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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. 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.

  3. Structural dynamics of hydrogen bonded methanol oligomers: Vibrational transient hole burning studies of spectral diffusion

    NASA Astrophysics Data System (ADS)

    Piletic, I. R.; Gaffney, K. J.; Fayer, M. D.

    2003-07-01

    Frequency resolved pump-probe experiments have been conducted on the deuterated hydroxyl stretch of methanol-d in a solution containing 0.8% methanol-d/23% methanol-h in carbon tetrachloride. Methanol-d molecules that both donate and receive hydrogen bonds have an inhomogeneously broadened hydroxyl stretch absorption line centered at 2487 cm-1. With a laser tuned to 2513 cm-1, the high-frequency side of the absorption spectrum is excited. The equilibration of the excited state peak and the ground-state hole results in the time-dependent shift in the frequency of the signal, which is used to monitor the dynamics of spectral diffusion. Model calculations were conducted to address the influence of spectral diffusion in the ground and excited states on the experimental observables when the vibrational lifetime is comparable to the spectral diffusion time. The model calculations illustrate the influence on the signal of absorbers in the ground state that have relaxed from the excited state. This aspect of the problem has not been addressed in previous descriptions of frequency resolved pump-probe spectroscopy. The calculations were used to fit the time-dependent peak maximum, resulting in a bi-exponential frequency-frequency correlation function, with a fast time constant of roughly 0.1 ps and a slower time constant of 1.6±0.3 ps. The observed dynamics have been compared with the predictions of dielectric continuum theory. The inability of a simple dielectric continuum theory to predict the observed spectral diffusion dynamics suggests that these dynamics do not result from the long-wavelength, collective orientational relaxation of the solvent. Instead the dynamics are attributed to fluctuations in the local hydrogen bond network, which is consistent with recent molecular-dynamics simulations of vibrational transient hole burning in water.

  4. Dynamics of supercritical methanol of varying density from first principles simulations: hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation.

    PubMed

    Yadav, Vivek Kumar; Chandra, Amalendu

    2013-06-14

    A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects

  5. Diffusion bonding of Stratapax for drill bits

    SciTech Connect

    Middleton, J.N.; Finger, J.T.

    1983-01-01

    A process has been developed for the diffusion bonding of General Electric's Stratapax drill blanks to support studs for cutter assemblies in drill bits. The diffusion bonding process is described and bond strength test data are provided for a variety of materials. The extensive process details, provided in the Appendices, should be sufficient to enable others to successfully build diffusion-bonded drill bit cutter assemblies.

  6. Diffusion bonding of copper to niobium

    NASA Astrophysics Data System (ADS)

    Wagner, Adrian R.

    Processes used to join metal to ceramic at low temperatures have proven to be inefficient because multiple brazing cycles with different brazing temperatures and braze filler metals are required. Even though this is reproducible and robust, it is not ideal due to the manufacturing time and cost associated with multiple brazing cycles. A more efficient and cost effective process is to utilize the diffusion bonding technique to join different metallic layers prior to joining the entire ceramic assembly in one brazing cycle. In this study, the diffusion bonding of copper to niobium was examined. To the author's knowledge, the diffusion bonding of Cu to Nb has not been researched, and the diffusion of Cu into Nb or Nb into Cu has not been observed. A series of diffusion bonding experiments were conducted to determine the optimal bonding time, temperature, and pressure for the Cu-Nb system. The diffusion bonded samples were evaluated using mechanical testing and microscopy. Results from characterization indicate that diffusion of Nb into Cu occurs, and a robust bond with no interfacial voids is formed using different combinations of bonding parameters. The diffusion of Nb into Cu and with failure occurring outside the diffusion bonded region during all mechanical testing indicate that Cu can be bonded to Nb via the diffusion bonding technique.

  7. Hydrogen bond dynamics in bulk alcohols.

    PubMed

    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. Hydrogen bond dynamics in bulk alcohols

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  9. 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.

  10. HIP diffusion bonding for gear materials

    SciTech Connect

    Ashworth, M.A.; Jacobs, M.H.; Armstrong, G.R.; Freeman, R.; Rickinson, B.A.; King, S.

    1996-12-31

    Mechanical actuators used on aircraft flight control systems contain highly stressed gears which are made from low alloy steels; either through or surface hardened. Corrosion protection has traditionally been provided by cadmium plating. Conventional stainless steels, even when given surface treatments do not provide the necessary strength, wear and corrosion properties for such gears. HIP processing has been used on cobalt based alloy powders as a new approach to produce gears for mechanical and corrosion testing. The technology has been used both to consolidate the powder and HIP diffusion bond the alloy to conventional stainless steels. The microstructure and properties of the consolidated alloy are presented together with preliminary results from component testing. The diffusion bonding route has produced gears which have much better wear and corrosion resistance than conventional steel gears whilst retaining equivalent fatigue properties. The economics of the process are discussed together with the concept of using the HIP process to shape as well as consolidate the material.

  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. Diffusion doping in quantum dots: bond strength and diffusivity.

    PubMed

    Saha, Avijit; Makkar, Mahima; Shetty, Amitha; Gahlot, Kushagra; A R, Pavan; Viswanatha, Ranjani

    2017-02-23

    Semiconducting materials uniformly doped with optical or magnetic impurities have been useful in a number of potential applications. However, clustering or phase separation during synthesis has made this job challenging. Recently the "inside out" diffusion doping was proposed to be successful in obtaining large sized quantum dots (QDs) uniformly doped with a dilute percentage of dopant atoms. Herein, we demonstrate the use of basic physical chemistry of diffusion to control the size and concentration of the dopants within the QDs for a given transition metal ion. We have studied three parameters; the bond strength of the core molecules and the diffusion coefficient of the diffusing metal ion are found to be important while the ease of cation exchange was not highly influential in the control of size and concentration of the single domain dilute magnetic semiconductor quantum dots (DMSQDs) with diverse dopant ions M(2+) (Fe(2+), Ni(2+), Co(2+), Mn(2+)). Steady state optical emission spectra reveal that the dopants are incorporated inside the semiconducting CdS and the emission can be tuned during shell growth. We have shown that this method enables control over doping percentage and the QDs show a superior ferromagnetic response at room temperature as compared to previously reported systems.

  13. Signal analysis approach to ultrasonic evaluation of diffusion bond quality

    SciTech Connect

    Chinn, D; Thomas, G

    1999-06-08

    Solid state bonds like the diffusion bond are attractive techniques for joining dissimilar materials since they are not prone to the defects that occur with fusion welding. Ultrasonic methods can detect the presence of totally unbonded regions but have difficulty sensing poor bonded areas where the substrates are in intimate contact. Standard ultrasonic imaging is based on amplitude changes in the signal reflected from the bond interface. Unfortunately amplitude alone is not sensitive to bond quality. We demonstrated that there is additional information in the ultrasonic signal that correlates with bond quality. In our approach we interrogated a set of dissimilar diffusion bonded samples with broad band ultrasonic signals. The signals were digitally processed and the characteristics of the signals that corresponded to bond quality were determined. These characteristics or features were processed with pattern recognition algorithms to produce predictions of bond quality. The predicted bond quality was then compared with the destructive measurement to assess the classification capability of the ultrasonic technique

  14. Ultrasonic NDT of titanium diffusion bonding with guided waves

    SciTech Connect

    Rose, J.L.; Zhu, W.; Zaidi, M.

    1998-04-01

    An ultrasonic guided wave technique is developed for the NDT of diffusion bonded titanium-to-titanium structures. A three-layer model based on the normal beam experimental results has been proposed. Dispersion curves and wave structure are analyzed to direct the experimental study. Two features related to Lamb waves propagating in diffusion bonded titanium plates, the spectral peak to peak ratios and the wave mode frequency shift, are extracted from the guided wave experimental results for both 2 mm (0.08 in.) and 4 mm (0.16 in.) diffusion bond panels. It is found for some specific modes and frequencies that these two features are sensitive to the diffusion bonding states and, therefore, could be used to distinguish good bond panels from poor bond ones.

  15. 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.

  16. 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.

  17. Ultrasonic evaluation of beryllium-copper diffusion bonds

    SciTech Connect

    Jamieson, E.E.

    2000-06-08

    A study was performed to compare the effectiveness of several advanced ultrasonic techniques when used to determine the strength of diffusion bonded beryllium-copper, which heretofore have each been applied to only a few material systems. The use of integrated backscatter calculations, frequency domain reflection coefficients, and time-of-flight variance was compared in their ability to characterize the bond strength in a series of beryllium-copper diffusion bond samples having a wide variation in bond quality. Correlation of integrated backscatter calculations and time-of-flight variance with bond strength was good. Some correlation of the slope of the frequency based reflection coefficient was shown for medium and high strength bonds, while its Y-intercept showed moderate correlation for all bond strengths.

  18. 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.

  19. 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.

  20. Metal honeycomb to porous wireform substrate diffusion bond evaluation

    NASA Technical Reports Server (NTRS)

    Vary, A.; Moorhead, P. E.; Hull, D. R.

    1982-01-01

    Two nondestructive techniques were used to evaluate diffusion bond quality between a metal foil honeycomb and porous wireform substrate. The two techniques, cryographics and acousto-ultrasonics, are complementary in revealing variations of bond integrity and quality in shroud segments from an experimental aircraft turbine engine.

  1. 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.

  2. 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.

  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. 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.

  5. 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.

  6. Characterization of metallic foil joints using diffusion bonding and diffusion soldering in micro-technology-based energy and chemical systems

    SciTech Connect

    Gabriel, Michael; Paul, B.K.; Wilson, R.D.

    2001-01-01

    The several 316 stainless steel mesoscopic devices were made using diffusing bonding and diffusion soldering. Tensile strength, pressure drop of the devices were measured, and metallurgical examinations were made of the joints. Continuous bonds were observed in both diffusion bonded and diffusion soldered samples. Strengths of the diffusion soldered samples were up to 80% of the strength of the Ag3Sn joint material or 125 MPa. The pressure drop in diffusion soldered samples was 0.76 psi at the highest flow rates of 2.08 L/min. Diffusion bonded joints had strengths of up to 700 MPa but the back pressures were higher at all flow rates.

  7. Characterization of metallic foil joints using diffusion bonding and diffusion soldering in micro-technology-based energy and chemical systems

    SciTech Connect

    Gabriel, Michael; Paul, Brian K.; Wilson, Rick D.; Alman, David E.

    2001-01-10

    The several 316 stainless steel mesoscopic devices were made using diffusing bonding and diffusion soldering. Tensile strength, pressure drop of the devices were measured, and metallurgical examinations were made of the joints. Continuous bonds were observed in both diffusion bonded and diffusion soldered samples. Strengths of the diffusion soldered samples were up to 80% of the strength of the Ag(sub3) Sn joint material or 125 MPa. The pressure drop in diffusion soldered samples was 0.76 psi at the highest flow rates of 2.08 L/min. Diffusion bonded joints had strengths of up to 700 MPa but the back pressures were higher at all flow rates.

  8. 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.

  9. Diffusive dynamics on paper matrix

    NASA Astrophysics Data System (ADS)

    Chaudhury, Kaustav; Kar, Shantimoy; Chakraborty, Suman

    2016-11-01

    Writing with ink on a paper and the rapid diagnostics of diseases using paper cartridge, despite their remarkable diversities from application perspective, both involve the motion of a liquid from a source on a porous hydrophilic substrate. Here we bring out a generalization in the pertinent dynamics by appealing to the concerned ensemble-averaged transport with reference to the underlying molecular picture. Our results reveal that notwithstanding the associated complexities and diversities, the resultant liquid transport characteristics on a paper matrix, in a wide variety of applications, resemble universal diffusive dynamics. Agreement with experimental results from diversified applications is generic and validates our unified theory.

  10. Tunable infrared generation with diffusion-bonded-stacked gallium arsenide

    NASA Astrophysics Data System (ADS)

    Zheng, Dong

    Mid-infrared (MIR) radiation finds increasing applications in remote sensing, spectroscopy and military counter-measures. Nonlinear optical interactions provide one approach to tunable MIR sources generation. The development of MIR nonlinear optical crystals with excellent performance at a reasonable cost is essential for applications. Diffusion-bonded-stacked (DBS) GaAs periodic structures are a new family of quasi-phasematched (QPM) nonlinear optical crystals. The bonding process preserves the optical and mechanical properties of the bulk material, while the periodic modulation of the nonlinear coefficient permits QPM interactions. DBS GaAs bonding requirements, such as number of bonded layers and tolerable optical loss, are discussed. Nonlinear optical properties like mixing gain, wavelength, temperature and angular acceptance of the bonded structure, are predicted. DBS GaAs devices with up to 50 layers were bonded and characterized. Optical loss from interfacial voids and gaps at shorter wavelengths, from processing induced p- type free carrier absorption at longer wavelengths was characterized. 'Lithographic dicing' was invented and demonstrated as a replacement for mechanical dicing, resulting in the capability to handle thin wafers and cleaner interfaces for better bonding. Absorption due to semi-insulating-to-p-type conversion, a bulk crystal loss mechanism, was found to be induced by high bonding temperatures, and dependent on wafer sources and materials in contact with the stack. Optimized bonding parameters reduced the optical loss of 36-layer DBS GaAs to less than 0.2 cm-1 at long wavelengths. Tunable 15.6 to 17.6 μm coherent radiation at 90-ps pulse width was generated by difference frequency mixing in a 24-layer DBS GaAs device. The wavelength tuning curve agreed with theoretical predictions demonstrating that the bonding process maintained nonlinear optical phasematching over the 6 mm interaction length. Maximum mixing gain of 0.7%, or 5% internal

  11. 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.

  12. 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.

  13. Thermographic Inspection Of Superplastically Formed Diffusion Bonded Titanium Panels

    NASA Astrophysics Data System (ADS)

    Haavig, David L.; King, Daniel C.

    1988-01-01

    Infrared thermographic nondestructive inspection of superplastically formed diffusion bonded (SPF/DB) titanium structures is discussed. Nondestructive testing (NDT) of the structures produced by this recently developed method is vital for construction of modern fighter aircraft. Forming and bonding parameters can be optimized by proper interpretation of NDT results. Currently, ultrasonic inspection is used for NDT on these parts. In an effort to reduce cost and inspection time required by ultrasonic testing, a thermographic investigation of panel response to rapid heating was undertaken. Panels were uniformly illuminated for a duration of up to four seconds by high intensity lamps. Infrared images of temperature variation due to panel thickness were observed. Correlation of thermograms with ultrasonic and destructive investigations indicate that lack of bonding and panel formations can easily be observed. We have demonstrated that thermographic inspection provides an equally sensitive and lower cost alternative to ultrasonic inspection. Finally, thermographic inspection facilities for large scale inspection are suggested.

  14. 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

  15. Delayed mechanical failure of silver-interlayer diffusion bonds

    SciTech Connect

    Kassner, M.E. ); Rosen, R.S.; Henshall, G.A. . Physical Metallurgy and Joining Section)

    1990-12-01

    Silver-interlayer diffusion bonds were fabricated using planar-magnetron sputtering (PMS). The bonds exhibit very high tensile strengths, despite the soft interlayer, because of the constraint by the base metal. However, these joints undergo delayed failure at relatively low tensile stresses at ambient temperatures, apparently by a ductile microvoid coalescence mechanism at the bond interfaces. Two classes of delayed tensile failure were investigated. In the first case, the applied stress does not produced any plastic deformation in the base metal, and failure appears to be controlled by time-dependent plasticity within the silver interlayer as a result of the effective stress in the interlayer. The plasticity causes cavity nucleation and, eventually, interlinkage and failure. In the second case, time-dependent plasticity is observed in base metals, and concomitant shear occurs within the softer silver under a high triaxial stress state. Here, the time-dependent plasticity of the base metal accelerates plasticity and failure in the interlayer. These models were substantiated by careful analysis of the stress and temperature dependence of the rupture times, finite element analysis of the stress state within the interlayer, and microscopy of the fracture surfaces and interfaces loaded to various fractions of the expected rupture times. These findings are applicable to bonds in which the interlayers are prepared by processes other than physical vapor deposition.

  16. Diffusion Bonding and Characterization of a Dispersion Strengthened Aluminum Alloy

    NASA Astrophysics Data System (ADS)

    Cooke, Kavian Omar

    Aluminum metal matrix composites (Al-MMC's) containing silicon carbide or alumina particle reinforcements are used extensively in automotive and aircraft industries. The addition of a reinforcing phase has led to significant improvements in the mechanical properties of these alloys. However, despite substantial improvements in the properties, the lack of a reliable joining method has restricted their full potential. The differences in physical and metallurgical properties between the ceramic phase and the Al-MMC, prevents the successful application of the fusion welding processes, conventionally used for joining monolithic aluminum alloys. Therefore, alternative techniques that prevent microstructural changes in the base metal need to be developed. In this study, the transient liquid phase diffusion bonding and eutectic bonding of a particle reinforced Al 6061-MMC was investigated to identify a method that could control particle segregation within the joint and increase the final joint strength. The results showed that TLP bonding using Ni-foil was possible at 600°C for 10 minutes using a pressure of 0.01 MPa. However, characterization of the bond interface showed a wide particle segregated zone due to the "pushing effect" of the solid/liquid interface during isothermal solidification stage of bonding. The presence of this particle segregated zone was shown to cause low joint strengths. In order to overcome these problems, TLP bonding was performed using electrodeposited coatings of Ni and Ni-Al 2O3 as a way of controlling the volume of eutectic liquid formed at the joint. Theoretical and experimental work showed that the use of thin coatings was successful in reducing the width of the segregated zone formed at the joint and this had the effect of increasing joint shear strength values. Furthermore, lower bonding temperature could also be used as a method of reducing particle segregation and therefore, a Cu-Sn interlayer was used to form a eutectic bond. The

  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. Diffusion of co-sputtered metals as bonding materials for 3D interconnects during thermal treatments.

    PubMed

    Hsu, S Y; Chen, H Y; Chen, K N

    2012-03-01

    Diffusion behaviors of co-sputtered metals during thermal treatments were investigated, where these co-sputtered metals can be used as bonding materials for 3D Interconnects. In this paper, we report the diffusion behaviors and discuss the diffusion mechanisms of co-sputtered metals before and after annealing. Atom and vacancy volume, vacancy formation energy, and activation energy are proposed to explain the diffusion direction and diffusion rate among different co-sputtered metals. Based on the excellent bonding performance of this method, Cu/metal co-sputtering bonding is considered as a potential candidate for advanced bonding technology.

  19. Molecular dynamics simulations of substitutional diffusion

    SciTech Connect

    Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

    2016-12-18

    In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example, we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.

  20. Molecular dynamics simulations of substitutional diffusion

    DOE PAGES

    Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

    2016-12-18

    In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

  1. 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.

  2. The metallurgical integrity of the frit vent assembly diffusion bond

    NASA Astrophysics Data System (ADS)

    Ulrich, G. B.

    1994-06-01

    Iridium alloy clad vent sets (CVS's) are now being made by Energy Systems at the Oak Ridge Y-12 Plant. These CVS's are being made for the US Department of Energy's (NE-53) General Purpose Heat Source- Radioisotope Thermoelectric Generator (GPHS-RTG) program, which is to supply electrical power for the National Aeronautics and Space Administration's Cassini mission to Saturn. A GPHS-RTG has 72 CVS'. Each CVS encapsulates one (238)PuO2 fuel pellet. The helium gas produced from the alpha decay of the (238)Pu is vented through a nominal 0.45-mm-diam hole in the vent cup of each CVS. A frit vent assembly that is electron beam welded over the vent hole allows helium gas to escape but prevents plutonia fines from exiting. The metallurgical integrity of frit vent assemblies produced by Martin Marietta Energy Systems, Inc. (Energy Systems) were compared with those produced earlier by EG&G-Mound Applied Technology, Inc. (EG&G-MAT). Scanning electron microscope (SEM) photographs were taken (at magnifications of from 126x to 1,000x) of the starting frit vent powder and the diffusion-bonded powder in finished frit vent assemblies produced by Energy Systems and EG&G-MAT. Frit vent assemblies also were metallographically prepared and visually examined/photographed at magnifications of from 50x to 1,000x. The SEM and metallographic examinations of the particle-to-particle and particle-to-foil component diffusion bonds indicated that the Energy Systems-produced and EG&G-MAT-produced frit vent assemblies have comparable metallurgical integrity. Statistical analysis of the Energy Systems production data shows that the frit vent manufacturing yield is 91%.

  3. 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.

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

    DOE PAGES

    Shen, B.; Wang, Z. Y.; Dong, F.; ...

    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. Dripping dynamics at high Bond numbers

    NASA Astrophysics Data System (ADS)

    Rubio-Rubio, Mariano; Taconet, Paloma; Sevilla, Alejandro

    2014-11-01

    When dispensing liquid from a vertically oriented injector under gravity, drops grow at the outlet until the surface tension forces can no longer balance their weight, and the pinch-off occurs. This dripping regime no longer exists above a critical flow rate, at which an abrupt transition to jetting takes place. These phenomena are governed by the liquid properties, the injector size and the injection flow rate, or non-dimensionally, by the Bond, Bo , Weber, We , and Kapitza, Γ, numbers. Detailed accounts of the rich dynamics of the dripping regime and the transition leading to jetting can be found in the literature (e.g. Phys. Rev. Lett. vol. 93, 2004, and Phys. Fluids vol. 18, 2006), but only for two different values of Bo . Therefore, we present new experiments on the dripping dynamics and jetting transition for a wide range of both the liquid viscosity and the size of the injector, reaching values of Bo up to one order-of-magnitude larger than those present in the literature. Our results reveal the existence of new dynamics in the dripping regime not observed at small Bond numbers. In addition, we quantify the hysteresis present in the dripping-jetting transition, previously measured only for the inviscid case. Supported by Spanish MINECO under Project DPI 2011-28356-C03-02.

  6. Leakage rates and thermal requirements for the diffusion bonding of microchannel arrays via internal convective heating

    SciTech Connect

    Bose, Sumantra; Palo, Daniel R.; Paul, Brian

    2007-07-24

    Diffusion bonding cycle times can be a large cost factor in the production of metal microchannel devices. The challenge is to significantly minimize this cost by reducing the bonding cycle time through rapid and uniform heating and cooling within the bonding process. Heating rates in diffusion bonding processes are typically limited by the need to minimize thermal gradients during bonding. A novel method is described which takes advantage of the internal flow passages within microchannel devices for convective heat transfer during the bonding process. The internal convective heating (ICH) technique makes use of heated inert gas to provide the microchannel assembly with rapid and uniform heat input. This paper will demonstrate the ability to effectively diffusion bond microchannel laminae using the ICH method by investigating the leakage rates.

  7. The dynamics of unsteady detonation with diffusion

    SciTech Connect

    Aslam, Tariq Dennis; Romick, Christopher; Powers, Joseph

    2010-01-01

    Here we consider an unsteady detonation with diffusion included. This introduces an interaction between the reaction length scales and diffusion length scales. Detailed kinetics introduce multiple length scales as shown though the spatial eigenvalue analysis of hydrogen-oxygen system; the smallest length scale is {approx} 10{sup 7} m and the largest {approx} 10{sup -2} m; away from equilibrium, the breadth can be larger. In this paper, we consider a simpler set of model equations, similar to the inviscid reactive compressible fluid equations, but include diffusion (in the form of thermal/energy, momentum, and mass diffusion). We will seek to reveal how the complex dynamics already discovered in one-step systems in the inviscid limit changes with the addition of diffusion.

  8. 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.

  9. 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

  10. Levitation effect: role of symmetry and dependence of diffusivity on the bond length of homonuclear and heteronuclear diatomic species.

    PubMed

    Sharma, Manju; Yashonath, S

    2011-04-07

    Molecular dynamics investigation of model diatomic species confined to the α-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O(2), the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

  11. Process optimization for diffusion bonding of tungsten with EUROFER97 using a vanadium interlayer

    NASA Astrophysics Data System (ADS)

    Basuki, Widodo Widjaja; Aktaa, Jarir

    2015-04-01

    Solid-state diffusion bonding is a selected joining technology to bond divertor components consisting of tungsten and EUROFER97 for application in fusion power plants. Due to the large mismatch in their coefficient of thermal expansions, which leads to serious thermally induced residual stresses after bonding, a thin vanadium plate is introduced as an interlayer. However, the diffusion of carbon originated from EUROFER97 in the vanadium interlayer during the bonding process can form a vanadium carbide layer, which has detrimental influences on the mechanical properties of the joint. For optimal bonding results, the thickness of this layer and the residual stresses has to be decreased sufficiently without a significant reduction of material transport especially at the vanadium/tungsten interface, which can be achieved by varying the diffusion bonding temperature and duration. The investigation results show that at a sufficiently low bonding temperature of 700 °C and a bonding duration of 4 h, the joint reaches a reasonable high ductility and toughness especially at elevated test temperature of 550 °C with elongation to fracture of 20% and mean absorbed Charpy impact energy of 2 J (using miniaturized Charpy impact specimens). The strength of the bonded materials is about 332 MPa at RT and 291 MPa at 550 °C. Furthermore, a low bonding temperature of 700 °C can also help to avoid the grain coarsening and the alteration of the grain structure especially of the EUROFER97 close to the bond interface.

  12. General theory of heat diffusion dynamics

    NASA Astrophysics Data System (ADS)

    Tröster, A.; Schranz, W.

    2002-11-01

    A detailed theoretical investigation of the influence of heat diffusion processes on the low-frequency dispersion in macroscopic elastic susceptibilities is presented. In particular, a general solution of the heat diffusion equation is derived for arbitrary boundary conditions and externally imposed periodic and spatially inhomogeneous stress. In contrast to other calculations found in the literature, our results indicate that in elastic experiments on monodomain samples of macroscopic dimensions the isothermal-adiabatic crossover function necessarily reduces to a Debye-like dispersion. Experimentally, this is illustated by measurements of the complex dynamic elastic susceptibilities of KSCN and KMnF3. Our approach also allows to discuss heat diffusion in polydomain crystals and heterogeneous systems, for which one obtains dispersions of a non-Debye type. While explicitly derived in an elastic context, the present theory also applies to heat diffusion in dielectric materials.

