen Bonds on the Vibrational Relaxation and Orientational Relaxation Dynamics of HN3 and N3(-) in Solutions.

    PubMed

    Lee, Chiho; Son, Hyewon; Park, Sungnam

    2016-09-15

    Hydrogen bonds (H-bonds) play an important role in determining the structures and dynamics of molecular systems. In this work, we investigated the effect of H-bonds on the vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in methanol (CH3OH) and N,N-dimethyl sulfoxide (DMSO) using polarization-controlled infrared pump-probe spectroscopy and quantum chemical calculations. Our detailed analysis of experimental and computational results reveals that both vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in CH3OH and DMSO are substantially dependent on the strength of the H-bonds between the probing solute and its surrounding solvent. Especially in the case of N3(-) in CH3OH, the vibrational population relaxation of N3(-) is found to occur by a direct intermolecular vibrational energy transfer to CH3OH due to large vibrational coupling strength. The orientational relaxation dynamics of HN3 and N3(-), which are well fit by a biexponential function, are analyzed by the wobbling-in-a-cone model and extended Debye-Stokes-Einstein equation. Depending on the intermolecular interactions, the slow overall orientational relaxation occurs under slip, stick, and superstick boundary conditions. For HN3 and N3(-) in CH3OH and DMSO, the vibrational population relaxation becomes faster but the orientational relaxation becomes slower as the H-bond strength is increased. Our current results imply that H-bonds have significant effects on the vibrational population relaxation and orientational relaxation dynamics of a small solute whose size is comparable to the size of the solvent. PMID:27537433

  3. Quantification of sampling uncertainty for molecular dynamics simulation: Time-dependent diffusion coefficient in simple fluids

    NASA Astrophysics Data System (ADS)

    Kim, Changho; Borodin, Oleg; Karniadakis, George Em

    2015-12-01

    We analyze two standard methods to compute the diffusion coefficient of a tracer particle in a medium from molecular dynamics (MD) simulation, the velocity autocorrelation function (VACF) method, and the mean-squared displacement (MSD) method. We show that they are equivalent in the sense that they provide the same mean values with the same level of statistical errors. We obtain analytic expressions for the level of the statistical errors present in the time-dependent diffusion coefficient as well as the VACF and the MSD. Under the assumption that the velocity of the tracer particle is a Gaussian process, all results are expressed in terms of the VACF. Hence, the standard errors of all relevant quantities are computable once the VACF is obtained from MD simulation. By using analytic models described by the Langevin equations driven by Gaussian white noise and Poissonian white shot noise, we verify our theoretical error estimates and discuss the non-Gaussianity effect in the error estimates when the Gaussian process approximation does not hold exactly. For validation, we perform MD simulations for the self-diffusion of a Lennard-Jones fluid and the diffusion of a large and massive colloid particle suspended in the fluid. Our theoretical framework is also applicable to mesoscopic simulations, e.g., Langevin dynamics and dissipative particle dynamics.

  4. Global dynamic modeling of electro-hydraulic 3-UPS/S parallel stabilized platform by bond graph

    NASA Astrophysics Data System (ADS)

    Zhang, Lijie; Guo, Fei; Li, Yongquan; Lu, Wenjuan

    2016-08-01

    Dynamic modeling of a parallel manipulator(PM) is an important issue. A complete PM system is actually composed of multiple physical domains. As PMs are widely used in various fields, the importance of modeling the global dynamic model of the PM system becomes increasingly prominent. Currently there lacks further research in global dynamic modeling. A unified modeling approach for the multi-energy domains PM system is proposed based on bond graph and a global dynamic model of the 3-UPS/S parallel stabilized platform involving mechanical and electrical-hydraulic elements is built. Firstly, the screw bond graph theory is improved based on the screw theory, the modular joint model is modeled and the normalized dynamic model of the mechanism is established. Secondly, combined with the electro-hydraulic servo system model built by traditional bond graph, the global dynamic model of the system is obtained, and then the motion, force and power of any element can be obtained directly. Lastly, the experiments and simulations of the driving forces, pressure and flow are performed, and the results show that, the theoretical calculation results of the driving forces are in accord with the experimental ones, and the pressure and flow of the first limb and the third limb are symmetry with each other. The results are reasonable and verify the correctness and effectiveness of the model and the method. The proposed dynamic modeling method provides a reference for modeling of other multi-energy domains system which contains complex PM.

  5. Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Solomentsev, Gleb Y.; English, Niall J.; Mooney, Damian A.

    2010-12-01

    Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å-1. A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-à-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Molecular Dynamics Simulation Study of Two-Dimensional Diffusion Behavior in Smectic Liquid Crystalline Monolayers

    NASA Astrophysics Data System (ADS)

    Watanabe, Go; Saito, Jun-ichi; Fujita, Yusuke; Tabe, Yuka

    2013-08-01

    We have carried out molecular dynamics (MD) simulations for monolayers of smectic A and C liquid crystal (LC) phases in order to investigate the in-plane molecular diffusion from the microscopic point of view. In contrast to similar complex two-dimensional systems (e.g., biomembranes) whose molecular diffusion is anomalous, in-plane mean square displacements (MSDs) for both phases increase linearly with passing time similar to typical fluids on the nanosecond time scale. By following the relation between the diffusion and the viscosity in the fluids, we estimated the viscosity coefficients for both LC monolayers, and the obtained values indicate that the smectic A monolayer has a higher viscosity than the smectic C one. Moreover, we investigate the in-plane self-diffusion anisotropy D\\|/D\\bot for smectic C and found that the diffusion parallel to the molecular tilt is 1.5 times larger than that in the perpendicular direction. This anisotropic diffusion property in the smectic C monolayer has not been clearly confirmed thus far.

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

    NASA Astrophysics Data System (ADS)

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

    SciTech Connect

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

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    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.

  12. Role of the interfacial thermal barrier in the effective thermal diffusivity/conductivity of SiC-fiber-reinforced reaction-bonded silicon nitride

    NASA Technical Reports Server (NTRS)

    Bhatt, Hemanshu; Donaldson, Kimberly Y.; Hasselman, D. P. H.; Bhatt, R. T.

    1990-01-01

    Experimental thermal diffusivity data transverse to the fiber direction for composites composed of a reaction bonded silicon nitride matrix reinforced with uniaxially aligned carbon-coated silicon carbide fibers indicate the existence of a significant thermal barrier at the matrix-fiber interface. Calculations of the interfacial thermal conductances indicate that at 300 C and 1-atm N2, more than 90 percent of the heat conduction across the interface occurs by gaseous conduction. Good agreement is obtained between thermal conductance values for the oxidized composite at 1 atm calculated from the thermal conductivity of the N2 gas and those inferred from the data for the effective composite thermal conductivity.

  13. Rayleigh scattering correlation spectroscopy on diffusion dynamics of nanoparticles under intense laser irradiation

    NASA Astrophysics Data System (ADS)

    Hee, Ping-Yu; Uwada, Takayuki; Okano, Kazunori; Miura, Atsushi; Masuhara, Hiroshi

    2013-09-01

    Rayleigh scattering correlation microspectroscopy is developed and applied to study diffusion dynamics of some nanospheres in water. It was clearly found that the diffusion constant of gold nanoparticles decreased with increasing excitation laser power at the excitation wavelength of higher absorption cross section. This behavior was explained in terms of a coupling between laser trapping by the scattering excitation laser itself and laser heating of the particle. In the case of non-absorbing nanospheres such as silica and polystyrene, the excitation power dependence can be ascribed only to the laser trapping. Experimental setup is introduced, theoretical formulation is described, and future development of this measurement is considered.

  14. Non-diffusive spin dynamics in a two-dimensional electron gas

    SciTech Connect

    Weber, C.P.

    2010-04-28

    We describe measurements of spin dynamics in the two-dimensional electron gas in GaAs/GaAlAs quantum wells. Optical techniques, including transient spin-grating spectroscopy, are used to probe the relaxation rates of spin polarization waves in the wavevector range from zero to 6 x 10{sup 4} cm{sup -1}. We find that the spin polarization lifetime is maximal at nonzero wavevector, in contrast with expectation based on ordinary spin diffusion, but in quantitative agreement with recent theories that treat diffusion in the presence of spin-orbit coupling.

  15. Numerical Study of Buoyancy and Differential Diffusion Effects on the Structure and Dynamics of Triple Flames

    NASA Technical Reports Server (NTRS)

    Chen, J. -Y.; Echekki, T.

    1999-01-01

    Triple flames arise in a number of practical configurations where fuel and oxidizer are partially premixed, such as in the base of a lifted jet flame. Past experimental studies, theoretical analyses, and numerical modeling of triple flames suggested the potential role of triple flames in stabilizing turbulent flames and in promoting flame propagation. From recent numerical simulations of laminar triple flames, a strong influence of differential diffusion among species and heat on the triple flame structure has been gradually appreciated. This paper reports preliminary numerical results on the influence of gravity and differential diffusion effects on the structure and dynamics of triple flames with a one-step global irreversible chemistry model.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. Role of interfacial carbon layer in the thermal diffusivity/conductivity of silicon carbide fiber-reinforced reaction-bonded silicon nitride matrix composites

    NASA Technical Reports Server (NTRS)

    Bhatt, Hemanshu; Donaldson, Kimberly Y.; Hasselman, D. P. H.; Bhatt, Ramakrishna T.

    1992-01-01

    Experiments were carried out on samples of reaction-bonded silicon nitride uniaxially reinforced by SiC monofilaments with and without a 3-micron-thick carbon-rich coating. It is found that a combination of a carbon coatings on the fibers and an interfacial gap due to the thermal expansion mismatch in the composite can significantly (by a factor of 2) lower the effective thermal diffusivity in the direction transverse to the fiber. At atmospheric pressure, gaseous conduction across the interfacial gap makes a significant contribution to the heat transfer across the interface, indicated by significantly lower values of the effective thermal diffusivity under vacuum than in nitrogen or helium at atmospheric pressure.

  18. Characterization of a transition in the transport dynamics of a diffusive sandpile by means of recurrence quantification analysis

    NASA Astrophysics Data System (ADS)

    Mier, J. A.; Sánchez, R.; Newman, D. E.

    2016-08-01

    Recurrence quantification analysis (RQA) is used to characterize a dynamical transition that takes place in the diffusive sandpile. The transition happens when a combination of the drive strength, diffusivity, and overturning size exceeds a critical value. Above the transition, the self-similar transport dynamics associated to the classical (nondiffusive) sandpile is replaced by new transport dynamics dominated by near system-size, quasiperiodic avalanche events. The deterministic content of transport dynamics, as quantified by RQA, turns out to be quite different in both phases. The time series analyzed with RQA in this work correspond to local sand fluxes at different radial locations across the diffusive sandpile.

  19. Characterization of a transition in the transport dynamics of a diffusive sandpile by means of recurrence quantification analysis.

    PubMed

    Mier, J A; Sánchez, R; Newman, D E

    2016-08-01

    Recurrence quantification analysis (RQA) is used to characterize a dynamical transition that takes place in the diffusive sandpile. The transition happens when a combination of the drive strength, diffusivity, and overturning size exceeds a critical value. Above the transition, the self-similar transport dynamics associated to the classical (nondiffusive) sandpile is replaced by new transport dynamics dominated by near system-size, quasiperiodic avalanche events. The deterministic content of transport dynamics, as quantified by RQA, turns out to be quite different in both phases. The time series analyzed with RQA in this work correspond to local sand fluxes at different radial locations across the diffusive sandpile. PMID:27627267

  20. Proton dynamics in the hydrogen bonds of 4-amino-3,5-dihalogenobenzoic acid

    NASA Astrophysics Data System (ADS)

    Asaji, Tetsuo; Ueda, Kouhei; Oguni, Masaharu

    2015-08-01

    On the polycrystalline sample of 4-amino-3,5-dihalogenobenzoic acid, 4-NH2-3,5-X2C6H2COOH, which has a symmetric dimer structure in the crystal, the proton tunneling in the hydrogen bonds has been investigated by NQR and NMR spin-lattice relaxation times T1 measurements. Two 35Cl NQR lines of the X = Cl derivative show the existence of two crystallographically inequivalent chlorine atoms in the high-temperature phase, in consistency with the reported crystal structure. Below 138 K, each splits into a doublet indicating the symmetry breaking of the benzoic acid dimer. The proton dynamics was analyzed by a coherent and incoherent tunneling models, for the high- and low-temperature phases, respectively. The temperature dependence of the correlation time of proton translation was estimated. As for the X = I derivative, the proton dynamics was discussed similarly by 1H NMR T1 data by assuming occurrence of a phase transition at low-temperature.

  1. Energy dependent sticking coefficients of trimethylamine on Si(001)-Influence of the datively bonded intermediate state on the adsorption dynamics

    NASA Astrophysics Data System (ADS)

    Lipponer, M. A.; Reutzel, M.; Dürr, M.; Höfer, U.

    2016-11-01

    The adsorption dynamics of the datively bonded trimethylamine (TMA) on Si(001) was investigated by means of molecular beam techniques. The initial sticking probability s0 of TMA on Si(001) was measured as a function of kinetic energy at two different surface temperatures (230 and 550 K). At given surface temperature, s0 was found to decrease with increasing kinetic energy (0.1 to 0.6 eV) indicating a non-activated reaction channel. At increased surface temperature, s0 is reduced due to the onset of desorption into the gas phase. The energy dependence of s0 is compared to the results for the adsorption of tetrahydrofuran (THF) on Si(001), which reacts via a datively bonded intermediate into a covalently bound final state. As s0 follows the same energy dependence both for TMA and THF, the datively bonded intermediate state is concluded to dominate the reaction dynamics in the latter case as well.

  2. Dielectric spectroscopy of a polymerizing liquid and the evolution of molecular dynamics with increase in the number of covalent bonds

    NASA Astrophysics Data System (ADS)

    Parthun, M. G.; Johari, G. P.

    1995-07-01

    Dielectric spectroscopy and calorimetry studies of a low viscosity, initially monomeric liquid undergoing spontaneous chemical reaction, to form a linear chain polymer while maintaining isothermal conditions, have been used to determine how the number of covalent bonds formed during the growth of a linear chain affects the dielectric permittivity, relaxation time, and the spectral shape. During this reaction, the static permittivity decreased and the relaxation time increased towards limiting values. As the number of covalent bonds increased towards the Avogadro number, the change in the complex permittivity as measured for a fixed frequency was phenomenologically similar to that observed on varying the frequency, although the exact formalisms in both cases differed. In both cases the relaxation function could be well described by a stretched exponential or sum of exponentials, with a width that decreased as the liquid's state changed from monomeric liquid to a fully reacted chain polymer. The observed increase in the relaxation time with the number of bonds formed seems consistent with the decrease in the configurational entropy or the number of accessible configurations available to the structure, under isothermal conditions. It decreases progressively more slowly as the number of covalent bonds in the structure increases. As this occurs, a second relaxation process at higher frequencies is revealed. The dielectric manifestation of the irreversible process of covalent bond formation is remarkably similar to that observed on supercooling a molecular or polymeric liquid. The study demonstrates how negative feedback between molecular diffusion and chemical reaction vitrifies a liquid isothermally.

