Science.gov

Sample records for intramolecular diffusive motion

  1. Extremely slow intramolecular diffusion in unfolded protein L.

    PubMed

    Waldauer, Steven A; Bakajin, Olgica; Lapidus, Lisa J

    2010-08-03

    A crucial parameter in many theories of protein folding is the rate of diffusion over the energy landscape. Using a microfluidic mixer we have observed the rate of intramolecular diffusion within the unfolded B1 domain of protein L before it folds. The diffusion-limited rate of intramolecular contact is about 20 times slower than the rate in 6 M GdnHCl, and because in these conditions the protein is also more compact, the intramolecular diffusion coefficient decreases 100-500 times. The dramatic slowdown in diffusion occurs within the 250 micros mixing time of the mixer, and there appears to be no further evolution of this rate before reaching the transition state of folding. We show that observed folding rates are well predicted by a Kramers model with a denaturant-dependent diffusion coefficient and speculate that this diffusion coefficient is a significant contribution to the observed rate of folding.

  2. Extremely slow intramolecular diffusion in unfolded protein L

    PubMed Central

    Waldauer, Steven A.; Bakajin, Olgica; Lapidus, Lisa J.

    2010-01-01

    A crucial parameter in many theories of protein folding is the rate of diffusion over the energy landscape. Using a microfluidic mixer we have observed the rate of intramolecular diffusion within the unfolded B1 domain of protein L before it folds. The diffusion-limited rate of intramolecular contact is about 20 times slower than the rate in 6 M GdnHCl, and because in these conditions the protein is also more compact, the intramolecular diffusion coefficient decreases 100–500 times. The dramatic slowdown in diffusion occurs within the 250 μs mixing time of the mixer, and there appears to be no further evolution of this rate before reaching the transition state of folding. We show that observed folding rates are well predicted by a Kramers model with a denaturant-dependent diffusion coefficient and speculate that this diffusion coefficient is a significant contribution to the observed rate of folding. PMID:20643973

  3. Molecular crowding inhibits intramolecular breathing motions in proteins.

    SciTech Connect

    Makowski, L.; Rodi, D. J.; Mandava, S.; Minh, D.; Gore, D. B.; Fischetti, R. F.; Biosciences Division; IIT

    2008-01-11

    In aqueous solution some proteins undergo large-scale movements of secondary structures, subunits or domains, referred to as protein 'breathing', that define a native-state ensemble of structures. These fluctuations are sensitive to the nature and concentration of solutes and other proteins and are thereby expected to be different in the crowded interior of a cell than in dilute solution. Here we use a combination of wide angle X-ray scattering (WAXS) and computational modeling to derive a quantitative measure of the spatial scale of conformational fluctuations in a protein solution. Concentration-dependent changes in the observed scattering intensities are consistent with a model of structural fluctuations in which secondary structures undergo rigid-body motions relative to one another. This motion increases with decreasing protein concentration or increasing temperature. Analysis of a set of five structurally and functionally diverse proteins reveals a diversity of kinetic behaviors. Proteins with multiple disulfide bonds exhibit little or no increase in breathing in dilute solutions. The spatial extent of structural fluctuations appears highly dependent on both protein structure and concentration and is universally suppressed at very high protein concentrations.

  4. Detailed tuning of structure and intramolecular communication are dispensable for processive motion of myosin VI.

    PubMed

    Elting, Mary Williard; Bryant, Zev; Liao, Jung-Chi; Spudich, James A

    2011-01-19

    Dimeric myosin VI moves processively hand-over-hand along actin filaments. We have characterized the mechanism of this processive motion by measuring the impact of structural and chemical perturbations on single-molecule processivity. Processivity is maintained despite major alterations in lever arm structure, including replacement of light chain binding regions and elimination of the medial tail. We present kinetic models that can explain the ATP concentration-dependent processivities of myosin VI constructs containing either native or artificial lever arms. We conclude that detailed tuning of structure and intramolecular communication are dispensable for processive motion, and further show theoretically that one proposed type of nucleotide gating can be detrimental rather than beneficial for myosin processivity. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. Electron diffraction analysis for the molecules with degenerate large amplitude motions: Intramolecular dynamics in arsenic pentafluoride

    NASA Astrophysics Data System (ADS)

    Kochikov, Igor V.; Kovtun, Dmitry M.; Tarasov, Yury I.