  13. Diffusion bonding between ODS ferritic steel and F82H steel for fusion applications

    NASA Astrophysics Data System (ADS)

    Noh, Sanghoon; Kim, Byungjun; Kasada, Ryuta; Kimura, Akihiko

    2012-07-01

    Diffusion bonding techniques were employed to join high Cr oxide dispersion strengthened (ODS) ferritic steel (Fe-15Cr-2W-0.2Ti-0.35Y2O3) and F82H steel under uni-axial hydrostatic pressure using a high vacuum hot press, and the microstructure and mechanical properties of the joints were investigated. The dissimilar joints were bonded by solid-state diffusion bonding (SSDB) and liquid phase diffusion bonding (LPDB). After bonding process, heat treatments were conducted to utilize the phase transformation of F82H steel for recovering the martensitic structure. Tensile tests with miniaturized specimens were carried out to investigate and compare the bonding strengths of each joint. Microstructure was observed for the bonding interface, and fracture mode was investigated after the tensile tests. LPDB joint of interfacial F82H steel fully recovered to martensite phase by post-joining heat treatments, while SSDB joint had ferrite phases at the interface even after heat treatment, which is considered to be due to decarburization of F82H steel during the bonding process. Therefore it is considered that the insert material plays a role as diffusion barrier of carbon during LPDB process. Microstructure observations and tensile tests of the joints revealed that the LPDB joints possess suitable tensile properties which are comparable to that of F82H steel. This indicates that LPDB is more promising method to bond ODS-FS and F82H steel than SSDB.

  14. Diffusion bonding and brazing of high purity copper for linear collider accelerator structures

    NASA Astrophysics Data System (ADS)

    Elmer, J. W.; Klingmann, J.; van Bibber, K.

    2001-05-01

    Diffusion bonding and brazing of high purity copper were investigated to develop procedures for joining precision machined copper components for the Next Linear Collider (NLC). Diffusion bonds were made over a range of temperatures from 400 °C to 1000 °C, under two different loading conditions [3.45 kPa (0.5 psi) and 3.45 MPa (500 psi)], and on two different diamond machined surface finishes. Brazes were made using pure silver, pure gold, and gold-nickel alloys, and different heating rates produced by both radiation and induction heating. Braze materials were applied by both physical vapor deposition (PVD) and conventional braze alloy shims. Results of the diffusion bonding experiments showed that bond strengths very near that of the copper base metal could be made at bonding temperatures of 700 °C or higher at 3.45 MPa bonding pressure. At lower temperatures, only partial strength diffusion bonds could be made. At low bonding pressures (3.45 kPa), full strength bonds were made at temperatures of 800 °C and higher, while no bonding (zero strength) was observed at temperatures of 700 °C and lower. Observations of the fracture surfaces of the diffusion bonded samples showed the effects of surface finish on the bonding mechanism. These observations clearly indicate that bonding began by point asperity contact, and flatter surfaces resulted in a higher percentage of bonded area under similar bonding conditions. Results of the brazing experiments indicated that pure silver worked very well for brazing under both conventional and high heating rate scenarios. Similarly, pure silver brazed well for both the PVD layers and the braze alloy shims. The gold and gold-containing brazes had problems, mainly due to the high diffusivity of gold in copper. These problems led to the necessity of overdriving the temperature to ensure melting, the presence of porosity in the joint, and very wide braze joints. Based on the overall findings of this study, a two-step joining method

  15. 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.

  16. Method of fluxless brazing and diffusion bonding of aluminum containing components

    NASA Technical Reports Server (NTRS)

    Featherston, A. B.; Okelly, K. P. (Inventor)

    1976-01-01

    A method of diffusion bonding and fluxless brazing of aluminum containing components is reported. The aluminum surfaces are freed of any aluminum oxide coating and are coated with a polymeric sealer which can be thermally removed leaving essentially no residue. The polymeric sealer is being removed in a substantially oxygen free environment, and the aluminum components are then being brazed or diffusion bonded without the use of a flux to remove oxide coating.

  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. Ultrasonically Activated Diffusion Bonding for Fluidic Control Assembly

    DTIC Science & Technology

    1979-02-01

    commercially available vacuum bell jar. Provisions for elevated temperature operation included an induction heating coil surrounding the welding and...Ultrasonic bonding times of 2 to 4 seconds are orders of magnitude faster than thermally activated bonding and require no furnaces or high vacuum ...sonic spot welding system appropriately modified for use under high vacuum conditions, with a shortened reed member for containment within a

  19. Molecular dynamics simulation of fractal aggregate diffusion

    NASA Astrophysics Data System (ADS)

    Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis

    2010-11-01

    The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.

  20. 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.

  1. Diffusion bonding of a superplastic Inconel 718SPF superalloy by electroless nickel plating

    SciTech Connect

    Yeh, M.S.; Chang, C.B.; Chuang, T.H.

    2000-02-01

    Although intimate contact can be obtained for diffusion bonding of a superplastic Inconel 718SPF superalloy under a low pressure of 7 MPa, the precipitates formed at the interface retarded achievement of a sound joint. The shear strength was only 41.5 MPa for an overlap length of 12 T (T = 1.3 mm, sheet thickness). The diffusion bondability of t his Inconel 718SPF superalloy was enhanced by electroless nickel plating. In this situation, the bonding shear strength increased to 70.4 MPa for the same overlap length of 12 T under the same bonding condition, regardless of the roughness of the surface to be bonded. Upon decreasing the overlap length from 12 to 6T, the bonding strength remained constant.

  2. 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.

  3. 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).

  4. Enhanced nonlinear inspection of diffusion bonded interfaces using reflected non-collinear ultrasonic wave mixing

    NASA Astrophysics Data System (ADS)

    Zhang, Ziyin; Nagy, Peter B.; Hassan, Waled

    2016-02-01

    Ultrasonic wave mixing has shown promising potential for assessing otherwise hidden subtle imperfections in imperfect diffusion bonds between Ti-6Al-4V components. When interrogating a diffusion bonded specimen using non-collinear shear wave mixing, both bulk and interface nonlinearity will contribute to the transmitted nonlinear signal. Although a recent study has shown that changing the transducer alignment can suppress the intrinsic nonlinearity of the surrounding material to some extent so that the interface nonlinearity could be detected more selectively, it is still difficult to distinguish different levels of bond quality based on the detected transmitted signal only. Analytical and numerical studies showed that an imperfect interface generates the same amount of nonlinear displacement in the reflected and transmitted fields. In this study, we used the reflected nonlinear interface signature to characterize diffusion bonded interfaces. Our results indicate that it is better to use the reflected nonlinear interface signature to assess the bond quality, which is in agreement with our previous analytical and numerical predictions. However, the observed random phase of the reflected signature indicates that existing nonlinear interface models are insufficient for accurately describing the nonlinear interaction of shear incident waves with high-quality diffusion bonded interfaces.

  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. AN INTERNAL CONVECTIVE HEATING TECHNIQUE FOR DIFFUSION BONDING ARRAYED MICROCHANNEL ARCHITECTURES

    SciTech Connect

    Paul, Brian; Bose, Sumantra; Palo, Daniel R.

    2010-01-08

    Diffusion bonding cycle times can be a large factor in the production cost of metal microchannel devices. The challenge is to significantly minimize bonding cycle times through rapid heating and cooling within the bonding process. A novel method is described which takes advantage of the internal flow passages within microchannel devices for convective heat transfer during the bonding process. The internal convective heating (ICH) technique makes use of heated inert gas to provide the microchannel assembly with rapid and uniform heat input. Results demonstrate that the ICH technique is feasible, capable of producing microchannels with higher dimensional integrity and shorter bonding cycle times than traditional vacuum hot press methods. Results suggest that this may be due to smaller thermal gradients within microchannel devices during the ICH bonding cycle.

  7. LAMMPS framework for dynamic bonding and an application modeling DNA

    NASA Astrophysics Data System (ADS)

    Svaneborg, Carsten

    2012-08-01

    We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly

  8. Diffusion bonding titanium to stainless steel using Nb/Cu/Ni multi-interlayer

    SciTech Connect

    Li Peng; Li Jinglong; Xiong Jiangtao; Zhang Fusheng; Raza, Syed Hamid

    2012-06-15

    By using Nb/Cu/Ni structure as multi-interlayer, diffusion bonding titanium to austenitic stainless steel has been conducted. The effects of bonding temperature and bonding time on the interfacial microstructure were analyzed by scanning electron microscope equipped with energy dispersive spectroscope, and the joint strength was evaluated by tensile test. The results showed that Ni atoms aggregated at the Cu-Nb interface, which promoted Cu solution in Nb. This phenomenon forms a Cu-Nb solution strengthening effect. However, such effect would decay by using long bonding time that dilutes Ni atom aggregation, or be suppressed by using high bonding temperature that embrittles the Cu-Nb interface due to the formation of large grown intermetallic compounds. The sound joint was obtained by promoted parameters as 850 Degree-Sign C for 30-45 min, under which a bonding strength around 300 MPa could be obtained. - Highlights: Black-Right-Pointing-Pointer Titanium was diffusion bonded to stainless steel using Nb/Cu/Ni multi-interlayer. Black-Right-Pointing-Pointer The effects of bonding parameters on microstructure and joint strength were studied. Black-Right-Pointing-Pointer Nickel aggregation promotes Cu solution in Nb which can strengthen the joint. Black-Right-Pointing-Pointer The sound joint with strength of around 300 MPa was obtained by promoted parameters.

  9. 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.

  10. 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.

  11. Diffusive thermal dynamics for the Ising ferromagnet.

    PubMed

    Buonsante, P; Burioni, R; Cassi, D; Vezzani, A

    2002-09-01

    We introduce a thermal dynamics for the Ising ferromagnet where the energy variations occurring within the system exhibit a diffusive character typical of thermalizing agents such as, e.g., localized excitations. Time evolution is provided by a walker hopping across the sites of the underlying lattice according to local probabilities depending on the usual Boltzmann weight at a given temperature. Despite the canonical hopping probabilities the walker drives the system to a stationary state which is not reducible to the canonical equilibrium state in a trivial way. The system still exhibits a magnetic phase transition occurring at a finite value of the temperature larger than the canonical one. The dependence of the model on the density of walkers realizing the dynamics is also discussed. Interestingly the differences between the stationary state and the Boltzmann equilibrium state decrease with increasing number of walkers.

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

    PubMed

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

    2016-05-28

    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 (Im1,2 (+)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.

  13. Reaction-diffusion analysis for one-step plasma etching and bonding of microfluidic devices

    SciTech Connect

    Rosso, Michel; Steijn, Volkert van; Smet, Louis C. P. M. de; Sudhoelter, Ernst J. R.; Kreutzer, Michiel T.; Kleijn, Chris R.

    2011-04-25

    A self-similar reaction front develops in reactive ion etching when the ions penetrate channels of shallow height h. This relates to the patterning of microchannels using a single-step etching and bonding, as described by Rhee et al. [Lab Chip 5, 102 (2005)]. Experimentally, we report that the front location scales as x{sub f{approx}}ht{sup 1/2} and the width is time-invariant and scales as {delta}{approx}h. Mean-field reaction-diffusion theory and Knudsen diffusion give a semiquantitative understanding of these observations and allow optimization of etching times in relation to bonding requirements.

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

    SciTech Connect

    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 the 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.

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

    DOE PAGES

    Greathouse, Jeffery A.; Cygan, Randall T.; Fredrich, Joanne T.; ...

    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

  16. TEM Analysis of Interfaces in Diffusion-Bonded Silicon Carbide Ceramics Joined Using Metallic Interlayers

    NASA Technical Reports Server (NTRS)

    Ozaki, T.; Tsuda, H.; Halbig, M. C.; Singh, M.; Hasegawa, Y.; Mori, S.; Asthana R.

    2016-01-01

    Silicon Carbide (SiC) is a promising material for thermo-structural applications due to its excellent high-temperature mechanical properties, oxidation resistance, and thermal stability. However, joining and integration technologies are indispensable for this material in order to fabricate large size and complex shape components with desired functionalities. Although diffusion bonding techniques using metallic interlayers have been commonly utilized to bond various SiC ceramics, detailed microstructural observation by Transmission Electron Microscopy (TEM) of the bonded area has not been carried out due to difficulty in preparing TEM samples. In this study, we tried to prepare TEM samples from joints of diffusion bonded SiC ceramics by Focused Ion Beam (FIB) system and carefully investigated the interfacial microstructure by TEM analysis. The samples used in this study were SiC fiber bonded ceramics (SA-Tyrannohex: SA-THX) diffusion bonded with metallic interlayers such as Ti, TiMo, and Mo-B. In this presentation, the result of microstructural analysis obtained by TEM observations and the influence of metallic interlayers and fiber orientation of SA-THX on the joint microstructure will be discussed.

  17. Directional diffusion and void formation at a Si (001) bonded wafer interface

    NASA Astrophysics Data System (ADS)

    Esser, R. H.; Hobart, K. D.; Kub, F. J.

    2002-08-01

    Low-temperature hydrophobic bonding is an enabling technology allowing the fabrication of device structures. Current research into improvement of hydrophobic bonding has focused on the elimination of thermally generated voids. It has been observed that a regular grid etched into the bonding interface can eliminate the thermally generated voids. By manipulation of patterns etched into the bond interface, it was possible to ascertain that the diffusion of interfacial gasses that form the thermally generated voids is enhanced along the <110> directions. This is shown by an analysis of the void density at various locations in relation to the etched trenches at the bonded interface. Void density between trenches is shown to be 12% of the void density near trenches but nto along a <110> direction.

  18. 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.

  19. 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.

  20. The Breathing Orbital Valence Bond Method in Diffusion Monte Carlo: C-H Bond Dissociation ofAcetylene

    SciTech Connect

    Domin, D.; Braida, Benoit; Lester Jr., William A.

    2008-05-30

    This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 {+-} 0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 {+-} 0.7 kcal/mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 {+-} 0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 {+-} 0.5 kcal/mol).

  1. Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach.

    PubMed

    Raiteri, Paolo; Gale, Julian D; Bussi, Giovanni

    2011-08-24

    A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO(3) has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO(3) have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.

  2. Ambient-temperature creep failure of silver-aided diffusion bonds between steel

    SciTech Connect

    Henshall, G.A.; Kassner, M.E.; Rosen, R.S.

    1990-01-15

    It has long been known that thin (e.g., 1 {mu}m {minus} 1 mm) interlayer bonds between higher strength base materials may have high ultimate tensile or rupture strengths despite the relatively low strength of the filler metal. The high strength of the joint is due to the mechanical constraint provided by the stronger base metals which restricts transverse contraction of the interlayer. The constraint produces a triaxial state or stress and reduces the effective stress, thus reducing the tendency for the interlayer to plastically deform. Plasticity of the base metal reduces the constraint and decreases the strength of the bond. The purpose of this work was twofold. First, the validity of the base-metal- accelerated'' delayed-failure theory for bonds utilizing plastic base metals was checked. Creep-rupture tests were performed on diffusion-bonded specimens using silver interlayers deposited by planar-magnetron sputtering (PMS), a physical vapor-deposition process. The PMS process was preferred because of the superior quality and strength of the bond and because this modern low-temperature joining process is increasingly utilized for joining ceramic and composite materials. The role of plastic base metals in the fracture process was further investigated by conducting tensile-rupture tests of diffusion bonds made with stainless steel base metals of different yield strengths, and therefore different creep rates. The second purpose was to determine whether delayed failure occurs in interlayer bonds between elastic base metals, which do not creep over the range of applied stresses. This question is particularly relevant since many alloys, ceramics and composites fall within this category. Again, ambient and near-ambient temperature creep-rupture tests were performed at a variety of stresses below the UTS of the bond. 25 refs., 7 figs.

  3. 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.

  4. 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.

  5. 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

    2015-07-15

    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.

  6. 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.

  7. The hydrogen-bond collective dynamics in liquid methanol

    NASA Astrophysics Data System (ADS)

    Bellissima, Stefano; de Panfilis, Simone; Bafile, Ubaldo; Cunsolo, Alessandro; González, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-12-01

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

  8. The hydrogen-bond collective dynamics in liquid methanol

    PubMed Central

    Bellissima, Stefano; De Panfilis, Simone; Bafile, Ubaldo; Cunsolo, Alessandro; González, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-01-01

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature. PMID:27996056

  9. The hydrogen-bond collective dynamics in liquid methanol

    DOE PAGES

    Bellissima, Stefano; Cunsolo, Alessandro; DePanfilis, Simone; ...

    2016-12-20

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HBmore » dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.« less

  10. The hydrogen-bond collective dynamics in liquid methanol

    SciTech Connect

    Bellissima, Stefano; Cunsolo, Alessandro; DePanfilis, Simone; Bafile, Ubaldo; Gonzalez, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-12-20

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

  11. Hydrogen bonding definitions and dynamics in liquid water.

    PubMed

    Kumar, R; Schmidt, J R; Skinner, J L

    2007-05-28

    X-ray and neutron diffractions, vibrational spectroscopy, and x-ray Raman scattering and absorption experiments on water are often interpreted in terms of hydrogen bonding. To this end a number of geometric definitions of hydrogen bonding in water have been developed. While all definitions of hydrogen bonding are to some extent arbitrary, those involving one distance and one angle for a given water dimer are unnecessarily so. In this paper the authors develop a systematic procedure based on two-dimensional potentials of mean force for defining cutoffs for a given pair of distance and angular coordinates. They also develop an electronic structure-based definition of hydrogen bonding in liquid water, related to the electronic occupancy of the antibonding OH orbitals. This definition turns out to be reasonably compatible with one of the distance-angle geometric definitions. These two definitions lead to an estimate of the number of hydrogen bonds per molecule in liquid simple point charge/extended (SPC/E) water of between 3.2 and 3.4. They also used these and other hydrogen-bond definitions to examine the dynamics of local hydrogen-bond number fluctuations, finding an approximate long-time decay constant for SPC/E water of between 0.8 and 0.9 ps, which corresponds to the time scale for local structural relaxation.

  12. Structure and dynamics of diffusion flames in microgravity

    NASA Technical Reports Server (NTRS)

    Matalon, Moshe

    1995-01-01

    The objectives of this project are to gain insight into diffusion flames by modeling various configurations related to ongoing experimental investigations in the microgravity combustion science program. The emphasis of the work is to understand the structure and dynamics of diffusion flames. Improving our fundamental understanding of diffusion flames is most relevant to issues related to fire safety and fire prevention because most fires consist of diffusion flames.

  13. 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

  14. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

    NASA Astrophysics Data System (ADS)

    Alexandrov, B. S.; Stanev, V. G.; Bishop, A. R.; Rasmussen, K. Ø.

    2012-12-01

    We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H⋯N and N-H⋯O hydrogen bonding, we identify a high-frequency (˜96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (˜300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

  15. Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity.

    PubMed

    Nandi, Prithwish K; English, Niall J

    2016-12-01

    Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, ηS. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Hydrophobic molecules slow down the hydrogen-bond dynamics of water.

    PubMed

    Bakulin, Artem A; Pshenichnikov, Maxim S; Bakker, Huib J; Petersen, Christian

    2011-03-17

    We study the spectral and orientational dynamics of HDO molecules in solutions of tertiary-butyl-alcohol (TBA), trimethyl-amine-oxide (TMAO), and tetramethylurea (TMU) in isotopically diluted water (HDO:D(2)O and HDO:H(2)O). The spectral dynamics are studied with femtosecond two-dimensional infrared spectroscopy and the orientational dynamics with femtosecond polarization-resolved vibrational pump-probe spectroscopy. We observe a strong slowing down of the spectral diffusion around the central part of the absorption line that increases with increasing solute concentration. At low concentrations, the fraction of water showing slow spectral dynamics is observed to scale with the number of methyl groups, indicating that this effect is due to slow hydrogen-bond dynamics in the hydration shell of the methyl groups of the solute molecules. The slowing down of the vibrational frequency dynamics is strongly correlated with the slowing down of the orientational mobility of the water molecules. This correlation indicates that these effects have a common origin in the effect of hydrophobic molecular groups on the hydrogen-bond dynamics of water.

  1. 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.

  2. Diffusion bonding of commercially pure titanium to low carbon steel using a silver interlayer

    SciTech Connect

    Atasoy, Evren; Kahraman, Nizamettin

    2008-10-15

    Titanium and low carbon steel plates were joined through diffusion bonding using a silver interlayer at various temperatures for various diffusion times. In order to determine the strength of the resulting joints, tensile-shear tests and hardness tests were applied. Additionally, optical, scanning electron microscopy examinations and energy dispersive spectrometry elemental analyses were carried out to determine the interface properties of the joint. The work showed that the highest interface strength was obtained for the specimens joined at 850 deg. C for 90 min. It was seen from the hardness results that the highest hardness value was obtained for the interlayer material and the hardness values on the both sides of the interlayer decreased gradually as the distance from the joint increased. In energy dispersive spectrometry analyses, it was seen that the amount of silver in the interlayer decreased markedly depending on the temperature rise. In addition, increasing diffusion time also caused some slight decrease in the amount of silver.

  3. Reflexion measurements for inverse characterization of steel diffusion bond mechanical properties

    NASA Astrophysics Data System (ADS)

    Le Bourdais, Florian; Cachon, Lionel; Rigal, Emmanuel

    2017-02-01

    The present work describes a non-destructive testing method aimed at securing high manufacturing quality of the innovative compact heat exchanger developed under the framework of the CEA R&D program dedicated to the Advanced Sodium Technological Reactor for Industrial Demonstration (ASTRID). The heat exchanger assembly procedure currently proposed involves high temperature and high pressure diffusion welding of stainless steel plates. The aim of the non-destructive method presented herein is to characterize the quality of the welds obtained through this assembly process. Based on a low-frequency model developed by Baik and Thompson [1], pulse-echo normal incidence measurements are calibrated according to a specific procedure and allow the determination of the welding interface stiffness using a nonlinear fitting procedure in the frequency domain. Performing the characterization of plates after diffusion welding using this method allows a useful assessment of the material state as a function of the diffusion bonding process.

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

    SciTech Connect

    Sai K. Mylavarapu; Richard N. Christensen; Raymond R. Unocic; Richard E. Glosup; Mike W. Patterson

    2012-08-01

    The Very High Temperature Reactor (VHTR) using gas-cooled reactor technology is anticipated to be the reactor type for the Next Generation Nuclear Plant (NGNP). In this reactor concept 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 a secondary fluid for electricity generation, hydrogen production, and/or industrial process heat applications. At present, there is no proven IHX concept for VHTRs. The current Technology Readiness Level (TRL) status issued by NGNP to all components associated with the IHX for reduced nominal reactor outlet temperatures of 750–800 degrees C is 3 on a 1–10 scale, with 10 indicating omplete technological maturity. Among 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 with Alloy 617, a candidate high-temperature structural material for NGNP applications, are the primary focus of this paper. In the current study, diffusion bonding of Alloy 617 has been demonstrated, although the optimum diffusion bonding process parameters to engineer a quasi interface-free joint are yet to be determined. The PCHE fabrication related processes, i.e., photochemical etching and diffusion bonding are discussed for Alloy 617 plates. In addition, the authors’ experiences with these non-conventional machining and joining techniques are discussed. Two PCHEs are fabricated using Alloy 617 plates and are being experimentally investigated for their thermal-hydraulic performance in a High-Temperature Helium Facility (HTHF). The HTHF is primarily of Alloy 800H construction and is designed to facilitate experiments at temperatures and pressures up to 800 degrees C and 3 MPa, respectively. Furthermore, some preliminary

  5. 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

  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.

  7. 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.

  8. Diffusion bonding of Al7075 alloy to titanium aluminum vanadate alloy

    NASA Astrophysics Data System (ADS)

    Alhazaa, Abdulaziz Nasser

    The aluminum alloy (Al7075) and titanium alloy (Ti-6Al-4V) are used in a variety of applications in the aerospace industry. However, the high cost of Ti-6Al-4V alloy has been a major factor which has limited its use and therefore, the ability to join Al7075 alloy to Ti-6Al-4V alloy can provide a product that is less costly, but retains the high strength and light weight properties necessary for the transport industry. However, the large difference in the physical properties between these two alloys prevents the use of conventional joining techniques such as fusion welding to join these dissimilar alloys. Therefore, the diffusion bonding technique was used to join Al7075 alloy to Ti-6Al-4V alloy with the objective of minimizing microstructural changes of the two alloys during the bonding process. In this thesis, solid state and liquid phase bonding processes were undertaken. Solid state bonding was employed without interlayers and was successful at 510°C and 7 MPa. The bond interface showed an absence of the oxides due to the dissolution of oxygen into the titanium solution. Bonds made using copper interlayers at a temperature sufficient enough to form eutectic liquid formation between copper and aluminum were produced. The intermetallics theta(Al2Cu), S(Al2CuMg) and T(Al2Mg3Zn3) were identified at the aluminum interface while Cu3Ti2 intermetallic was identified at the titanium interface. Bonds made using tin based alloys interlayers and copper coatings were successful and gave the highest shear strength. The eutectic formation on the Al7075 alloy was responsible for joint formation at the aluminum interface while the formation of Sn3Ti5 intermetallic was responsible for the joint formation at titanium interface. The corrosion rate of the bonds decreased with increasing bonding time for joints made using the tin based interlayer in 3% NaCl solution. However, the presence of copper within the joint increased the corrosion rate of the bonds and this was attributed to

  9. Bonding dynamics of compliant microbump during ultrasonic bonding investigated by using Si strain gauge

    NASA Astrophysics Data System (ADS)

    Iwanabe, Keiichiro; Nakadozono, Kenichi; Senda, Yousuke; Asano, Tanemasa

    2016-06-01

    The bonding dynamics of a cone-shaped microbump during ultrasonic bonding are investigated by in situ measurements of the strain generated in a substrate using a piezoresistance strain sensor. The strain sensor is composed of a pair of p- and n-type piezoresistance gauges to extract strain components in the ultrasonic vibration along the plane parallel to the substrate surface and along the direction perpendicular to the surface. Flip-chip bonding is performed at room-temperature. The time evolution of the strain generated in the substrate according to the load-up of pressing force and application of ultrasonic vibration is clearly detected. The softening of the bump metal during the application of ultrasonic vibration is clearly observed. Results of a comparative study between the bonding of a cone-shaped microbump and that of a flat-top microbump suggest mechanical stress concentration near the top end of the cone-shaped microbump, which results in the transformation of the crystal texture of the bump from grains to fine crystallites.

  10. 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.

  11. Gas Diffusion in Polyethylene Terepthalate By Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Butler, Simon; Adolf, David

    2006-03-01

    Molecular dynamics simulations of the diffusion of small penetrants through PET have been performed utilising the anisotropic united atom model [1] and a virtual liquid technique. [2] The accuracy and reliability of these two approaches has been assessed in terms of the improvement in equation of state behaviour and of diffusion co-efficients and solubilities. The effect of the diffusion of nitrogen, carbon dioxide, and oxygen on the local dynamics of PET have been investigated as a result. Attention has been focused on the dual mode effect [3] observed during mixed gas diffusion. [1] Molecular dynamics calculation of the equation of state of alkanes, J. Chem. Phys. 93, 6 (1990) [2] Kikuchi, Kuwajima, Fukada, Novel method to estimate the solubility of small molecules in cis-polyisoprene by molecular dynamics simulations, J. Chem. Phys, 115, 13 (2001) [3] Lewis, Duckett, Ward, Fairclough, Ryan, The barrier properties of polyethylene terephthalate to mixtures of oxygen, carbon dioxide and nitrogen, Polymer, 1631, 44 (2003)

  12. Molecular dynamics simulations on local structure and diffusion in liquid Ti x Al 1- x alloys

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Liu, C. S.; Cheng, Z. F.; Shi, D. P.