  3. Unified model of brain tissue microstructure dynamically binds diffusion and osmosis with extracellular space geometry

    NASA Astrophysics Data System (ADS)

    Yousefnezhad, Mohsen; Fotouhi, Morteza; Vejdani, Kaveh; Kamali-Zare, Padideh

    2016-09-01

    We present a universal model of brain tissue microstructure that dynamically links osmosis and diffusion with geometrical parameters of brain extracellular space (ECS). Our model robustly describes and predicts the nonlinear time dependency of tortuosity (λ =√{D /D* } ) changes with very high precision in various media with uniform and nonuniform osmolarity distribution, as demonstrated by previously published experimental data (D = free diffusion coefficient, D* = effective diffusion coefficient). To construct this model, we first developed a multiscale technique for computationally effective modeling of osmolarity in the brain tissue. Osmolarity differences across cell membranes lead to changes in the ECS dynamics. The evolution of the underlying dynamics is then captured by a level set method. Subsequently, using a homogenization technique, we derived a coarse-grained model with parameters that are explicitly related to the geometry of cells and their associated ECS. Our modeling results in very accurate analytical approximation of tortuosity based on time, space, osmolarity differences across cell membranes, and water permeability of cell membranes. Our model provides a unique platform for studying ECS dynamics not only in physiologic conditions such as sleep-wake cycles and aging but also in pathologic conditions such as stroke, seizure, and neoplasia, as well as in predictive pharmacokinetic modeling such as predicting medication biodistribution and efficacy and novel biomolecule development and testing.

  4. Dynamics of supercooled water in nanotubes: Cage correlation function and diffusion coefficient

    NASA Astrophysics Data System (ADS)

    Khademi, Mahdi; Kalia, Rajiv K.; Sahimi, Muhammad

    2015-09-01

    Dynamics of low-temperature water in nanostructured materials is important to a variety of phenomena, ranging from transport in cement and asphaltene, to conformational dynamics of proteins in "crowded" cellular environments, survival of microorganisms at very low temperatures, and diffusion in nanogeoscience. Using silicon-carbide nanotubes as a prototype of nanostructured materials, extensive molecular dynamics simulations were carried out to study the cage correlation function C (t ) and self-diffusivity D of supercooled water in the nanotubes. C (t ) , which measures changes in the atomic surroundings inside the nanotube, follows the Kohlrausch-Williams-Watts law, C (t ) ˜exp[-(t/τ ) β] , where τ is a relaxation time and β is a topological exponent. For the temperature range 220 Kdiffusivity manifests a transition around 230 K, very close to 228 K, the temperature at which a fragile-to-strong dynamic crossover is supposed to happen. Thus the results indicate that water does not freeze in the nanotube over the studied temperature range, and that the Stokes-Einstein relation breaks down.

  5. INTRODUCTION: Surface Dynamics, Phonons, Adsorbate Vibrations and Diffusion

    NASA Astrophysics Data System (ADS)

    Bruch, L. W.

    2004-07-01

    well infrared photodetectors (QWIPs) and resonant cavity-enhanced photodiodes (RCEPDs) based on dilute nitrides need to be investigated extensively. To date, most theoretical attention has been focused on understanding the band structure of the GaInAsN/GaAs system and on evaluating gain spectra and threshold conditions for 1.3 µm lasers. However, as our understanding of band structure and the effects of strain, defects, etc in dilute nitrides improves we can calculate the electrical and optical properties, including radiative and non-radiative recombination for the materials and structures of interest. The spontaneous and stimulated emission rates have already been calculated for GaInNAs at 1.3 µm by many authors, but extension to other dilute nitrides and other wavelength ranges still represents a major challenge. Many-body effects, including exchange-correlation effects, are essential for accurate models of gain spectra in lasers and optical amplifiers. The differential gain is a key parameter for laser modulation and remains an important subject of study as new materials and structures are explored. Similarly the differential refractive index and linewidth enhancement factor have strong influences on laser spectrum (chirp, linewidth), dynamics and noise, and these must also be studied theoretically. As regards to non-radiative recombination, in addition to recombination through defects, the Auger effect is of especial significance for wavelengths beyond 1 µm and is a worthy subject for theoretical study. The converse effect, impact ionization, is of key importance for avalanche photodiodes (APDs) and has yet to be evaluated for the dilute nitride materials. Inter-valence band absorption (IVBA) is of significance, as a possible cause of temperature sensitivity in lasers and this must be investigated theoretically in the dilute nitrides. Third-order non-linear optical coefficients should be calculated in order to assess the scope for all-optical signal processing

  6. Some applications of nonlinear diffusion to processing of dynamic evolution images

    SciTech Connect

    Goltsov, Alexey N.; Nikishov, Sergey A.

    1997-05-15

    Model nonlinear diffusion equation with the most simple Landau-Ginzburg free energy functional was applied to locate boundaries between meaningful regions of low-level images. The method is oriented to processing images of objects that are a result of dynamic evolution: images of different organs and tissues obtained by radiography and NMR methods, electron microscope images of morphogenesis fields, etc. In the methods developed by us, parameters of the nonlinear diffusion model are chosen on the basis of the preliminary treatment of the images. The parameters of the Landau-Ginzburg free energy functional are extracted from the structure factor of the images. Owing to such a choice of the model parameters, the image to be processed is located in the vicinity of the steady-state of the diffusion equation. The suggested method allows one to separate distinct structures having specific space characteristics from the whole image. The method was applied to processing X-ray images of the lung.

  7. Diffusion dynamics near critical bifurcations in a nonlinearly damped pendulum system

    NASA Astrophysics Data System (ADS)

    Sakthivel, G.; Rajasekar, S.

    2012-03-01

    We numerically study the diffusion dynamics near critical bifurcations such as sudden widening of the size of a chaotic attractor, intermittency and band-merging of a chaotic attractor in a nonlinearly damped and periodically driven pendulum system. The system is found to show only normal diffusion. Near sudden widening and intermittency crisis power-law variation of diffusion constant with the control parameter ω of the external periodic force f sin ωt is found while linear variation of it is observed near band-merging crisis. The value of the exponent in the power-law relation varies with the damping coefficient and the strength of the added Gaussian white noise.

  8. Hydrogen-bond vibrational and energetic dynamical properties in sI and sII clathrate hydrates and in ice Ih: Molecular dynamics insights

    NASA Astrophysics Data System (ADS)

    Chakraborty, Somendra Nath; English, Niall J.

    2015-10-01

    Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein.

  9. Hydrogen-bond vibrational and energetic dynamical properties in sI and sII clathrate hydrates and in ice Ih: Molecular dynamics insights.

    PubMed

    Chakraborty, Somendra Nath; English, Niall J

    2015-10-21

    Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein. PMID:26493912

  10. Hydrogen-bond vibrational and energetic dynamical properties in sI and sII clathrate hydrates and in ice Ih: Molecular dynamics insights.

    PubMed

    Chakraborty, Somendra Nath; English, Niall J

    2015-10-21

    Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein.

  11. Bond Formation and Bond Scission Dynamics in Polyatomic Molecules Revealed by Momentum Imaging Experiments and Electron Scattering Calculations

    NASA Astrophysics Data System (ADS)

    Slaughter, Daniel; Trevisan, Cynthia; Weyland, Marvin; Dorn, Alexander; Douguet, Nicolas; Orel, Ann; Adaniya, Hidehito; McCurdy, Bill; Belkacem, Ali; Rescigno, Tom

    2016-05-01

    We present combined experimental and theoretical studies of dissociative electron attachment (DEA) dynamics in methane and ammonia. DEA in each of these systems proceeds through electronic Feshbach resonances, where a valence electron is excited and captured with the incident electron in the lowest unoccupied orbital. In methane, one triply-degenerate resonance undergoes Jahn-Teller splitting through molecular distortions, leading to four observed final states, each having a 2-body and a 3-body dissociation with anionic products H- and CH2-and neutrals CH3, CH2, H2 or H. In ammonia, one resonance leads to H- + NH2 and NH2-+ H, the latter resulting from non-adiabatic charge transfer. A higher energy resonance leads directly to H- + NH2* and indirectly to NH2-+ H. We examine the dynamics of the transient anion in each of these processes. work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  12. Trojan resonant dynamics, stability, and chaotic diffusion, for parameters relevant to exoplanetary systems

    NASA Astrophysics Data System (ADS)

    Páez, Rocío Isabel; Efthymiopoulos, Christos

    2015-02-01

    The possibility that giant extrasolar planets could have small Trojan co-orbital companions has been examined in the literature from both viewpoints of the origin and dynamical stability of such a configuration. Here we aim to investigate the dynamics of hypothetical small Trojan exoplanets in domains of secondary resonances embedded within the tadpole domain of motion. To this end, we consider the limit of a massless Trojan companion of a giant planet. Without other planets, this is a case of the elliptic restricted three body problem (ERTBP). The presence of additional planets (hereafter referred to as the restricted multi-planet problem, RMPP) induces new direct and indirect secular effects on the dynamics of the Trojan body. The paper contains a theoretical and a numerical part. In the theoretical part, we develop a Hamiltonian formalism in action-angle variables, which allows us to treat in a unified way resonant dynamics and secular effects on the Trojan body in both the ERTBP or the RMPP. In both cases, our formalism leads to a decomposition of the Hamiltonian in two parts, . , called the basic model, describes resonant dynamics in the short-period (epicyclic) and synodic (libration) degrees of freedom, while contains only terms depending trigonometrically on slow (secular) angles. is formally identical in the ERTBP and the RMPP, apart from a re-definition of some angular variables. An important physical consequence of this analysis is that the slow chaotic diffusion along resonances proceeds in both the ERTBP and the RMPP by a qualitatively similar dynamical mechanism. We found that this is best approximated by the paradigm of `modulational diffusion'. In the paper's numerical part, we then focus on the ERTBP in order to make a detailed numerical demonstration of the chaotic diffusion process along resonances. Using color stability maps, we first provide a survey of the resonant web for characteristic mass parameter values of the primary, in which the

  13. Diffusion-assisted selective dynamical recoupling: A new approach to measure background gradients in magnetic resonance

    NASA Astrophysics Data System (ADS)

    Álvarez, Gonzalo A.; Shemesh, Noam; Frydman, Lucio

    2014-02-01

    Dynamical decoupling, a generalization of the original NMR spin-echo sequence, is becoming increasingly relevant as a tool for reducing decoherence in quantum systems. Such sequences apply non-equidistant refocusing pulses for optimizing the coupling between systems, and environmental fluctuations characterized by a given noise spectrum. One such sequence, dubbed Selective Dynamical Recoupling (SDR) [P. E. S. Smith, G. Bensky, G. A. Álvarez, G. Kurizki, and L. Frydman, Proc. Natl. Acad. Sci. 109, 5958 (2012)], allows one to coherently reintroduce diffusion decoherence effects driven by fluctuations arising from restricted molecular diffusion [G. A. Álvarez, N. Shemesh, and L. Frydman, Phys. Rev. Lett. 111, 080404 (2013)]. The fully-refocused, constant-time, and constant-number-of-pulses nature of SDR also allows one to filter out "intrinsic" T1 and T2 weightings, as well as pulse errors acting as additional sources of decoherence. This article explores such features when the fluctuations are now driven by unrestricted molecular diffusion. In particular, we show that diffusion-driven SDR can be exploited to investigate the decoherence arising from the frequency fluctuations imposed by internal gradients. As a result, SDR presents a unique way of probing and characterizing these internal magnetic fields, given an a priori known free diffusion coefficient. This has important implications in studies of structured systems, including porous media and live tissues, where the internal gradients may serve as fingerprints for the system's composition or structure. The principles of this method, along with full analytical solutions for the unrestricted diffusion-driven modulation of the SDR signal, are presented. The potential of this approach is demonstrated with the generation of a novel source of MRI contrast, based on the background gradients active in an ex vivo mouse brain. Additional features and limitations of this new method are discussed.

  14. Diffusion-assisted selective dynamical recoupling: A new approach to measure background gradients in magnetic resonance

    SciTech Connect

    Álvarez, Gonzalo A.; Shemesh, Noam; Frydman, Lucio

    2014-02-28

    Dynamical decoupling, a generalization of the original NMR spin-echo sequence, is becoming increasingly relevant as a tool for reducing decoherence in quantum systems. Such sequences apply non-equidistant refocusing pulses for optimizing the coupling between systems, and environmental fluctuations characterized by a given noise spectrum. One such sequence, dubbed Selective Dynamical Recoupling (SDR) [P. E. S. Smith, G. Bensky, G. A. Álvarez, G. Kurizki, and L. Frydman, Proc. Natl. Acad. Sci. 109, 5958 (2012)], allows one to coherently reintroduce diffusion decoherence effects driven by fluctuations arising from restricted molecular diffusion [G. A. Álvarez, N. Shemesh, and L. Frydman, Phys. Rev. Lett. 111, 080404 (2013)]. The fully-refocused, constant-time, and constant-number-of-pulses nature of SDR also allows one to filter out “intrinsic” T{sub 1} and T{sub 2} weightings, as well as pulse errors acting as additional sources of decoherence. This article explores such features when the fluctuations are now driven by unrestricted molecular diffusion. In particular, we show that diffusion-driven SDR can be exploited to investigate the decoherence arising from the frequency fluctuations imposed by internal gradients. As a result, SDR presents a unique way of probing and characterizing these internal magnetic fields, given an a priori known free diffusion coefficient. This has important implications in studies of structured systems, including porous media and live tissues, where the internal gradients may serve as fingerprints for the system's composition or structure. The principles of this method, along with full analytical solutions for the unrestricted diffusion-driven modulation of the SDR signal, are presented. The potential of this approach is demonstrated with the generation of a novel source of MRI contrast, based on the background gradients active in an ex vivo mouse brain. Additional features and limitations of this new method are discussed.

  15. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    NASA Astrophysics Data System (ADS)

    Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

    2013-11-01

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  16. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    SciTech Connect

    Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

    2013-11-15

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  17. Mathematical model of diffusion-limited gas bubble dynamics in unstirred tissue with finite volume.

    PubMed

    Srinivasan, R Srini; Gerth, Wayne A; Powell, Michael R

    2002-02-01

    Models of gas bubble dynamics for studying decompression sickness have been developed by considering the bubble to be immersed in an extravascular tissue with diffusion-limited gas exchange between the bubble and the surrounding unstirred tissue. In previous versions of this two-region model, the tissue volume must be theoretically infinite, which renders the model inapplicable to analysis of bubble growth in a finite-sized tissue. We herein present a new two-region model that is applicable to problems involving finite tissue volumes. By introducing radial deviations to gas tension in the diffusion region surrounding the bubble, the concentration gradient can be zero at a finite distance from the bubble, thus limiting the tissue volume that participates in bubble-tissue gas exchange. It is shown that these deviations account for the effects of heterogeneous perfusion on gas bubble dynamics, and are required for the tissue volume to be finite. The bubble growth results from a difference between the bubble gas pressure and an average gas tension in the surrounding diffusion region that explicitly depends on gas uptake and release by the bubble. For any given decompression, the diffusion region volume must stay above a certain minimum in order to sustain bubble growth.

  18. Mathematical model of diffusion-limited gas bubble dynamics in unstirred tissue with finite volume

    NASA Technical Reports Server (NTRS)

    Srinivasan, R. Srini; Gerth, Wayne A.; Powell, Michael R.

    2002-01-01

    Models of gas bubble dynamics for studying decompression sickness have been developed by considering the bubble to be immersed in an extravascular tissue with diffusion-limited gas exchange between the bubble and the surrounding unstirred tissue. In previous versions of this two-region model, the tissue volume must be theoretically infinite, which renders the model inapplicable to analysis of bubble growth in a finite-sized tissue. We herein present a new two-region model that is applicable to problems involving finite tissue volumes. By introducing radial deviations to gas tension in the diffusion region surrounding the bubble, the concentration gradient can be zero at a finite distance from the bubble, thus limiting the tissue volume that participates in bubble-tissue gas exchange. It is shown that these deviations account for the effects of heterogeneous perfusion on gas bubble dynamics, and are required for the tissue volume to be finite. The bubble growth results from a difference between the bubble gas pressure and an average gas tension in the surrounding diffusion region that explicitly depends on gas uptake and release by the bubble. For any given decompression, the diffusion region volume must stay above a certain minimum in order to sustain bubble growth.