    2017-03-01

    There exists a noticeable disagreement in the difference of axial and equatorial bond lengths in D3h symmetry arsenic and phosphorus pentafluorides between the GED data and high level quantum chemical results. In order to resolve this disagreement, a new structural analysis of the original experiment of (Clippard & Bartell, Inorg. Chem., 9 (1970) 805-811) was undertaken on the basis of modern approach incorporating spectroscopic evidence and quantum chemical information and allowing for intramolecular large-amplitude motion. The results of the analysis prove the internal insufficiency of the experimental material in the description of the accurate positions of the peaks on the radial distribution function. Additional experimental investigation of pentahalide molecules, especially at high temperatures, is of interest.

  6. Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions.

    PubMed

    Tan, R K; Sprous, D; Harvey, S C

    1996-08-01

    Small (600 base pair) DNA plasmids were modeled with a simplified representation (3DNA) and the intramolecular motions were studied using molecular mechanics and molecular dynamics techniques. The model is detailed enough to incorporate sequence effects. At the same time, it is simple enough to allow long molecular dynamics simulations. The simulations revealed that large-scale slithering occurs in a homogeneous sequence. In a heterogeneous sequence, containing numerous small intrinsic curves, the centers of the curves are preferentially positioned at the tips of loops. With more curves than loop tips (two in unbranched supercoiled DNA), the heterogeneous sequence plasmid slithers short distances to reposition other curves into the loop tips. However, the DNA is immobilized most of the time, with the loop tips positioned over a few favored curve centers. Branching or looping also appears in the heterogeneous sequence as a new method of repositioning the loop tips. Instead of a smooth progression of increasing writhing with increasing linking difference, theoretical studies have predicted that there is a threshold between unwrithed and writhed DNA at a linking difference between one and two. This has previously been observed in simulations of static structures and is demonstrated here for dynamic homogeneous closed DNA. Such an abrupt transition is not found in the heterogeneous sequence in both the static and dynamic cases.

  7. Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

    NASA Astrophysics Data System (ADS)

    Ichiyanagi, Kouhei; Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Hoshisashi, Kentaro; Jae-won, Chang; Tokue, Maki; Matsushita, Yufuku; Nishijima, Masaki; Inoue, Yoshihisa; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru; Yagi, Naoto; Sasaki, Yuji C.

    2013-10-01

    Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10-20 keV (△E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

  8. Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

    SciTech Connect

    Ichiyanagi, Kouhei; Sasaki, Yuji C.; Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru; Hoshisashi, Kentaro; Jae-won, Chang; Tokue, Maki; Matsushita, Yufuku; Nishijima, Masaki; Inoue, Yoshihisa; Yagi, Naoto

    2013-10-15

    Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10–20 keV (△E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

  9. Quantum effect of intramolecular high-frequency vibrational modes on diffusion-controlled electron transfer rate: From the weak to the strong electronic coupling regions

    SciTech Connect

    Zhu, Wenjuan; Zhao, Yi

    2007-05-14

    The Sumi-Marcus theory is extended by introducing two approaches to investigate electron transfer reactions from weak-to-strong electronic coupling regime. One of these approaches is the quantum R-matrix theory, useful for dealing with the intramolecular vibrational motions in the whole electronic coupling domain. The other is the split operator approach that is employed to solve the reaction-diffusion equation. The approaches are then applied to electron transfer in the Marcus inverted regime to investigate the nuclear tunneling effect on the long time rate and the survival probabilities. The numerical results illustrate that the adiabatic suppression obtained from the R-matrix approach is much smaller than that from the Landau-Zener theory whereas it cannot be predicted by the perturbation theory. The jointed effects of the electronic coupling and solvent relaxation time on the rates are also explored.