    2011-10-01

    The microscopic structure and dynamics of liquid Ti xAl 1- x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti 0.75Al 0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.

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

    SciTech Connect

    Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell; Lordi, Vincenzo; Draeger, Erik; Pask, John; Pascucci, Valerio; Bremer, Peer -Timo

    2016-09-27

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

  14. Diffusion mechanism of hydrogen in amorphous silicon - Ab initio molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Su, Y.-S.; Pantelides, S. T.

    2001-03-01

    Diffusion of hydrogen in hydrogenated amorphous silicon (a-Si:H) is an important process, but the mechanism is still not well understood and even controversial. The observed activation energy is only about 1.5 eV, whereas the energy to dissociate Si-H bonds is much larger ( 2.5 eV). H is generally believed to migrate as an interstitial, perhaps as in crystalline Si. We report first-principles density-functional molecular dynamics simulations and identify a wealth of processes that occur. The main mechanism for the release of H from Si-H bonds is the conversion of the Si atom to fivefold coordination by the arrival of a floating bond, as suggested by one of us (STP, Phys. Rev. Lett. 58, 1344 (1987)) but the H atom is not released in the interstitial regions. Migration occurs by a bond-interconversion process, with the H atom acting as the analog of a floating bond. Estimates of the diffusion constant are in agreement with observations. Work supported in part by NSF.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  19. Superplastic Formed and Diffusion Bonded Titanium Landing Gear Component Feasibility Study.

    DTIC Science & Technology

    1980-07-01

    Gear Superplastic Forming Shock Strut SPF/DB Outer Cylinder Titanium Diffusion Bonding Cylindrical Sandwich Structure Z% ABSTRACT (Continue en ro,eree...lO0 Fighter Aircraft 6 5 F-lO0 Main Landing Gear 6 6 F-lO0 Landing Gear Strut Section Selected for this Program 7 7 SPF/DB Titanium Landing Gear... Assembly with a Diaphram Seal for DB Cycle. 18 15 MLG SPF/DB Titanium Outer Cylinder Segment DB Cycle Using a Diaphram Seal 19 16 Hot Sizing Tool 20 17

  20. Elastic stability of superplastically formed/diffusion-bonded orthogonally corrugated core sandwich plates

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1980-01-01

    The paper concerns the elastic buckling behavior of a newly developed superplastically formed/diffusion-bonded (SPF/DB) orthogonally corrugated core sandwich plate. Uniaxial buckling loads were calculated for this type of sandwich plate with simply supported edges by using orthotropic sandwich plate theory. The buckling behavior of this sandwich plate was then compared with that of an SPF/DB unidirectionally corrugated core sandwich plate under conditions of equal structural density. It was found that the buckling load for the former was considerably higher than that of the latter.

  1. 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.

  2. 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.

  3. Diffusion Bonding of Ti-6Al-4V Sheet with Ti-6Al-4V Foam for Biomedical Implant Applications

    NASA Astrophysics Data System (ADS)

    Hamilton, Brittany; Oppenheimer, Scott; Dunand, David C.; Lewis, Daniel

    2013-12-01

    Advanced metallic bone implants are designed to have a porous surface to improve osseointegration and reduce risks of loosening. An alternative approach to existing surface treatments to create a porous surface is to bond separately produced metallic foams onto the implant. To assess the feasibility of this approach, a Ti-6Al-4V foam was diffusion bonded onto bulk Ti-6Al-4V in an argon atmosphere at temperatures between 1173 K and 1223 K (900 °C and 950 °C) for times between 45 and 75 minutes. These specimens were tested in tension to determine bond quality: failures occurred in the foam, indicating a strong diffusion-bonded interface. The quality of the bond was confirmed by metallographic studies, indicating that this approach, which can also be applied to creating of sandwich with porous cores, is successful.

  4. 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.

  5. Microstructure and mechanical strength of diffusion bonded joints between silicon carbide and F82H steel

    NASA Astrophysics Data System (ADS)

    Zhong, Zhihong; Hinoki, Tatsuya; Kohyama, Akira

    2011-10-01

    The combination of SiC and reduced activation ferritic/martensitic steels is attractive for fusion applications because it is expected to offer high thermal efficiency, high reliability and superior safety characteristic under a neutron irradiation environment. In this paper, diffusion bonding of SiC to F82H steel has been investigated. Direct joining of SiC to F82H was unsuccessful due to a large residual stress generated in the joint. A double W/Cu and a multiple W/Ni/Cu/Ni interlayer were used to reduce the residual stress, and encouraging results were obtained. The interfacial microstructure examination revealed that the various interfaces were bonded well. Diffusion products in the reaction zones were identified. The shear strength of the SiC/F82H joints measured by knife-edge tests at room temperature was found to increase with the increase in the joining temperature, and reached a maximum of 41.3 MPa. The fracture surfaces of the joints were also analyzed.

  6. Release of polyphenolic drugs from dynamically bonded layer-by-layer films.

    PubMed

    Zhou, Lin; Chen, Mao; Tian, Lili; Guan, Ying; Zhang, Yongjun

    2013-05-01

    Layer-by-layer (LbL) assembled films have been exploited for surface-mediated drug delivery. The drugs loaded in the films were usually released via diffusion or the degradation of one of the film components. Here we demonstrate that drug release can also be achieved by exploiting the dynamic nature of hydrogen-bonded LbL films. The films were fabricated from tannic acid (TA), a model polyphenolic drug, and poly(vinyl pyrrolidone) (PVPON). The driving force for the film buildup is the hydrogen bonding between the two components, which was confirmed by Fourier transform infrared (FTIR) spectra. The film growth is linear, and the growth rate of the film decreases with increasing assembly temperature. Because of the reversible/dynamic nature of hydrogen bonding, when soaked in aqueous solutions, the PVPON/TA films disassemble gradually and thus release TA to the media. The release rate of TA increases with increasing pH and temperature but decreases with increasing ionic strength. Scanning electron microscopy (SEM) studies on the surface morphology of the film during TA release reveal that the film surface becomes smoother and then rougher again because of the dewetting of the film. The released TA can scavenge ABTS(+•) cation radicals, indicating it retains its antioxidant activity, a major biological activity of polyphenols.

  7. 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.

  8. 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.

  9. Diffusive dynamics of nanoparticles in ultra-confined media

    DOE PAGES

    Jacob, Jack Deodato; Conrad, Jacinta; Krishnamoorti, Ramanan; ...

    2015-08-10

    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 accountedmore » for steric restrictions and hydrodynamic interactions. The stretching exponent decreased linearly as the nanoparticles were increasingly confined by the posts. Altogether, 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.« less

  10. Diffusive dynamics of nanoparticles in ultra-confined media

    SciTech Connect

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

    2015-08-10

    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. Altogether, 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.

  11. 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

  12. 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.

  13. A Comparison Between Cold-Welded and Diffusion-Bonded Al/Cu Bimetallic Rods Produced by ECAE Process

    NASA Astrophysics Data System (ADS)

    Eslami, P.; Karimi Taheri, A.; Zebardast, M.

    2013-10-01

    In this research, the application of equal channel angular extrusion process to produce both the cold-welded and diffusion-bonded Al/Cu bimetallic rods is assessed. The joints shear strength for both of the methods are measured and compared. The microstructure examinations were also carried out using scanning electron microscope equipped with EDX system and x-ray diffraction analysis. The results exhibit that the strength of the bond in cold-welded specimens is dependent on the amount of stretch and pressure at the materials interface. But in the diffusion-bonded specimens, it is depended on the struggle between the oxidation rate of the mating surfaces accompanied by inter-metallic compounds formation and the aluminum and copper atoms ability to diffuse in the joint interface.

  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. Equilibrium and dynamic pleating of a crystalline bonded network

    NASA Astrophysics Data System (ADS)

    Ganguly, Saswati; Nath, Parswa; Horbach, Jürgen; Sollich, Peter; Karmakar, Smarajit; Sengupta, Surajit

    2017-03-01

    We describe a phase transition that gives rise to structurally non-trivial states in a two-dimensional ordered network of particles connected by harmonic bonds. Monte Carlo simulations reveal that the network supports, apart from the homogeneous phase, a number of heterogeneous "pleated" phases, which can be stabilised by an external field. This field is conjugate to a global collective variable quantifying "non-affineness," i.e., the deviation of local particle displacements from local affine deformation. In the pleated phase, stress is localised in ordered rows of pleats and eliminated from the rest of the lattice. The kinetics of the phase transition is unobservably slow in molecular dynamics simulation near coexistence, due to very large free energy barriers. When the external field is increased further to lower these barriers, the network exhibits rich dynamic behaviour: it transforms into a metastable phase with the stress now localised in a disordered arrangement of pleats. The pattern of pleats shows ageing dynamics and slow relaxation to equilibrium. Our predictions may be checked by experiments on tethered colloidal solids in dynamic laser traps.

  16. 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.

  17. Lasing and thermal characteristics of Yb:YAG/YAG composite with atomic diffusion bonding

    NASA Astrophysics Data System (ADS)

    Sankar Nagisetty, Siva; Severova, Patricie; Miura, Taisuke; Smrž, Martin; Kon, Hitoe; Uomoto, Miyuki; Shimatsu, Takehito; Kawasaki, Masato; Higashiguchi, Takeshi; Endo, Akira; Mocek, Tomáš

    2017-01-01

    We demonstrated the laser performance of an Yb:YAG/YAG composite ceramic laser medium mounted on an aluminium heatsink via atomic diffusion bonding (ADB) technique using nanocrystalline metal films at room temperature in air. The surface temperature rise of the ADB bonded laser medium was linear with 57 °C lower than that of the commercially available soldered Yb:YAG thin disk at the pump power of 280 W. Moreover, the ADB disk was pumped 1.5 times higher (7.3 kW cm-2) than the typical damage threshold of the soldered disk without any sign of damage. The undoped capping may be effective for the suppression of ASE heating; however, according to the in situ OPD measurement it induces strong thermal lensing. The CW laser output power of 177 W was obtained at the pump power of 450 W with the optical-to-optical efficiency of 40% using V-shape cavity.

  18. 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.

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

    PubMed Central

    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. PMID:25573551

  20. 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.

  1. The quantum nature of the hydrogen bond: insight from path-integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Walker, Brent; Li, Xin-Zheng; Michaelides, Angelos

    2011-03-01

    Hydrogen (H) bonds are weak, generally intermolecular bonds, that hold together much of soft matter, the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of H means H-bonds are inherently quantum mechanical; effects such as zero point motion and tunneling should be considered, although often are not. In particular, a consistent picture of quantum nuclear effects on the strength of H-bonds and consequently the structure of H-bonded systems is still absent. Here, we report ab initio path-integral molecular dynamics studies on the quantum nature of the H-bond. Systematic examination of a range of H-bonded systems shows that quantum nuclei weaken weak H-bonds but strengthen relatively strong ones. This correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb enables predictions to be made for H-bonded bonded materials in general with merely classical knowledge (e.g. H-bond strength or H-bond length). Our work rationalizes the contrasting influence of quantum nuclear dynamics on a wide variety of materials, including liquid water and HF, and highlights the need for flexible molecules in force-field based studies of quantum nuclear dynamics.

  2. 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.

  3. 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.

  4. Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing

    NASA Astrophysics Data System (ADS)

    Wang, Zhongrui; Joshi, Saumil; Savel'Ev, Sergey E.; Jiang, Hao; Midya, Rivu; Lin, Peng; Hu, Miao; Ge, Ning; Strachan, John Paul; Li, Zhiyong; Wu, Qing; Barnell, Mark; Li, Geng-Lin; Xin, Huolin L.; Williams, R. Stanley; Xia, Qiangfei; Yang, J. Joshua

    2017-01-01

    The accumulation and extrusion of Ca2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. To emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca2+, respectively. The diffusive memristor and its dynamics enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.

  5. Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing

    SciTech Connect

    Wang, Zhongrui; Joshi, Saumil; Savel’ev, Sergey E.; Jiang, Hao; Midya, Rivu; Lin, Peng; Hu, Miao; Ge, Ning; Strachan, John Paul; Li, Zhiyong; Wu, Qing; Barnell, Mark; Li, Geng-Lin; Xin, Huolin L.; Williams, R. Stanley; Xia, Qiangfei; Yang, J. Joshua

    2016-09-26

    The accumulation and extrusion of Ca2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. In order to emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca2+, respectively. Furthermore, the diffusive memristor and its dynamics enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.

  6. Decoupling of surface diffusion and relaxation dynamics of molecular glasses.

    PubMed

    Zhang, Yue; Fakhraai, Zahra

    2017-04-03

    Tobacco mosaic virus is used as a probe to measure surface diffusion of ultrathin films of N,N'-Bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD) (12 nm [Formula: see text] 53 nm, where [Formula: see text] is the film thickness) at various temperatures below the glass transition temperature, [Formula: see text], of all films. As the film thickness is decreased, [Formula: see text] decreases rapidly and the average film dynamics are enhanced by 6-14 orders of magnitude. We show that the surface diffusion is invariant of the film thickness decrease and the resulting enhanced overall mobility. The values of the surface diffusion coefficient and its temperature dependence are invariant of film thickness and are the same as the corresponding bulk values ([Formula: see text]400 nm). For the thinnest films ([Formula: see text]20 nm), the effective activation energy for rearrangement (temperature dependence of relaxation times) becomes smaller than the activation energy for surface diffusion. These results suggest that the fast surface diffusion is decoupled from film relaxation dynamics and is a solely free surface property.

  7. Molecular dynamics simulations of hydrogen diffusion in aluminum

    SciTech Connect

    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 how 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.

  8. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGES

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

    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

  9. Post-processing interstitialcy diffusion from molecular dynamics simulations

    SciTech Connect

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-15

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

  10. 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

  11. Protonation Dynamics and Hydrogen Bonding in Aqueous Sulfuric Acid.

    PubMed

    Niskanen, Johannes; Sahle, Christoph J; Juurinen, Iina; Koskelo, Jaakko; Lehtola, Susi; Verbeni, Roberto; Müller, Harald; Hakala, Mikko; Huotari, Simo

    2015-09-03

    Hydration of sulfuric acid plays a key role in new-particle formation in the atmosphere. It has been recently proposed that proton dynamics is crucial in the stabilization of these clusters. One key question is how water molecules mediate proton transfer from sulfuric acid, and hence how the deprotonation state of the acid molecule behaves as a function concentration. We address the proton transfer in aqueous sulfuric acid with O K edge and S L edge core-excitation spectra recorded using inelastic X-ray scattering and with ab initio molecular dynamics simulations in the concentration range of 0-18.0 M. Throughout this range, we quantify the acid-water interaction with atomic resolution. Our simulations show that the number of donated hydrogen bonds per Owater increases from 1.9 to 2.5 when concentration increases from 0 to 18.0 M, in agreement with a rapid disappearance of the pre-edge feature in the O K edge spectrum. The simulations also suggest that for 1.5 M sulfuric acid SO4(2-) is most abundant and that its concentration falls monotonously with increasing concentration. Moreover, the fraction of HSO4(-) peaks at ∼12 M.

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

    PubMed

    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-urea)s 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.

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

    NASA Astrophysics Data System (ADS)

    Ying, Hanze; Zhang, Yanfeng; Cheng, Jianjun

    2014-02-01

    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-urea)s 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.

  14. 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

  15. 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.

  16. 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.

  17. Single-file dynamics with different diffusion constants.

    PubMed

    Ambjörnsson, Tobias; Lizana, Ludvig; Lomholt, Michael A; Silbey, Robert J

    2008-11-14

    We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two-particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally efficient stochastic simulation technique based on the Gillespie algorithm. We find that the mean square displacement for a tagged particle scales as the square root of time (as for identical particles) for long times, with a prefactor which depends on the diffusion constants for the particles; these results are in excellent agreement with very recent analytic predictions in the mathematics literature.

  18. Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing

    DOE PAGES

    Wang, Zhongrui; Joshi, Saumil; Savel’ev, Sergey E.; ...

    2016-09-26

    The accumulation and extrusion of Ca2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. In order to emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca2+, respectively. Furthermore, the diffusive memristor and its dynamicsmore » enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.« less

  19. 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.

  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. 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.

  2. Mesoscopic dynamics of diffusion-influenced enzyme kinetics

    NASA Astrophysics Data System (ADS)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-01

    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.

  3. Sodium diffusion through amorphous silica surfaces: a molecular dynamics study.

    PubMed

    Rarivomanantsoa, Michaël; Jund, Philippe; Jullien, Rémi

    2004-03-08

    We have studied the diffusion inside the silica network of sodium atoms initially located outside the surfaces of an amorphous silica film. We have focused our attention on structural and dynamical quantities, and we have found that the local environment of the sodium atoms is close to the local environment of the sodium atoms inside bulk sodo-silicate glasses obtained by quench. This is in agreement with recent experimental results.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter.

    PubMed

    del Val, Coral; Bondar, Luiza; Bondar, Ana-Nicoleta

    2014-04-01

    Long-distance proton transfers by proton pumps occurs in discrete steps that may involve the direct participation of protein sidechains and water molecules, and coupling of protonation changes to structural rearrangements of the protein matrix. Here we explore the role of inter-helical hydrogen bonding in long-distance protein conformational coupling and dynamics of internal water molecules. From molecular dynamics simulations of wild type and nine different bacteriorhodopsin mutants we find that both intra- and inter-helical hydrogen bonds are important determinants of the local protein structure, dynamics, and water interactions. Based on molecular dynamics and bioinformatics analyses, we identify an aspartate/threonine inter-helical hydrogen-bonding motif involved in controlling the local conformational dynamics. Perturbation of inter-helical hydrogen bonds can couple to rapid changes in water dynamics.

  13. Molecular dynamics simulation of water at mineral surfaces: Structure, dynamics, energetics and hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Kalinichev, A. G.; Wang, J.; Kirkpatrick, R.

    2006-05-01

    Fundamental molecular-level understanding of the properties of aqueous mineral interfaces is of great importance for many geochemical and environmental systems. Interaction between water and mineral surfaces substantially affects the properties of both phases, including the reactivity and functionality of the substrate surface, and the structure, dynamics, and energetics of the near surface aqueous phase. Experimental studies of interfacial water structure and dynamics using surface-sensitive techniques such as sum-frequency vibrational spectroscopy or X-ray and neutron reflectivity are not always possible for many practically important substrates, and their results often require interpretation concerning the atomistic mechanisms responsible for the observed behavior. Molecular computer simulations can provide new insight into the underlying molecular- level relationships between the inorganic substrate structure and composition and the structure, ordering, and dynamics of interfacial water. We have performed a series of molecular dynamics (MD) computer simulations of aqueous interfaces with several silicates (quartz, muscovite, and talc) and hydroxides (brucite, portlandite, gibbsite, Ca/Al and Mg/Al double hydroxides) to quantify the effects of the substrate mineral structure and composition on the structural, transport, and thermodynamic properties of water on these mineral surfaces. Due to the prevalent effects of the development of well-interconnected H-bonding networks across the mineral- water interfaces, all the hydroxide surfaces (including a fully hydroxylated quartz surface) show very similar H2O density profiles perpendicular to the interface. However, the predominant orientations of the interfacial H2O molecules and their detailed 2-dimensional near-surface structure and dynamics parallel to the interface are quite different reflecting the differences in the substrate structural charge distribution and the density and orientations of the surface OH

  14. Spatial dynamics of a population with stage-dependent diffusion

    NASA Astrophysics Data System (ADS)

    Azevedo, F.; Coutinho, R. M.; Kraenkel, R. A.

    2015-05-01

    We explore the spatial dynamics of a population whose individuals go through life stages with very different dispersal capacities. We model it through a system of partial differential equations of the reaction-diffusion kind, with nonlinear diffusion terms that may depend on population density and on the stage. This model includes a few key biological ingredients: growth and saturation, life stage structure, small population effects, and diffusion dependent on the stage. In particular, we consider that adults exhibit two distinct classes: one highly mobile and the other less mobile but with higher fecundity rate, and the development of juveniles into one or the other depends on population density. We parametrize the model with estimated parameters of an insect species, the brown planthopper. We focus on a situation akin to an invasion of the species in a new habitat and find that the front of invasion is led by the most mobile adult class. We also show that the trade-off between dispersal and fecundity leads to invasion speed attaining its maximum at an intermediate value of the diffusion coefficient of the most mobile class.

  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. 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.

  17. 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.

  18. Dynamic cross-correlations between entangled biofilaments as they diffuse.

    PubMed

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

    2017-03-10

    Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 10(4) times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales.

  19. Dynamic cross-correlations between entangled biofilaments as they diffuse

    PubMed Central

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

    2017-01-01

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

  20. Diffusive and Arrestedlike Dynamics in Currency Exchange Markets

    NASA Astrophysics Data System (ADS)

    Clara-Rahola, J.; Puertas, A. M.; Sánchez-Granero, M. A.; Trinidad-Segovia, J. E.; de las Nieves, F. J.

    2017-02-01

    This work studies the symmetry between colloidal dynamics and the dynamics of the Euro-U.S. dollar currency exchange market (EURUSD). We consider the EURUSD price in the time range between 2001 and 2015, where we find significant qualitative symmetry between fluctuation distributions from this market and the ones belonging to colloidal particles in supercooled or arrested states. In particular, we find that models used for arrested physical systems are suitable for describing the EURUSD fluctuation distributions. Whereas the corresponding mean-squared price displacement (MSPD) to the EURUSD is diffusive for all years, when focusing in selected time frames within a day, we find a two-step MSPD when the New York Stock Exchange market closes, comparable to the dynamics in supercooled systems. This is corroborated by looking at the price correlation functions and non-Gaussian parameters and can be described by the theoretical model. We discuss the origin and implications of this analogy.

  1. 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.

  2. Testing and modeling of diffusion bonded prototype optical windows under ITER conditions

    SciTech Connect

    Jacobs, M.; Van Oost, G.; Degrieck, J.; De Baere, I.; Gusarov, A.; Gubbels, F.; Massaut, V.

    2011-07-01

    Glass-metal joints are a part of ITER optical diagnostics windows. These joints must be leak tight for the safety (presence of tritium in ITER) and to preserve the vacuum. They must also withstand the ITER environment: temperatures up to 220 deg.C and fast neutron fluxes of {approx}3.10{sup 9} n/cm{sup 2}.s. At the moment, little information is available about glass-metal joints suitable for ITER. Therefore, we performed mechanical and thermal tests on some prototypes of an aluminium diffusion bonded optical window. Finite element modeling with Abaqus code was used to understand the experimental results. The prototypes were helium leaking probably due to very tiny cracks in the interaction layer between the steel and the aluminium. However, they were all able to withstand a thermal cycling test up to 200 deg. C; no damage could be seen after the tests by visual inspection. The prototypes successfully passed push-out test with a 500 N load. During the destructive push-out tests the prototypes broke at a 6-12 kN load between the aluminium layer and the steel or the glass, depending on the surface quality of the glass. The microanalysis of the joints has also been performed. The finite element modeling of the push-out tests is in a reasonable agreement with the experiments. According to the model, the highest thermal stress is created in the aluminium layer. Thus, the aluminium joint seems to be the weakest part of the prototypes. If this layer is improved, it will probably make the prototype helium leak tight and as such, a good ITER window candidate. (authors)

  3. Diffusion in crowded biological environments: applications of Brownian dynamics

    PubMed Central

    2011-01-01

    Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions. PMID:21595998

  4. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  5. 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

  6. Molecular Dynamics Simulations of Diffusion in a Silica Melt

    NASA Astrophysics Data System (ADS)

    Gemmell, A.; Fraser, D.; Refson, K.

    2003-12-01

    Computer modelling of silicate melts enables the study of pressure-temperature conditions not easily obtainable by traditional experimentation (e.g. 1). Diffusion in melts under various conditions is critical to our understanding of a variety of processes such as melt crystallisation, magma mixing and the behaviour of trace elements during magma ascent that underpins the field of igneous petrogenesis. It can also provide information on melt structure via diffusion mechanisms and their activation energies. In the present paper, the magnitude and mechanism of diffusion of silicon and oxygen in molten silica has been investigated by molecular dynamics using a modified BKS potential (2). A range of melt temperatures and pressures were studied with a view to understanding the relationship between temperature, pressure, diffusion and melt structure. At each P-T point studied, the system was equilibrated for between 1 million and 40 million 1fs steps depending on the conditions, with data collection over the same time range. The potential was adjusted to overcome problems with instability in the particle velocities at high temperature. The simulations were run at the Oxford University Supercomputing centre, UK. Systems of 144, 288, 576 and 1152 particles were investigated. In addition, two different sets of periodic boundary conditions were used - cubic and truncated octahedral. The latter was found to provide a better ratio of simulated time to compute time. The present data extend the range of data available and indicate a pronounced non-linearity in the temperature dependence of diffusion, as shown by plots of log10D with 1/T. The second derivative is greatest around 3500K. At least two different diffusion mechanisms may operate at lower and higher temperatures with differing activation energies. Comparison with previous molecular dynamics data shows broad agreement with most studies. Although the data presented do include some low temperature runs, comparison with

  7. 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.

  8. Thermal fatigue testing of a diffusion-bonded beryllium divertor mock-up under ITER relevant conditions

    SciTech Connect

    Youchison, D.L.; Guiniiatouline, R.; Watson, R.D.

    1994-12-31

    Thermal response and thermal fatigue tests of four 5 mm thick beryllium tiles on a Russian divertor mock-up were completed on the Electron Beam Test System at Sandia National Laboratories. The beryllium tiles were diffusion bonded onto an OFHC copper saddleblock and a DSCu (MAGT) tube containing a porous coating. Thermal response tests were performed on the tiles to an absorbed heat flux of 5 MW/m{sup 2} and surface temperatures near 300{degrees}C using 1.4 MPa water at 5.0 m/s flow velocity and an inlet temperature of 8-15{degrees}C. One tile was exposed to incrementally increasing heat fluxes up to 9.5 MW/m{sup 2} and surface temperatures up to 690{degrees}C before debonding at 10 MW/m{sup 2}. A third tile debonded after 9200 thermal fatigue cycles at 5 MW/m{sup 2}, while another debonded after 6800 cycles. In all cases, fatigue failure occurred in the intermetallic layers between the beryllium and copper. No fatigue cracking of the bulk beryllium was observed. During thermal cycling, a gradual loss of porous coating produced increasing sample temperatures. These experiments indicate that diffusion-bonded beryllium tiles can survive several thousand thermal cycles under ITER relevant conditions without failure. However, the reliability of the diffusion bonded Joint remains a serious issue.