  19. Molecular dynamics simulation of amorphous indomethacin-poly(vinylpyrrolidone) glasses: solubility and hydrogen bonding interactions.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-03-01

    Amorphous drug dispersions are frequently employed to enhance solubility and dissolution of poorly water-soluble drugs and thereby increase their oral bioavailability. Because these systems are metastable, phase separation of the amorphous components and subsequent drug crystallization may occur during storage. Computational methods to determine the likelihood of these events would be very valuable, if their reliability could be validated. This study investigates amorphous systems of indomethacin (IMC) in poly(vinylpyrrolidone) (PVP) and their molecular interactions by means of molecular dynamics (MD) simulations. IMC and PVP molecules were constructed using X-ray diffraction data, and force-field parameters were assigned by analogy with similar groups in Amber-ff03. Five assemblies varying in PVP and IMC composition were equilibrated in their molten states then cooled at a rate of 0.03 K/ps to generate amorphous glasses. Prolonged aging dynamic runs (100 ns) at 298 K and 1 bar were then carried out, from which solubility parameters, the Flory-Huggins interaction parameter, and associated hydrogen bonding properties were obtained. Calculated glass transition temperature (T(g)) values were higher than experimental results because of the faster cooling rates in MD simulations. Molecular mobility as characterized by atomic fluctuations was substantially reduced below the T(g) with IMC-PVP systems exhibiting lower mobilities than that found in amorphous IMC, consistent with the antiplasticizing effect of PVP. The number of IMC-IMC hydrogen bonds (HBs) formed per IMC molecule was substantially lower in IMC-PVP mixtures, particularly the fractions of IMC molecules involved in two or three HBs with other IMC molecules that may be potential precursors for crystal growth. The loss of HBs between IMC molecules in the presence of PVP was largely compensated for by the formation of IMC-PVP HBs. The difference (6.5 MPa(1/2)) between the solubility parameters in amorphous IMC

  20. Fast dynamics and relaxation of colloidal drops during the drying process using multispeckle diffusing wave spectroscopy.

    PubMed

    Lee, Jeong Yong; Hwang, Ji Won; Jung, Hyun Wook; Kim, Sung Hyun; Lee, Seong Jae; Yoon, Kisun; Weitz, David A

    2013-01-22

    The fast dynamics generated by the Brownian motion of particles in colloidal drops, and the related relaxation during drying, which play key roles in suspension systems, were investigated incorporating multispeckle diffusing wave spectroscopy (MSDWS). MSDWS equipment was implemented to analyze the relaxation properties of suspensions under a nonergodic and nonstationary drying process, which cannot be elucidated by conventional light scattering methods, such as dynamic light scattering and diffusing wave spectroscopy. Rapid particle movement can be identified by the characteristic relaxation time, which is closely related to the Brownian motion due to thermal fluctuations of the particles. In the compacting stage of the drying process, the characteristic relaxation time increased gradually with the drying time because the particles in the colloidal drop were constrained by themselves. Moreover, variations of the initial concentration and particle size considerably affected the complete drying time and characteristic relaxation time, producing a shorter relaxation time for a low concentrated suspension with small particles. PMID:23281633

  1. Random Vibration Tests for Prediction of Fatigue Life of Diffuser Structure for Gas Dynamic Laser

    NASA Astrophysics Data System (ADS)

    Maurer, O. F.; Banaszak, D. L.

    1980-01-01

    Static and dynamic strain measurements which were taken during test stand operations of the gas dynamic laser (GDL) for the AF Airborne Laser Laboratory indicated that higher than expected vibrational stress levels may possibly limit the fatigue life of the laser structure. Particularly the diffuser sidewall structure exhibited large amplitude random vibrations which were excited by the internal gas flow. The diffuser structure consists of two layers of brazed stainless steel, AISI-347, panels. Cooling ducts were milled into the outer face sheet. These in turn are backed by the inner face sheet. So called T-rail stiffeners silver-brazed to the outer face sheets add the required stiffness and divide the sidewall into smaller rectangular plate sections.

  2. Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

    DOE PAGESBeta

    Diallo, S. O.; Vlcek, L.; Mamontov, E.; Keum, J. K.; Chen, Jihua; Hayes, J. S.; Chialvo, A. A.

    2015-02-17

    When water molecules are confined to nanoscale spacings, such as in the nanometer-size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures (~150 K), leading to a metastable liquid state with remarkable physical properties. Here we have investigated the ambient pressure diffusive dynamics of water in microporous Kynol ACF-10 (average pore size ~11.6 Å, with primarily slit-like pores) from temperature T = 280 K in its stable liquid state down to T = 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be, respectively, higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time (more » $${{\\tau}}$$) when compared to previous findings indicate that it is the width of the slit pores-not their curvature-that primarily affects the dynamics of water for pore sizes larger than 10 Å. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 Å gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer Q (Q ≤ 0.9 Å-1). At high Q, however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. Consequently, the simulations are compared to the experiments at low Q, where the two can be best reconciled. The best agreement is obtained for the diffusion parameter D associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bimodal exponential model, is used to parametrize the self-correlation function I (Q,t).« less

  3. Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

    SciTech Connect

    Diallo, S. O.; Vlcek, L.; Mamontov, E.; Keum, J. K.; Chen, Jihua; Hayes, J. S.; Chialvo, A. A.

    2015-02-17

    When water molecules are confined to nanoscale spacings, such as in the nanometer-size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures (~150 K), leading to a metastable liquid state with remarkable physical properties. Here we have investigated the ambient pressure diffusive dynamics of water in microporous Kynol ACF-10 (average pore size ~11.6 Å, with primarily slit-like pores) from temperature T = 280 K in its stable liquid state down to T = 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be, respectively, higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time (${{\\tau}}$) when compared to previous findings indicate that it is the width of the slit pores-not their curvature-that primarily affects the dynamics of water for pore sizes larger than 10 Å. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 Å gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer Q (Q ≤ 0.9 Å-1). At high Q, however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. Consequently, the simulations are compared to the experiments at low Q, where the two can be best reconciled. The best agreement is obtained for the diffusion parameter D associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bimodal exponential model, is used to parametrize the self-correlation function I (Q,t).

  4. Investigation of the diffuse ultraviolet background using satellite data: Dynamics explorer guest investigator program

    NASA Technical Reports Server (NTRS)

    Fix, J. D.

    1986-01-01

    The imaging instrumentation for the Dynamics Explorer Mission was designed primarily to obtain global auroral images. The instrument, however, was also used successfully to study marine bioluminescence, the geocorona, and the global distribution of atmospheric ozone. The imager has considerable potential for the study of astronomical sources of ultraviolet radiation as well. The data produced by the imager is used to study the brightness and isotrophy of the diffuse ultraviolet background.

  5. Relationship between maximum principle and dynamic programming for stochastic differential games of jump diffusions

    NASA Astrophysics Data System (ADS)

    Shi, Jingtao

    2014-04-01

    This paper is concerned with the relationship between maximum principle and dynamic programming for zero-sum stochastic differential games of jump diffusions. Under the assumption that the value function is smooth enough, relations among the adjoint processes, the generalised Hamiltonian function and the value function are given. A portfolio optimisation problem under model uncertainty in an incomplete financial market is discussed to show the applications of our result.

  6. Exploring the dynamics of balance data — movement variability in terms of drift and diffusion

    NASA Astrophysics Data System (ADS)

    Gottschall, Julia; Peinke, Joachim; Lippens, Volker; Nagel, Volker

    2009-02-01

    We introduce a method to analyze postural control on a balance board by reconstructing the underlying dynamics in terms of a Langevin model. Drift and diffusion coefficients are directly estimated from the data and fitted by a suitable parametrization. The governing parameters are utilized to evaluate balance performance and the impact of supra-postural tasks on it. We show that the proposed method of analysis gives not only self-consistent results but also provides a plausible model for the reconstruction of balance dynamics.

  7. Microstructures and Mechanical Properties of Transient Liquid-Phase Diffusion-Bonded Ti3Al/TiAl Joints with TiZrCuNi Interlayer

    NASA Astrophysics Data System (ADS)

    Ren, H. S.; Xiong, H. P.; Pang, S. J.; Chen, B.; Wu, X.; Cheng, Y. Y.; Chen, B. Q.

    2016-04-01

    Transient liquid-phase diffusion bonding of Ti3Al-based alloy to TiAl intermetallics was conducted using Ti-13Zr-21Cu-9Ni (wt pct) interlayer foil. The joint microstructures were examined using a scanning electron microscope (SEM) equipped with an electron probe micro-analyzer (EPMA). The microhardness across the joint was measured and joint strengths were tested. The results show that the Ti3Al/TiAl joint mainly consists of Ti-rich phase, Ti2Al layer, α 2-Ti3Al band, and residual interlayer alloy dissolved with Al. The amount of residual interlayer at the central part of the joint is decreased with the increase of the bonding temperature, and meantime the Ti2Al and α 2-Ti3Al reaction bands close to the joined Ti3Al-based alloy become thickened gradually. Furthermore, the central part of the joint exhibits the maximum microhardness across the whole joint. The joints bonded at 1193 K (920 °C) for 600 seconds with a pressure of 2 MPa presented the maximum shear strength of 417 MPa at room temperature, and the strength of 234 MPa was maintained at 773 K (500 °C).

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

    SciTech Connect

    Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

    2015-07-07

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

  9. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  10. Vibrational dynamics of hydrogen-bonded complexes in solutions studied with ultrafast infrared pump-probe spectroscopy.

    PubMed

    Banno, Motohiro; Ohta, Kaoru; Yamaguchi, Sayuri; Hirai, Satori; Tominaga, Keisuke

    2009-09-15

    In aqueous solution, the basis of all living processes, hydrogen bonding exerts a powerful effect on chemical reactivity. The vibrational energy relaxation (VER) process in hydrogen-bonded complexes in solution is sensitive to the microscopic environment around the oscillator and to the geometrical configuration of the hydrogen-bonded complexes. In this Account, we describe the use of time-resolved infrared (IR) pump-probe spectroscopy to study the vibrational dynamics of (i) the carbonyl CO stretching modes in protic solvents and (ii) the OH stretching modes of phenol and carboxylic acid. In these cases, the carbonyl group acts as a hydrogen-bond acceptor, whereas the hydroxyl group acts as a hydrogen-bond donor. These vibrational modes have different properties depending on their respective chemical bonds, suggesting that hydrogen bonding may have different mechanisms and effects on the VER of the CO and OH modes than previously understood. The IR pump-probe signals of the CO stretching mode of 9-fluorenone and methyl acetate in alcohol, as well as that of acetic acid in water, include several components with different time constants. Quantum chemical calculations indicate that the dynamical components are the result of various hydrogen-bonded complexes that form between solute and solvent molecules. The acceleration of the VER is due to the increasing vibrational density of states caused by the formation of hydrogen bonds. The vibrational dynamics of the OH stretching mode in hydrogen-bonded complexes were studied in several systems. For phenol-base complexes, the decay time constant of the pump-probe signal decreases as the band peak of the IR absorption spectrum shifts to lower wavenumbers (the result of changing the proton acceptor). For phenol oligomers, the decay time constant of the pump-probe signal decreases as the probe wavenumber decreases. These observations show that the VER time strongly correlates with the strength of hydrogen bonding. This

  11. Dynamic contact-free continuous-wave diffuse optical tomography system for the detection of vascular dynamics within the foot

    NASA Astrophysics Data System (ADS)

    Khalil, M. A.; Hoi, J.; Kim, H. K.; Hielscher, A. H.

    2013-03-01

    We present a dynamic contact-free continuous-wave diffuse optical tomography system for the detection and monitoring of peripheral arterial disease (PAD) in the foot. Peripheral Arterial Disease (PAD) is the narrowing of the functional area of the artery generally due to atherosclerosis. It affects between 8-12 million people in the United States and if untreated this can lead to ulceration, gangrene and ultimately amputation. Contact-Free imaging is highly desirable, due to the presence of ulcerations and gangrene in many patients affected by PAD. The system uses an electron multiplying charge coupled device (EMCCD) camera for detection to achieve a dynamic range of 86 dB with a frame rate of 1 Hz using 20 collimated source fibers and 2 wavelengths. We present first clinical results showing 3D images of total hemoglobin changes in response to a dynamic thigh cuff.

  12. Forbidden phonon: Dynamical signature of bond symmetry breaking in the iron chalcogenides

    NASA Astrophysics Data System (ADS)

    Fobes, David M.; Zaliznyak, Igor A.; Tranquada, John M.; Xu, Zhijun; Gu, Genda; He, Xu-Gang; Ku, Wei; Zhao, Yang; Matsuda, Masaaki; Garlea, V. Ovidiu; Winn, Barry

    2016-09-01

    Investigation of the inelastic neutron scattering spectra in Fe1 +yTe1 -xSex near a signature wave vector Q =(1 ,0 ,0 ) for the bond-order wave (BOW) formation of parent compound Fe1 +yTe [D. Fobes et al., Phys. Rev. Lett. 112, 187202 (2014), 10.1103/PhysRevLett.112.187202] reveals an acoustic-phonon-like dispersion present in all structural phases. While a structural Bragg peak accompanies the mode in the low-temperature phase of Fe1 +yTe , it is absent in the high-temperature tetragonal phase, where Bragg scattering at this Q is forbidden by symmetry. Notably, this mode is also observed in superconducting FeTe0.55Se0.45 , where structural and magnetic transitions are suppressed, and no BOW has been observed. The presence of this "forbidden" phonon indicates that the lattice symmetry is dynamically or locally broken by magneto-orbital BOW fluctuations, which are strongly coupled to lattice in these materials.

  13. Site and bond-specific dynamics of reactions at the gas-liquid interface.

    PubMed

    Tesa-Serrate, Maria A; King, Kerry L; Paterson, Grant; Costen, Matthew L; McKendrick, Kenneth G

    2014-01-01

    The dynamics of the interfacial reactions of O((3)P) with the hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene) have been studied experimentally. Laser-induced fluorescence (LIF) was used to detect the nascent gas-phase OH products. The O((3)P) atoms are acutely sensitive to the chemical differences of the squalane and squalene surfaces. The larger exothermicity of abstraction from allylic C-H sites in squalene is reflected in markedly hotter OH rotational and vibrational distributions. There is a more modest increase in translational energy release. A larger fraction of the available energy is deposited in the liquid for squalene than for squalane, consistent with a more extensive geometry change on formation of the allylic radical co-product. Although the dominant reaction mechanism is direct, impulsive scattering, there is some evidence for OH being accommodated at both liquid surfaces, resulting in thermalised translation and rotational distributions. Despite the H-abstraction reaction being strongly favoured energetically for squalene, the yield of OH is substantially lower than for squalane. This is very likely due to competitive addition of O((3)P) to the unsaturated sites in squalene, implying that double bonds are extensively exposed at the liquid surface.

  14. Enzymatic hydroxylation of an unactivated methylene C-H bond guided by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Narayan, Alison R. H.; Jiménez-Osés, Gonzalo; Liu, Peng; Negretti, Solymar; Zhao, Wanxiang; Gilbert, Michael M.; Ramabhadran, Raghunath O.; Yang, Yun-Fang; Furan, Lawrence R.; Li, Zhe; Podust, Larissa M.; Montgomery, John; Houk, K. N.; Sherman, David H.