  10. Ultrafast twisting motions and intramolecular charge-transfer reaction in a cyanine dye trapped in molecular nanocavities

    NASA Astrophysics Data System (ADS)

    Fayed, T. A.; Organero, J. A.; Garcia-Ochoa, I.; Tormo, L.; Douhal, A.

    2002-09-01

    Emission properties of the cyanine dye, 1-(2-naphthyl)-2-ethenyl-(2-benzothiazolium) iodide, in aqueous nanocavities offered by cyclodextrins and in a film of a polymeric matrix were studied by means of steady-state and picosecond time-resolved emission spectroscopy. The results show the occurrence of a fast twisting motion and a subsequent intramolecular charge-transfer reaction. The initial step can be prevented by the size of the nanocavity which governs the spectral position of the fluorescence band and lifetime of the excited encapsulated host.

  11. Prospective motion correction of segmented diffusion weighted EPI.

    PubMed

    Herbst, Michael; Zahneisen, Benjamin; Knowles, Benjamin; Zaitsev, Maxim; Ernst, Thomas

    2015-12-01

    Recently, a new algorithm was introduced to combine segments of under-sampled diffusion weighted data using multiplexed sensitivity encoding. While the algorithm provides good results in cooperative volunteers, motion during the data acquisition is not accounted for. In this work, the continuous prospective motion correction of a segmented diffusion weighted acquisition is combined with multiplexed sensitivity encoding. Simulations investigate the influence of motion on the reconstruction. Additionally, the change in coil sensitivities due to patient motion is taken into consideration. Finally, in vivo experiments display the effects of motion and its prospective correction on high resolution diffusion weighted imaging. Inconsistencies of the imaging plane lead to artifacts and blurring in the reconstructed dataset. Additionally, motion during the diffusion weighting period can lead to substantial image artifacts and signal dropouts. The change in coil sensitivities shows minor effect for the simulated range of motion (5°). Prospective motion correction is shown to improve image quality in the case of large motion (5°) and to reliably correct for small motion (1°). The combination of prospective motion correction and multiplexed sensitivity encoding allows for high resolution diffusion weighted imaging even in the presence of substantial head motion. © 2014 Wiley Periodicals, Inc.

  12. Real-time optical motion correction for diffusion tensor imaging.

    PubMed

    Aksoy, Murat; Forman, Christoph; Straka, Matus; Skare, Stefan; Holdsworth, Samantha; Hornegger, Joachim; Bammer, Roland

    2011-08-01

    Head motion is a fundamental problem in brain MRI. The problem is further compounded in diffusion tensor imaging because of long acquisition times, and the sensitivity of the tensor computation to even small misregistration. To combat motion artifacts in diffusion tensor imaging, a novel real-time prospective motion correction method was introduced using an in-bore monovision system. The system consists of a camera mounted on the head coil and a self-encoded checkerboard marker that is attached to the patient's forehead. Our experiments showed that optical prospective motion correction is more effective at removing motion artifacts compared to image-based retrospective motion correction. Statistical analysis revealed a significant improvement in similarity between diffusion data acquired at different time points when prospective correction was used compared to retrospective correction (P<0.001). Copyright © 2011 Wiley-Liss, Inc.

  13. Approximate constants of motion for classically chaotic vibrational dynamics - Vague tori, semiclassical quantization, and classical intramolecular energy flow

    NASA Technical Reports Server (NTRS)

    Shirts, R. B.; Reinhardt, W. P.

    1982-01-01

    Substantial short time regularity, even in the chaotic regions of phase space, is found for what is seen as a large class of systems. This regularity manifests itself through the behavior of approximate constants of motion calculated by Pade summation of the Birkhoff-Gustavson normal form expansion; it is attributed to remnants of destroyed invariant tori in phase space. The remnant torus-like manifold structures are used to justify Einstein-Brillouin-Keller semiclassical quantization procedures for obtaining quantum energy levels, even in the absence of complete tori. They also provide a theoretical basis for the calculation of rate constants for intramolecular mode-mode energy transfer. These results are illustrated by means of a thorough analysis of the Henon-Heiles oscillator problem. Possible generality of the analysis is demonstrated by brief consideration of classical dynamics for the Barbanis Hamiltonian, Zeeman effect in hydrogen and recent results of Wolf and Hase (1980) for the H-C-C fragment.