  9. 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.

  10. 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.

  11. Radial propagation in population dynamics with density-dependent diffusion

    NASA Astrophysics Data System (ADS)

    Ngamsaad, Waipot

    2014-01-01

    Population dynamics that evolve in a radial symmetric geometry are investigated. The nonlinear reaction-diffusion model, which depends on population density, is employed as the governing equation for this system. The approximate analytical solution to this equation is found. It shows that the population density evolves from the initial state and propagates in a traveling-wave-like manner for a long-time scale. If the distance is insufficiently long, the curvature has an ineluctable influence on the density profile and front speed. In comparison, the analytical solution is in agreement with the numerical solution.

  12. Stochastic actions for diffusive dynamics: reweighting, sampling, and minimization.

    PubMed

    Adib, Artur B

    2008-05-15

    In numerical studies of diffusive dynamics, two different action functionals are often used to specify the probability distribution of trajectories, one of which requires the evaluation of the second derivative of the potential in addition to the force. Here it is argued that both actions are equivalent prescriptions for the purposes of reweighting and sampling trajectories, whereas the most probable path is more generally given by the global minimum of the action involving the second derivative term. The answer to this apparent paradox lies in the nondifferentiable character of Brownian paths, as well as in the "entropy" associated with a given trajectory.

  13. 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.

  14. Valence-bond description of chemical reactions on Born-Oppenheimer molecular dynamics trajectories

    NASA Astrophysics Data System (ADS)

    Noguchi, Nao; Nakano, Haruyuki

    2009-04-01

    The nature of chemical bonds on dynamic paths was investigated using the complete active space valence-bond (CASVB) method and the Born-Oppenheimer dynamics. To extract the chemical bond picture during reactions, a scheme to collect contributions from several VB (resonance) structures into a small numbers of indices was introduced. In this scheme, a tree diagram for the VB structures is constructed with the numbers of the ionic bonds treated as generation. A pair of VB structures is related to each other if one VB structure is transferred into the other by changing a covalent bond to an ionic bond. The former and latter VB structures are named parent and child structures, respectively. The weights of the bond pictures are computed as the sum of the CASVB occupation numbers running from the top generation to the bottom along the descent of the VB structures. Thus, a number of CASVB occupation numbers are collected into a small number of indices, and a clear bond picture may be obtained from the CASVB wave function. The scheme was applied to the hydrogen exchange reaction H2+F→H+HF and the Diels-Alder reaction C5H6(cyclopentadiene)+CH2=CH2(ethylene)→C7H10(norbornene). In both the reactions, the scheme gave a clear picture for the Born-Oppenheimer dynamics trajectories. The reconstruction of the bonds during reactions was well described by following the temporal changes in weight.

  15. Cooperative dynamic and diffusion behavior above and below the dynamical crossover of supercooled water

    NASA Astrophysics Data System (ADS)

    Picasso, Germán C.; Malaspina, David C.; Carignano, Marcelo A.; Szleifer, Igal

    2013-07-01

    Using extensive molecular dynamics simulations combined with a novel approach to analyze the molecular displacements we analyzed the change in the dynamics above and below the crossover temperature Tx for supercooled water. Our findings suggest that the crossover from fragile to strong glass former occurring at Tx is related with a change in the diffusion mechanism evidencing the presence of jump-like diffusion at lower temperatures. Also we observe that fluctuations of the local environments are intimately connected with fluctuations in the size and the amount of cooperative cluster of mobile molecules, and in particular we find a highly cooperative nature of the motion at low temperatures.

  16. 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

  17. Hydrogen Bonding Controls the Dynamics of Catechol Adsorbed on a TiO2(110) Surface

    NASA Astrophysics Data System (ADS)

    Diebold, Ulrike; Li, Shao-Chun; Chu, Li-Na; Gong, Xue-Qing

    2011-03-01

    Direct studies of how organic molecules diffuse on metal oxide surfaces can provide insights into catalysis and molecular assembly processes. We studied individual catechol molecules, C6 H4 (OH)2 , on a rutile Ti O2 (110) surface with scanning tunnelingmicroscopy. Surface hydroxyls enhanced the diffusivity of adsorbed catecholates. The capture and release of a proton caused individual molecules to switch between mobile and immobile states within a measurement period of minutes. Density functional theory calculations showed that the transfer of hydrogen from surface hydroxyls to the molecule and its interaction with surface hydroxyls substantially lowered the activation barrier for rotational motion across the surface. Hydrogen bonding can play an essential role in the initial stages of the dynamics of molecular assembly.

  18. 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.

  19. Diffusive and dynamical radiating stars with realistic equations of state

    NASA Astrophysics Data System (ADS)

    Brassel, Byron P.; Maharaj, Sunil D.; Goswami, Rituparno

    2017-03-01

    We model the dynamics of a spherically symmetric radiating dynamical star with three spacetime regions. The local internal atmosphere is a two-component system consisting of standard pressure-free, null radiation and an additional string fluid with energy density and nonzero pressure obeying all physically realistic energy conditions. The middle region is purely radiative which matches to a third region which is the Schwarzschild exterior. A large family of solutions to the field equations are presented for various realistic equations of state. We demonstrate that it is possible to obtain solutions via a direct integration of the second order equations resulting from the assumption of an equation of state. A comparison of our solutions with earlier well known results is undertaken and we show that all these solutions, including those of Husain, are contained in our family. We then generalise our class of solutions to higher dimensions. Finally we consider the effects of diffusive transport and transparently derive the specific equations of state for which this diffusive behaviour is possible.

  20. 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.

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

    PubMed Central

    Eslami, P.; Taheri, A. Karimi

    2011-01-01

    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

  2. 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.

  3. 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.

  4. Hydrogen bond lifetime for water in classic and quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Antipova, M. L.; Petrenko, V. E.

    2013-07-01

    The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.

  5. 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.

  6. 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.

  7. Tensile and creep properties of diffusion bonded titanium alloy IMI 834 to gamma titanium aluminide IHI alloy 01A

    SciTech Connect

    Holmquist, M.; Recina, V.; Pettersson, B.

    1999-04-23

    Diffusion bonding of the Ti-alloy Ti-5.8Al-4.0Sn-3.5Zr-0.7Nb-0.5Mo-0.35Se-0.06C (wt%) to the intermetallic {gamma}-based alloy Ti-33Al-2Fe-1.8V-0.1B (wt%) using hot isostatic pressing at 900 C, 200 MPa held for 1 h was studied. Sound joints without any pores or cracks with a width of approximately 5--7 {micro}m could be produced. Tensile testing showed that the strengths of the joints are similar to the strength of the {gamma}-TiAl base material at temperatures between room temperature and 600 C. The fracture occurs either at the joint or in the {gamma}-TiAl material. The fracture initiation process is a competition between initiation in the {gamma}-TiAl base material and initiation at the {gamma}-TiAl/diffusion bond interface. Creep testing showed that most of the creep elongation occurs in the Ti-alloy, but failure is initiated in the joint bond line. Creep causes degradation and pore formation in this line. Interlinkage of these pores creates a crack which grows slowly until the fracture toughness of the {gamma}-TiAl is exceeded and the crack starts to propagate in the {gamma}-TiAl material and terminates creep life.

  8. 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.

  9. 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.

  10. Hydrogen bonding in a mixture of protic ionic liquids: a molecular dynamics simulation study.

    PubMed

    Paschek, Dietmar; Golub, Benjamin; Ludwig, Ralf

    2015-04-07

    We report results of molecular dynamics (MD) simulations characterising the hydrogen bonding in mixtures of two different protic ionic liquids sharing the same cation: triethylammonium-methylsulfonate (TEAMS) and triethylammonium-triflate (TEATF). The triethylammonium-cation acts as a hydrogen-bond donor, being able to donate a single hydrogen-bond. Both, the methylsulfonate- and the triflate-anions can act as hydrogen-bond acceptors, which can accept multiple hydrogen bonds via their respective SO3-groups. In addition, replacing a methyl-group in the methylsulfonate by a trifluoromethyl-group in the triflate significantly weakens the strength of a hydrogen bond from an adjacent triethylammonium cation to the oxygen-site in the SO3-group of the anion. Our MD simulations show that these subtle differences in hydrogen bond strength significantly affect the formation of differently-sized hydrogen-bonded aggregates in these mixtures as a function of the mixture-composition. Moreover, the reported hydrogen-bonded cluster sizes can be predicted and explained by a simple combinatorial lattice model, based on the approximate coordination number of the ions, and using statistical weights that mostly account for the fact that each anion can only accept three hydrogen bonds.

  11. Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

    PubMed

    Kashid, Somnath M; Jin, Geun Young; Bagchi, Sayan; Kim, Yung Sam

    2015-12-10

    Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

  12. 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.

  13. Solvent dynamical behavior in an organogel phase as studied by NMR relaxation and diffusion experiments.

    PubMed

    Yemloul, Mehdi; Steiner, Emilie; Robert, Anthony; Bouguet-Bonnet, Sabine; Allix, Florent; Jamart-Grégoire, Brigitte; Canet, Daniel

    2011-03-24

    An organogelation process depends on the gelator-solvent pair. This study deals with the solvent dynamics once the gelation process is completed. The first approach used is relaxometry, i.e., the measurement of toluene proton longitudinal relaxation time T(1) as a function of the proton NMR resonance frequency (here in the 5 kHz to 400 MHz range). Pure toluene exhibits an unexpected T(1) variation, which has been identified as paramagnetic relaxation resulting from an interaction of toluene with dissolved oxygen. In the gel phase, this contribution is retrieved with, in addition, a strong decay at low frequencies assigned to toluene molecules within the gel fibers. Comparison of dispersion curves of pure toluene and toluene in the gel phase leads to an estimate of the proportion of toluene embedded within the organogel (found around 40%). The second approach is based on carbon-13 T(1) and nuclear Overhauser effect measurements, the combination of these two parameters providing direct information about the reorientation of C-H bonds. It appears clearly that reorientation of toluene is the same in pure liquid and in the gel phase. The only noticeable changes in carbon-13 longitudinal relaxation times are due to the so-called chemical shift anisotropy (csa) mechanism and reflect slight modifications of the toluene electronic distribution in the gel phase. NMR diffusion measurements by the pulse gradient spin-echo (PGSE) method allow us to determine the diffusion coefficient of toluene inside the organogel. It is roughly two-thirds of the one in pure toluene, thus indicating that self-diffusion is the only dynamical parameter to be slightly affected when the solvent is inside the gel structure. The whole set of experimental observations leads to the conclusion that, once the gel is formed, the solvent becomes essentially passive, although an important fraction is located within the gel structure.

  14. 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.

  15. Dynamic diffuse optical tomography imaging of peripheral arterial disease.

    PubMed

    Khalil, Michael A; Kim, Hyun K; Kim, In-Kyong; Flexman, Molly; Dayal, Rajeev; Shrikhande, Gautam; Hielscher, Andreas H

    2012-09-01

    Peripheral arterial disease (PAD) is the narrowing of arteries due to plaque accumulation in the vascular walls. This leads to insufficient blood supply to the extremities and can ultimately cause cell death. Currently available methods are ineffective in diagnosing PAD in patients with calcified arteries, such as those with diabetes. In this paper we investigate the potential of dynamic diffuse optical tomography (DDOT) as an alternative way to assess PAD in the lower extremities. DDOT is a non-invasive, non-ionizing imaging modality that uses near-infrared light to create spatio-temporal maps of oxy- and deoxy-hemoglobin in tissue. We present three case studies in which we used DDOT to visualize vascular perfusion of a healthy volunteer, a PAD patient and a diabetic PAD patient with calcified arteries. These preliminary results show significant differences in DDOT time-traces and images between all three cases, underscoring the potential of DDOT as a new diagnostic tool.

  16. 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.

  17. 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.

  18. Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes

    NASA Astrophysics Data System (ADS)

    Bodis, Pavol; Yeremenko, Sergiy; Berná, José; Buma, Wybren J.; Leigh, David A.; Woutersen, Sander

    2011-04-01

    We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-HṡṡṡO=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ⩾200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-HṡṡṡO=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales.

  19. Critical Dynamics Behavior of the Wolff Algorithm in the Site-Bond-Correlated Ising Model

    NASA Astrophysics Data System (ADS)

    Campos, P. R. A.; Onody, R. N.

    Here we apply the Wolff single-cluster algorithm to the site-bond-correlated Ising model and study its critical dynamical behavior. We have verified that the autocorrelation time diminishes in the presence of dilution and correlation, showing that the Wolff algorithm performs even better in such situations. The critical dynamical exponents are also estimated.

  20. Topological Properties of Chemical Bonds from Static and Dynamic Electron Densities.

    PubMed

    Jagannatha Prathapa, Siriyara; Held, Jeanette; van Smaalen, Sander

    2013-09-01

    Dynamic and static electron densities (EDs) based on the independent spherical atom model (IAM) and multipole (MP) models of crambin were successfully computed, holding no series-termination effects. The densities are compared to EDs of small biological molecules at diverse temperatures. It is outlined that proteins exhibit an intrinsic flexibility, present as frozen disorder at 100 K, in contrast to small molecules. The flexibility of the proteins is reflected by atomic displacement parameters (B-factors), which are considerably larger than for small molecules at 298 K. Thus, an optimal deconvolution of deformation density and thermal motion is not guaranteed, which prevents a free refinement of MP parameters but allows an application of transferable, fixed MP parameters. The analysis of the topological properties, such as the density at bond critical points (BCPs) and the Laplacian, reveals systematic differences between static and dynamic EDs. Zero-point-vibrations, yet present in dynamic EDs at low temperature, affect but marginally the EDs of small molecules. The zero-point-vibrations cause a smearing of the ED, which becomes more pronounced with increasing temperature. Topological properties, primarily the Laplacian, of covalent bonds appear to be more sensitive to effects by temperature and the polarity of the bonds. However, dynamic EDs at ca. 20 K based on MP models provide a good characterization of chemical bonding. Both the density at BCPs and the Laplacian of hydrogen bonds constitute similar values from static and dynamic EDs for all studied temperatures. Deformation densities demonstrate the necessity of the employment of MP parameters in order to comprise the nature of covalent bonds. The character of hydrogen bonds can be roughly pictured by IAM, whereas MP parameters are recommended for a classification of hydrogen bonds beyond a solely interpretation of topological properties.

  1. Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens.

    PubMed

    Liu, Fang; Du, Likai; Lan, Zhenggang; Gao, Jun

    2017-02-15

    Sinapic acid derivatives are important sunscreen species in natural plants, which could provide protection from solar UV radiation. Using a combination of ultrafast excited state dynamics, together with classical molecular dynamics studies, we demonstrate that there is direct coupling of hydrogen bond motion with excited state photoprotection dynamics as part of the basic mechanism in solution. Beyond the intra-molecular degree of freedom, the inter-molecular motions on all timescales are potentially important for the photochemical or photophysical events, ranging from the ultrafast hydrogen bond motion to solvent rearrangements. This provides not only an enhanced understanding of the anomalous experimental spectroscopic results, but also the key idea in the development of sunscreen agents with improved photo-chemical properties. We suggest that the hydrogen bond dynamics coupled excited state photoprotection mechanism may also be possible in a broad range of bio-related molecules in the condensed phase.

  2. HBonanza: A Computer Algorithm for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis

    PubMed Central

    Durrant, Jacob D.; McCammon, J. Andrew

    2011-01-01

    In the current work, we present a hydrogen-bond analysis of 2,673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its protein receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. PMID:21880522

  3. Thermodynamics of hydration of fullerols [C60(OH)n] and hydrogen bond dynamics in their hydration shells

    NASA Astrophysics Data System (ADS)

    Keshri, Sonanki; Tembe, B. L.

    2017-02-01

    Molecular dynamics simulations of fullerene and fullerols [C60(OH)n, where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules. We have found that water molecules form two solvation shells around the central solute molecule. Hydrogen bonding in the bulk solvent is unaffected by increasing n. The large decrease in solvation enthalpies of these solute molecules for n > 14 enhances solubilisation. The diffusion constants of solute molecules decrease with increasing n. The solvation free energy of C60 in water is positive (52.8 kJ/mol), whereas its value for C60(OH)30 is highly negative (-427.1 kJ/mol). The effects of surface hydroxylation become more dominant once the fullerols become soluble.

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

    PubMed

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

    2010-01-28

    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 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/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 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/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

  5. NMR spectra and translational diffusion of protons in crystals with hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Timokhin, V. M.; Garmash, V. M.; Tarasov, V. P.

    2015-07-01

    Investigation of proton transport in hydrogen-bond crystals at low temperatures is currently one of important problems in the semiconductor physics. With the use of the NMR spectra of wide-band-gap hydrogen-bond crystals grown in H2O and D2O solutions, we have succeeded in finding a direct proof of the presence of protons in the mobile phase, determined their activation energy in good agreement with the spectra of thermally stimulated depolarization currents and with the infrared spectra, and, as a result, clarified the mechanism of proton transport and tunneling.

  6. Diffusion dynamics of synaptic molecules during inhibitory postsynaptic plasticity

    PubMed Central

    Petrini, Enrica Maria; Barberis, Andrea

    2014-01-01

    The plasticity of inhibitory transmission is expected to play a key role in the modulation of neuronal excitability and network function. Over the last two decades, the investigation of the determinants of inhibitory synaptic plasticity has allowed distinguishing presynaptic and postsynaptic mechanisms. While there has been a remarkable progress in the characterization of presynaptically-expressed plasticity of inhibition, the postsynaptic mechanisms of inhibitory long-term synaptic plasticity only begin to be unraveled. At postsynaptic level, the expression of inhibitory synaptic plasticity involves the rearrangement of the postsynaptic molecular components of the GABAergic synapse, including GABAA receptors, scaffold proteins and structural molecules. This implies a dynamic modulation of receptor intracellular trafficking and receptor surface lateral diffusion, along with regulation of the availability and distribution of scaffold proteins. This Review will focus on the mechanisms of the multifaceted molecular reorganization of the inhibitory synapse during postsynaptic plasticity, with special emphasis on the key role of protein dynamics to ensure prompt and reliable activity-dependent adjustments of synaptic strength. PMID:25294987

  7. 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

  8. Molecular dynamics simulations reveal that water diffusion between graphene oxide layers is slow

    SciTech Connect

    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 a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. 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 spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 14% 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. As a result, 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.

  9. Molecular dynamics simulations reveal that water diffusion between graphene oxide layers is slow

    DOE PAGES

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; ...

    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 a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. 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 spacing from about 0.7 nm to 0.8 nm and an increase in mass ofmore » about 14% 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. As a result, 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.« less

  10. Light-induced hydrogen evolution from hydrogenated amorphous silicon: Hydrogen diffusion by formation of bond centered hydrogen

    NASA Astrophysics Data System (ADS)

    Tanimoto, H.; Arai, H.; Mizubayashi, H.; Yamanaka, M.; Sakata, I.

    2014-02-01

    The light-induced hydrogen evolution (LIHE) from amorphous (a-) Si:H by the order of at. % is observed during white light soaking (WLS) of 100-400 mW/cm2 at 350-500 K or ultra violet light soaking (UVLS) of 30-120 mW/cm2 at 305-320 K in a vacuum. The thermal desorption spectroscopy indicates that LIHE originated from bonded hydrogen takes place through the diffusion of light-induced mobile hydrogen (LIMH) with the activation energy of 0.5 eV. LIMH is assigned to bond centered hydrogen and the hydrogen diffusion process becomes prominent when LIMH can leave from a-Si:H such under light soaking in a vacuum above room temperature. For H2 in microvoids, the hydrogen evolution rate is governed by the surface barrier and its activation energy of 1.0 eV in dark decreases to 0.4 eV under WLS or UVLS.

  11. Intermolecular dynamical charge fluctuations in water: a signature of the H-bond network.

    PubMed

    Sharma, Manu; Resta, Raffaele; Car, Roberto

    2005-10-28

    We report a simulation of deuterated water using a Car-Parrinello approach based on maximally localized Wannier functions. This provides local information on the dynamics of the hydrogen-bond network and on the origin of the low-frequency infrared activity. The oscillator strength of the translational modes, peaked around approximately 200 cm-1, is anisotropic and originates from intermolecular--not intramolecular--charge fluctuations. These fluctuations are a signature of a tetrahedral hydrogen-bonding environment.

  12. Catastrophic fault diagnosis in dynamic systems using bond graph methods

    SciTech Connect

    Yarom, Tamar.

    1990-01-01

    Detection and diagnosis of faults has become a critical issue in high performance engineering systems as well as in mass-produced equipment. It is particularly helpful when the diagnosis can be made at the initial design level with respect to a prospective fault list. A number of powerful methods have been developed for aiding in the general fault analysis of designs. Catastrophic faults represent the limit case of complete local failure of connections or components. They result in the interruption of energy transfer between corresponding points in the system. In this work the conventional approach to fault detection and diagnosis is extended by means of bond-graph methods to a wide variety of engineering systems. Attention is focused on catastrophic fault diagnosis. A catastrophic fault dictionary is generated from the system model based on topological properties of the bond graph. The dictionary is processed by existing methods to extract a catastrophic fault report to aid the engineer in performing a design analysis.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    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 Vo/(kBT /e ) , where Vo is the amplitude of the driving voltage and kBT /e is the thermal voltage with kB 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 /λDL , where D is the ion diffusivity, λD 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 (Vo3) 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 Vo. 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 Vo. 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.

  15. Diffusion Bonding of TA15 and Ti2AlNb Alloys: Interfacial Microstructure and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Li, Ping; Ji, Xiaohu; Xue, Kemin

    2017-03-01

    TA15 and Ti2AlNb alloys were joined by diffusion welding. The influence of holding time on morphology and mechanical properties of the joint was studied under two conditions of different bonding pressure and temperature. The interface structure was analyzed by BSE and EDS. The mechanical properties of joints were tested. The results show that the typical interfacial microstructure consists of lath α-phase (TA15 alloy)/flake α phase + α-interfacial phase + α2 phase/B2-rich phase/Ti2AlNb alloy. When bonding at 920 °C and 15 MPa with increasing holding time, the interface microstructure evolves into flake α phase and distributes as a basket-weave and the interfacial coarse spherical α phase distributes as a line. α2 phase and O phase disappear gradually while the content of the B2 phase increases. The tensile strength of the joints is 870, 892 and 903 MPa, for 120, 150 and 210 min holding time, respectively, while the elongation rises as well. When bonding at 940 °C and 10 MPa with increasing holding time, the interfacial area includes more Widmanstatten structure and B2 phase. The tensile strength of joints decreases from 921 to 908 MPa, while the elongation increases from 12 to 15.5%, for holding 120 and 210 min, respectively. The tendency of plastic fracture also increases with holding time for both temperature-pressure combinations.

  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. Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study.

    PubMed

    Zhang, Liqun

    2017-04-01

    Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665-681. © 2016 Wiley Periodicals, Inc.

  18. Structure and hydrogen bond dynamics of water-dimethyl sulfoxide mixtures by computer simulations

    NASA Astrophysics Data System (ADS)

    Luzar, Alenka; Chandler, David

    1993-05-01

    We have used two different force field models to study concentrated dimethyl sulfoxide (DMSO)-water solutions by molecular dynamics. The results of these simulations are shown to compare well with recent neutron diffraction experiments using H/D isotope substitution [A. K. Soper and A. Luzar, J. Chem. Phys. 97, 1320 (1992)]. Even for the highly concentrated 1 DMSO : 2 H2O solution, the water hydrogen-hydrogen radial distribution function, gHH(r), exhibits the characteristic tetrahedral ordering of water-water hydrogen bonds. Structural information is further obtained from various partial atom-atom distribution functions, not accessible experimentally. The behavior of water radial distribution functions, gOO(r) and gOH(r) indicate that the nearest neighbor correlations among remaining water molecules in the mixture increase with increasing DMSO concentration. No preferential association of methyl groups on DMSO is detected. The pattern of hydrogen bonding and the distribution of hydrogen bond lifetimes in the simulated mixtures is further investigated. Molecular dynamics results show that DMSO typically forms two hydrogen bonds with water molecules. Hydrogen bonds between DMSO and water molecules are longer lived than water-water hydrogen bonds. The hydrogen bond lifetimes determined by reactive flux correlation function approach are about 5 and 3 ps for water-DMSO and water-water pairs, respectively, in 1 DMSO : 2 H2O mixture. In contrast, for pure water, the hydrogen bond lifetime is about 1 ps. We discuss these times in light of experimentally determined rotational relaxation times. The relative values of the hydrogen bond lifetimes are consistent with a statistical (i.e., transition state theory) interpretation.

  19. EFFECT OF TEMPERATURE AND GLYCEROL ON THE HYDROGEN-BOND DYNAMICS OF WATER

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, the effect of varying glycerol concentration and temperature on the dynamics of water has not received due attention. We have studied the effect of concentration and temperature on the hydrogen bonded network formed by water molecules. A strong correlation between the relaxation time of the network and average number of hydrogen bonds per water molecules was found. The radial distribution function of water oxygens and hydrogens clarifies the effect of concentration on the structure and clustering of water.

  20. 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.

  1. The dynamics of multimodal integration: The averaging diffusion model.

    PubMed

    Turner, Brandon M; Gao, Juan; Koenig, Scott; Palfy, Dylan; L McClelland, James

    2017-03-08

    We combine extant theories of evidence accumulation and multi-modal integration to develop an integrated framework for modeling multimodal integration as a process that unfolds in real time. Many studies have formulated sensory processing as a dynamic process where noisy samples of evidence are accumulated until a decision is made. However, these studies are often limited to a single sensory modality. Studies of multimodal stimulus integration have focused on how best to combine different sources of information to elicit a judgment. These studies are often limited to a single time point, typically after the integration process has occurred. We address these limitations by combining the two approaches. Experimentally, we present data that allow us to study the time course of evidence accumulation within each of the visual and auditory domains as well as in a bimodal condition. Theoretically, we develop a new Averaging Diffusion Model in which the decision variable is the mean rather than the sum of evidence samples and use it as a base for comparing three alternative models of multimodal integration, allowing us to assess the optimality of this integration. The outcome reveals rich individual differences in multimodal integration: while some subjects' data are consistent with adaptive optimal integration, reweighting sources of evidence as their relative reliability changes during evidence integration, others exhibit patterns inconsistent with optimality.

  2. 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.