    2015-08-01

    The hallmark of enzymes from secondary metabolic pathways is the pairing of powerful reactivity with exquisite site selectivity. The application of these biocatalytic tools in organic synthesis, however, remains under-utilized due to limitations in substrate scope and scalability. Here, we report how the reactivity of a monooxygenase (PikC) from the pikromycin pathway is modified through computationally guided protein and substrate engineering, and applied to the oxidation of unactivated methylene C-H bonds. Molecular dynamics and quantum mechanical calculations were used to develop a predictive model for substrate scope, site selectivity and stereoselectivity of PikC-mediated C-H oxidation. A suite of menthol derivatives was screened computationally and evaluated through in vitro reactions, where each substrate adhered to the predicted models for selectivity and conversion to product. This platform was also expanded beyond menthol-based substrates to the selective hydroxylation of a variety of substrate cores ranging from cyclic to fused bicyclic and bridged bicyclic compounds.

  15. Transformation of the Strongly Hydrogen Bonded System into van der Waals one Reflected in Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Kamiński, K.; Kamińska, E.; Grzybowska, K.; Włodarczyk, P.; Pawlus, S.; Paluch, M.; Zioło, J.; Rzoska, S. J.; Pilch, J.; Kasprzycka, A.; Szeja, W.

    Dielectric relaxation studies on disaccharides lactose and octa-O-acetyl-lactose are reported. The latter is a hydrogen bonded system while the former is a van der Waals glass former. The transformation between them was arranged by substituting hydrogen atoms in lactose by acetyl groups. Hereby the influence of differences in bounding on dynamics of both systems is discussed. We showed that the faster secondary relaxation (labeled γ) in octa-O-acetyl-lactose has much lower amplitude than that of lactose. The relaxation time and activation energy remain unchanged in comparison to the γ- relaxation of lactose. We did not observe the slow secondary relaxation (labeled β), clearly visible in lactose, in its acethyl derivative. Detailed analysis of the dielectric spectra measured for octa-O-acetyl-lactose in its glassy state (not standard change in the shape of the γ- peak with lowering temperature) enabled us to provide probable explanation of our finding. No credible comparative analysis of the α- relaxation process of the lactose and octa-O-acetyl-lactose are presented, because loss spectra of the former carbohydrate were affected by the huge contribution of the dc conductivity. Notwithstanding, one can expect that octa-O-acetyl-lactose has lower glass transition temperature and steepness index than lactose.

  16. Catalytic performance and molecular dynamic simulation of immobilized CC bond hydrolase based on carbon nanotube matrix.

    PubMed

    Zhou, Hao; Qu, Yuanyuan; Kong, Chunlei; Li, Duanxing; Shen, E; Ma, Qiao; Zhang, Xuwang; Wang, Jingwei; Zhou, Jiti

    2014-04-01

    Carbon nanotube (CNT) has been proved to be a kind of novel support for enzyme immobilization. In this study, we tried to find the relationship between conformation and catalytic performance of immobilized enzyme. Two CC bond hydrolases BphD and MfphA were immobilized on CNTs (SWCNT and MWCNT) via physical adsorption and covalent attachment. Among the conjugates, the immobilized BphD on chemically functionalized SWCNT (BphD-CSWCNT) retained the highest catalytic efficiency (kcat/Km value) compared to free BphD (92.9%). On the other hand, when MfphA bound to pristine SWCNT (MfphA-SWCNT), it was completely inactive. Time-resolved fluorescence spectrum indicated the formation of static ground complexes during the immobilization processes. Circular dichroism (CD) showed that the secondary structures of immobilized enzymes changed in varying degrees. In order to investigate the inhibition mechanism of MfphA by SWCNT, molecular dynamics simulation was employed to analyze the adsorption process, binding sites and time evolution of substrate tunnels. The results showed that the preferred binding sites (Trp201 and Met81) of MfphA for SWCNT blocked the main substrate access tunnel, thus making the enzyme inactive. The "tunnel-block" should be a novel possible inhibition mechanism for enzyme-nanotube conjugate.

  17. Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential.

    PubMed

    Zhou, Xiaowang; Ward, Donald K; Wong, Bryan M; Doty, F Patrick; Zimmerman, Jonathan A

    2012-08-23

    Cd(1-x)Zn(x)Te (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals.

  18. Enzymatic Hydroxylation of an Unactivated Methylene C–H Bond Guided by Molecular Dynamics Simulations

    PubMed Central

    Narayan, Alison R. H.; Jiménez-Osés, Gonzalo; Liu, Peng; Negretti, Solymar; Zhao, Wanxiang; Gilbert, Michael M.; Ramabhadran, Raghunath O.; Yang, Yun-Fang; Furan, Lawrence R.; Li, Zhe; Podust, Larissa M.; Montgomery, John; Houk, K. N.; Sherman, David H.

    2015-01-01

    The hallmark of enzymes from secondary metabolic pathways is the pairing of powerful reactivity with exquisite site selectivity. The application of these biocatalytic tools in organic synthesis, however, remains under-utilized due to limitations in substrate scope and scalability. Here we report the reactivity of a monooxygenase (PikC) from the pikromycin pathway is modified through computationally-guided protein and substrate engineering, and applied to the oxidation of unactivated methylene C-H bonds. Molecular dynamics and quantum mechanical calculations were employed to develop a predictive model for substrate scope, site selectivity, and stereoselectivity of PikC mediated C-H oxidation. A suite of menthol derivatives was screened computationally and evaluated through in vitro reactions where each substrate adhered to the predicted models for selectivity and conversion to product. This platform was also expanded beyond menthol-based substrates to the selective hydroxylation of a variety of substrate cores ranging from cyclic to fused bicyclic and bridged bicyclic compounds. PMID:26201742

  19. Diffusion of Small Solute Particles in Viscous Liquids: Cage Diffusion, a Result of Decoupling of Solute-Solvent Dynamics, Leads to Amplification of Solute Diffusion.

    PubMed

    Acharya, Sayantan; Nandi, Manoj K; Mandal, Arkajit; Sarkar, Sucharita; Bhattacharyya, Sarika Maitra

    2015-08-27

    We study the diffusion of small solute particles through solvent by keeping the solute-solvent interaction repulsive and varying the solvent properties. The study involves computer simulations, development of a new model to describe diffusion of small solutes in a solvent, and also mode coupling theory (MCT) calculations. In a viscous solvent, a small solute diffuses via coupling to the solvent hydrodynamic modes and also through the transient cages formed by the solvent. The model developed can estimate the independent contributions from these two different channels of diffusion. Although the solute diffusion in all the systems shows an amplification, the degree of it increases with solvent viscosity. The model correctly predicts that when the solvent viscosity is high, the solute primarily diffuses by exploiting the solvent cages. In such a scenario the MCT diffusion performed for a static solvent provides a correct estimation of the cage diffusion.

  20. Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics

    PubMed Central

    Veshtort, Mikhail; Griffin, Robert G.

    2011-01-01

    Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R2). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two 13C nuclei and about ten 1H nuclei from their nearest environment. Spin diffusion constants computed by this method

  1. Dynamics of Weak, Bifurcated and Strong Hydrogen Bonds in Lithium Nitrate Trihydrate

    SciTech Connect

    Werhahn, Jasper C.; Pandelov, S.; Xantheas, Sotiris S.; Iglev, H.

    2011-07-07

    The properties of three distinct types of hydrogen bonds, namely a weak, a bifurcated and a strong one, all present in/the LiNO3 (HDO)(D2O)2 hydrate lattice unit cell are studied using steady-state and time-resolved spectroscopy. The lifetimes of the OH stretching vibrations for the three individual bonds are 2.2 ps (weak), 1.7 ps (bifurcated), and 1.2 ps (strong), respectively. For the first time the properties of bifurcated H bonds can thus be unambiguously directly compared to those of weak and strong H bonds in the same system. The values of their OH stretching vibration lifetime, anharmonicity, red shift and bond strength lie between those for the strong and weak H bonds. The experimentally observed inhomogeneous broadening of their spectral signature is attributed to the coupling with a low frequency intermolecular wagging vibration/

  2. Effects of ion dynamics on kinetic structures of the diffusion region during magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Chen, L. J.; Shuster, J. R.; Bessho, N.; Li, G.; Torbert, R. B.; Daughton, W. S.

    2014-12-01

    Based on results from Particle-in-cell (PIC) simulations, we report how ion dynamics influencethe Hall electric field and electron velocity distributions in the diffusion region of magnetic reconnection.The Hall electric field is due to charge imbalance in the diffusion region. At early times, within a few ion cyclotron oscillations from the peak reconnection,electron orbit dynamics dominate, and the Hall electric field layer assumes the width of the electron current layer.As the pre-existing current sheet ions are accelerated and jetted away, inflowing ions form an ion phase space hole structure.The ion hole structure is self-consistently supported by the Hall electric field. The ion meandering orbit width increasesover the course of about 10 ion cyclotron oscillations from several to approximately 40 electron skin depths (two ion skin depths,where the skin depth is based on the initial current sheet density), and theHall electric field layer widens in the same manner to become much broader than the electron diffusion region.The electron velocity distributions upstream of the electron diffusion region and within the regionof counter streaming ions become fragmented as the ion hole establishes itself.The fragmentation is carried into the electron diffusion region, and through the electron outflow jet, leading to a multitude of arcs in the electron distributions at the end of the jet. The broadening of the Hall electric field layer resolves a longstanding discrepancy concerning whether the narrowest width of the layer is of the electron [Chen et al., 2008] or ion [Mozer et al., 2002] scale. The fragmentation of the electron distributions may be due to an electron-ion instability, and is underinvestigation.

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

    SciTech Connect

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

    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

  4. Effects of heterogeneous structure and diffusion permeability of body tissues on decompression gas bubble dynamics.

    PubMed

    Nikolaev, V P

    2000-07-01

    To gain insight into the special nature of gas bubbles that may form in astronauts, aviators and divers, we developed a mathematical model which describes the following: 1) the dynamics of extravascular bubbles formed in intercellular cavities of a hypothetical tissue undergoing decompression; and 2) the dynamics of nitrogen tension in a thin layer of intercellular fluid and in a thick layer of cells surrounding the bubbles. This model is based on the assumption that, due to limited cellular membrane permeability for gas, a value of effective nitrogen diffusivity in the massive layer of cells in the radial direction is essentially lower compared to conventionally accepted values of nitrogen diffusivity in water and body tissues. Due to rather high nitrogen diffusivity in intercellular fluid, a bubble formed just at completion of fast one-stage reduction of ambient pressure almost instantly grows to the size determined by the initial volume of the intercellular cavity, surface tension of the fluid, the initial nitrogen tension in the tissue, and the level of final pressure. The rate of further bubble growth and maximum bubble size depend on comparatively low effective nitrogen diffusivity in the cell layer, the tissue perfusion rate, the initial nitrogen tension in the tissue, and the final ambient pressure. The tissue deformation pressure performs its conservative action on bubble dynamics only in a limited volume of tissue (at a high density of formed bubbles). Our model is completely consistent with the available data concerning the random latency times to the onset of decompression sickness (DCS) symptoms associated with hypobaric decompressions simulating extravehicular activity. We believe that this model could be used as a theoretical basis for development of more adequate methods for the DCS risk prediction.

  5. Solvent influence on cellulose 1,4-β-glycosidic bond cleavage: a molecular dynamics and metadynamics study.

    PubMed

    Loerbroks, Claudia; Boulanger, Eliot; Thiel, Walter

    2015-03-27

    We explore the influence of two solvents, namely water and the ionic liquid 1-ethyl-3-methylimidazolium acetate (EmimAc), on the conformations of two cellulose models (cellobiose and a chain of 40 glucose units) and the solvent impact on glycosidic bond cleavage by acid hydrolysis by using molecular dynamics and metadynamics simulations. We investigate the rotation around the glycosidic bond and ring puckering, as well as the anomeric effect and hydrogen bonds, in order to gauge the effect on the hydrolysis mechanism. We find that EmimAc eases hydrolysis through stronger solvent-cellulose interactions, which break structural and electronic barriers to hydrolysis. Our results indicate that hydrolysis in cellulose chains should start from the ends and not in the centre of the chain, which is less accessible to solvent. PMID:25689773

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

    PubMed

    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].

  7. Rotational diffusion affects the dynamical self-assembly pathways of patchy particles.

    PubMed

    Newton, Arthur C; Groenewold, Jan; Kegel, Willem K; Bolhuis, Peter G

    2015-12-15

    Predicting the self-assembly kinetics of particles with anisotropic interactions, such as colloidal patchy particles or proteins with multiple binding sites, is important for the design of novel high-tech materials, as well as for understanding biological systems, e.g., viruses or regulatory networks. Often stochastic in nature, such self-assembly processes are fundamentally governed by rotational and translational diffusion. Whereas the rotational diffusion constant of particles is usually considered to be coupled to the translational diffusion via the Stokes-Einstein relation, in the past decade it has become clear that they can be independently altered by molecular crowding agents or via external fields. Because virus capsids naturally assemble in crowded environments such as the cell cytoplasm but also in aqueous solution in vitro, it is important to investigate how varying the rotational diffusion with respect to transitional diffusion alters the kinetic pathways of self-assembly. Kinetic trapping in malformed or intermediate structures often impedes a direct simulation approach of a kinetic network by dramatically slowing down the relaxation to the designed ground state. However, using recently developed path-sampling techniques, we can sample and analyze the entire self-assembly kinetic network of simple patchy particle systems. For assembly of a designed cluster of patchy particles we find that changing the rotational diffusion does not change the equilibrium constants, but significantly affects the dynamical pathways, and enhances (suppresses) the overall relaxation process and the yield of the target structure, by avoiding (encountering) frustrated states. Besides insight, this finding provides a design principle for improved control of nanoparticle self-assembly.

  8. The gravel-sand transition: Sediment dynamics in a diffuse extension

    NASA Astrophysics Data System (ADS)

    Venditti, Jeremy G.; Domarad, Natalia; Church, Michael; Rennie, Colin D.

    2015-06-01

    As gravel-bedded rivers fine in the downstream direction, they characteristically exhibit an abrupt transition from gravel- to sand-bedded conditions. The prevailing theory for why abrupt gravel-sand transitions emerge is based on bed load sorting of a bimodal sediment. The abruptness is thought to be a consequence of sand overwhelming the gravel-sand mixture once it reaches a critical coverage on the bed. The role suspension plays in the development of gravel-sand transitions has not been fully appreciated. The Fraser River, British Columbia, is an archetypical abrupt gravel-sand transition with a "diffuse extension" composed of a sand bed with some patches of gravel. We examine flow, shear stress, and suspended sediment flux in the diffuse extension to better understand sediment dynamics where the sand bed emerges. Sand is carried in suspension upstream of the primary abrupt gravel-sand transition, but in the diffuse extension, sand is moved as both bed load and suspended load. We do not observe downstream gradients in shear stress or suspended sand flux through the diffuse extension that would suggest a gradual "rain out" of sand moving downstream, which raises the question, how is the sand bed formed? Sediment advection length scales indicate that with the exception of very fine sand that moves as wash load in the diffuse extension, fractions coarser than the median sand size cannot be carried in suspension for more than one channel width. This suggests that sand is deposited en masse at the beginning of the diffuse extension, forming a sediment slug at low flood flows that is smeared downstream at high flood flows to form the sand reach.

  9. Rotational diffusion affects the dynamical self-assembly pathways of patchy particles

    PubMed Central

    Newton, Arthur C.; Groenewold, Jan; Kegel, Willem K.; Bolhuis, Peter G.

    2015-01-01

    Predicting the self-assembly kinetics of particles with anisotropic interactions, such as colloidal patchy particles or proteins with multiple binding sites, is important for the design of novel high-tech materials, as well as for understanding biological systems, e.g., viruses or regulatory networks. Often stochastic in nature, such self-assembly processes are fundamentally governed by rotational and translational diffusion. Whereas the rotational diffusion constant of particles is usually considered to be coupled to the translational diffusion via the Stokes–Einstein relation, in the past decade it has become clear that they can be independently altered by molecular crowding agents or via external fields. Because virus capsids naturally assemble in crowded environments such as the cell cytoplasm but also in aqueous solution in vitro, it is important to investigate how varying the rotational diffusion with respect to transitional diffusion alters the kinetic pathways of self-assembly. Kinetic trapping in malformed or intermediate structures often impedes a direct simulation approach of a kinetic network by dramatically slowing down the relaxation to the designed ground state. However, using recently developed path-sampling techniques, we can sample and analyze the entire self-assembly kinetic network of simple patchy particle systems. For assembly of a designed cluster of patchy particles we find that changing the rotational diffusion does not change the equilibrium constants, but significantly affects the dynamical pathways, and enhances (suppresses) the overall relaxation process and the yield of the target structure, by avoiding (encountering) frustrated states. Besides insight, this finding provides a design principle for improved control of nanoparticle self-assembly. PMID:26621742

  10. Dynamics of a reaction-diffusion system with Brusselator kinetics under feedback control

    NASA Astrophysics Data System (ADS)

    Karafyllis, Iasson; Christofides, Panagiotis D.; Daoutidis, Prodromos

    1999-01-01

    This paper studies the dynamics of the reaction-diffusion Brusselator model with Neumann and Dirichlet boundary conditions, under linear and nonlinear modal feedback control. The bifurcation parameters are for the Neumann problem the concentration of one of the reactants and for the Dirichlet problem the diffusion coefficient of one of the reactants. The study of the dynamics of the system is based on methods of bifurcation theory and the application of Poincaré maps. A direct comparison of the dynamics of the open-loop and closed-loop systems establishes that the use of feedback control significantly suppresses the rich open-loop dynamics. In addition, the superiority of the nonlinear controller over a linear controller, in attenuating the effect of bifurcations on the output of the closed-loop system, and the ability of the nonlinear controller to stabilize the system states at the spatially uniform solution provided the number of manipulated inputs is sufficiently large are shown for both the Neumann and Dirichlet problems.

  11. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering

    NASA Astrophysics Data System (ADS)

    Kim, Jae-Yeol; Kim, Cheolhee; Lee, Nam Ki

    2015-04-01

    Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s-1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution.

  12. An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion

    NASA Astrophysics Data System (ADS)

    Gou, J.; Ward, M. J.

    2016-08-01

    A class of coupled cell-bulk ODE-PDE models is formulated and analyzed in a two-dimensional domain, which is relevant to studying quorum-sensing behavior on thin substrates. In this model, spatially segregated dynamically active signaling cells of a common small radius ɛ ≪ 1 are coupled through a passive bulk diffusion field. For this coupled system, the method of matched asymptotic expansions is used to construct steady-state solutions and to formulate a spectral problem that characterizes the linear stability properties of the steady-state solutions, with the aim of predicting whether temporal oscillations can be triggered by the cell-bulk coupling. Phase diagrams in parameter space where such collective oscillations can occur, as obtained from our linear stability analysis, are illustrated for two specific choices of the intracellular kinetics. In the limit of very large bulk diffusion, it is shown that solutions to the ODE-PDE cell-bulk system can be approximated by a finite-dimensional dynamical system. This limiting system is studied both analytically, using a linear stability analysis and, globally, using numerical bifurcation software. For one illustrative example of the theory, it is shown that when the number of cells exceeds some critical number, i.e., when a quorum is attained, the passive bulk diffusion field can trigger oscillations through a Hopf bifurcation that would otherwise not occur without the coupling. Moreover, for two specific models for the intracellular dynamics, we show that there are rather wide regions in parameter space where these triggered oscillations are synchronous in nature. Unless the bulk diffusivity is asymptotically large, it is shown that a diffusion-sensing behavior is possible whereby more clustered spatial configurations of cells inside the domain lead to larger regions in parameter space where synchronous collective oscillations between the small cells can occur. Finally, the linear stability analysis for these cell

  13. Range-separated approach to the RPA correlation applied to the van der Waals Bond and to diffusion of defects.

    PubMed

    Bruneval, Fabien

    2012-06-22

    The random-phase approximation (RPA) is a promising approximation to the exchange-correlation energy of density functional theory, since it contains the van der Waals (vdW) interaction and yields a potential with the correct band gap. However, its calculation is computationally very demanding. We apply a range-separation concept to RPA and demonstrate how it drastically speeds up the calculations without loss of accuracy. The scheme is then successfully applied to a layered system subjected to weak vdW attraction and is used to address the controversy of the self-diffusion in silicon. We calculate the formation and migration energies of self-interstitials and vacancies taking into account atomic relaxations. The obtained activation energies deviate significantly from the earlier calculations and challenge some of the experimental interpretations: the diffusion of vacancies and interstitials has almost the same activation energy.

  14. Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid.

    PubMed

    Cao, Bing-Yang; Dong, Ruo-Yu

    2014-01-21

    Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein-Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient. PMID:25669403

  15. A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase

    SciTech Connect

    Nagashima, Hiroki; Tokumasu, Takashi; Tsuda, Shin-ichi; Tsuboi, Nobuyuki; Koshi, Mitsuo; Hayashie, A. Koichi

    2014-10-06

    In this paper, the quantum effect of hydrogen molecule on its diffusivity is analyzed using Molecular Dynamics (MD) method. The path integral centroid MD (CMD) method is applied for the reproduction method of time evolution of the molecules. The diffusion coefficient of liquid hydrogen is calculated using the Green-Kubo method. The simulation is performed at wide temperature region and the temperature dependence of the quantum effect of hydrogen molecule is addressed. The calculation results are compared with those of classical MD results. As a result, it is confirmed that the diffusivity of hydrogen molecule is changed depending on temperature by the quantum effect. It is clarified that this result can be explained that the dominant factor by quantum effect on the diffusivity of hydrogen changes from the swollening the potential to the shallowing the potential well around 30 K. Moreover, it is found that this tendency is related to the temperature dependency of the ratio of the quantum kinetic energy and classical kinetic energy.

  16. Population dynamics and wave propagation in a Lotka-Volterra system with spatial diffusion.

    PubMed

    Wang, Mao-Xiang; Lai, Pik-Yin

    2012-11-01

    We consider the competitive population dynamics of two species described by the Lotka-Volterra model in the presence of spatial diffusion. The model is described by the diffusion coefficient (d(α)) and proliferation rate (r(α)) of the species α (α = 1,2 is the species label). Propagating wave front solutions in one dimension are investigated analytically and by numerical solutions. It is found that the wave profiles and wave speeds are determined by the speed parameters, v(α) ≡ 2 sqrt [d(α)r(α)], of the two species, and the phase diagrams for various inter- and intracompetitive scenarios are determined. The steady wave front speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. The effect of the intermediate stationary state is investigated and propagating wave profiles beyond the simple Fisher wave fronts are revealed. The wave front speed of a species can display abrupt increase as its speed parameter is increased. In particular for the case in which both species are aggressive, our results show that the speed parameter is the deciding factor that determines the ultimate surviving species, in contrast to the case without diffusion in which the final surviving species is decided by its initial population advantage. Possible relations to the biological relevance of modeling cancer development and wound healing are also discussed.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Experimental Validation of FE/BEM Dynamic Strain Model Under Diffuse Acoustic Field Loading

    NASA Technical Reports Server (NTRS)

    Tsoi, W. Ben; Gardner, Bryce; Cotoni, Vincent

    2010-01-01

    Structural finite element (FE) models naturally output displacement or acceleration response data. However, they can also be used to compute stress, internal forces, and strain response. When coupled with a boundary element model (BEM) of the fluid surrounding the structure, a fully coupled analysis can be performed. Modeling a diffuse acoustic field in the BEM fluid provides an excitation like that found when the structure is placed in a reverberation chamber. Fully coupling the structural FE model to the acoustic BEM model provides a means to predict not only the acceleration response of the panel to diffuse field loading, but also the ability to predict the dynamic stress and strain response. This type of model has been available with current predictive tools, but experimental validation of the prediction of dynamic stress or strain is difficult to find. An aluminum panel was instrumented with accelerometers and strain gages and hung in a reverberation room and subjected to a diffuse acoustic field. This paper presents the comparison of the experimental and predicted results.

  19. Population dynamics and wave propagation in a Lotka-Volterra system with spatial diffusion.

    PubMed

    Wang, Mao-Xiang; Lai, Pik-Yin

    2012-11-01

    We consider the competitive population dynamics of two species described by the Lotka-Volterra model in the presence of spatial diffusion. The model is described by the diffusion coefficient (d(α)) and proliferation rate (r(α)) of the species α (α = 1,2 is the species label). Propagating wave front solutions in one dimension are investigated analytically and by numerical solutions. It is found that the wave profiles and wave speeds are determined by the speed parameters, v(α) ≡ 2 sqrt [d(α)r(α)], of the two species, and the phase diagrams for various inter- and intracompetitive scenarios are determined. The steady wave front speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. The effect of the intermediate stationary state is investigated and propagating wave profiles beyond the simple Fisher wave fronts are revealed. The wave front speed of a species can display abrupt increase as its speed parameter is increased. In particular for the case in which both species are aggressive, our results show that the speed parameter is the deciding factor that determines the ultimate surviving species, in contrast to the case without diffusion in which the final surviving species is decided by its initial population advantage. Possible relations to the biological relevance of modeling cancer development and wound healing are also discussed. PMID:23214815

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-07-01

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

  4. In situ measurement and dynamic control of the evaporation rate in vapor diffusion crystallization of proteins

    NASA Astrophysics Data System (ADS)

    Shu, Zhan-Yong; Gong, Hai-Yun; Bi, Ru-Chang

    1998-08-01

    A special device with a weight-sensitive facility was designed for monitoring and controlling the water evaporation in vapor diffusion protein crystallization. The device made it possible to measure the weight of the drop in real time while the crystallization experiment was going on normally. The precise water equilibration curves under different crystallization conditions could be obtained automatically. By monitoring and controlling the evaporation rate, the crystallization of hen egg-white lysozyme and trichosanthin, a plant protein from Chinese herb, was optimized by regulating the reservoir solution dynamically. The experimental results of these two proteins indicate both the feasibility of the device and the usefulness of dynamic control technique. Compared with traditional crystallization experiments, dynamically controlled crystallization can reduce the number of nuclei, increase the crystal size and save experimental time effectively.

  5. Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions.

    PubMed

    Li, Minfeng; Yamato, Kazuhiro; Ferguson, Joseph S; Gong, Bing

    2006-10-01

    Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.

  6. Dynamics and patterns of a diffusive Leslie-Gower prey-predator model with strong Allee effect in prey

    NASA Astrophysics Data System (ADS)

    Ni, Wenjie; Wang, Mingxin

    2016-10-01

    This paper is devoted to study the dynamical properties and stationary patterns of a diffusive Leslie-Gower prey-predator model with strong Allee effect in the prey population. We first analyze the nonnegative constant equilibrium solutions and their stabilities, and then study the dynamical properties of time-dependent solutions. Moreover, we investigate the stationary patterns induced by diffusions (Turing pattern). Our results show that the impact of the strong Allee effect essentially increases the system spatiotemporal complexity.

  7. Modelling the dynamics of motion integration with a new luminance-gated diffusion mechanism.

    PubMed

    Tlapale, Emilien; Masson, Guillaume S; Kornprobst, Pierre

    2010-08-01

    The dynamics of motion integration show striking similarities when observed at neuronal, psychophysical, and oculomotor levels. Based on the inter-relation and complementary insights given by those dynamics, our goal was to test how basic mechanisms of dynamical cortical processing can be incorporated in a dynamical model to solve several aspects of 2D motion integration and segmentation. Our model is inspired by the hierarchical processing stages of the primate visual cortex: we describe the interactions between several layers processing local motion and form information through feedforward, feedback, and inhibitive lateral connections. Also, following perceptual studies concerning contour integration and physiological studies of receptive fields, we postulate that motion estimation takes advantage of another low-level cue, which is luminance smoothness along edges or surfaces, in order to gate recurrent motion diffusion. With such a model, we successfully reproduced the temporal dynamics of motion integration on a wide range of simple motion stimuli: line segments, rotating ellipses, plaids, and barber poles. Furthermore, we showed that the proposed computational rule of luminance-gated diffusion of motion information is sufficient to explain a large set of contextual modulations of motion integration and segmentation in more elaborated stimuli such as chopstick illusions, simulated aperture problems, or rotating diamonds. As a whole, in this paper we proposed a new basal luminance-driven motion integration mechanism as an alternative to less parsimonious models, we carefully investigated the dynamics of motion integration, and we established a distinction between simple and complex stimuli according to the kind of information required to solve their ambiguities.

  8. Critical Role of Dynamic Flexibility in Ge-Containing Zeolites: Impact on Diffusion.

    PubMed

    Gutiérrez-Sevillano, Juan José; Calero, Sofía; Hamad, Said; Grau-Crespo, Ricardo; Rey, Fernando; Valencia, Susana; Palomino, Miguel; Balestra, Salvador R G; Ruiz-Salvador, A Rabdel

    2016-07-11

    Incorporation of germanium in zeolites is well known to confer static flexibility to their framework, by stabilizing the formation of small rings. In this work, we show that the flexibility associated to Ge atoms in zeolites goes beyond this static effect, manifesting also a clear dynamic nature, in the sense that it leads to enhanced molecular diffusion. Our study combines experimental and theoretical methods providing evidence for this effect, which has not been described previously, as well as a rationalization for it, based on atomistic grounds. We have used both pure-silica and silico-germanate ITQ-29 (LTA topology) zeolites as a case study. Based on our simulations, we identify the flexibility associated to the pore breathing-like behavior induced by the Ge atoms, as the key factor leading to the enhanced diffusion observed experimentally in Ge-containing zeolites. PMID:27305363

  9. Confinement and Diffusion Effects in Dynamical Nuclear Polarization in Low Dimensional Nanostructures

    NASA Astrophysics Data System (ADS)

    Henriksen, Dan; Tifrea, Ionel

    2012-02-01

    We investigate the dynamic nuclear polarization as it results from the hyperfine coupling between nonequilibrium electronic spins and nuclear spins in semiconductor nanostructures. The natural confinement provided by low dimensional nanostructures is responsible for an efficient nuclear spin - electron spin hyperfine coupling [1] and for a reduced value of the nuclear spin diffusion constant [2]. In the case of optical pumping, the induced nuclear spin polarization is position dependent even in the presence of nuclear spin diffusion. This effect should be measurable via optically induced nuclear magnetic resonance or time-resolved Faraday rotation experiments. We discuss the implications of our calculations for the case of GaAs quantum well structures.[4pt] [1] I. Tifrea and M. E. Flatt'e, Phys. Rev. B 84, 155319 (2011).[0pt] [2] A. Malinowski and R. T. Harley, Solid State Commun. 114, 419 (2000).

  10. Gas dynamics in high-luminosity polarized He-3 targets using diffusion and convection

    SciTech Connect

    Dolph, P.A. M; Averett, T; Kelleher, A; Mooney, K E; Nelyubin, V; Tobias, W A; Wojsekhowski, B; Cates, G D

    2011-12-01

    The dynamics of the movement of gas is discussed for two-chambered polarized He-3 target cells of the sort that have been used successfully for many electron scattering experiments. A detailed analysis is presented showing that diffusion is a limiting factor in target performance, particularly as these targets are run at increasingly high luminosities. Measurements are presented on a new prototype polarized He-3 target cell in which the movement of gas is due largely to convection instead of diffusion. NMR tagging techniques have been used to visualize the gas flow, showing velocities along a cylindrically-shaped target of between 5-80 cm/min. The new target design addresses one of the principle obstacles to running polarized He-3 targets at substantially higher luminosities while simultaneously providing new flexibility in target geometry.