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

    PubMed

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

    2017-02-07

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

  4. Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

    PubMed

    Gaspari, Roberto; Rapallo, Arnaldo

    2008-06-28

    In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum

  5. Scaling of the dynamics of flexible Lennard-Jones chains: Effects of harmonic bonds.

    PubMed

    Veldhorst, Arno A; Dyre, Jeppe C; Schrøder, Thomas B

    2015-11-21

    The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic bonds. The introduction of harmonic bonds almost completely destroys the correlations in the equilibrium fluctuations of the potential energy and the virial. According to the isomorph theory, if these correlations are strong a system has isomorphs, curves in the phase diagram along which structure, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bonds does have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as "pseudoisomorphs." In particular, this means that Rosenfeld's excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds.

  6. Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

    The contacts between the N-terminal domain of heat shock protein 90 (N-Hsp90) and ADP involve both direct and water-mediated hydrogen bonds in X-ray crystallographic structure. We perform all-atom molecular dynamics (MD) simulations of N-Hsp90 and ADP to investigate the changes of the hydrogen bond lengths during ADP dissociation. We show the difference between the hydrogen bonds in the crystal structure and MD simulations. Moreover, the N6 group of ADP does not contact with the Cγ group of Asp93, and the hydrogen bonds between Asn51 side chain and ADP are stable in the early step of ADP dissociation.

  7. Hydrogen bonding in liquid methanol, methylamine, and methanethiol studied by molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kosztolányi, T.; Bakó, I.; Pálinkás, G.

    2003-03-01

    Molecular-dynamics computer simulations have been carried out on liquid methanol, methylamine, and methanethiol. The local structure of the liquids was studied based on radial distribution functions and the density projections of the neighboring molecules obtained on the basis of simulated molecular configurations. The extent of hydrogen bonding was investigated by direct analysis of the connectivity of molecules forming hydrogen-bonded clusters in these liquids. By this analysis, the methanol molecules were found to form linear chainlike structures. The local structure of hydrogen-bonded molecules of methylamine proved to be rather space filling due to the great extent of chain branching. Methanethiol molecules also proved to form hydrogen bonds forming small compact clusters. No evidence was found, however, for the clustering of hydrophobic methyl groups in any of the liquids. The quality of simulations was checked by derivation of neutron total and composite radial distribution functions and by comparison of those with available experimental data.

  8. Static and dynamic descriptions of bond breaking/formation: A complementary view?

    NASA Astrophysics Data System (ADS)

    Joubert, Laurent; Adamo, Carlo

    2005-12-01

    Ab initio molecular-dynamic simulations using density-functional theory and the recent atom-centered density-matrix propagation (ADMP) method were used to study the bond breaking and formation for a case-study substitution nucleophilic bimolecular reaction, namely, the Walden inversion. Using the atoms-in-molecule approach, we have performed a detailed analysis to investigate intra- and intermolecular charge transfer along the ADMP trajectory. These results were compared to those obtained considering a static approach, such as the intrinsic reaction path. In particular, the topological properties computed along the dynamic trajectory well evidence a stronger electron exchange tending to spontaneously maximize the rising covalent interaction. Furthermore, their analysis suggests that the bond formation mechanism involves a reactive intermediate with a bonding interaction stronger than in the final product.

  9. The impact of interface bonding efficiency on high-burnup spent nuclear fuel dynamic performance

    SciTech Connect

    Jiang, Hao; Wang, Jy-An John; Wang, Hong

    2016-09-26

    Finite element analysis (FEA) was used to investigate the impact of interfacial bonding efficiency at pellet-pellet and pellet-clad interfaces of high-burnup (HBU) spent nuclear fuel (SNF) on system dynamic performance. Bending moments M were applied to FEA model to evaluate the system responses. From bending curvature, κ, flexural rigidity EI can be estimated as EI = M/κ. The FEA simulation results were benchmarked with experimental results from cyclic integrated reversal bending fatigue test (CIRFT) of HBR fuel rods. The consequence of interface debonding between fuel pellets and cladding is a redistribution of the loads carried by the fuel pellets to the clad, which results in a reduction in composite rod system flexural rigidity. Furthermore, the interface bonding efficiency at the pellet-pellet and pellet-clad interfaces can significantly dictate the SNF system dynamic performance. With the consideration of interface bonding efficiency, the HBU SNF fuel property was estimated with CIRFT test data.

  10. 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).

  11. 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.

  12. Constructing covalent organic frameworks in water via dynamic covalent bonding

    PubMed Central

    Thote, Jayshri; Barike Aiyappa, Harshitha; Rahul Kumar, Raya; Kandambeth, Sharath; Biswal, Bishnu P.; Balaji Shinde, Digambar; Chaki Roy, Neha; Banerjee, Rahul

    2016-01-01

    The formation of keto-enamine based crystalline, porous polymers in water is investigated for the first time. Facile access to the Schiff base reaction in water has been exploited to synthesize stable porous structures using the principles of Dynamic Covalent Chemistry (DCC). Most credibly, the water-based Covalent Organic Frameworks (COFs) possess chemical as well as physical properties such as crystallinity, surface area and porosity, which is comparable to their solvothermal counterparts. The formation of COFs in water is further investigated by understanding the nature of the monomers formed using hydroxy and non-hydroxy analogues of the aldehyde. This synthetic route paves a new way to synthesize COFs using a viable, greener route by utilization of the DCC principles in conjunction with the keto–enol tautomerism to synthesize useful, stable and porous COFs in water. PMID:27840679

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. Liquid-phase diffusion bonding: Temperature effects and solute redistribution in high temperature lead-free composite solders

    SciTech Connect

    Anderson, Iver; Choquette, Stephanie

    2015-05-17

    Liquid-phase diffusion bonding (LPDB) is being studied as the primary phenomena occurring in the development of a high temperature lead-free composite solder paste composed of gas-atomized Cu-10Ni, wt.% (Cu-11Ni, at.%) powder blended with Sn-0.7Cu-0.05Ni-0.01Ge (Sn-1.3Cu-0.1Ni-0.02Ge, at.%) Nihon-Superior SN100C solder powder. Powder compacts were used as a model system. LPDB promotes enhanced interdiffusion of the low-melting alloy matrix with the solid Cu-10Ni reinforcement powder above the matrix liquidus temperature. The initial study involved the effective intermetallic compound (IMC) compositions and microstructures that occur at varying reflow temperatures and times between 250-300°C and 30-60s, respectively. Certain reflow temperatures encourage adequate interdiffusion to form a continuous highly-conductive network throughout the composite solder joints. The diffusion of nickel, in particular, has a disperse pattern that foreshadows the possibility of a highly-conductive low-melting solder that can be successfully utilized at high temperatures.

  19. New results on non-CP dynamics unearthed from urtexts of quantum state diffusion

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos

    2017-04-01

    Thirty years ago, the present author discussed the pure state unraveling (stochastic quantum trajectories) of Markovian open system dynamics. The fact that he considered all positive dynamics, not restricted to the Lindblad–Gorini–Kossakowski–Sudarshan complete-positive subclass, has remained unnoticed so far. We emphasize the importance of the transition-rate-operator W and the merit of the invariant (representation-independent) approach. From the urtexts we point out the condition W≥slant 0 of positive dynamics, the extension of quantum state diffusion for positive dynamics, and as a major new result, the description of all the diffusive unravelings of positive dynamics.

  20. 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.

  1. A Modified Shake Algorithm for Maintaining Rigid Bonds in Molecular Dynamics Simulations of Large Molecules

    NASA Astrophysics Data System (ADS)

    Lambrakos, S. G.; Boris, J. P.; Oran, E. S.; Chandrasekhar, I.; Nagumo, M.

    1989-12-01

    We present a new modification of the SHAKE algorithm, MSHAKE, that maintains fixed distances in molecular dynamics simulations of polyatomic molecules. The MSHAKE algorithm, which is applied by modifying the leapfrog algorithm to include forces of constraint, computes an initial estimate of constraint forces, then iteratively corrects the constraint forces required to maintain the fixed distances. Thus MSHAKE should always converge more rapidly than SHAKE. Further, the explicit determination of the constraint forces at each timestep makes MSHAKE convenient for use in molecular dynamics simulations where bond stress is a significant dynamical quantity.

  2. 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.

  3. Inter-diffusion and its correlation with dynamical cross correlation in liquid Ce80Ni20

    NASA Astrophysics Data System (ADS)

    Hu, J. L.; Zhong, L. X.; Zhu, C. A.; Zhang, B.

    2017-03-01

    We reported the inter-diffusion coefficients in liquid Ce_{80}Ni_{20} measured by the sliding cell technique. Combined with the self-diffusion data of Ni measured by quasi-elastic neutron scattering in the literature, it was found that the relationship between inter-diffusion and self-diffusion in liquid Ce_{80}Ni_{20} was strongly deviated from the standard Darken equation with an abnormally small dynamical cross correlation factor S (the so called Manning factor) in a range of 0.6-0.8, less than unity in standard systems. Through the calculated distinct diffusion coefficient and its deviation from the standard one, it was discovered that the small S value was directly originated from enhanced distinct diffusion between Ce and Ni atoms and reduced distinct diffusion between Ni and Ni atoms. Because the inter-atomic interaction was not considered in the standard liquids, the present small S factor and intrinsic distinct diffusion coefficients were believed to be resulted from the chemical interaction between Ce and Ni in the liquid. The results provide new evidence of the dynamic cross correlation in liquid diffusion, and thus shed light on the understanding of the correlation between dynamics and structure in liquid alloys.

  4. Investigation on W/Fe diffusion bonding using Ti foil and Ti powder interlayer by SPS

    NASA Astrophysics Data System (ADS)

    Chen, Hong-Yu; Luo, Lai-Ma; Zhang, Jun; Zan, Xiang; Zhu, Xiao-Yong; Luo, Guang-Nan; Wu, Yu-Cheng

    2015-12-01

    W/steel composites are being developed for potential application in He gas-cooled divertors and plasma-facing components in fusion reactors. In this study, the dissimilar metal joints between W and Fe were fabricated at 950 °C via spark plasma sintering method with Ti foil (Ti-F) and Ti powder (Ti-P) as the interlayer under Ar atmosphere for 5 min at 57 MPa. Microscopic structures of the W/Fe diffusion joints with Ti-F and Ti-P were investigated and compared via field-emission scanning electron microscopy and energy-dispersive X-ray spectroscopy. Thermal cycling tests were employed to measure the thermal stability of different types of W/Ti/Fe samples. The hardness distribution across joining interfaces was also determined. After thermal cycling tests, a crack occurred along the W/Ti-P interface in the W/Ti-P/Fe samples, whereas the W/Ti-F/Fe samples were intact at the interfaces. Results revealed that Ti-F is more suitable as an interlayer than Ti-P, and the interfaces of the W/Ti-F/Fe samples have better thermal stability than those of the W/Ti-P/Fe ones.

  5. Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

    PubMed Central

    Yamamoto, Eiji; Akimoto, Takuma; Kalli, Antreas C.; Yasuoka, Kenji; Sansom, Mark S. P.

    2017-01-01

    Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:28116358

  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. Dynamics of Plug Formation in a Circular Cylinder Under Low Bond Number Conditions: Experiment and Simulation

    NASA Astrophysics Data System (ADS)

    Hallaby, Ghazi; Kizito, John P.

    2016-08-01

    The goal of the current study is to investigate the dynamics of two phase interface under a low Bond number condition. Silicone oil is injected into a cylinder under a Bond number of about 0.47 via a side tube forming a T-junction with the former. The time evolution of the interface of silicon oil in a cylinder is captured using a high speed camera. The volume at which the plug is formed is then determined using an image processing tool to analyze the captured images. A numerical simulation is carried out where fluid is injected into a cylinder, under a less than unity Bond number condition, via a side tube. Numerical and experimental results are then compared.

  8. 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.

  9. LETTER TO THE EDITOR: Fractal diffusion coefficient from dynamical zeta functions

    NASA Astrophysics Data System (ADS)

    Cristadoro, Giampaolo

    2006-03-01

    Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero.

  10. Molecular Simulations of Hydrogen Bond Cluster Size and Reorientation Dynamics in Liquid and Glassy Azole Systems.

    PubMed

    Sun, Qinfang; Harvey, Jacob A; Greco, Katharine V; Auerbach, Scott M

    2016-10-06

    We simulated the dynamics of azole groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole) as neat liquids and tethered via linkers to aliphatic backbones to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors which are thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to simulate tethered systems over the temperature range 200-900 K and the corresponding neat liquids under liquid state temperatures at standard pressure. We computed hydrogen bond cluster sizes; orientational order parameters; orientational correlation functions associated with functional groups, linkers, and backbones; time scales; and activation energies associated with orientational randomization. All tethered systems exhibit a liquid to glassy-solid transition upon cooling from 600 to 500 K, as evidenced by orientational order parameters and correlation functions. Tethering the azoles was generally found to produce hydrogen bond cluster sizes similar to those in untethered liquids and hydrogen bond lifetimes longer than those in liquids. The simulated rates of functional group reorientation decreased dramatically upon tethering. The activation energies associated with orientational randomization agree well with NMR data for tethered imidazole systems at lower temperatures and for tethered 1,2,3-triazole systems at both low- and high-temperature ranges. Overall, our simulations corroborate the notion that tethering functional groups dramatically slows the process of reorientation. We found a linear correlation between gas-phase hydrogen bond energies and tethered functional group reorientation barriers for all azoles except for imidazole, which acts as an outlier because of both atomic charges and molecular structure.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. "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.

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

    SciTech Connect

    Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; Gainaru, Catalin P.; Sokolov, Alexei P.

    2016-04-06

    Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxy alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.

  20. Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

    DOE PAGES

    Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

    2016-04-06

    Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

  1. 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

    2015-11-05

    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.

  2. 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

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

    SciTech Connect

    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.

    2016-06-23

    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 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.

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

    DOE PAGES

    Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang; ...

    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

  6. A molecular dynamics study of radiation induced diffusion in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Martin, G.; Maillard, S.; Brutzel, L. Van; Garcia, P.; Dorado, B.; Valot, C.

    2009-03-01

    The nuclear oxide fuels are submitted 'in-pile' to strong structural and chemical modifications due to the fissions and temperature. The diffusion of species is notably the result of a thermal activation and of radiation induced diffusion. This study proposes to estimate to what extent the radiation induced diffusion contributes to the diffusion of lattice atoms in UO2. Irradiations are simulated using molecular dynamics simulation by displacement cascades induced by uranium primary knock-on atoms between 1 and 80 keV. As atoms are easier to displace when their vibration amplitude increases, the temperature range which have been investigated is 300-1400 K. Cascade overlaps were also simulated. The material is shown to melt at the end of cascades, yielding a reduced threshold energy displacement. The nuclear contribution to the radiation induced diffusion is compared to thermally activated diffusion under in-reactor and long-term storage conditions.

  7. Magnetic diffusion and ion nonlinear dynamics in magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Zenitani, S.; Shinohara, I.; Nagai, T.; Wada, T.

    2013-12-01

    Magnetic reconnection is a fundamental process in many plasma systems, ranging from laboratory and solar-terrestrial environments to extreme astrophysical settings. The reconnection process is controlled by magnetic dissipation physics in a small-scale region near the reconnection point (X-line), and therefore the structure of the reconnection site is of strong interest. According to the standard picture of collisionless reconnection, the X-line is surrounded by a compact electron diffusion region and by an outer ion diffusion region. While the electron region has been extensively studied, much less is known about the ion region. In this work, we examine key aspects of the ion region in magnetic reconnection. First, we evaluate the ''diffusion'' of magnetic field lines, going back to the topology theorems. Unlike in the MHD, the idealness, the frozen-in, magnetic diffusion, and the energy dissiation can be all different in a kinetic plasma. We will apply these concepts to the reconnection site in two-dimensional particle-in-cell (PIC) simulations. Importantly, in the outer part of the ion region, even though the ion ideal condition is violated, the magnetic fields are frozen to plasma fluids. This raises a serious question to the widespread definition of the ion diffusion region, based on the ion nonidealness. We further examine the ion velocity distribution function in the same region. The distribution function contains multiple populations such as global Speiser ions, local Speiser ions, and trapped ions. The particle motion of the local Speiser ions in an appropriately rotated frame explains the plasma nonidealness. The trapped ions are the first demonstration of the regular orbits in Chen & Palmadesso (1986), in self-consistent PIC simulations. They would be observational signatures in the ion current layer near reconnection sites.

  8. 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.

  9. 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.

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

    PubMed Central

    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. PMID:24748697

  11. 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.

  12. Determination of rotary diffusivity of poly(n-propyl isocyanate) by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Laso, M.; Jimeno, N.; Muneta, L. M.; Müller, M.

    2006-12-01

    The rotational dynamics of a nondilute solution of the rodlike polymer poly(n-propyl isocyanate) (PPIC) has been studied on an atomistic model by means of a large-scale classical molecular dynamics investigation. The rotary diffusivity of PPIC in toluene solution has been determined from the Einsteinian diffusion regime of the end-to-end vector on the surface of the unit sphere and has been found to be Dr=10.5×105(±2.7)s-1, which falls in the range of the experimental data available. A comparison of molecular dynamics predictions with theoretical and perturbation expansion predictions has also been performed.

  13. Determination of rotary diffusivity of poly(n-propyl isocyanate) by molecular dynamics.

    PubMed

    Laso, M; Jimeno, N; Muneta, L M; Müller, M

    2006-12-28

    The rotational dynamics of a nondilute solution of the rodlike polymer poly(n-propyl isocyanate) (PPIC) has been studied on an atomistic model by means of a large-scale classical molecular dynamics investigation. The rotary diffusivity of PPIC in toluene solution has been determined from the Einsteinian diffusion regime of the end-to-end vector on the surface of the unit sphere and has been found to be Dr=10.5x10(5)(+/-2.7) s-1, which falls in the range of the experimental data available. A comparison of molecular dynamics predictions with theoretical and perturbation expansion predictions has also been performed.

  14. 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.

  15. 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 ...

  16. Massively parallel dual control volume grand canonical molecular dynamics with LADERA II. Gradient driven diffusion through polymers

    NASA Astrophysics Data System (ADS)

    Ford Grant, David M.; Heffelfinger, S.

    This paper, the second part of a series, extends the capabilities of the LADERA FORTRAN code for massively parallel dual control volume grand canonical molecular dynamics (DCVGCMD). DCV-GCMD is a hybrid of two more common molecular simulation techniques (grand canonical Monte Carlo and molecular dynamics) which allows the direct molecularlevel modelling of diffusion under a chemical potential gradient. The present version of the code, LADERA-B has the capability of modelling systems with explicit intramolecular interactions such as bonds, angles, and dihedral rotations. The utility of the new code for studying gradient-driven diffusion of small molecules through polymers is demonstrated by applying it to two model systems. LADERA-B includes another new feature, which is the use of neighbour lists in force calculations. This feature increases the speed of the code but presents several challenges in the parallel hybrid algorithm. There is discussion on how these problems were addressed and how our implementation results in a significant increase in speed over the original LADERA. Scaling results are presented for LADERA-B on two massively parallel message-passing machines.

  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. The impact of interface bonding efficiency on high-burnup spent nuclear fuel dynamic performance

    DOE PAGES

    Jiang, Hao; Wang, Jy-An John; Wang, Hong

    2016-09-26

    Finite element analysis (FEA) was used to investigate the impact of interfacial bonding efficiency at pellet-pellet and pellet-clad interfaces of high-burnup (HBU) spent nuclear fuel (SNF) on system dynamic performance. Bending moments M were applied to FEA model to evaluate the system responses. From bending curvature, κ, flexural rigidity EI can be estimated as EI = M/κ. The FEA simulation results were benchmarked with experimental results from cyclic integrated reversal bending fatigue test (CIRFT) of HBR fuel rods. The consequence of interface debonding between fuel pellets and cladding is a redistribution of the loads carried by the fuel pellets tomore » the clad, which results in a reduction in composite rod system flexural rigidity. Furthermore, the interface bonding efficiency at the pellet-pellet and pellet-clad interfaces can significantly dictate the SNF system dynamic performance. With the consideration of interface bonding efficiency, the HBU SNF fuel property was estimated with CIRFT test data.« less

  19. 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

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

    PubMed

    Yang, Jianjun; Tse, John S

    2011-11-17

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

  1. 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.

  2. Computation of the hindrance factor for the diffusion for nanoconfined ions: molecular dynamics simulations versus continuum-based models

    NASA Astrophysics Data System (ADS)

    Zhu, Haochen; Ghoufi, Aziz; Szymczyk, Anthony; Balannec, Béatrice; Morineau, Denis

    2012-06-01

    We report the self-diffusion coefficients and hindrance factor for the diffusion of ions into cylindrical hydrophilic silica nanopores (hydrated silica) determined from molecular dynamics (MD) simulations. We make a comparison with the hindered diffusion coefficients used in continuum-based models of nanofiltration (NF). Hindrance factors for diffusion estimated from the macroscopic hydrodynamic theory were found to be in fair quantitative agreement with MD simulations for a protonated pore, but they strongly overestimate diffusion inside a deprotonated pore.

  3. 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 .

  4. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

    PubMed

    Park, Kyung-Lae

    2017-01-01

    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  5. 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.

  6. 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.

  7. Diffusion of molecules in the bulk of a low density amorphous ice from molecular dynamics simulations.

    PubMed

    Ghesquière, P; Mineva, T; Talbi, D; Theulé, P; Noble, J A; Chiavassa, T

    2015-05-07

    The diffusion of molecules in interstellar ice is a fundamental phenomenon to take into account while studying the formation of complex molecules in this ice. This work presents a theoretical study on the diffusion of H2O, NH3, CO2, CO, and H2CO in the bulk of a low density amorphous (LDA) ice, while taking into account the physical conditions prevailing in space, i.e. temperatures below 150 K and extremely low pressure. This study was undertaken by means of molecular dynamics simulations. For CO2 for which no experimental data were available we conducted our own experiments. From our calculations we show that, at low temperatures, the diffusion of molecules in the bulk of a LDA ice is driven by the self-diffusion of water molecules in the ice. With this study we demonstrate that molecular dynamics allows the calculation of diffusion coefficients for small molecules in LDA ice that are convincingly comparable to experimentally measured diffusion coefficients. We also provide diffusion coefficients for a series of molecules of astrochemical interest.

  8. 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

  9. Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2

    NASA Astrophysics Data System (ADS)

    Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori

    2005-07-01

    An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.

  10. Synchronization and local convergence analysis of networks with dynamic diffusive coupling

    NASA Astrophysics Data System (ADS)

    Burbano Lombana, Daniel Alberto; di Bernardo, Mario

    2016-11-01

    In this paper, we address the problem of achieving synchronization in networks of nonlinear units coupled by dynamic diffusive terms. We present two types of couplings consisting of a static linear term, corresponding to the diffusive coupling, and a dynamic term which can be either the integral or the derivative of the sum of the mismatches between the states of neighbouring agents. The resulting dynamic coupling strategy is a distributed proportional-integral (PI) or a proportional-derivative (PD) law that is shown to be effective in improving the network synchronization performance, for example, when the dynamics at nodes are nonidentical. We assess the stability of the network by extending the classical Master Stability Function approach to the case where the links are dynamic ones of PI/PD type. We validate our approach via a set of representative examples including networks of chaotic Lorenz and networks of nonlinear mechanical systems.

  11. Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Desai, Tapan; Keblinski, Pawel

    2003-03-01

    SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

  12. A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2.

    PubMed

    Alavi, Saman; Ohmura, Ryo; Ripmeester, John A

    2011-02-07

    Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO(2) molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

  13. Dynamical Symmetry Breaking and Phase Transitions in Driven Diffusive Systems

    NASA Astrophysics Data System (ADS)

    Baek, Yongjoo; Kafri, Yariv; Lecomte, Vivien

    2017-01-01

    We study the probability distribution of a current flowing through a diffusive system connected to a pair of reservoirs at its two ends. Sufficient conditions for the occurrence of a host of possible phase transitions both in and out of equilibrium are derived. These transitions manifest themselves as singularities in the large deviation function, resulting in enhanced current fluctuations. Microscopic models which implement each of the scenarios are presented, with possible experimental realizations. Depending on the model, the singularity is associated either with a particle-hole symmetry breaking, which leads to a continuous transition, or in the absence of the symmetry with a first-order phase transition. An exact Landau theory which captures the different singular behaviors is derived.

  14. 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

  15. Dynamical behavior of a dangling bond dimer on a hydrogenated semiconductor: Ge(001):H

    NASA Astrophysics Data System (ADS)

    Godlewski, Szymon; Kolmer, Marek; Lis, Jakub; Zuzak, Rafal; Such, Bartosz; Gren, Wojciech; Szymonski, Marek; Kantorovich, Lev

    2015-09-01

    We show that a dangling bond (DB) dimer on Ge(001):H exhibits a dynamical behavior when the empty states are imaged with scanning tunneling microscopy (STM) at liquid helium temperature. Large amplitude Ge atom vibrations are decisive in facilitating a specific appearance of the structure in the STM images. The underlying mechanism is unraveled using a theoretical model and calculations within the density functional theory framework. Furthermore, we demonstrate the ability to induce controlled switching of the DB dimer with noncontact atomic force microscope and the stabilizing role of the dimer-dimer interaction.

  16. Monte Carlos studies of critical and dynamic phenomena in mixed bond Ising model

    NASA Astrophysics Data System (ADS)

    Santos-Filho, J. B.; Moreno, N. O.; de Albuquerque, Douglas F.

    2010-11-01

    The phase transition of a random mixed-bond Ising ferromagnet on a cubic lattice model is studied both numerically and analytically. In this work, we use the Metropolis and Wolff algorithm with histogram technique and finite size scaling theory to simulate the dynamics of the system. We obtained the thermodynamic quantities such as magnetization, susceptibility, and specific heat. Our results were compared with those obtained using a new technique in effective field theory that employs similar probability distribution within the framework of two-site clusters.

  17. Using molecular dynamics to obtain Maxwell-Stefan diffusion coefficients in liquid systems

    NASA Astrophysics Data System (ADS)

    van de Ven-Lucassen Thijs, Irma M. J. J.; Vlugt Antonius, J. H.; van der Zanden Piet, J. J.; Kerkhof, J. A. M.

    Two methods are compared for the calculation of Maxwell-Stefan diffusion coefficients. The first method is a non-equilibrium molecular dynamics (NEMD) algorithm, in which the system is driven away from equilibrium and the system response is monitored. The second method is the equilibrium molecular dynamics (EMD) calculation of the appropriate GreenKubo equation. Simulations were performed for systems of 250 and 300 Lennard-Jones particles at various densities and temperatures. The systems were divided into two or three components by attaching a colour label to the particles. Since a colour label plays no role in the dynamics, the Maxwell-Stefan diffusion coefficients of the binary and ternary systems are equal to the self-diffusion coefficient. In dense fluids, the system response to an external perturbation is not a first-order process, and the diffusion coefficients cannot be determined from the short term response in the NEMD method. Only the long term response can be used, after a steady state has been reached. In binary systems the Maxwell-Stefan diffusion coefficients, determined by the Green-Kubo (EMD) method, are more accurate than the NEMD coefficients. Since in the NEMD method only the long term response can be used, the GreenKubo method is also less time consuming and is therefore preferred for the calculation of the Maxwell-Stefan diffusion coefficients. In ternary systems the Green-Kubo method is tested for the 250 particle system. The Maxwell-Stefan diffusion coefficients agree well with the selfdiffusion coefficient. For low mole fractions of the coloured components the diffusion coefficients were less accurate.