  11. Self-diffusion coefficients of ions in electrolyte solutions by nonequilibrium Brownian dynamics

    NASA Astrophysics Data System (ADS)

    Raineri, Fernando O.; Wood, Mark D.; Friedman, Harold L.

    1990-01-01

    The self-diffusion coefficients of the ions in a model electrolyte solution are calculated with a novel implementation of the nonequilibrium Brownian dynamics technique. The ions are coupled to an external color field E by color charges in such a way that each ionic species as a whole is electrically neutral to E. The ion-ion forces are not directly affected by the color charges or E. The method is tested on a model of a 1 M NaCl aqueous solution without hydrodynamic interactions and the results are compared with those of a previous equilibrium simulation for the same model system. The self-diffusion coefficients of Na+ and Cl- are determined with 2%-3% accuracy and, within this margin, agree with the results of the equilibrium simulation obtained with more than twice the computational effort. Furthermore, within the range of field strengths studied, the average color flows depend linearly on E.

  12. Gold nanoparticle translocation dynamics and electrical detection of single particle diffusion using solid-state nanopores.

    PubMed

    Goyal, Gaurav; Freedman, Kevin J; Kim, Min Jun

    2013-09-01

    This paper describes the use of gold nanoparticles to study particle translocation dynamics through silicon nitride solid-state nanopores. Gold nanoparticles were dispersed in 20 mM KCl solution containing nonionic surfactant Triton X-100 and their translocation was studied at different applied voltages. The use of low electrolyte concentration resulted in current enhancement upon particle translocation. The counterion cloud around the nanoparticles is proposed to be the reason for current enhancement phenomena because associated counterion cloud is believed to increase the ion density inside the pore during particle translocation. Further, single particle diffusion events were also recorded at 0 mV voltage bias and 0 pA background ionic current with high signal-to-noise ratio as the particles moved down their concentration gradient. The ability of nanopore sensors to detect single particle diffusion can be extended to field-free analysis of biomolecules in their native state and at or near physiological salt concentrations.

  13. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

  14. Transition from diffusive to ballistic dynamics for a class of finite quantum models.

    PubMed

    Steinigeweg, Robin; Breuer, Heinz-Peter; Gemmer, Jochen

    2007-10-12

    The transport of excitation probabilities amongst weakly coupled subunits is investigated for a class of finite quantum systems. It is demonstrated that the dynamical behavior of the transported quantity depends on the considered length scale; e.g., the introduced distinction between diffusive and ballistic transport appears to be a scale-dependent concept, especially since a transition from diffusive to ballistic behavior is found in the limit of small as well as in the limit of large length scales. All these results are derived by an application of the time-convolutionless projection operator technique and are verified by the numerical solution of the full time-dependent Schrödinger equation which is obtained by exact diagonalization for a range of model parameters. PMID:17995149

  15. Atomic packing and diffusion in Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy analyzed by ab initio molecular dynamics simulation

    SciTech Connect

    Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki

    2015-05-07

    In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.

  16. Dynamic properties and third order diffusion coefficients of ions in electrostatic fields

    NASA Astrophysics Data System (ADS)

    Koutselos, Andreas D.

    1997-05-01

    Velocity correlation functions and third order diffusion coefficients of ions moving in a buffer gas under the influence of an electrostatic field are determined via molecular dynamics simulation. For the closed shell system of K+ in Ar using a universal interaction model potential, the general form of the third order correlation functions is found to be monotonically decaying in time except in the cases of <ΔvZ(0)ΔvX(t)2>, <ΔvZ(0)ΔvY(t)2>, and <ΔvZ(0)ΔvZ(t)2>, with Δv(t)=v(t) - and the field in the z direction. These functions acquire positive slope at short times showing enhancement of correlations between instantaneous vz components of the ions and their future kinetic energies or velocity measures. This feature is shown to quantify the dynamics of correlations between velocity components suggested in the past by Ong, Hogan, Lam and Viehland [Phys. Rev. A 45, 3997 (1992)] in order to explain the form of an ion velocity distribution function calculated through a Monte Carlo simulation method. In addition, within a stochastic analysis which establishes a relation between velocity correlation functions and third order diffusion coefficients, only two independent components of the diffusion tensor, Q∥ and Q⊥, are predicted. We thereby calculate the Q⊥ component, which has not been determined so far, over a wide field range. The magnitudes of the resulting third order diffusion coefficients indicate that their contribution to the ion transport in usual drift-tube measurements should be very small.

  17. Lateral diffusivity coefficients from the dynamics of a SF6 patch in a coastal environment

    NASA Astrophysics Data System (ADS)

    Kersalé, M.; Petrenko, A. A.; Doglioli, A. M.; Nencioli, F.; Bouffard, J.; Blain, S.; Diaz, F.; Labasque, T.; Quéguiner, B.; Dekeyser, I.

    2016-01-01

    The dispersion of a patch of the tracer sulfur hexafluoride (SF6) is used to assess the lateral diffusivity in the coastal waters of the western part of the Gulf of Lion (GoL), northwestern Mediterranean Sea, during the Latex10 experiment (September 2010). Immediately after the release, the spreading of the patch is associated with a strong decrease of the SF6 concentrations due to the gas exchange from the ocean to the atmosphere. This has been accurately quantified, evidencing the impact of the strong wind conditions during the first days of this campaign. Few days after the release, as the atmospheric loss of SF6 decreased, lateral diffusivity coefficient at spatial scales of 10 km has been computed using two approaches. First, the evolution of the patch with time was combined with a diffusion-strain model to obtain estimates of the strain rate (γ = 2.5 10- 6 s- 1) and of the lateral diffusivity coefficient (Kh = 23.2 m2 s- 1). Second, a steady state model was applied, showing Kh values similar to the previous method after a period of adjustment between 2 and 4.5 days. This implies that after such period, our computation of Kh becomes insensitive to the inclusion of further straining of the patch. Analysis of sea surface temperature satellite imagery shows the presence of a strong front in the study area. The front clearly affected the dynamics within the region and thus the temporal evolution of the patch. Our results are consistent with previous studies in open ocean and demonstrate the success and feasibility of those methods also under small-scale, rapidly-evolving dynamics typical of coastal environments.

  18. Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

    PubMed

    Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

    2014-09-28

    Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities. PMID:25102451

  19. Dynamics of surface thermal expansion and diffusivity using two-color reflection transient gratings

    SciTech Connect

    Pennington, D.M.; Harris, C.B.

    1993-02-01

    We report ultrafast measurements of the dynamic thermal expansion of a surface and the temperature dependent surface thermal diffusivity using a two-color reflection transient grating technique. Studies were performed on p-type, n-type, and undoped GaAs(100) samples at several temperatures. Using a 75 fs ultraviolet probe with visible excitation beams, the electronic effects that dominate single color experiments become negligible; thus surface expansion due to heating and the subsequent contraction caused by cooling provide the dominant influence on the diffracted probe. The diffracted signal was composed of two components, thermal expansion of the surface and heat flow away from the surface, allowing the determination of the rate of expansion as well as the surface thermal diffusivity. At room temperature a signal rise due to thermal expansion was observed, corresponding to a maximum average displacement of {approx} 1 {angstrom} at 32 ps. Large fringe spacings were used, thus the dominant contributions to the signal were expansion and diffusion perpendicular to the surface. Values for the surface thermal diffusivity of GaAs were measured and found to be in reasonable agreement with bulk values above 50{degrees}K. Below 50{degrees}K, the diffusivity at the surface was more than an order of magnitude slower than in the bulk due to increased phonon boundary scattering. Comparison of the results with a straightforward thermal model yields good agreement over a range of temperatures (12--300{degrees}K). The applicability and advantages of the transient grating technique for studying photothermal and photoacoustic phenomena are discussed.

  20. Dissipative particle dynamics study of translational diffusion of rigid-chain rodlike polymer in nematic phase

    NASA Astrophysics Data System (ADS)

    Zhao, Tongyang; Wang, Xiaogong

    2013-09-01

    In this study, dissipative particle dynamics (DPD) method was employed to investigate the translational diffusion of rodlike polymer in its nematic phase. The polymer chain was modeled by a rigid rod composed of consecutive DPD particles and solvent was represented by independent DPD particles. To fully understand the translational motion of the rods in the anisotropic phase, four diffusion coefficients, D_{||}u, D_ bot u, D_{||}n, D_ bot n were obtained from the DPD simulation. By definition, D_{||}n and D_ bot n denote the diffusion coefficients parallel and perpendicular to the nematic director, while D_{||}u and D_ bot u denote the diffusion coefficients parallel and perpendicular to the long axis of a rigid rod u. In the simulation, the velocity auto-correlation functions were used to calculate the corresponding diffusion coefficients from the simulated velocity of the rods. Simulation results show that the variation of orientational order caused by concentration and temperature changes has substantial influences on D_{||}u and D_ bot u. In the nematic phase, the changes of concentration and temperature will result in a change of local environment of rods, which directly influence D_{||}u and D_ bot u. Both D_{||}n and D_ bot n can be represented as averages of D_{||}u and D_ bot u, and the weighted factors are functions of the orientational order parameter S2. The effect of concentration and temperature on D_{||}n and D_ bot n demonstrated by the DPD simulation can be rationally interpreted by considering their influences on D_{||}u, D_ bot u and the order parameter S2.

  1. Studying Dynamic Myofiber Aggregate Reorientation in Dilated Cardiomyopathy Using In Vivo Magnetic Resonance Diffusion Tensor Imaging

    PubMed Central

    von Deuster, Constantin; Sammut, Eva; Asner, Liya; Nordsletten, David; Lamata, Pablo; Stoeck, Christian T.; Razavi, Reza

    2016-01-01

    Background— The objective of this study is to assess the dynamic alterations of myocardial microstructure and strain between diastole and systole in patients with dilated cardiomyopathy relative to healthy controls using the magnetic resonance diffusion tensor imaging, myocardial tagging, and biomechanical modeling. Methods and Results— Dual heart-phase diffusion tensor imaging was successfully performed in 9 patients and 9 controls. Tagging data were acquired for the diffusion tensor strain correction and cardiac motion analysis. Mean diffusivity, fractional anisotropy, and myocyte aggregate orientations were compared between both cohorts. Cardiac function was assessed by left ventricular ejection fraction, torsion, and strain. Computational modeling was used to study the impact of cardiac shape on fiber reorientation and how fiber orientations affect strain. In patients with dilated cardiomyopathy, a more longitudinal orientation of diastolic myofiber aggregates was measured compared with controls. Although a significant steepening of helix angles (HAs) during contraction was found in the controls, consistent change in HAs during contraction was absent in patients. Left ventricular ejection fraction, cardiac torsion, and strain were significantly lower in the patients compared with controls. Computational modeling revealed that the dilated heart results in reduced HA changes compared with a normal heart. Reduced torsion was found to be exacerbated by steeper HAs. Conclusions— Diffusion tensor imaging revealed reduced reorientation of myofiber aggregates during cardiac contraction in patients with dilated cardiomyopathy relative to controls. Left ventricular remodeling seems to be an important factor in the changes to myocyte orientation. Steeper HAs are coupled with a worsening in strain and torsion. Overall, the findings provide new insights into the structural alterations in patients with dilated cardiomyopathy. PMID:27729361

  2. Hydrogen bonding constrains free radical reaction dynamics at serine and threonine residues in peptides.

    PubMed

    Thomas, Daniel A; Sohn, Chang Ho; Gao, Jinshan; Beauchamp, J L

    2014-09-18

    Free radical-initiated peptide sequencing (FRIPS) mass spectrometry derives advantage from the introduction of highly selective low-energy dissociation pathways in target peptides. An acetyl radical, formed at the peptide N-terminus via collisional activation and subsequent dissociation of a covalently attached radical precursor, abstracts a hydrogen atom from diverse sites on the peptide, yielding sequence information through backbone cleavage as well as side-chain loss. Unique free-radical-initiated dissociation pathways observed at serine and threonine residues lead to cleavage of the neighboring N-terminal Cα-C or N-Cα bond rather than the typical Cα-C bond cleavage observed with other amino acids. These reactions were investigated by FRIPS of model peptides of the form AARAAAXAA, where X is the amino acid of interest. In combination with density functional theory (DFT) calculations, the experiments indicate the strong influence of hydrogen bonding at serine or threonine on the observed free radical chemistry. Hydrogen bonding of the side-chain hydroxyl group with a backbone carbonyl oxygen aligns the singly occupied π orbital on the β-carbon and the N-Cα bond, leading to low-barrier β-cleavage of the N-Cα bond. Interaction with the N-terminal carbonyl favors a hydrogen-atom transfer process to yield stable c and z(•) ions, whereas C-terminal interaction leads to effective cleavage of the Cα-C bond through rapid loss of isocyanic acid. Dissociation of the Cα-C bond may also occur via water loss followed by β-cleavage from a nitrogen-centered radical. These competitive dissociation pathways from a single residue illustrate the sensitivity of gas-phase free radical chemistry to subtle factors such as hydrogen bonding that affect the potential energy surface for these low-barrier processes.

  3. Correlated random walk on lattices. II. Tracer diffusion through a two-component dynamic background

    NASA Astrophysics Data System (ADS)

    Tahir-Kheli, R. A.

    1983-06-01

    A detailed calculation of frequency- and wave-vector-dependent correlation functions for an arbitrary tracer diffusing in a regular crystal against a background of hopping classical particles has recently been given by Tahir-Kheli and Elliott

    [Phys. Rev. B 27, 844 (1983)]
    . Here we present an important generalization of this work to a system with a dynamic background consisting of two arbitrary species of particles. In particular, the generalization includes a system where the tracer concentration itself is finite while an arbitrary concentration of other atoms is also present in the dynamic stream. The theory is exact to the leading nontrivial order in particle concentration xA and xB. In the intermediate-concentration regime, the theory incorporates dominant fluctuations from the mean field. The present model can serve to usefully describe incoherent neutron scattering in metal-hydride interstitial solutions such as MAxABxB with A,B≡H, D, and T and M≡Pd and Ti. Moreover, it can be used to treat tracer diffusion dynamics in nonstoichiometric metal oxides and, somewhat more simplistically, ionic conduction in the superionic state.

  4. Simple analytical forms of the perpendicular diffusion coefficient for two-component turbulence. II. Dynamical turbulence with constant correlation time

    SciTech Connect

    Shalchi, A.

    2014-01-10

    We explore perpendicular diffusion based on the unified nonlinear transport theory. In Paper I, we focused on magnetostatic turbulence, whereas in the present article we include dynamical turbulence effects. For simplicity, we assume a constant correlation time. We show that there is now a nonvanishing contribution of the slab modes. We explore the parameter regimes in which the turbulence dynamics becomes important for perpendicular diffusion. Analytical forms for the perpendicular diffusion coefficient are derived, which can be implemented easily in solar modulation or shock acceleration codes.

  5. Use of bond-valence sums in modelling the diffuse scattering from PZN (PbZn1/3Nb2/3O3)

    PubMed Central

    Whitfield, R. E.; Welberry, T. R.; Paściak, M.; Goossens, D. J.

    2014-01-01

    This work extends previous efforts to model diffuse scattering from PZN (PbZn1/3Nb2/3O3). Earlier work [Welberry et al. (2005 ▶). J. Appl. Cryst. 38, 639–647; Welberry et al. (2006 ▶). Phys. Rev. B, 74, 224108] is highly prescriptive, using Monte Carlo simulation with very artificial potentials to induce short-range-order structures which were deduced as necessary from inspection of the data. While this gives valid results for the nature of the local structure, it does not strongly relate these structures to underlying crystal chemistry. In that work, the idea of the bond-valence sum was used as a guide to the expected behaviour of the atoms. This paper extends the use of the bond-valence sum from a qualitative guide to becoming a key aspect of the potential experienced by the atoms, through the idea of the global instability index, whose square has been shown to be proportional to the density functional theory energy of some systems when close to the minimum energy configuration.

  6. Quantum dynamics study of fulvene double bond photoisomerization: The role of intramolecular vibrational energy redistribution and excitation energy

    SciTech Connect

    Blancafort, Lluis; Gatti, Fabien; Meyer, Hans-Dieter

    2011-10-07

    The double bond photoisomerization of fulvene has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method. Fulvene is a test case to develop optical control strategies based on the knowledge of the excited state decay mechanism. The decay takes place on a time scale of several hundred femtoseconds, and the potential energy surface is centered around a conical intersection seam between the ground and excited state. The competition between unreactive decay and photoisomerization depends on the region of the seam accessed during the decay. The dynamics are carried out on a four-dimensional model surface, parametrized from complete active space self-consistent field calculations, that captures the main features of the seam (energy and locus of the seam and associated branching space vectors). Wave packet propagations initiated by single laser pulses of 5-25 fs duration and 1.85-4 eV excitation energy show the principal characteristics of the first 150 fs of the photodynamics. Initially, the excitation energy is transferred to a bond stretching mode that leads the wave packet to the seam, inducing the regeneration of the reactant. The photoisomerization starts after the vibrational energy has flowed from the bond stretching to the torsional mode. In our propagations, intramolecular energy redistribution (IVR) is accelerated for higher excess energies along the bond stretch mode. Thus, the competition between unreactive decay and isomerization depends on the rate of IVR between the bond stretch and torsion coordinates, which in turn depends on the excitation energy. These results set the ground for the development of future optical control strategies.

  7. Diffusion Rates for Hydrogen on Pd(111) from Molecular Quantum Dynamics Calculations.

    PubMed

    Firmino, Thiago; Marquardt, Roberto; Gatti, Fabien; Dong, Wei

    2014-12-18

    The van Hove formula for the dynamical structure factor (DSF) related to particle scattering at mobile adsorbates is extended to include the relaxation of the adsorbates' vibrational states. The total rate obtained from the DSF is assumed to be the sum of a diffusion and a relaxation rate. A simple kinetic model to support this assumption is presented. To illustrate its potential applicability, the formula is evaluated using wave functions, energies, and lifetimes of vibrational states obtained for H/Pd(111) from first-principle calculations. Results show that quantum effects can be expected to be important even at room temperature.

  8. Dynamic diffuse optical tomography for assessing changes of breast tumors during neoadjuvant chemotherapy

    NASA Astrophysics Data System (ADS)

    Gunther, Jacqueline E.; Lim, Emerson; Kim, Hyun Keol; Brown, Mindy; Refice, Susan; Kalinsky, Kevin; Hershman, Dawn; Hielscher, Andreas H.

    2015-03-01

    We have developed a dynamic diffuse optical tomography imaging system that is capable of 3D imaging of both breasts simultaneously. In an ongoing study subjects receiving neoadjuvant chemotherapy are imaged at 6 time points throughout their 5-month treatment. At each time point the subjects preform a breath hold to observe the hemodynamic effects in the breasts. For each session the percent change of various hemodynamic parameters during the breath hold is determined. Preliminary results from show statistically significant differences in washout rates and deoxyhemoglobin changes at the 2-week imaging point between subjects that respond and do not respond to treatment.

  9. Large time behavior in a nonlinear age-dependent population dynamics problem with spatial diffusion.

    PubMed

    Langlais, M

    1988-01-01

    In this work we analyze the large time behavior in a nonlinear model of population dynamics with age-dependence and spatial diffusion. We show that when t----+ infinity either the solution of our problem goes to 0 or it stabilizes to a nontrivial stationary solution. We give two typical examples where the stationary solutions can be evaluated upon solving very simple partial differential equations. As a by-product of the extinction case we find a necessary condition for a nontrivial periodic solution to exist. Numerical computations not described below show a rapid stabilization.

  10. Water vapor diffusion effects on gas dynamics in a sonoluminescing bubble.

    PubMed

    Xu, Ning; Apfel, Robert E; Khong, Anthony; Hu, Xiwei; Wang, Long

    2003-07-01

    Calculations based on a consideration of gas diffusion of gas dynamics in a sonoluminescing bubble filled with a noble gas and water vapor are carried out. Xenon-, argon-, and helium-filled bubbles are studied. In the absence of shock waves, bubble temperatures are found to be decreased, a decrease attributable to the large heat capacity of water vapor. Peak bubble temperature reductions are seen in bubbles containing Xe or Ar but not in those containing He. Further extrapolations provide evidence for the occurrence of shock waves in bubbles with Xe and water vapor. No shock waves are observed in bubbles with Ar or He.

  11. Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions

    NASA Astrophysics Data System (ADS)

    Kamerlin, Natasha; Elvingson, Christer

    2016-11-01

    We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution.

  12. Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions.

    PubMed

    Kamerlin, Natasha; Elvingson, Christer

    2016-11-30

    We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution. PMID:27662260

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Quantum phase communication channels in the presence of static and dynamical phase diffusion

    NASA Astrophysics Data System (ADS)

    Trapani, Jacopo; Teklu, Berihu; Olivares, Stefano; Paris, Matteo G. A.

    2015-07-01

    We address quantum communication channels based on phase modulation of coherent states and analyze in detail the effects of static and dynamical (stochastic) phase diffusion. We evaluate mutual information for an ideal phase receiver and for a covariant phase-space-based receiver, and compare their performances by varying the number of symbols in the alphabet and/or the overall energy of the channel. Our results show that phase communication channels are generally robust against phase noise, especially for large alphabets in the low-energy regime. In the presence of dynamical (non-Markovian) noise the mutual information is preserved by the time correlation of the environment, and when the noise spectra are detuned with respect to the information carrier, revivals of mutual information appear.

  15. Diffusion Dynamics of Charged Dust Particles in Capacitively Coupled RF Discharge System

    SciTech Connect

    Chew, W. X.; Muniandy, S. V.; Wong, C. S.; Yap, S. L.; Tan, K. S.

    2011-03-30

    Dusty plasma is loosely defined as electron-ion plasma with additional charged components of micron-sized dust particles. In this study, we developed a particle diagnostic technique based on light scattering and particle tracking velocimetry to investigate the dynamics of micron-sized titanium oxide particles in Argon gas capacitively coupled rf-discharge. The particle trajectories are constructed from sequence of image frames and treated as sample paths of charged Brownian motion. At specific sets of plasma parameters, disordered liquid-like dust particle configuration are observed. Mean-square-displacement of the particle trajectories are determined to characterize the transport dynamics. We showed that the dust particles in disordered liquid phase exhibit anomalous diffusion with different scaling exponents for short and large time scales, indicating the presence of slow and fast modes which can be related to caging effect and dispersive transport, respectively.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. The Ionic DTI Model (iDTI) of Dynamic Diffusion Tensor Imaging (dDTI).

    PubMed

    Makris, Nikos; Gasic, Gregory P; Garrido, Leoncio

    2014-01-01

    Measurements of water molecule diffusion along fiber tracts in CNS by diffusion tensor imaging (DTI) provides a static map of neural connections between brain centers, but does not capture the electrical activity along axons for these fiber tracts. Here, a modification of the DTI method is presented to enable the mapping of active fibers. It is termed dynamic diffusion tensor imaging (dDTI) and is based on a hypothesized "anisotropy reduction due to axonal excitation" ("AREX"). The potential changes in water mobility accompanying the movement of ions during the propagation of action potentials along axonal tracts are taken into account. Specifically, the proposed model, termed "ionic DTI model", was formulated as follows. First, based on theoretical calculations, we calculated the molecular water flow accompanying the ionic flow perpendicular to the principal axis of fiber tracts produced by electrical conduction along excited myelinated and non-myelinated axons.Based on the changes in molecular water flow we estimated the signal changes as well as the changes in fractional anisotropy of axonal tracts while performing a functional task.The variation of fractional anisotropy in axonal tracts could allow mapping the active fiber tracts during a functional task. Although technological advances are necessary to enable the robust and routine measurement of this electrical activity-dependent movement of water molecules perpendicular to axons, the proposed model of dDTI defines the vectorial parameters that will need to be measured to bring this much needed technique to fruition. PMID:25431757

  18. Classical Molecular Dynamics and Self-Consistent Tight-Binding Simulations of Si-Si Wafer Bonding.

    NASA Astrophysics Data System (ADS)

    Lepage, J. G.; Kim, Jeongnim; Wilkins, John W.; Kirchhoff, Florian

    2000-03-01

    We have carried out a series of atomistic simulations of the room temperature bonding of clean, defect-free Si wafers under UHV conditions using Classical Molecular Dynamics (CMD) and Self-Consistent Tight-Binding (SCTB) Our simulations indicate that even when the wafers are perfectly aligned, bonding does not typically result in the formation of bulk crystalline Si. Instead, the basic geometry of the original dimerized surface tends to persist, producing an interface characterized by linked dimers. As the wafers bond, considerable chemical energy is released resulting in rapid heating (up to 800 K) at the interface. However, this heat is rapidly conducted away from the interface and so does not have an appreciable annealing effect. Large-scale CMD calculations show that the ground state energy of the bonded system is sensitively dependent on twist angle. The SCTB calculations were performed using the using the parameterization of Lenosky et al.( Thomas J. Lenosky, Joel D. Kress, Inhee Kwon, Arthur F. Voter, Byard Edwards, David F. Richards, Sang Yang, and James B. Adams, Phys. Rev. B 55), 1528 (1997).

  19. Simulating dislocation loop internal dynamics and collective diffusion using stochastic differential equations

    SciTech Connect

    Derlet, P. M.; Gilbert, M. R.; Dudarev, S. L.

    2011-10-01

    Nanoscale prismatic loops are modeled via a partial stochastic differential equation that describes an overdamped continuum elastic string, with a view to describing both the internal and collective dynamics of the loop as a function of temperature. Within the framework of the Langevin equation, expressions are derived that relate the empirical parameters of the model, the friction per unit length, and the elastic stiffness per unit length, to observables that can be obtained directly via molecular-dynamics simulations of interstitial or vacancy prismatic loop mobility. The resulting expressions naturally exhibit the properties that the collective diffusion coefficient of the loop (i) scales inversely with the square root of the number of interstitials, a feature that has been observed in both atomistic simulation and in situ TEM investigations of loop mobility, and (ii) the collective diffusion coefficient is not at all dependent on the internal interactions within the loop, thus qualitatively rationalizing past simulation results showing that the characteristic migration energy barrier is comparable to that of a single interstitial, and cluster migration is a result of individual (but correlated) interstitial activity.

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

    NASA Astrophysics Data System (ADS)

    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. Modeling of advection-diffusion-reaction processes using transport dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. In particular, the transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of Lagrangian particles. To validate the proposed tDPD model and the boundary conditions, three benchmark simulations of one-dimensional diffusion with different boundary conditions are performed, and the results show excellent agreement with the theoretical solutions. Also, two-dimensional simulations of ADR systems are performed and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, an application of tDPD to the spatio-temporal dynamics of blood coagulation involving twenty-five reacting species is performed to demonstrate the promising biological applications of the tDPD model. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.

  2. Dynamics of velocity gradient invariants in turbulence: Restricted Euler and linear diffusion models

    NASA Astrophysics Data System (ADS)

    Martín, Jesús; Dopazo, César; Valiño, Luis

    1998-08-01

    A complete system of dynamical equations for the invariants of the velocity gradient, the strain rate, and the rate-of-rotation tensors is deduced for an incompressible flow. The equations for the velocity gradient invariants R and Q were first deduced by Cantwell [Phys. Fluids A 4, 782 (1992)] in terms of Hij, the tensor containing the anisotropic part of the pressure Hessian and the viscous diffusion term in the velocity gradient equation. These equations are extended here for the strain rate tensor invariants, RS and QS, and for the rate-of-rotation tensor invariant, QW, using HijS and HijW, the symmetric and the skew-symmetric parts of Hij, respectively. In order to obtain a complete system, an equation for the square of the vortex stretching vector, Vi≡Sijωj, is required. The resulting dynamical system of invariants is closed using a simple model for the velocity gradient evolution: an isotropic approximation for the pressure term and a linear model for the viscous diffusion term. The local topology and the resulting statistics implied by this model reproduce a number of trends similar to known results from numerical experiments for the small scales of turbulence.

  3. Application of Molecular Dynamics Simulations in Molecular Property Prediction II: Diffusion Coefficient

    PubMed Central

    Wang, Junmei; Hou, Tingjun

    2011-01-01

    In this work, we have evaluated how well the General AMBER force field (GAFF) performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, 5 organic compounds in aqueous solutions, 4 proteins in aqueous solutions, and 9 organic compounds in non-aqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned error (AUE) and the root-mean-square error (RMSE) are 0.137 and 0.171 ×10−5 cm−2s−1, respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for 8 organic solvents with experimental data (R2 = 0.784), 4 proteins in aqueous solutions (R2 = 0.996) and 9 organic compounds in non-aqueous solutions (R2 = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide (DMSO) and cyclohexane have been studied. The major MD settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement (MSD) collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. PMID:21953689

  4. Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

    PubMed Central

    2014-01-01

    Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block

  5. Crowding Induces Complex Ergodic Diffusion and Dynamic Elongation of Large DNA Molecules

    PubMed Central

    Chapman, Cole D.; Gorczyca, Stephanie; Robertson-Anderson, Rae M.

    2015-01-01

    Despite the ubiquity of molecular crowding in living cells, the effects of crowding on the dynamics of genome-sized DNA are poorly understood. Here, we track single, fluorescent-labeled large DNA molecules (11, 115 kbp) diffusing in dextran solutions that mimic intracellular crowding conditions (0–40%), and determine the effects of crowding on both DNA mobility and conformation. Both DNAs exhibit ergodic Brownian motion and comparable mobility reduction in all conditions; however, crowder size (10 vs. 500 kDa) plays a critical role in the underlying diffusive mechanisms and dependence on crowder concentration. Surprisingly, in 10-kDa dextran, crowder influence saturates at ∼20% with an ∼5× drop in DNA diffusion, in stark contrast to exponentially retarded mobility, coupled to weak anomalous subdiffusion, with increasing concentration of 500-kDa dextran. Both DNAs elongate into lower-entropy states (compared to random coil conformations) when crowded, with elongation states that are gamma distributed and fluctuate in time. However, the broadness of the distribution of states and the time-dependence and length scale of elongation length fluctuations depend on both DNA and crowder size with concentration having surprisingly little impact. Results collectively show that mobility reduction and coil elongation of large crowded DNAs are due to a complex interplay between entropic effects and crowder mobility. Although elongation and initial mobility retardation are driven by depletion interactions, subdiffusive dynamics, and the drastic exponential slowing of DNA, up to ∼300×, arise from the reduced mobility of larger crowders. Our results elucidate the highly important and widely debated effects of cellular crowding on genome-sized DNA. PMID:25762333

  6. Investigations of interhydrogen bond dynamical coupling effects in the polarized IR spectra of acetanilide crystals.

    PubMed

    Flakus, Henryk T; Michta, Anna

    2010-02-01

    This Article presents the investigation results of the polarized IR spectra of the hydrogen bond in acetanilide (ACN) crystals measured in the frequency range of the proton and deuteron stretching vibration bands, nu(N-H) and nu(N-D). The basic spectral properties of the crystals were interpreted quantitatively in terms of the "strong-coupling" theory. The model of the centrosymmetric dimer of hydrogen bonds postulated by us facilitated the explanation of the well-developed, two-branch structure of the nu(N-H) and nu(N-D) bands as well as the isotopic dilution effects in the spectra. On the basis of the linear dichroic and temperature effects in the polarized IR spectra of ACN crystals, the H/D isotopic "self-organization" effects were revealed. A nonrandom distribution of hydrogen isotope atoms (H or D) in the lattice was deduced from the spectra of isotopically diluted ACN crystals. It was also determined that identical hydrogen isotope atoms occupy both hydrogen bonds in the dimeric systems, where each hydrogen bond belongs to a different chain. A more complex fine structure pattern of nu(N-H) and nu(N-D) bands in ACN spectra in comparison with the spectra of other secondary amides (e.g., N-methylacetamide) can be explained in terms of the "relaxation" theory of the IR spectra of hydrogen-bonded systems. PMID:20055492

  7. Molecular dynamics simulation of the formation of sp3 hybridized bonds in hydrogenated diamondlike carbon deposition processes.