  18. Dynamical effect of confining wall on diffusion of fluid at nanoscale

    NASA Astrophysics Data System (ADS)

    Devi, Reena; Srivastava, Sunita; Tankeshwar, K.

    2016-05-01

    The dynamical effect of wall-fluid interaction on diffusion in direction perpendicular to confining walls has been studied, theoretically. The properties of fluids which incorporates the effect of static changes in confined fluid has been modified to include, directly, the dynamical effects of wall on the motion of particles. The results obtained for VACF in perpendicular direction of channel of width of two atomic diameters are presented and compared with the molecular dynamic (MD) simulation results as well as the results obtained without including the dynamical effect.

  19. 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

  20. 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

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

    PubMed

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

    2011-12-13

    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.

  2. Effect of cell and microvillus mechanics on the transmission of applied loads to single bonds in dynamic force spectroscopy

    NASA Astrophysics Data System (ADS)

    Gupta, V. K.; Eggleton, C. D.

    2011-07-01

    Receptor-ligand interactions that mediate cellular adhesion are often subjected to forces that regulate their detachment via modulating off-rates. Although the dynamics of detachment is primarily controlled by the physical chemistry of adhesion molecules, cellular features such as cell deformability and microvillus viscoelasticity have been shown to affect the rolling velocity of leukocytes in vitro through experiments and simulation. In this work, we demonstrate via various micromechanical models of two cells adhered by a single (intramolecular) bond that cell deformability and microvillus viscoelasticity modulate transmission of an applied external load to an intramolecular bond, and thus the dynamics of detachment. Specifically, it is demonstrated that the intermolecular bond force is not equivalent to the instantaneous applied force and that the instantaneous bond force decreases with cellular and microvillus compliance. As cellular compliance increases, not only does the time lag between the applied load and the bond force increase, an initial response time is observed during which cell deformation is observed without transfer of force to the bond. It is further demonstrated that following tether formation the instantaneous intramoleular bond force increases linearly at a rate dependent on microvillus viscosity. Monte Carlo simulations with fixed kinetic parameters predict that both cell and microvillus compliance increase the average rupture time, although the average rupture force based on bond length remains nearly unchanged.

  3. 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.

  4. 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.

  5. The Dynamics of Controlled Flow Separation within a Diverter Duct Diffuser

    NASA Astrophysics Data System (ADS)

    Peterson, C. J.; Vukasinovic, B.; Glezer, A.

    2016-11-01

    The evolution and receptivity to fluidic actuation of the flow separation within a rectangular, constant-width, diffuser that is branched off of a primary channel is investigated experimentally at speeds up to M = 0.4. The coupling between the diffuser's adverse pressure gradient and the internal separation that constricts nearly half of the flow passage through the duct is controlled using a spanwise array of fluidic actuators on the surface upstream of the diffuser's inlet plane. The dynamics of the separating surface vorticity layer in the absence and presence of actuation are investigated using high-speed particle image velocimetry combined with surface pressure measurements and total pressure distributions at the primary channel's exit plane. It is shown that the actuation significantly alters the incipient dynamics of the separating vorticity layer as the characteristic cross stream scales of the boundary layer upstream of separation and of the ensuing vorticity concentrations within the separated flow increase progressively with actuation level. It is argued that the dissipative (high frequency) actuation alters the balance between large- and small-scale motions near separation by intensifying the large-scale motions and limiting the small-scale dynamics. Controlling separation within the diffuser duct also has a profound effect on the global flow. In the presence of actuation, the mass flow rate in the primary duct increases 10% while the fraction of the diverted mass flow rate in the diffuser increases by more than 45% at 0.7% actuation mass fraction. Supported by the Boeing Company.

  6. 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.

  7. A chiroptical switch based on supramolecular chirality transfer through alkyl chain entanglement and dynamic covalent bonding.

    PubMed

    Lv, Kai; Qin, Long; Wang, Xiufeng; Zhang, Li; Liu, Minghua

    2013-12-14

    Chirality transfer is an interesting phenomenon in Nature, which represents an important step to understand the evolution of chiral bias and the amplification of the chirality. In this paper, we report the chirality transfer via the entanglement of the alkyl chains between chiral gelator molecules and achiral amphiphilic Schiff base. We have found that although an achiral Schiff base amphiphile could not form organogels in any kind of organic solvents, it formed co-organogels when mixed with a chiral gelator molecule. Interestingly, the chirality of the gelator molecules was transferred to the Schiff base chromophore in the mixed co-gels and there was a maximum mixing ratio for the chirality transfer. Furthermore, the supramolecular chirality was also produced based on a dynamic covalent chemistry of an imine formed by the reaction between an aldehyde and an amine. Such a covalent bond of imine was formed reversibly depending on the pH variation. When the covalent bond was formed the chirality transfer occurred, when it was destroyed, the transfer stopped. Thus, a supramolecular chiroptical switch is obtained based on supramolecular chirality transfer and dynamic covalent chemistry.

  8. Elucidation of the relationships between H-bonding patterns and excited state dynamics in cyclovalone.

    PubMed

    Lamperti, Marco; Maspero, Angelo; Tønnesen, Hanne H; Bondani, Maria; Nardo, Luca

    2014-08-28

    Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should produce an enhanced phototoxicity. Indeed, although curcumin exhibits photosensitized antibacterial activity, this compound is characterized by very fast excited-state dynamics which limit its efficacy as a photosensitizer. In previous works we showed that the main non-radiative decay pathway of keto-enolic curcuminoids is through excited-state transfer of the enolic proton to the keto-oxygen. Another effective deactivation pathway involves an intermolecular charge transfer mechanism occurring at the phenyl rings, made possible by intramolecular H-bonding between the methoxy and the hydroxyl substituent. In this paper we present UV-Vis and IR absorption spectra data with the aim of elucidating the intramolecular charge distribution of this compound and its solvation patterns in different environments, with particular focus on solute-solvent H-bonding features. Moreover, we discuss steady state and time-resolved fluorescence data that aim at characterizing the excited-state dynamics of cyclovalone, and we compare its decay photophysics to that of curcumin. Finally, because during the characterization procedures we found evidence of very fast photodegradation of cyclovalone, its photostability in four organic solvents was studied by HPLC and the corresponding relative degradation rates were calculated.

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

    DOE PAGES

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

    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

  10. Shape optimization of the diffuser blade of an axial blood pump by computational fluid dynamics.

    PubMed

    Zhu, Lailai; Zhang, Xiwen; Yao, Zhaohui

    2010-03-01

    Computational fluid dynamics (CFD) has been a viable and effective way to predict hydraulic performance, flow field, and shear stress distribution within a blood pump. We developed an axial blood pump with CFD and carried out a CFD-based shape optimization of the diffuser blade to enhance pressure output and diminish backflow in the impeller-diffuser connecting region at a fixed design point. Our optimization combined a computer-aided design package, a mesh generator, and a CFD solver in an automation environment with process integration and optimization software. A genetic optimization algorithm was employed to find the pareto-optimal designs from which we could make trade-off decisions. Finally, a set of representative designs was analyzed and compared on the basis of the energy equation. The role of the inlet angle of the diffuser blade was analyzed, accompanied by its relationship with pressure output and backflow in the impeller-diffuser connecting region.

  11. 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.

  12. 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.

  13. 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.

  14. Molecular dynamics simulations of the rotational and translational diffusion of a Janus rod-shaped nanoparticle

    NASA Astrophysics Data System (ADS)

    Kharazmi, Ali; Priezjev, Nikolai

    2016-11-01

    We investigate the diffusion of a Janus nanoparticle immersed in a dense Lennard-Jones fluid using molecular dynamic simulations. In particular we consider a rod-shaped particle with different surface wettability on each half-side of the particle and analyze the mean square displacement and the translational and rotational velocity autocorrelation functions. It is found that diffusion is enhanced when the wettability contrast is high and the local slip length on the nonwetting side is relatively large. We also examine the time evolution of the orientation tensor and correlate it with the particle displacement. These results are compared with our previously published results on diffusive dynamics of a Janus sphere with two hemispheres of different wettability.

  15. 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.

  16. Studying complex fluids and crystal formation using Dynamic Light Scattering and Optical Probe Diffusion

    NASA Astrophysics Data System (ADS)

    Streletzky, Kiril A.

    2004-10-01

    Dynamic light scattering (DLS) spectroscopy provides non-destructive analytic technique for probing structure and dynamics of polymer solutions, colloids, micellar systems, liquid crystals, and, in some cases, observation of nucleation and crystal growth. The method of optical probe diffusion uses DLS to measure transport of dilute mesoscopic probes in a complex fluid solution. If tracer particles are the dominant scatterers in solution, their diffusion provides important information for inferring physical properties of the complex fluid. In situ nature of DLS allows non-invasive studies of different chemical and physical processes such as polymer and colloidal diffusion, gelation, micellar aggregation and dynamics. DLS is also useful for studying critical behavior of liquid crystals and for observing crystallization from clear solutions. The highlights of our results obtained using DLS and optical probe diffusion are presented. These examples include: a) research on polymer dynamics in dilute and concentrated solutions of a neutral HPC polymer; b) project on aggregation and transport of spherical Tx-100 micelles; c) study of crystallization of molecular sieve zeolite NaA.

  17. 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.

  18. 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

  19. Molecular dynamics study of polystyrene bond-breaking and crosslinking under C60 and Arn cluster bombardment

    NASA Astrophysics Data System (ADS)

    Czerwinski, Bartlomiej; Postawa, Zbigniew; Garrison, Barbara J.; Delcorte, Arnaud

    2013-05-01

    Molecular dynamics computer simulations are used to elucidate the bond-breaking and crosslinking processes induced by 2.5 keV C60 and Arn cluster bombardment in an amorphous sec-butyl-terminated polystyrene sample. The obtained results indicate that replacement of C60 by Ar18 or Ar60 projectiles leads to the decrease of the number of broken bonds and, hence, to the decrease of formation of new intra- and intermolecular (crosslinking) bonds. When the number of atoms in the Arn cluster is increased from 60 to 250 or more, the total number of broken bonds and the total number of newly created bonds reach a zero value. Additional comparison to the case of a fullerite crystal reveals that the change of material properties leads to almost 7.5-fold reduction of the efficiency of the crosslinking process.

  20. 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.

  1. 'Dynamic Distance' Reaction Coordinate for Competing Bonds:  Applications in Classical and Ab Initio Simulations.

    PubMed

    Burisch, Christian; Markwick, Phineus R L; Doltsinis, Nikos L; Schlitter, Jürgen

    2008-01-01

    A versatile reaction coordinate, the "dynamic distance", is introduced for the study of reactions involving the rupture and formation of a series of chemical bonds or contacts. The dynamic distance is a mass-weighted mean of selected distances. When implemented as a generalized constraint, the dynamic distance is particularly suited for driving activated processes by controlled increase during a simulation. As a single constraint acting upon multiple degrees of freedom, the sequence of events along the resulting reaction pathway is determined unambiguously by the underlying energy landscape. Free energy profiles can be readily obtained from the mean constraint force. In this paper both theoretical aspects and numerical implementation are discussed, and the unique and diverse properties of this reaction coordinate are demonstrated using three examples:  In the framework of Car-Parrinello molecular dynamics, we present results for the prototypical double proton-transfer reaction in formic acid dimer and the photocycle of the guanine-cytosine DNA base pair. As a classical mechanical example, the opening of the binding pocket of the enzyme rubisco is analyzed.

  2. Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics.

    PubMed

    Zhou, Da; Qian, Hong

    2011-09-01

    Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical "device" that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.

  3. Effects of Heterogeneous Diffuse Fibrosis on Arrhythmia Dynamics and Mechanism

    NASA Astrophysics Data System (ADS)

    Kazbanov, Ivan V.; Ten Tusscher, Kirsten H. W. J.; Panfilov, Alexander V.

    2016-02-01

    Myocardial fibrosis is an important risk factor for cardiac arrhythmias. Previous experimental and numerical studies have shown that the texture and spatial distribution of fibrosis may play an important role in arrhythmia onset. Here, we investigate how spatial heterogeneity of fibrosis affects arrhythmia onset using numerical methods. We generate various tissue textures that differ by the mean amount of fibrosis, the degree of heterogeneity and the characteristic size of heterogeneity. We study the onset of arrhythmias using a burst pacing protocol. We confirm that spatial heterogeneity of fibrosis increases the probability of arrhythmia induction. This effect is more pronounced with the increase of both the spatial size and the degree of heterogeneity. The induced arrhythmias have a regular structure with the period being mostly determined by the maximal local fibrosis level. We perform ablations of the induced fibrillatory patterns to classify their type. We show that in fibrotic tissue fibrillation is usually of the mother rotor type but becomes of the multiple wavelet type with increase in tissue size. Overall, we conclude that the most important factor determining the formation and dynamics of arrhythmia in heterogeneous fibrotic tissue is the value of maximal local fibrosis.

  4. 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.

  5. Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis.

    PubMed

    Globus, Tatiana; Sizov, Igor; Gelmont, Boris

    2014-01-01

    Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35-0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, OH-N and OH-C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2-3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

  6. 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.

  7. 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.

  8. Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface.

    PubMed

    Vila Verde, Ana; Bolhuis, Peter G; Campen, R Kramer

    2012-08-09

    We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

  9. 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%).

  10. Study of the continuous/diffuse aurora using particle observations from the Dynamics Explorer satellites

    NASA Astrophysics Data System (ADS)

    Sharber, J. R.; Winningham, J. D.

    1988-10-01

    The continuous/diffuse (C/D) aurora and related auroral studies are used as the primary data observations from instruments on the Dynamics Explorer satellites. These satellites carried particle detection instrumentation referred to as the High Altitude Plasma Instrument (HAPI) on the DE-1 and the Low Altitude Plasma Instrument (LAPI) on DE-2, and together provided high resolution spectral and angular measurements of electron and positive ions at altitudes between 500 km and 4 R sub E above the auroral region. The objectives of the research are: (1) to provide a thorough description of the particle populations which produce the quiet and activated continuous/diffuse aurora, (2) to attempt to determine what mechanisms act within the plasma sheet and on supra-auroral field lines to precipitate the continuous/diffuse auroral particles, (3) to attempt to find a simple and effective way to model the effects of this aurora and (4), added during the first year of the contract, applying the Dynamics Explorer database to selective investigations of of the high-latitude auroral regions. Research has included a description of quiet and disturbed diffuse auroral particles, a study of particles and waves in the diffuse aurora, an attempt to determine the mechanisms of the precipitation, and studies of polar arcs, ionization, and convection in the high-latitude regions.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  13. Dynamics of surface catalyzed reactions; the roles of surface defects, surface diffusion, and hot electrons.

    PubMed

    Somorjai, Gabor A; Bratlie, Kaitlin M; Montano, Max O; Park, Jeong Y

    2006-10-12

    The mechanism that controls bond breaking at transition metal surfaces has been studied with sum frequency generation (SFG), scanning tunneling microscopy (STM), and catalytic nanodiodes operating under the high-pressure conditions. The combination of these techniques permits us to understand the role of surface defects, surface diffusion, and hot electrons in dynamics of surface catalyzed reactions. Sum frequency generation vibrational spectroscopy and kinetic measurements were performed under 1.5 Torr of cyclohexene hydrogenation/dehydrogenation in the presence and absence of H(2) and over the temperature range 300-500 K on the Pt(100) and Pt(111) surfaces. The structure specificity of the Pt(100) and Pt(111) surfaces is exhibited by the surface species present during reaction. On Pt(100), pi-allyl c-C6H9, cyclohexyl (C6H11), and 1,4-cyclohexadiene are identified adsorbates, while on the Pt(111) surface, pi-allyl c-C6H9, 1,4-cyclohexadiene, and 1,3-cyclohexadiene are present. A scanning tunneling microscope that can be operated at high pressures and temperatures was used to study the Pt(111) surface during the catalytic hydrogenation/dehydrogenation of cyclohexene and its poisoning with CO. It was found that catalytically active surfaces were always disordered, while ordered surface were always catalytically deactivated. Only in the case of the CO poisoning at 350 K was a surface with a mobile adsorbed monolayer not catalytically active. From these results, a CO-dominated mobile overlayer that prevents reactant adsorption was proposed. By using the catalytic nanodiode, we detected the continuous flow of hot electron currents that is induced by the exothermic catalytic reaction. During the platinum-catalyzed oxidation of carbon monoxide, we monitored the flow of hot electrons over several hours using a metal-semiconductor Schottky diode composed of Pt and TiO2. The thickness of the Pt film used as the catalyst was 5 nm, less than the electron mean free path

  14. 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.

  15. 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.

  16. Theory of relaxation dynamics in glass-forming hydrogen-bonded liquids

    NASA Astrophysics Data System (ADS)

    Hentschel, H. G. E.; Procaccia, Itamar

    2008-03-01

    We address the relaxation dynamics in hydrogen-bonded supercooled liquids near (but above) the glass transition, measured via broadband dielectric spectroscopy (BDS). We propose a theory based on decomposing the relaxation of the macroscopic dipole moment into contributions from hydrogen-bonded clusters of s molecules, with smin≤s≤smax . The existence of smax is translated into a sum rule on the concentrations of clusters of size s . We construct the statistical mechanics of the supercooled liquid subject to this sum rule as a constraint, to estimate the temperature-dependent density of clusters of size s . With a theoretical estimate of the relaxation time of each cluster, we provide predictions for the real and imaginary parts of the frequency-dependent dielectric response. The predicted spectra and their temperature dependence are in accord with measurements, explaining a host of phenomenological fits like the Vogel-Fulcher fit and the stretched exponential fit. Using glycerol as a particular example, we demonstrate quantitative correspondence between theory and experiments. The theory also demonstrates that the α peak and the “excess wing” stem from the same physics in this material. The theory also shows that in other hydrogen-bonded glass formers the excess wing can develop into a β peak, depending on the molecular material parameters (predominantly the surface energy of the clusters). We thus argue that α and β peaks can stem from the same physics. We address the BDS in constrained geometries (pores) and explain why recent experiments on glycerol did not show a deviation from bulk spectra. Finally, we discuss the dc part of the BDS spectrum and argue why it scales with the frequency of the α peak, providing an explanation for the remarkable data collapse observed in experiments.

  17. 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.

  18. 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.

  19. 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).

  20. 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

  1. 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

  2. On the Dynamics of Some Discretizations of Convection-Diffusion Equations

    NASA Technical Reports Server (NTRS)

    Sweby, Peter K.; Yee, H. C.; Rai, Man Mohan (Technical Monitor)

    1995-01-01

    Numerical discretizations of differential equations which model physical processes can possess dynamics quite different from that of the equations themselves. Recently the emphasis has been on the the dynamics of numerical discretizations for Ordinary Differential Equations (ODEs). For Partial Differential Equations (PDEs) using a method of lines approach the situation is more complex. First, the spatial discretisation may introduce dynamics not present in the original equations; second, the solution of the resulting system of ODEs is open to the modified dynamics of the ODE solver used. These two effects may interact in a complex manner. In this talk we present some results of our recent work on the dynamics of discretizations of convection-diffusion equations, including those produced using Total Variation Diminishing (TVD) schemes and adaptive grid techniques. A more general overview of the area may be found on our accompanying poster presentation.

  3. Dynamical invariants in a non-Markovian quantum-state-diffusion equation

    NASA Astrophysics Data System (ADS)

    Luo, Da-Wei; Pyshkin, P. V.; Lam, Chi-Hang; Yu, Ting; Lin, Hai-Qing; You, J. Q.; Wu, Lian-Ao

    2015-12-01

    We find dynamical invariants for open quantum systems described by the non-Markovian quantum-state-diffusion (QSD) equation. In stark contrast to closed systems where the dynamical invariant can be identical to the system density operator, these dynamical invariants no longer share the equation of motion for the density operator. Moreover, the invariants obtained with a biorthonormal basis can be used to render an exact solution to the QSD equation and the corresponding non-Markovian dynamics without using master equations or numerical simulations. Significantly we show that we can apply these dynamical invariants to reverse engineering a Hamiltonian that is capable of driving the system to the target state, providing a different way to design control strategy for open quantum systems.

  4. 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.

  5. 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

    2016-09-08

    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.

  6. 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.

  7. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

    Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

  8. Unified model of brain tissue microstructure dynamically binds diffusion and osmosis with extracellular space geometry.

    PubMed

    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=sqrt[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.

  9. 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.

  10. 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.

  11. 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

  12. Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections.

    PubMed

    Nakamura, Masaaki; Tsai, Po-Yu; Kasai, Toshio; Lin, King-Chuen; Palazzetti, Federico; Lombardi, Andrea; Aquilanti, Vincenzo

    2015-01-01

    Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v=1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v=0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through "roaming" pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

  13. Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases.

    PubMed

    Shih, Andrew J; Telesco, Shannon E; Choi, Sung-Hee; Lemmon, Mark A; Radhakrishnan, Ravi

    2011-06-01

    The EGFR (epidermal growth factor receptor)/ErbB/HER (human EGFR) family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signalling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of three members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4), in different molecular contexts: monomer against dimer and wild-type against mutant. Using bioinformatics and fluctuation analyses of the molecular dynamics trajectories, we relate sequence similarities to correspondence of specific bond-interaction networks and collective dynamical modes. We find that in the active conformation of the ErbB kinases, key subdomain motions are co-ordinated through conserved hydrophilic interactions: activating bond-networks consisting of hydrogen bonds and salt bridges. The inactive conformations also demonstrate conserved bonding patterns (albeit less extensive) that sequester key residues and disrupt the activating bond network. Both conformational states have distinct hydrophobic advantages through context-specific hydrophobic interactions. We show that the functional (activating) asymmetric kinase dimer interface forces a corresponding change in the hydrophobic and hydrophilic interactions that characterize the inactivating bond network, resulting in motion of the αC-helix through allostery. Several of the clinically identified activating kinase mutations of EGFR act in a similar fashion to disrupt the inactivating bond network. The present molecular dynamics study reveals a fundamental difference in the sequence of events in EGFR activation compared with that described for the Src kinase Hck.

  14. Sub-diffusion and population dynamics of water confined in soft environments

    NASA Astrophysics Data System (ADS)

    Hanot, Samuel; Lyonnard, Sandrine; Mossa, Stefano

    2016-02-01

    We have studied by using molecular dynamics computer simulations the dynamics of water confined in ionic surfactant phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed in depth the main dynamical features in terms of mean-squared displacements and intermediate scattering functions, and found clear evidence of sub-diffusive behaviour. We have identified water molecules lying at the charged interface with the hydrophobic confining matrix as the main factor responsible for this unusual feature, and given a comprehensive picture of dynamics based on a very precise analysis of lifetimes at the interface. We conclude by providing, for the first time to our knowledge, a unique framework for rationalizing the existence of important dynamical heterogeneities in fluids adsorbed in soft confining environments.We have studied by using molecular dynamics computer simulations the dynamics of water confined in ionic surfactant phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed in depth the main dynamical features in terms of mean-squared displacements and intermediate scattering functions, and found clear evidence of sub-diffusive behaviour. We have identified water molecules lying at the charged interface with the hydrophobic confining matrix as the main factor responsible for this unusual feature, and given a comprehensive picture of dynamics based on a very precise analysis of lifetimes at the interface. We conclude by providing, for the first time to our knowledge, a unique framework for rationalizing the existence of important dynamical heterogeneities in fluids adsorbed in soft confining environments. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR05853H

  15. Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite.

    PubMed

    van den Berg, A W C; Bromley, S T; Flikkema, E; Wojdel, J; Maschmeyer, Th; Jansen, J C

    2004-06-01

    In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700-1200 K, the diffusion coefficient is found to range from 1.610(-10) to 1.810(-9) m(2)/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the application of transition state theory, which, together with the finding that the pre-exponential factor in the Arrhenius-type equation for the hopping rate is temperature-independent, enables extrapolation of our results to lower temperatures. Estimates based on mass penetration theory calculations indicate a promising hydrogen uptake rate at 573 K.

  16. Nonlinear Diffusion Filtering of the GOCE-Based Satellite-Only Mean Dynamic Topography

    NASA Astrophysics Data System (ADS)

    Cunderlik, Robert; Mikula, Karol

    2015-03-01

    The paper presents nonlinear diffusion filtering of the GOCE-based satellite-only mean dynamic topography (MDT). Our approach is based on a numerical solution to the nonlinear diffusion equation defined on the discretized Earth’s surface using the regularized surface Perona-Malik Model. For its numerical discretization we use a surface finite volume method. A key idea is that the diffusivity coefficient depends on the edge detector. It allows effectively reduce the stripping noise while preserve important gradients in filtered data. Numerical experiments present nonlinear filtering of the geopotential evaluated from the GO_CONS_GCF_2_ DIR_R5 model on the DTU13 mean sea surface. After filtering the geopotential is transformed into the MDT.

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  1. 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.

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

    PubMed Central

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

    2016-01-01

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene. PMID:27922072

  3. Chain Dynamics in Single Chain Limit by Rheological and Diffusion Measurements

    NASA Astrophysics Data System (ADS)

    Wang, Shi-Qing; Wang, Shanfeng

    2004-03-01

    Our recent trace and self diffusion measurements , indicate (a) (b) that the molecular weight scaling of the self-diffusion coefficient is non-reptative for moderately entangled polymer melts as noted previously (c) but asymptotically approaches the reptative exponent of -2.0 for sufficiently entangled polymers, whereas the trace diffusion coefficient, measured by immersing a dilute amount of probe chains in a matrix of sufficiently entangled polymer of the same species, scales reptatively even for the probe chains of moderate entanglement. To further understand the behavior of probe chain dynamics in a matrix, we have measured the intrinsic viscosity and intrinsic storage and loss moduli of dilute solutions made of long chains (in dilution) and short chains, where both chain lengths can be much longer than the entanglement chain length. A rich variety of chain dynamics is observed including Stokes-Zimm behavior and Rouse like behavior as a function of the long and short chain lengths and concentration. (a) S.Q. Wang, Highlight Article, J. Polym. Sci. Polym. Phys., 41, 1589 (2003). (b) "Diffusion and Rheology of Binary Polymer Mixtures", S. Wang et al, Macromolecules, in press (2003). (c) T.P. Lodge, Phys. Rev. Lett. 83, 3218 (1999).

  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. 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.