    PubMed

    Murakami, Yasuo; Horiguchi, Seishi; Hamaguchi, Satoshi

    2010-04-01

    The formation process of sp3 hybridized carbon networks (i.e., diamondlike structures) in hydrogenated diamondlike carbon (DLC) films has been studied with the use of molecular-dynamics simulations. The processes simulated in this study are injections of hydrocarbon (CH3 and CH) beams into amorphous carbon (a-C) substrates. It has been shown that diamondlike sp3 structures are formed predominantly at a subsurface level when the beam energy is relatively high, as in the "subplantation" process for hydrogen-free DLC deposition. However, for hydrogenated DLC deposition, the presence of abundant hydrogen at subsurface levels, together with thermal spikes caused by energetic ion injections, substantially enhances the formation of carbon-to-carbon sp3 bonds. Therefore, the sp3 bond formation process for hydrogenated DLC films essentially differs from that for hydrogen-free DLC films.

  8. Particle bonding, annealing response, and mechanical properties of dynamically consolidated type 304 stainless steel powders

    NASA Astrophysics Data System (ADS)

    Wright, R. N.; Korth, G. E.; Flinn, J. E.

    1989-11-01

    The nature of interparticle bonding in explosively consolidated, centrifugally atomized (CA), and vacuum gas-atomized (VGA) Type 304 stainless steel powders has been examined. Stress waves with sufficient amplitude to produce full density do not necessarily produce metallurgical bonds between particles; the local strain and strain rate are found to determine the degree of local heating and, in turn, the degree of particle fusion. Particle interaction is found to be limited to nearest neighbors. The as-consolidated CA material has approximately twice the ultimate tensile strength of mill-annealed wrought Type 304 stainless steel. Consolidated CA powder has a higher defect density than VGA powder consolidated under the same conditions; however, the VGA material recrystallizes at a lower temperature due to a lower concentration of carbides. Annealing explosively consolidated material produced from either powder results in sintering, improved particle bonding, and greater ductility.

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

    PubMed

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

    2015-07-01

    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. PMID:26075680

  10. Core structure of a dissociated edge dislocation and pipe diffusion in copper investigated by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Huang, J.; Meyer, M.; Pontikis, V.

    1991-06-01

    The atomic core structure of two Schockley partial dislocations in copper has been investigated as a function of temperature using molecular dynamics. We employed a resonant model pseudopotential adapted to copper. Our results show that at increasing temperature, the core of the partials becomes increasingly extended and invades entirely the fault ribbon, yet, the separation distance between the partials remains unchanged. At high temperatures vibrational amplitudes of atoms are much larger in the core of the partials than in the bulk of the perfect crystal and the local atomic structure becomes highly disordered. Although disordered, the core structure remains solid-like up to temperatures close to the melting point. Pipe diffusion along this dissociated dislocation has also been investigated. The formation energies of a vacancy and an interstitial are obtained by quasi-dynamics relaxation at T = 0 K while the migration energies for pipe diffusion are calculated at high temperature. Contrary to current assumptions in favour of a vacancy mechanism, we found that in our model the two types of defects may contribute comparably to pipe diffusion since their activation energies are very close. The trajectories of the migrating defects involve not only the partials' cores but also the stacking fault ribbon extending between them, thus explaining why pipe diffusion is slower when the dislocations are dissociated. La structure de coeur de deux dislocations partielles de Schockley a été étudiée, par dynamique moléculaire, en fonction de la température. Nous avons utilisé un pseudopotentiel calculé pour le cuivre à l'aide d'un modèle de résonance. Nos résultats montrent que le coeur des partielles s'étend de plus en plus à mesure que la température augmente et qu'il recouvre complètement le ruban de faute. Cependant la distance de dissociation entre les partielles ne change pas. A haute température, les amplitudes de vibration atomique sont nettement plus

  11. Calculation of surface diffusivity and residence time by molecular dynamics with application to nanoscale selective-area growth

    NASA Astrophysics Data System (ADS)

    Almeida, S.; Ochoa, E.; Chavez, J. J.; Zhou, X. W.; Zubia, D.

    2015-08-01

    The surface diffusivity and residence time were calculated by molecular dynamics simulations in order to solve the surface diffusion equations for selective-area growth. The calculations for CdTe/CdS material system were performed in substrates with Cd termination and S termination. The surface diffusivity and residence time were obtained at different temperatures (600 K, 800 K, 1000 K, 1200 K, and 1400 K). The thermal activation energies were extracted from Arrhenius equation for each substrate termination. Thereafter, values obtained by molecular dynamics were used in a surface diffusion model to calculate the surface concentration profile of adatoms. Alternating the surface termination has the potential to achieve nanoscale selective-area growth without the need of a dielectric film as a mask.

  12. Room temperature single-crystal diffuse scattering and ab initio lattice dynamics in CaTiSiO5

    NASA Astrophysics Data System (ADS)

    Gutmann, M. J.; Refson, K.; Zimmermann, M. v.; Swainson, I. P.; Dabkowski, A.; Dabkowska, H.

    2013-08-01

    Single-crystal diffuse scattering data have been collected at room temperature on synthetic titanite using both neutrons and high-energy x-rays. A simple ball-and-springs model reproduces the observed diffuse scattering well, confirming its origin to be primarily due to thermal motion of the atoms. Ab initio phonons are calculated using density-functional perturbation theory and are shown to reproduce the experimental diffuse scattering. The observed diffuse x-ray and neutron scattering patterns are consistent with a summation of mode frequencies and displacement eigenvectors associated with the entire phonon spectrum, rather than with a simple, short-range static displacement. A band gap is observed between 600 and 700 cm-1 with only two modes crossing this region, both associated with antiferroelectric Ti-O motion along a. One of these modes (of Bu symmetry), displays a large LO-TO mode-splitting (562-701.4 cm-1) and has a dominant component coming from Ti-O bond-stretching and, thus, the mode-splitting is related to the polarizability of the Ti-O bonds along the chain direction. Similar mode-splitting is observed in piezo- and ferroelectric materials. The calculated phonon dispersion model may be of use to others in future to understand the phase transition at higher temperatures, as well as in the interpretation of measured phonon dispersion curves.

  13. Fractional and fractal dynamics approach to anomalous diffusion in porous media: application to landslide behavior

    NASA Astrophysics Data System (ADS)

    Martelloni, Gianluca; Bagnoli, Franco

    2016-04-01

    Richardson's treatise on turbulent diffusion in 1926 [24] and today, the list of system displaying anomalous dynamical behavior is quite extensive. We only report some examples: charge carrier transport in amorphous semiconductors [25], porous systems [26], reptation dynamics in polymeric systems [27, 28], transport on fractal geometries [29], the long-time dynamics of DNA sequences [30]. In this scenario, the fractional calculus is used to generalized the Fokker-Planck linear equation -∂P (x,t)=D ∇2P (x,t), ∂t (3) where P (x,t) is the density of probability in the space x=[x1, x2, x3] and time t, while D >0 is the diffusion coefficient. Such processes are characterized by Eq. (1). An example of Eq. (3) generalization is ∂∂tP (x,t)=D∇ αP β(x,t) ‑ ∞ < α ≤ 2 β > ‑ 1 , (4) where the fractional based-derivatives Laplacian Σ(∂α/∂xα)i, (i = 1, 2, 3), of non-linear term Pβ(x,t) is taken into account [31]. Another generalized form is represented by equation ∂∂tδδP(x,t)=D ∇ αP(x,t) δ > 0 α ≤ 2 , (5) that considers also the fractional time-derivative [32]. These fractional-described processes exhibit a power law patters as expressed by Eq. (2). This general introduction introduces the presented work, whose aim is to develop a theoretical model in order to forecast the triggering and propagation of landslides, using the techniques of fractional calculus. The latter is suitable for modeling the water infiltration (i.e., the pore water pressure diffusion in the soil) and the dynamical processes in the fractal media [33]. Alternatively the fractal representation of temporal and spatial derivative (the fractal order only appears in the denominator of the derivative) is considered and the results are compared to the fractional one. The prediction of landslides and the discovering of the triggering mechanism, is one of the challenging problems in earth science. Landslides can be triggered by different factors but in most cases the trigger is an

  14. Fractional and fractal dynamics approach to anomalous diffusion in porous media: application to landslide behavior

    NASA Astrophysics Data System (ADS)

    Martelloni, Gianluca; Bagnoli, Franco

    2016-04-01

    Richardson's treatise on turbulent diffusion in 1926 [24] and today, the list of system displaying anomalous dynamical behavior is quite extensive. We only report some examples: charge carrier transport in amorphous semiconductors [25], porous systems [26], reptation dynamics in polymeric systems [27, 28], transport on fractal geometries [29], the long-time dynamics of DNA sequences [30]. In this scenario, the fractional calculus is used to generalized the Fokker-Planck linear equation -∂P (x,t)=D ∇2P (x,t), ∂t (3) where P (x,t) is the density of probability in the space x=[x1, x2, x3] and time t, while D >0 is the diffusion coefficient. Such processes are characterized by Eq. (1). An example of Eq. (3) generalization is ∂∂tP (x,t)=D∇ αP β(x,t) - ∞ < α ≤ 2 β > - 1 , (4) where the fractional based-derivatives Laplacian Σ(∂α/∂xα)i, (i = 1, 2, 3), of non-linear term Pβ(x,t) is taken into account [31]. Another generalized form is represented by equation ∂∂tδδP(x,t)=D ∇ αP(x,t) δ > 0 α ≤ 2 , (5) that considers also the fractional time-derivative [32]. These fractional-described processes exhibit a power law patters as expressed by Eq. (2). This general introduction introduces the presented work, whose aim is to develop a theoretical model in order to forecast the triggering and propagation of landslides, using the techniques of fractional calculus. The latter is suitable for modeling the water infiltration (i.e., the pore water pressure diffusion in the soil) and the dynamical processes in the fractal media [33]. Alternatively the fractal representation of temporal and spatial derivative (the fractal order only appears in the denominator of the derivative) is considered and the results are compared to the fractional one. The prediction of landslides and the discovering of the triggering mechanism, is one of the challenging problems in earth science. Landslides can be triggered by different factors but in most cases the trigger is an

  15. Directionality of Double-Bond Photoisomerization Dynamics Induced by a Single Stereogenic Center.

    PubMed

    Marchand, Gabriel; Eng, Julien; Schapiro, Igor; Valentini, Alessio; Frutos, Luis Manuel; Pieri, Elisa; Olivucci, Massimo; Léonard, Jérémie; Gindensperger, Etienne

    2015-02-19

    In light-driven single-molecule rotary motors, the photoisomerization of a double bond converts light energy into the rotation of a moiety (the rotor) with respect to another (the stator). However, at the level of a molecular population, an effective rotary motion can only be achieved if a large majority of the rotors rotate in the same, specific direction. Here we present a quantitative investigation of the directionality (clockwise vs counterclockwise) induced by a single stereogenic center placed in allylic position with respect to the reactive double bond of a model of the biomimetic indanylidene-pyrrolinium framework. By computing ensembles of nonadiabatic trajectories at 300 K, we predict that the photoisomerization is >70% unidirectional for the Z → E and E → Z conversions. Most importantly, we show that such directionality, resulting from the asymmetry of the excited state force field, can still be observed in the presence of a small (ca. 2°) pretwist or helicity of the reactive double bond. This questions the validity of the conjecture that a significant double-bond pretwist (e.g., >10°) in the ground state equilibrium structure of synthetic or natural rotary motors would be required for unidirectional motion. PMID:26262473

  16. Dynamic nuclear polarization assisted spin diffusion for the solid effect case

    NASA Astrophysics Data System (ADS)

    Hovav, Yonatan; Feintuch, Akiva; Vega, Shimon

    2011-02-01

    The dynamic nuclear polarization (DNP) process in solids depends on the magnitudes of hyperfine interactions between unpaired electrons and their neighboring (core) nuclei, and on the dipole-dipole interactions between all nuclei in the sample. The polarization enhancement of the bulk nuclei has been typically described in terms of a hyperfine-assisted polarization of a core nucleus by microwave irradiation followed by a dipolar-assisted spin diffusion process in the core-bulk nuclear system. This work presents a theoretical approach for the study of this combined process using a density matrix formalism. In particular, solid effect DNP on a single electron coupled to a nuclear spin system is considered, taking into account the interactions between the spins as well as the main relaxation mechanisms introduced via the electron, nuclear, and cross-relaxation rates. The basic principles of the DNP-assisted spin diffusion mechanism, polarizing the bulk nuclei, are presented, and it is shown that the polarization of the core nuclei and the spin diffusion process should not be treated separately. To emphasize this observation the coherent mechanism driving the pure spin diffusion process is also discussed. In order to demonstrate the effects of the interactions and relaxation mechanisms on the enhancement of the nuclear polarization, model systems of up to ten spins are considered and polarization buildup curves are simulated. A linear chain of spins consisting of a single electron coupled to a core nucleus, which in turn is dipolar coupled to a chain of bulk nuclei, is considered. The interaction and relaxation parameters of this model system were chosen in a way to enable a critical analysis of the polarization enhancement of all nuclei, and are not far from the values of 13C nuclei in frozen (glassy) organic solutions containing radicals, typically used in DNP at high fields. Results from the simulations are shown, demonstrating the complex dependences of the DNP

  17. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    DOE PAGESBeta

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of frameworkmore » force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.« less

  18. Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

    SciTech Connect

    Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; Sholl, David S.; Greathouse, Jeffery A.; Allendorf, Mark D.

    2014-03-28

    Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.

  19. Importance of indole N-H hydrogen bonding in the organization and dynamics of gramicidin channels.

    PubMed

    Chaudhuri, Arunima; Haldar, Sourav; Sun, Haiyan; Koeppe, Roger E; Chattopadhyay, Amitabha

    2014-01-01

    The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a combination of steady state and time-resolved fluorescence approaches along with circular dichroism spectroscopy. We show here that in the absence of the hydrogen bonding ability of tryptophans, tetramethyltryptophan gramicidin (TM-gramicidin) is unable to maintain the single stranded, head-to-head dimeric channel conformation in membranes. Our results show that TM-gramicidin displays a red-shifted fluorescence emission maximum, lower red edge excitation shift (REES), and higher fluorescence intensity and lifetime, consistent with its nonchannel conformation. This is in agreement with the measured location (average depth) of the 1-methyltryptophans in TM-gramicidin using the parallax method. These results bring out the usefulness of 1-methyltryptophan as a fluorescent tool to examine the hydrogen bonding ability of tryptophans in proteins and peptides. W