  6. A novel chaotic image encryption algorithm using block scrambling and dynamic index based diffusion

    NASA Astrophysics Data System (ADS)

    Xu, Lu; Gou, Xu; Li, Zhi; Li, Jian

    2017-04-01

    In this paper, we propose a novel chaotic image encryption algorithm which involves a block image scrambling scheme and a new dynamic index based diffusion scheme. Firstly, the original image is divided into two equal blocks by vertical or horizontal directions. Then, we use the chaos matrix to construct X coordinate, Y coordinate and swapping control tables. By searching the X coordinate and Y coordinate tables, the swapping position of the processing pixel is located. The swapping control table is used to control the swapping of the pixel in the current block or the other block. Finally, the dynamic index scheme is applied to the diffusing of the scrambled image. The simulation results and performance analysis show that the proposed algorithm has an excellent safety performance with only one round.

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

    SciTech Connect

    Cheng, Shengfeng; Grest, Gary S.

    2012-01-01

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

  8. Molecular-Dynamics (MD) Simulations of Copper Diffusion in Copper Chalcogenides

    NASA Astrophysics Data System (ADS)

    Wang, Jing

    It was recently discovered that copper chalcogenides Cu2S and Cu2Se are viable candidates for thermoelectric materials with high figure of merit (ZT) values at temperatures around 1,000 K. And the possible reason for the high ZT is the low thermal conductivity arising from liquid-like Cu atoms in those phases. In this work, we perform first-principles molecular dynamics simulations to study the motion of Cu atoms in the high-temperature phases of Cu2S and Cu2Se and confirm the liquid nature of Cu atoms. To get a better understanding of the diffusion patterns of the systems, we have examined all the three phases of Cu2S (monoclinic, hexagonal and cubic phases with increasing temperature). Starting from the hexagonal phase the Cu atoms show a disordered/liquid-like feature with a jump diffusion pattern. We find that the diffusion is faster in x-y directions than in the z direction. A more isotropic diffusion pattern is found for high-temperature cubic phase with a much larger diffusion coefficient.

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

    NASA Astrophysics Data System (ADS)

    Moulod, M.; Hwang, G.

    2016-11-01

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

  10. 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.

  11. Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

    DOE PAGES

    Diallo, S. O.; Vlcek, L.; Mamontov, E.; ...

    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

  12. 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.

  13. 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).

  14. Impact of human activity patterns on the dynamics of information diffusion.

    PubMed

    Iribarren, José Luis; Moro, Esteban

    2009-07-17

    We study the impact of human activity patterns on information diffusion. To this end we ran a viral email experiment involving 31,183 individuals in which we were able to track a specific piece of information through the social network. We found that, contrary to traditional models, information travels at an unexpectedly slow pace. By using a branching model which accurately describes the experiment, we show that the large heterogeneity found in the response time is responsible for the slow dynamics of information at the collective level. Given the generality of our result, we discuss the important implications of this finding while modeling human dynamical collective phenomena.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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. Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation.

    PubMed

    Ding, Feng; Dokholyan, Nikolay V

    2008-12-16

    Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in neuronal death in amyotrophic lateral sclerosis. Each SOD1 monomer binds to 1 copper and 1 zinc ion and maintains its disulfide bond (Cys-57-Cys-146) in the reducing cytoplasm of cell. Mounting experimental evidence suggests that metal loss and/or disulfide reduction are important for initiating misfolding and aggregation of SOD1. To uncover the role of metals and the disulfide bond in the SOD1 folding, we systemically study the folding thermodynamics and structural dynamics of SOD1 monomer and dimer with and without metal binding and under disulfide-intact or disulfide-reduced environments in computational simulations. We use all-atom discrete molecular dynamics for sampling. Our simulation results provide dynamical evidence to the stabilizing role of metal ions in both dimer and monomer SOD1. The disulfide bond anchors a loop (Glu-49 to Asn-53) that contributes to the dimer interface. The reduction of the disulfide bond in SOD1 with metal ions depleted results in a flexible Glu-49-Asn-53 loop, which, in turn, disrupts dimer formation. Interestingly, the disulfide bond reduction does not affect the thermostability of monomer SOD1 as significantly as the metal ions do. We further study the structural dynamics of metal-free SOD1 monomers, the precursor for aggregation, in simulations and find inhomogeneous local unfolding of beta-strands. The strands protected by the metal-binding and electrostatic loops are found to unfold first after metal loss, leading to a partially unfolded beta-sheet prone to aggregation. Our simulation study sheds light on the critical role of metals and disulfide bond in SOD1 folding and aggregation.

  1. 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.

  2. Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics.

    PubMed

    Veshtort, Mikhail; Griffin, Robert G

    2011-10-07

    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 (R(2)). 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 (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this

  3. 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

  4. Guest-encapsulation properties of a self-assembled capsule by dynamic boronic ester bonds.

    PubMed

    Nishimura, Naoki; Yoza, Kenji; Kobayashi, Kenji

    2010-01-20

    Two molecules of tetrakis(dihydroxyboryl)-cavitand 1a as an aromatic cavity and four molecules of 1,2-bis(3,4-dihydroxyphenyl)ethane 2 as an equatorial linker self-assemble into capsule 3a via the formation of eight dynamic boronic ester bonds in CDCl(3) or C(6)D(6). Capsule 3a encapsulates one guest molecule, such as 4,4'-disubstituted-biphenyl and 2,6-disubstituted-anthracene derivatives, in a highly selective recognition event, wherein the guest substituents are oriented to both aromatic cavity ends of 3a, as confirmed by a (1)H NMR study and X-ray crystallographic analysis. Capsule 3a showed a significant solvent effect on guest encapsulation. The association constant (K(a)) of 3a with guests in C(6)D(6) was much greater than that in CDCl(3) (450-48,000-fold). The encapsulation of guests within 3a in C(6)D(6) was enthalpically driven, whereas that in CDCl(3) tended to be both enthalpically and entropically driven. Thermodynamic studies suggest that the small K(a) value in CDCl(3) arises from the character of CDCl(3) as a competitor guest molecule for 3a, and not from the difference in stability of the boronic ester bonds of 3a in both solvents. We propose a linker partial dissociation mechanism for the guest uptake and release into and out of 3a based on the kinetic studies of guest@3a using 2D EXSY analysis, as well as structural analysis of a guest@3b. The rotation behavior of 4,4'-diacetoxy-2,2'-disubstituted-biphenyls within 3a was also investigated, where the elongation of 2,2'-disubstituents of guests put the brakes on guest rotation within 3a.

  5. Conjugated Double Bonds in Lipid Bilayers: A Molecular Dynamic Simulation Study

    PubMed Central

    Zhao, Guijun; Subbaiah, P. V.; Chiu, See-Wing; Jakobsson, Eric; Scott, H. L.

    2011-01-01

    Conjugated linoleic acids (CLA) are found naturally in dairy products. Two isomers of CLA, that differ only in the location of cis and trans double bonds, are found to have distinct and different biological effects. The cis 9 trans 11 (C9T11) isomer is attributed to have the anti-carcinogenic effects, while the trans 10 cis 12 (T10C12) isomer is believed to be responsible for the anti-obesity effects. Since dietary CLA are incorporated into membrane phospholipids, we have used Molecular Dynamics (MD) simulations to investigate the comparative effects of the two isomers on lipid bilayer structure. Specifically, simulations of phosphatidylcholine lipid bilayers in which the sn-2 chains contained one of the two isomers of CLA were performed. Force field parameters for the torsional potential of double bonds were obtained from ab initio calculations. From the MD trajectories we calculated and compared structural properties of the two lipid bilayers, including areas per molecule, density profiles, thickness of bilayers, tilt angle of tail chains, order parameters profiles, radial distribution function (RDF) and lateral pressure profiles. The main differences found between bilayers of the two CLA isomers, are (1) the order parameter profile for C9T11 has a dip in the middle of sn-2 chain while the profile for T10C12 has a deeper dip close to terminal of sn-2 chain, and (2) the lateral pressure profiles show differences between the two isomers. Our simulation results reveal localized physical structural differences between bilayers of the two CLA isomers that may contribute to different biological effects through differential interactions with membrane proteins or cholesterol. PMID:21320475

  6. Dynamics of hydrogen-bonded liquids confined to mesopores: A dielectric and neutron spectroscopy study

    SciTech Connect

    Mel`nichenko, Y.B.; Schueller, J.; Richert, R.; Ewen, B.; Loong, C.

    1995-08-08

    In this paper we present and discuss experimental results on molecular mobility in propylene glycol and its three oligomers confined to the {similar_to}100 A pores of a controlled porous glass. The objective is to elucidate the finite size effects on the dynamics of hydrogen-bonded liquids of different molecular weights but identical chemical composition. The methods of dielectric and neutron spectroscopy have been employed to investigate both the low- and high-frequency features as a function of temperature. We find that all fluids in pores separate into two distinct liquid phases. (i) molecules physisorbed at the surface which exhibit a dramatic frustration of their mobility related to a substantial {ital positive} shift of the glass transition temperature {ital T}{sub {ital g}} by up to {Delta}{ital T}{sub {ital g}}{approx}+47 K; and (ii) relatively ``free`` molecules in the inner pore space subject to only moderate retardation of the {alpha} and normal mode relaxation and substantial broadening of the distribution of relaxation times. The shift in {ital T}{sub {ital g}} for the {alpha} process with {Delta}{ital T}{sub {ital g}}{approx}+5 K is maximal for the monomer liquid and gradually diminishes with increasing molecular weight or decreasing intermolecular hydrogen bonding. The inelastic neutron spectrum of confined propylene glycol shows the boson peak as expected in bulk strong and intermediate glass formers in the vicinity of {ital T}{sub {ital g}}. This effect can be attributed to the finite-size induced crossover from long wave vibrations characteristic of a continuous medium to localized vibrations in a confined geometry. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  7. 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.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  11. 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

  12. 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.

  13. Mutual diffusion in binary mixtures of ionic liquids and molecular liquids by dynamic light scattering (DLS).

    PubMed

    Rausch, Michael Heinrich; Lehmann, Julia; Leipertz, Alfred; Fröba, Andreas Paul

    2011-05-28

    The present study shows that dynamic light scattering (DLS) is capable of measuring mutual diffusion coefficients for binary mixtures of ionic liquids (ILs) with different molecular liquids over the complete composition range. Evidence is given that the light scattering signals are related to true molecular binary diffusion. The method stands out due to its ability to work non-invasively in macroscopic thermodynamic equilibrium with reasonable accuracy and within convenient measurement periods. Compared with other techniques, mixtures with distinctly higher viscosities can be probed. For exemplary binary mixtures of 1-ethyl-3-methylimidazolium ethylsulfate ([EMIM][EtSO(4)]) with acetone, acetonitrile, dichloromethane, ethanol, or water as well as of 1-ethyl-3-methylimidazolium methanesulfonate ([EMIM][MeSO(3)]) with acetone, water, or methanol, mutual diffusivity data were measured over a wide range of composition at a temperature of 293.15 K. In general, the mutual diffusivity increases with increasing mole fraction of the molecular liquid and similarities to aqueous solutions of classical inorganic salts can be found. The characteristic behavior of the mutual diffusion coefficients is influenced by the nature of the chosen molecular liquid. For IL water mixtures, low light scattering intensities were observed despite the large refractive index difference of the pure components. The reason for this behavior may be the existence of water clusters in the mixtures. Additional measurements for IL acetone mixtures at temperatures ranging from 278.15 K to 323.15 K showed that the temperature dependence of the mutual diffusivity can be represented by Arrhenius functions and is increasing for decreasing mole fractions of acetone.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  15. 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

  16. Direct assessment of quantum nuclear effects on hydrogen bond strength by constrained-centroid ab initio path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Walker, Brent; Michaelides, Angelos

    2010-11-01

    The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.

  17. Modified virtual internal bond model for concrete subjected to dynamic loading

    NASA Astrophysics Data System (ADS)

    Patil, Mayuri

    Concrete is often used as a primary material to build protective structures. There is a wide range of research work being performed to simulate the behavior of reinforced concrete under impact and blast loading. This behavior is studied from both material and structural points of view. The research study presented in this thesis focuses on material aspects of modeling. LS-DYNARTM is an effective software for modeling and finite element analysis of structural members. It allows the user to define the material through commercially available or user-defined constitutive material models. Each material model has a distinct set of parameters to define a material which is further assigned to elements and used for simulations. This research study presents a user defined material model called Modified Concrete Virtual Internal Bond Model (MC-VIB). The basic constitutive model of VIB assumes the body as a collection of randomly oriented material points interconnected by a network of internal bonds. The model was modified by several researchers for different purposes. This research presents the MC-VIB for concrete under dynamic loading and studies its implementation into LS-DYNARTM. The modifications include incorporation of shear behavior and accounting for the difference in behavior of concrete in tension and compression. This project includes the calibration of the model based on stress-strain behavior of single element and cylinder model of concrete. The parameters are based on concrete with a uniaxial compressive strength of 27.6 MPa (4 ksi). These numerical curves are compared to those obtained from conventionally used material models for concrete and standard curves obtained by accepted equations to check the accuracy of prediction. The material model available in LS-DYNARTM requires a number of input parameters to define concrete behavior. These properties are normally derived from actual tests performed on the concrete under consideration. Often the properties are

  18. 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

  19. 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.

  20. Self-diffusivity and interdiffusivity of molten aluminum-copper alloys under pressure, derived from molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rudd, Robert E.; Cabot, William H.; Caspersen, Kyle J.; Greenough, Jeffrey A.; Richards, David F.; Streitz, Frederick H.; Miller, Paul L.

    2012-03-01

    We use molecular dynamics (MD) to simulate diffusion in molten aluminum-copper (AlCu) alloys. The self-diffusivities and Maxwell-Stefan diffusivities are calculated for AlCu mixtures using the Green-Kubo formulas at temperatures from 1000 to 4000 K and pressures from 0 to 25 GPa, along with additional points at higher temperatures and pressures. The diffusivities are corrected for finite-size effects. The Maxwell-Stefan diffusivity is compared to the diffusivity calculated from the self-diffusivities using a generalization of the Darken equation. We find that the effects of cross-correlation are small. Using the calculated self-diffusivities, we have assessed whether dilute hard-sphere and dilute Lennard-Jones models apply to the molten mixture. Neither of the two dilute gas diffusivities describes the diffusivity in molten Al and Cu. We report generalized analytic models for the self-diffusivities and interdiffusivity (mutual diffusivity) that fit the MD results well. The MD-derived transport coefficients are in good agreement with the available experimental data. We also report MD calculations of the viscosity and an analytic fit to those results. The ionic thermal conductivity is discussed briefly.

  1. Dynamic response of a carbon nanotube-based rotary nano device with different carbon-hydrogen bonding layout

    NASA Astrophysics Data System (ADS)

    Yin, Hang; Cai, Kun; Wan, Jing; Gao, Zhaoliang; Chen, Zhen

    2016-03-01

    In a nano rotational transmission system (RTS) which consists of a single walled carbon nanotube (SWCNT) as the motor and a coaxially arranged double walled carbon nanotube (DWCNT) as a bearing, the interaction between the motor and the rotor in bearing, which has great effects on the response of the RTS, is determined by their adjacent edges. Using molecular dynamics (MD) simulation, the interaction is analyzed when the adjacent edges have different carbon-hydrogen (Csbnd H) bonding layouts. In the computational models, the rotor in bearing and the motor with a specific input rotational speed are made from the same armchair SWCNT. Simulation results demonstrate that a perfect rotational transmission could happen when the motor and rotor have the same Csbnd H bonding layout on their adjacent ends. If only half or less of the carbon atoms on the adjacent ends are bonded with hydrogen atoms, the strong attraction between the lower speed (100 GHz) motor and rotor leads to a synchronous rotational transmission. If only the motor or the rotor has Csbnd H bonds on their adjacent ends, no rotational transmission happens due to weak interaction between the bonded hydrogen atoms on one end with the sp1 bonded carbon atoms on the other end.

  2. 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

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

    NASA Astrophysics Data System (ADS)

    Mohammadzadeh, Roghayeh; Razmara, Naiyer; Razmara, Fereshteh

    2016-12-01

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

  4. A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase

    NASA Astrophysics Data System (ADS)

    Nagashima, Hiroki; Tsuda, Shin-ichi; Tsuboi, Nobuyuki; Koshi, Mitsuo; Hayashie, A. Koichi; Tokumasu, Takashi

    2014-10-01

    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.

  5. 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.

  6. Diffusive nature of xenon anesthetic changes properties of a lipid bilayer: molecular dynamics simulations.

    PubMed

    Yamamoto, Eiji; Akimoto, Takuma; Shimizu, Hiroyuki; Hirano, Yoshinori; Yasui, Masato; Yasuoka, Kenji

    2012-08-02

    Effects of general anesthesia can be controllable by the ambient pressure. We perform molecular dynamics simulations for a 1-palmitoyl-2-oleoyl phosphatidylethanolamine lipid bilayer with or without xenon molecules by changing the pressure to elucidate the mechanism of the pressure reversal of general anesthesia. According to the diffusive nature of xenon molecules in the lipid bilayer, a decrease in the orientational order of the lipid tails, an increase in the area and volume per lipid molecule, and an increase in the diffusivity of lipid molecules are observed. We show that the properties of the lipid bilayer with xenon molecules at high pressure come close to those without xenon molecules at 0.1 MPa. Furthermore, we find that xenon molecules are concentrated in the middle of the lipid bilayer at high pressures by the pushing effect and that the diffusivity of xenon molecules is suppressed. These results suggest that the pressure reversal originates from a jamming and suppression of the diffusivity of xenon molecules in lipid bilayers.

  7. Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid

    NASA Astrophysics Data System (ADS)

    Cao, Bing-Yang; Dong, Ruo-Yu

    2014-01-01

    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.

  8. Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix: I. Concentrated solutions of sucrose.

    PubMed

    Gutman, M; Nachliel, E; Kiryati, S

    1992-07-01

    Biochemical systems lose their homogeneity at a mesoscopic scale; physical parameters vary sharply over a scale of a few nanometers.In this manuscript, we demonstrate how proton diffusion studies can report the microscopic properties of inhomogeneous systems.The method used for this purpose was the laser induced proton pulse and the reaction followed was the recombination of a proton with pyranine anion (8 hydroxy pyrene 1,3,6 trisulfonate) either in the excited state (subnanosecond dynamics) or in the ground state (microsecond time-scale measurements). The observed signals were analyzed by numeric integration of differential rate equations pertinent to the diffusion controlled reaction between proton and pyranine anion.The accuracy of the methodology was verified by measuring the dielectric constant of sucrose solutions. The results we obtained are identical with those published in the International Critical Tables (1933. Vol. VI, 82-101).The diffusion coefficient of proton was found to be independent of the sucrose concentration, up to 2M solution where the sucrose makes up 45% of the volume. This observation is interpreted in terms of the microscopic heterogeneity of the solution: the proton diffuses in the aqueous space between the sucrose molecules, while the continuity of the aqueous phase is maintained by the Brownian motion of the sucrose molecule, which allows the proton to pass between them at an unhindered rate.

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  10. X-Ray Studies of Diffusion Dynamics in Nano-Confined Geometries

    NASA Astrophysics Data System (ADS)

    Boucheron, Leandra

    Since their discovery in the late 1800s, x-rays have taken the stage as one of the most powerful research techniques for materials science. Their element-specific absorption has allowed for everyday applications in security and medical imaging, while their short wavelength has a tremendous ability to resolve materials on a molecular or even atomic level. In this dissertation, I will discuss basic properties of x-rays as well as how they are produced and detected. I will also present x-ray scattering and analysis techniques before moving onto a discussion of my research on diffusion in soft-matter systems. I provide a full alignment guide for a lab-based dynamic light scattering (DLS) goniometer system, which I used for some preliminary studies of systems. I proceed to discuss diffusion on the nanoscale in quasi-1D (nanopores) and quasi-2D (liquid surface) systems. The latter of these systems was the main focus of my dissertation research. I utilized x-ray photon correlation spectroscopy (XPCS) to study the diffusion and interparticle dynamics of iron oxide nanoparticles at the air-water interface. Autocorrelation analysis revealed that these particles show signatures of a jammed system under lateral compression. I present these results as well as a description of their interpretation and importance in the main text.

  11. A diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Ma, Wanbiao; Lai, Xiulan

    2017-01-01

    From a biological perspective, a diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis is proposed. In the model, the diffusion of virus consists of two parts, the random diffusion and the chemotactic movement. The chemotaxis flux of virus depends not only on their own density, but also on the density of infected cells, and the density gradient of infected cells. The well posedness of the proposed model is deeply investigated. For the proposed model, the linear stabilities of the infection-free steady state E0 and the infection steady state E* are extensively performed. We show that the threshold dynamics can be expressed by the basic reproduction number R0 of the model without chemotaxis. That is, the infection-free steady state E0 is globally asymptotically stable if R0 < 1, and the virus is uniformly persistent if R0 > 1. In addition, we use the cross iteration method and the Schauder's fixed point theorem to prove the existence of travelling wave solutions connecting the infection-free steady state E0 and the infection steady state E* by constructing a pair of upper-lower solutions. At last, numerical simulations are presented to confirm theoretical findings.

  12. 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.

  13. 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

  14. Relaxation and self-diffusion of supercooled liquids derived from picosecond timescale dynamics

    NASA Astrophysics Data System (ADS)

    Cicerone, Marcus; Zhi, Miaochan; Blakely, Brandon; Tyagi, Madhusudan

    We use neutron scattering and nonlinear optical measurements to investigate ps-ns timescale dynamics in liquid, supercooled liquid, and glassy states. The experimental observables show evidence of dynamic heterogeneity on this timescale that supports a facilitated dynamics picture. We obtain a direct measure of the concentration of molecular excitations, or mobile regions, as a function of time and temperature. Using a model broadly consistent with that proposed by Chandler and co-workers, we are able to quantitatively predict self-diffusion rates and Stokes Einstein violation deep in the supercooled regime directly from ps timescale and Angstrom - nanometer length scale measurements for all systems we have investigated. The model we employ also provides a clear physical mechanism for the Johari-Goldstein relaxation process

  15. 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.

  16. Probing molecular dynamics in chromatographic systems using high-resolution 1H magic-angle-spinning NMR spectroscopy: interaction between p-Xylene and C18-bonded silica.

    PubMed

    Coen, Muireann; Wilson, Ian D; Nicholson, Jeremy K; Tang, Huiru; Lindon, John C

    2004-06-01

    The exact nature of the interaction between small molecules and chromatographic solid phases has been the subject of much research, but detailed understanding of the molecular dynamics in such systems remains elusive. High-resolution (1)H magic-angle-spinning (MAS) NMR spectroscopy has been applied to the investigation of C18-bonded silica material as used in chromatographic separation techniques together with an adsorbed model analyte, p-xylene. Two distinct p-xylene and water environments were identified within the C18-bonded silica through the measurement of (1)H NMR chemical shifts, T(1) and T(2) relaxation times and diffusion coefficients, including their temperature dependence. The results have been analyzed in terms of two environments, p-xylene within the C18 chains, in slow exchange on the NMR time scale with p-xylene in a more mobile state adsorbed as a layer in close proximity to the C18 particles, but which is distinct from free liquid p-xylene. The techniques used here could have more general applications, including the study of drug molecules bound into phospholipid membranes in micelles or vesicles.

  17. 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.

  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. 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.

  20. Forbidden phonon: Dynamical signature of bond symmetry breaking in the iron chalcogenides

    DOE PAGES

    Fobes, David M.; Zaliznyak, Igor A.; Tranquada, John M.; ...

    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 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. Lastly, the presence of this “forbidden” phonon indicates that the lattice symmetrymore » is dynamically or locally broken by magneto-orbital BOW fluctuations, which are strongly coupled to lattice in these materials.« less

  1. Molecular dynamics simulations of RDX and RDX-based plastic-bonded explosives.

    PubMed

    Zhu, Wei; Xiao, Jijun; Zhu, Weihua; Xiao, Heming

    2009-05-30

    Molecular dynamics simulations have been performed to investigate well-known energetic material cyclotrimethylene trinitramine (RDX) crystal and RDX-based plastic-bonded explosives (PBXs) with four typical fluorine-polymers, polyvinylidenedifluoride (PVDF), polychlorotri-fluoroethylene (PCTFE), fluorine rubber (F(2311)), and fluorine resin (F(2314)). The elastic coefficients, mechanical properties, binding energies, and detonation performances are obtained for the RDX crystal and RDX-based PBXs. The results indicate that the mechanical properties of RDX can be effectively improved by blending with a small amount of fluorine polymers and the overall effect of fluorine polymers on the mechanical properties of the PBXs along three crystalline surfaces is (001)>(010) approximately (100) and PVDF is regarded to best improve the mechanical properties of the PBXs on three surfaces. The order of the improvement in the ductibility made by the fluorine polymers on different surfaces is (001) approximately (010)>(100). The average binding energies between different RDX crystalline surfaces and different polymer binders are obtained, and the sequence of the binding energies of the PBXs with the four fluorine polymers on the three different surfaces is varied. Among the polymer binders, PVDF is considered as best one for RDX-based PBXs. The detonation performances of the PBXs decrease in comparison with the pure crystal but are superior to those of TNT.

  2. Forbidden phonon: Dynamical signature of bond symmetry breaking in the iron chalcogenides

    SciTech Connect

    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 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. Lastly, 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.

  3. Car-Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds.

    PubMed

    Brela, Mateusz Z; Wójcik, Marek J; Boczar, Marek; Witek, Łukasz; Yasuda, Mitsuru; Ozaki, Yukihiro

    2015-06-25

    We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid.

  4. 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).

  5. Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Liu, Xinjian; Jin, Yu; Huang, Congliang; He, Jingfeng; Rao, Zhonghao; Zhao, Yuemin

    2016-01-01

    Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

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

    PubMed

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

    2008-06-19

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

  7. 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/

  8. Diffusivities of Ternary Mixtures of n-Alkanes with Dissolved Gases by Dynamic Light Scattering.

    PubMed

    Heller, Andreas; Giraudet, Cédric; Makrodimitri, Zoi A; Fleys, Matthieu S H; Chen, Jiaqi; van der Laan, Gerard P; Economou, Ioannis G; Rausch, Michael H; Fröba, Andreas P

    2016-10-12

    Theoretical approaches suggest that dynamic light scattering (DLS) signals from low-molecular-weight ternary mixtures are governed by fluctuations in temperature as well as two individual contributions from fluctuations in concentration that are related to the eigenvalues of the Fick diffusion matrix. Until now, this could not be proven experimentally in a conclusive way. In the present study, a detailed analysis of DLS signals in ternary mixtures consisting of n-dodecane (n-C12H26) and n-octacosane (n-C28H58) with dissolved hydrogen (H2), carbon monoxide (CO), or water (H2O) as well as of n-C12H26 or n-C28H58 with dissolved H2 and CO is given for temperatures up to 523 K and pressures up to 4.1 MPa. Thermal diffusivities of pure n-C12H26 and n-C28H58 as well as thermal and mutual diffusivities of their binary mixtures being the basis for the ternary mixtures with dissolved gas were studied for comparison purposes. For the investigated ternary mixtures, three individual signals could be distinguished in the time-resolved analysis of scattered light intensity by using photon correlation spectroscopy (PCS). For the first time, it could be evidenced that these signals are clearly associated with hydrodynamic modes. In most cases, the fastest mode observable for ternary mixtures is associated with the thermal diffusivity. The two further modes obviously related to the molecular mass transport are observable on different time scales and comparable to the modes associated with the concentration fluctuations in the respective binary mixtures. Comparison of the experimental data with results from molecular dynamics simulations revealed very good agreement.

  9. 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.

  10. Molecular dynamics simulations of the diffusion and coalescence of helium in tungsten

    NASA Astrophysics Data System (ADS)

    Zhou, Y. L.; Wang, J.; Hou, Q.; Deng, A. H.

    2014-03-01

    Molecular dynamics (MD) simulations are performed on the diffusion and coalescence of helium in tungsten. A new method for determining the effective capture radii (ECRs) and the dissociation energies of helium-related defects is proposed in this work. It is observed that the ECR of an interstitial helium atom trapping helium interstitials (denoted as He-Hen, n = 1-3) decreases with increasing temperature, except for He-He2 at T < 400 K. The traditional view that the ECR is approximately equal to the lattice constant, which has been widely used in kinetic Monte Carlo (KMC) and rate theory (RT) models, is only valid in some cases. However, the ECR between an interstitial helium atom and a substitutional helium atom (denoted as He-HeV) always approximates the third nearest-neighbor tetrahedral positions of the HeV. The diffusion coefficients Dn for helium clusters are also investigated. He2 migrates more quickly than a single He atom does at T < 400 K, whereas the diffusion path of He2 changes at higher temperatures. Another counterintuitive observation is that D5 > D3 > D4 at T < 500 K, which can be attributed to the disordered structure of He5. The Arrhenius relation describes the diffusion of Hen well in the temperature range from 300 K to 550 K, whereas the diffusion is not a standard thermally activated process at higher temperatures. Taken together, these results help elucidate the initial stage of helium bubble formation in tungsten as well as the requirements of long-term evolution methods such as KMC or RT models.

  11. 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

  12. 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.

  13. 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.

  14. Nonequilibrium Mixed Quantum-Classical simulations of Hydrogen-bond Structure and Dynamics in Methanol-d Carbon tetrachloride liquid mixtures and its spectroscopic signature

    NASA Astrophysics Data System (ADS)

    Kwac, Kijeong; Geva, Eitan

    2011-03-01

    Liquid mixtures of methanol-d and carbon tetrachloride provide attractive model systems for investigating hydrogen-bond structure and dynamics. The hydrogen-bonded methanol oligomers in these mixtures give rise to a very broad hydroxyl stretch IR band (~ 150 cm-1). We have employed mixed quantum-classical molecular dynamics simulations to study the nature of hydrogen- bond structure and dynamics in this system and its spectroscopic signature. In our simulations, the hydroxyl stretch mode is treated quantum mechanically. We have found that the absorption spectrum is highly sensitive to the type of force fields used. Obtaining absorption spectra consistent with experiment required the use of corrected polarizabile force fields and a dipole damping scheme. We have established mapping relationships between the electric field along the hydroxyl bond and the hydrogen-stretch frequency and bond length thereby reducing the computational cost dramatically to simulate the complex nonequilibrium dynamics underlying pump-probe spectra.

  15. Dynamics of Pinned Membranes with Application to Protein Diffusion on the Surface of Red Blood Cells

    PubMed Central

    Lin, Lawrence C.-L.; Brown, Frank L. H.

    2004-01-01

    We present a theoretical treatment and simulation algorithm for the dynamics of Helfrich elastic membrane surfaces in the presence of general harmonic perturbations and hydrodynamic coupling to the surrounding solvent. In the limit of localized and strong interactions, this harmonic model can be used to pin the membrane to intracellular/intercellular structures. We consider the case of pinning to the cytoskeleton and use such a model to estimate the macroscopic diffusion constant for band 3 protein on the surface of human erythrocytes. Comparison to experimental results suggests that thermal undulations of the membrane surface should play a significant role in protein mobility on the red blood cell. PMID:14747313

  16. An adaptive streamline diffusion finite element method for hyperbolic systems in gas dynamics

    NASA Astrophysics Data System (ADS)

    Zhou, Guohui

    1992-09-01

    The paintwise error analysis of the streamline diffusion method for two dimensional stationary problem with constant coefficients is extended to the time dependent problem. The purpose of the study is to justify a local mesh refinement strategy. The one dimensional Euler equations coming from the shock tube and Riemann's problem in gas dynamics are used. The gas is assumed to be at rest on both sides of the membrane, with pressure and density different on each side. The case where the problem is scalar and linear is discussed. Linear systems of hyperbolic type in one space variable and nonlinear scalar problems are studied.

  17. 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.

  18. Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion.

    PubMed

    Gohlke, Holger; Hergert, Ulrike; Meyer, Tatu; Mulnaes, Daniel; Grieshaber, Manfred K; Smits, Sander H J; Schmitt, Lutz

    2013-10-28

    Opine dehydrogenases catalyze the reductive condensation of pyruvate with L-amino acids. Biochemical characterization of alanopine dehydrogenase from Arenicola marina revealed that this enzyme is highly specific for L-alanine. Unbiased molecular dynamics simulations with a homology model of alanopine dehydrogenase captured the binding of L-alanine diffusing from solvent to a putative binding region near a distinct helix-kink-helix motif. These results and sequence comparisons reveal how mutations and insertions within this motif dictate the L-amino acid specificity.

  19. 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.

  20. Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

    PubMed

    Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-05

    Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

  1. The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

    NASA Astrophysics Data System (ADS)

    Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; Shin, S. J.; Shao, L.; Kucheyev, S. O.

    2017-01-01

    The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from ‑20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV and 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies.

  2. The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

    PubMed Central

    Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; Shin, S. J.; Shao, L.; Kucheyev, S. O.

    2017-01-01

    The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from −20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV and 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies. PMID:28059109

  3. Interface Dynamics of a Metastable Mass-Conserving Spatially Extended Diffusion

    NASA Astrophysics Data System (ADS)

    Berglund, Nils; Dutercq, Sébastien

    2016-01-01

    We study the metastable dynamics of a discretised version of the mass-conserving stochastic Allen-Cahn equation. Consider a periodic one-dimensional lattice with N sites, and attach to each site a real-valued variable, which can be interpreted as a spin, as the concentration of one type of metal in an alloy, or as a particle density. Each of these variables is subjected to a local force deriving from a symmetric double-well potential, to a weak ferromagnetic coupling with its nearest neighbours, and to independent white noise. In addition, the dynamics is constrained to have constant total magnetisation or mass. Using tools from the theory of metastable diffusion processes, we show that the long-term dynamics of this system is similar to a Kawasaki-type exchange dynamics, and determine explicit expressions for its transition probabilities. This allows us to describe the system in terms of the dynamics of its interfaces, and to compute an Eyring-Kramers formula for its spectral gap. In particular, we obtain that the spectral gap scales like the inverse system size squared.

  4. 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.

  5. Strong bonding between sputtered bioglass-ceramic films and Ti-substrate implants induced by atomic inter-diffusion post-deposition heat-treatments

    NASA Astrophysics Data System (ADS)

    Stan, G. E.; Popa, A. C.; Galca, A. C.; Aldica, G.; Ferreira, J. M. F.

    2013-09-01

    Bioglasses (BG) are the inorganic materials exhibiting the highest indices of bioactivity. Their appliance as films for bio-functionalization of metallic implant surfaces has been regarded as an optimal solution for surpassing their limited bulk mechanical properties. This study reports on magnetron sputtering of alkali-free BG thin films by varying the target-to-substrate working distance, which proved to play an important role in determining the films’ properties. Post deposition heat-treatments at temperatures slightly above the glass transformation temperature were then applied to induce inter-diffusion processes at the BG/titanium substrate interface and strengthening the bonding as determined by pull-out adherence measurements. The morphological and structural features assessed by SEM-EDS, XRD, and FTIR revealed a good correlation between the formations of inter-metallic titanium silicide phases and the films’ bonding strength. The highest mean value of pull-out adherence (60.3 ± 4.6 MPa), which is adequate even for load-bearing biomedical applications, was recorded for films deposited at a working distance of 35 mm followed by a heat-treatment at 750 °C for 2 h in air. The experimental findings are explained on the basis of structural, compositional and thermodynamic considerations.

  6. Near-surface controls on the composition of growing crystals: Car-Parrinello molecular dynamics (CPMD) simulations of Ti energetics and diffusion in alpha quartz

    NASA Astrophysics Data System (ADS)

    Lanzillo, N. A.; Watson, E. B.; Thomas, J. B.; Nayak, S. K.; Curioni, A.

    2014-04-01

    Ab initio molecular dynamics simulations were used to explore changes in the vacancy-formation energy for Ti atoms and Ti-O bond characteristics in the outermost monolayers of the (1 0 0) and (0 1 0) prism faces of α quartz. Within 2 or 3 polyhedral layers of the crystal surface, the Ti vacancy-formation energy is substantially smaller than the bulk-lattice value of 11.8 eV. This is true of both oxygen-terminated surfaces and the geologically more realistic case in which the outermost oxygens are bonded to hydrogen. A key additional finding is that the Ti vacancy-formation energy near the H-terminated (1 0 0) surface differs by 1-2 eV from that near the H-terminated (0 1 0) surface. This difference means that the energy change accompanying Ti ↔ Si exchange between the bulk lattice and the near surface is also different for (1 0 0) and (0 1 0). Ultimately, therefore, the equilibrium concentrations of Ti near these two prism faces will not be the same. During crystal growth, this compositional difference may be “captured” by the quartz lattice and preserved as sectoral variation in Ti content-a feature commonly observed in both synthetic and natural α quartz. In this respect, the MD simulations provide direct support for the growth entrapment model (GEM; Watson, 2004) for non-equilibrium uptake of trace elements. To complement the vacancy-formation energy results, we used the first-principles metadynamics method to calculate diffusion pathways and free energy barriers for Ti diffusion in the bulk α quartz lattice and in the near-surface region. The computed estimate of the bulk-lattice activation energy compares favorably with the experimentally determined value of 2.8 eV (Cherniak et al., 2007), lending credence to the method. Diffusion results for the near-surface reveal a steep decrease in the activation energy for Ti diffusion approaching the surface in the outermost 2-3 polyhedral layers of the crystal. This finding implies depth-dependent Ti diffusion

  7. 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.

  8. Effect of self-interstitial diffusion anisotropy in electron-irradiated zirconium: A cluster dynamics modeling

    NASA Astrophysics Data System (ADS)

    Christien, F.; Barbu, A.

    2005-11-01

    A model based on the cluster dynamics approach was proposed in [A. Hardouin Duparc, C. Moingeon, N. Smetniansky-de-Grande, A. Barbu, J. Nucl. Mater. 302 (2002) 143] to describe point defect agglomeration in metals under irradiation. This model is restricted to materials where point defect diffusion is isotropic and is thus not applicable to anisotropic metals such as zirconium. Following the approach proposed by Woo [C.H. Woo, J. Nucl. Mater. 159 (1988) 237], we extended in this work the model to the case where self-interstitial atoms (SIA) diffusion is anisotropic. The model was then applied to the loop microstructure evolution of a zirconium thin foil irradiated with electrons in a high-voltage microscope. First, the inputs were validated by comparing the numerical results with Hellio et al. experimental results [C. Hellio, C.H. de Novion, L. Boulanger, J. Nucl. Mater. 159 (1988) 368]. Further calculations were made to evidence the effect of the thin foil orientation on the dislocation loop microstructure under irradiation. The result is that it is possible to reproduce for certain orientations the 'unexpected' vacancy loop growth experimentally observed in electron-irradiated zirconium [M. Griffiths, M.H. Loretto, R.E. Sallmann, J. Nucl. Mater. 115 (1983) 313; J. Nucl. Mater. 115 (1983) 323; Philos. Mag. A 49 (1984) 613]. This effect is directly linked to SIA diffusion anisotropy.

  9. Diffusion with micro-sorption in bentonite: evaluation by molecular dynamics and homogenization analysis

    NASA Astrophysics Data System (ADS)

    Prayongphan, Somchai; Ichikawa, Yasuaki; Kawamura, Katsuyuki; Suzuki, Satoru; Chae, Byung-Gon

    2006-03-01

    We here give a numerical analysis method of a diffusion problem including sorption chemistry for bentonite clay. Bentonite predominantly consists of the microscopic smectitic clay minerals (mainly montmorillonite and beidellite). Physico-chemical properties of smectite clays such as diffusivity of chemical species and adsorptivity on surface of clay mineral are characterized by crystalline structure of hydrated smectite minerals. To obtain the microscopic properties of the hydrated smectite, the molecular behavior is analyzed by a molecular dynamic (MD) simulation. We understand at least two types of adsorption are formed on the smectite surface; outer sphere complex and inner sphere complex. The inner sphere complex occurs on the edge sites of clay minerals. The amount of mono-layer of cations on the edge surface is considered as the adsorptivity of smectite in the microscopic level. A multiscale homogenization analysis (HA) is applied to extend the microscopic characteristics of the hydrated smectite to the macroscopic behavior. The diffusion and adsorption of a radioactive specie, cesium (Cs), is introduced by this analysis. The calculated results appear to be acceptable.

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

    NASA Astrophysics Data System (ADS)

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

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

  11. Analysis of dynamic diffuse wall based on two-dimensional twist wall

    NASA Astrophysics Data System (ADS)

    Fujii, T.; Kumosaki, K.; Inoue, M.

    1981-03-01

    The mechanism and the dynamic properties of the dynamic diffuse wall observed in Garnet bubbles have been analyzed based on two dimensional twist wall with a finite film thickness. The analysis reveals that during wall motion, 360 °-spin twist nucleates inside the wall and propagates along the film thickness. The wall distortion takes place where the 360 °-twist appears. Annihilation and/or accumulation of the 360 °-twist occurs at the film surface. The number of the 360 °-twists contained in a wall increases with increasing drive and in-plane fields, which leads to an increase of the apparent wall width obtained by domain walls observed by transmitted light (Faraday effect). Most of the experimental results may be well interpreted by the present analysis.

  12. Specific external forcing of spatiotemporal dynamics in reaction-diffusion systems.

    PubMed

    Lebiedz, Dirk; Brandt-Pollmann, Ulrich

    2005-06-01

    Self-organization behavior and in particular pattern forming spatiotemporal dynamics play an important role in far from equilibrium chemical and biochemical systems. Specific external forcing and control of self-organizing processes might be of great benefit in various applications ranging from technical systems to modern biomedical research. We demonstrate that in a cellular chemotaxis system modeled by one-dimensional reaction-diffusion equations particular forms of spatiotemporal dynamics can be induced and stabilized by controlling spatially distributed influx patterns of a chemical species as a function of time. In our model study we show that a propagating wave with certain shape and velocity and static symmetrical and asymmetrical patterns can be forced and manipulated by numerically computing open-loop optimal influx controls.

  13. Stochastic dynamics and control of a driven nonlinear spin chain: the role of Arnold diffusion

    NASA Astrophysics Data System (ADS)

    Chotorlishvili, L.; Toklikishvili, Z.; Berakdar, J.

    2009-09-01

    We study a chain of nonlinear interacting spins driven by a static and a time-dependent magnetic field. The aim is to identify the conditions for the locally and temporally controlled spin switching. Analytical and full numerical calculations show the possibility of stochastic control if the underlying semiclassical dynamics is chaotic. This is achievable by tuning the external field parameters according to the method described in this paper. We show analytically for a finite spin chain that Arnold diffusion is the underlying mechanism for the present stochastic control. Quantum mechanically we consider the regime where the classical dynamics is regular or chaotic. For the latter we utilize the random matrix theory. The efficiency and the stability of the non-equilibrium quantum spin states are quantified by the time dependence of the Bargmann angle related to the geometric phases of the states.

  14. Effects of dynamic disorder on exciton migration: Quantum diffusion, coherences, and energy transfer

    NASA Astrophysics Data System (ADS)

    Dutta, Rajesh; Bagchi, Biman

    2016-10-01

    We study excitation transfer and migration in a one-dimensional lattice characterized by dynamic disorder. The diagonal and off-diagonal energy disorders arise from the coupling of system and bath. We consider both same bath (when baths are spatially correlated) and independent bath (when baths are completely uncorrelated) limits. In the latter case, all diagonal and off-diagonal bath coupling elements fluctuate independently of each other and the dynamics is complicated. We obtain time dependent population distribution by solving Kubo's quantum stochastic Liouville equation. In the Markovian limit, both energy transfer dynamics and mean square displacement of the exciton behave the similar way in same and independent bath cases. However, these two baths can give rise to a markedly different behavior in the non-Markovian limit. We note that previously only the same bath case has been studied in the non-Markovian limit. The other main results of our study include the following. (i) For an average, non-zero off-diagonal coupling value J, exciton migration remains coherent in same bath case even at long times while it becomes incoherent in independent bath case in the Markovian limit. (ii) Coherent transfer is manifested in an oscillatory behavior of the energy transfer dynamics accompanied by faster-than diffusive spread of the exciton from the original position. (iii) Agreement with available analytical expression of mean squared displacement is good in Markovian limit for independent bath (off-diagonal fluctuation) case but only qualitative in non-Markovian limit for which no complete analytical solution is available. (iv) We observe transition from coherent to incoherent transport in independent bath (diagonal fluctuation) case when the bath is made progressively more Markovian. We present an analytical study that shows coherence to propagate through excited bath states. (v) The correlation time of the bath plays a unique role in dictating the diffusive spread

  15. 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.

  16. 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.

  17. Self-Diffusion and Non-Markovian Dynamics in Strongly Coupled Ultracold Neutral Plasmas

    NASA Astrophysics Data System (ADS)

    Strickler, Trevor; Langin, Thomas; McQuillen, Patrick; Killian, Thomas

    2015-05-01

    Collisional processes in weakly coupled plasmas are well-described by the Landau-Spitzer formalism. Classical plasma theory breaks down, however, in strongly coupled systems because of the non-perturbative nature of particle interactions, and improving our understanding of this regime is an important fundamental challenge. We present experimental measurements of the self-diffusion constant and observation of non-Markovian equilibration for strongly coupled ions in an ultracold neutral plasma (UCNP) created by photoionizing strontium atoms in a magneto-optical trap. Our diagnostic uses optical pumping to create ``spin-tagged'' subpopulations of ions having skewed velocity distributions that then relax back to equilibrium. A Green-Kubo relation is used to extract the self-diffusion constant from the equilibration curves. With improved time resolution (down to 30 ns), we have explored the early time dynamics of these skewed ion distributions within 100 ns after the optical pumping, where molecular dynamics simulations predict non-Markovian deviations from the exponential velocity damping expected for weakly coupled systems. At longer times, we observe oscillations of the average velocity during the relaxation, which indicate coupling of single-particle motion to collective modes. This work was supported by the United States National Science Foundation and the Department of Energy (PHY-0714603), and the Air Force Office of Scientific Research (FA9550-12-1-0267).

  18. Diffusivity and short-time dynamics in two models of silica

    NASA Astrophysics Data System (ADS)

    Lascaris, Erik; Hemmati, Mahin; Buldyrev, Sergey V.; Stanley, H. Eugene; Angell, C. Austen

    2015-03-01

    We discuss the dynamic behavior of two silica models, the BKS model (by van Beest, Kramer, and van Santen) and the WAC model (by Woodcock, Angell, and Cheeseman). Although BKS is considered the more realistic model for liquid silica, the WAC model has the unique property that it is very close to having a liquid-liquid critical point (LLCP), and this makes it particularly useful in studying the dynamics of models that do have a LLCP. We find that the diffusivity is a good indicator of how close a liquid is to criticality—the Si diffusivity shows a jump of 3-4 orders of magnitude when the pressure is reduced, which may be interpreted as an abrupt (though not first-order) transition from a high-density liquid state to a low-density liquid state. We show that this transition is captured by the Adam-Gibbs relation, which also allows us to estimate the configurational entropy of the system.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-07-01

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

  1. 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

  2. Slow-fast stochastic diffusion dynamics and quasi-stationarity for diploid populations with varying size.

    PubMed

    Coron, Camille

    2016-01-01

    We are interested in the long-time behavior of a diploid population with sexual reproduction and randomly varying population size, characterized by its genotype composition at one bi-allelic locus. The population is modeled by a 3-dimensional birth-and-death process with competition, weak cooperation and Mendelian reproduction. This stochastic process is indexed by a scaling parameter K that goes to infinity, following a large population assumption. When the individual birth and natural death rates are of order K, the sequence of stochastic processes indexed by K converges toward a new slow-fast dynamics with variable population size. We indeed prove the convergence toward 0 of a fast variable giving the deviation of the population from quasi Hardy-Weinberg equilibrium, while the sequence of slow variables giving the respective numbers of occurrences of each allele converges toward a 2-dimensional diffusion process that reaches (0,0) almost surely in finite time. The population size and the proportion of a given allele converge toward a Wright-Fisher diffusion with stochastically varying population size and diploid selection. We insist on differences between haploid and diploid populations due to population size stochastic variability. Using a non trivial change of variables, we study the absorption of this diffusion and its long time behavior conditioned on non-extinction. In particular we prove that this diffusion starting from any non-trivial state and conditioned on not hitting (0,0) admits a unique quasi-stationary distribution. We give numerical approximations of this quasi-stationary behavior in three biologically relevant cases: neutrality, overdominance, and separate niches.

  3. Diffusion-controlled intrachain reactions of supercoiled DNA: Brownian Dynamics simulations.

    PubMed Central

    Klenin, K V; Langowski, J

    2001-01-01

    The Brownian Dynamics technique was used to model a diffusion-controlled intramolecular reaction of supercoiled DNA (2500 basepairs) in 0.1 M sodium chloride solution. The distance between the reactive groups along the DNA contour was 470 basepairs. The reaction radius was varied from 6 to 20 nm. The results are presented in terms of the probability distribution P(F)(t) of the first collision time. The general form of the function P(F)(t) could be correctly predicted by a simple analytical model of one-dimensional diffusion of the superhelix ends along the DNA contour. The distribution P(F)(t) is essentially non-exponential: within a large initial time interval, it scales as P(F)(t) approximately t(-1/2), which is typical for one-dimensional diffusion. However, the mean time of the first collision is inversely proportional to the reaction radius, as in three dimensions. A visual inspection of the simulated conformations showed that a considerable part of the collisions is caused by the bending of the superhelix axis in the regions of the end loops, where the axis is most flexible. This fact explains why the distribution P(F)(t) combines the features of one- and three-dimensional diffusion. The simulations were repeated for a DNA chain with a permanent bend of 100 degrees in the middle position between the reactive groups along the DNA contour. The permanent bend changes dramatically the form of the distribution P(F)(t) and reduces the mean time of the first collision by approximately one order of magnitude. PMID:11159383

  4. Binary diffusion coefficients for mixtures of ionic liquids [EMIM][N(CN)2], [EMIM][NTf2], and [HMIM][NTf2] with acetone and ethanol by dynamic light scattering (DLS).

    PubMed

    Rausch, Michael H; Hopf, Lisa; Heller, Andreas; Leipertz, Alfred; Fröba, Andreas P

    2013-02-28

    Mutual diffusivities for binary mixtures of the ionic liquids (ILs) [EMIM][N(CN)2] (1-ethyl-3-methylimidazolium dicyanimide), [EMIM][NTf2] (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide), and [HMIM][NTf2] (1-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) with acetone and ethanol were studied in dependence on composition in the temperature range from 283.15 to 323.15 K, applying dynamic light scattering (DLS). The influence of experimental parameters on the achievable uncertainties was analyzed to ensure the acquisition of accurate data in adequate measurement times. For all probed systems, increasing binary diffusion coefficients were found for increasing temperatures. The systematic variation of anion and cation of the investigated ILs as well as a comparison with the literature data demonstrates the considerable influence of different ions on the resulting binary diffusion coefficients. Mutual diffusivities were found to be lower for the mixtures with ethanol than for those with acetone, which could be related to the formation of hydrogen bonds between ethanol and the ions. Most of the investigated IL solvent mixtures show increasing binary diffusion coefficients with increasing solvent concentration. For the mixtures of [EMIM][NTf2] with ethanol, however, a minimum of the mutual diffusivities was found in the ethanol mole fraction range from 0.7 to 0.8, which may hint at the vicinity of a critical demixing point. The viscosity of the pure ILs turned out to be no reliable indicator for the mutual diffusivity in mixtures with the same solvent.

  5. Dynamics of a thin film flowing down a heated wall with finite thermal diffusivity

    NASA Astrophysics Data System (ADS)

    Dallaston, Michael C.; Tseluiko, Dmitri; Kalliadasis, Serafim

    2016-11-01

    Consider the dynamics of a thin film flowing down a heated substrate. The substrate heating generates a temperature distribution on the free surface, which in turn induces surface-tension gradients and corresponding thermocapillary stresses that affect the free surface and therefore the fluid flow. We study here the effect of finite substrate thermal diffusivity on the film dynamics. Linear stability analysis of the full Navier-Stokes and heat transport equations indicates if the substrate diffusivity is sufficiently small, the film becomes unstable at a finite wavelength and at a Reynolds number smaller than that predicted in the long-wavelength limit. This property is captured in a reduced-order system of equations derived using a weighted-residual integral-boundary-layer method. This reduced-order model is also used to compute the bifurcation diagrams of solution branches connecting the trivial flat film to traveling waves including solitary pulses. The effect of finite diffusivity is to separate a simultaneous Hopf-transcritical bifurcation into its individual component bifurcations. The appropriate Hopf bifurcation then connects only to the solution branch of negative-hump pulses, with wave speed less than the linear wave speed, while the branch of positive-single-hump pulses merges with the branch of positive-two-hump pulses at a supercritical Reynolds number. In the regime where finite-wavelength instability occurs, there exists a Hopf-bifurcation pair connected by a branch of periodic solutions, whose period cannot be increased indefinitely. Numerical simulation of the reduced-order system shows the development of a train of coherent structures, each of which resembles a stationary positive-hump pulse, and, in the regime of finite-wavelength instability, wavelength selection and saturation to periodic traveling waves.

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

    NASA Astrophysics Data System (ADS)

    Chen, Chi; Lu, Ziheng; Ciucci, Francesco

    2017-01-01

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