  14. Approximate constants of motion for classically chaotic vibrational dynamics - Vague tori, semiclassical quantization, and classical intramolecular energy flow

    NASA Technical Reports Server (NTRS)

    Shirts, R. B.; Reinhardt, W. P.

    1982-01-01

    Substantial short time regularity, even in the chaotic regions of phase space, is found for what is seen as a large class of systems. This regularity manifests itself through the behavior of approximate constants of motion calculated by Pade summation of the Birkhoff-Gustavson normal form expansion; it is attributed to remnants of destroyed invariant tori in phase space. The remnant torus-like manifold structures are used to justify Einstein-Brillouin-Keller semiclassical quantization procedures for obtaining quantum energy levels, even in the absence of complete tori. They also provide a theoretical basis for the calculation of rate constants for intramolecular mode-mode energy transfer. These results are illustrated by means of a thorough analysis of the Henon-Heiles oscillator problem. Possible generality of the analysis is demonstrated by brief consideration of classical dynamics for the Barbanis Hamiltonian, Zeeman effect in hydrogen and recent results of Wolf and Hase (1980) for the H-C-C fragment.

  15. Diffusion Imaging with Prospective Motion Correction and Reacquisition

    PubMed Central

    Benner, Thomas; van der Kouwe, André J. W.; Sorensen, A. Gregory

    2011-01-01

    A major source of artifacts in diffusion-weighted imaging (DWI) is subject motion. Slow bulk subject motion causes misalignment of data when more than one average or diffusion gradient direction is acquired. Fast bulk subject motion can cause signal dropout artifacts in diffusion-weighted images and results in erroneous derived maps e.g. fractional anisotropy maps. To address both types of artifacts, a fully automatic method is presented that combines prospective motion correction with a reacquisition scheme. Motion correction is based on the Prospective Acquisition Correction (PACE) method modified to work with diffusion-weighted data (DW-PACE). The images to reacquire are determined automatically during the acquisition from the imaging data i.e. no extra reference scan, navigators or external devices are necessary. The number of reacquired images i.e. the additional scan duration can be adjusted freely. DW-PACE corrects slow bulk motion well and reduces misalignment artifacts like image blurring. Mean absolute residual values for translation and rotation were less than 0.6 mm and 0.5 degrees. Reacquisition of images affected by signal dropout artifacts results in diffusion maps and fiber tracking free of artifacts. The presented method allows the reduction of two types of common motion related artifacts at the cost of slightly increased acquisition time. PMID:21695721

  16. Real-time Optical Motion Correction for Diffusion Tensor Imaging

    PubMed Central

    Aksoy, Murat; Forman, Christoph; Straka, Matus; Skare, Stefan; Holdsworth, Samantha; Hornegger, Joachim; Bammer, Roland

    2011-01-01

    Head motion is a fundamental problem in brain MRI. The problem is further compounded in diffusion tensor imaging (DTI) because of long acquisition times, and the sensitivity of the tensor computation to even small misregistration. To combat motion artifacts in DTI, a novel real-time prospective motion correction method was introduced using an in-bore monovision system. The system consists of a camera mounted on the head coil and a self-encoded checkerboard marker that is attached to the patient’s forehead. Our experiments showed that optical prospective motion correction is more effective at removing motion artifacts compared to image-based retrospective motion correction. Statistical analysis revealed a significant improvement in similarity between diffusion data acquired at different time points when prospective correction was used compared to retrospective correction (p<0.001). PMID:21432898

  17. Head injury or head motion? Assessment and quantification of motion artifacts in diffusion tensor imaging studies.

    PubMed

    Ling, Josef; Merideth, Flannery; Caprihan, Arvind; Pena, Amanda; Teshiba, Terri; Mayer, Andrew R

    2012-01-01

    The relationship between head motion and diffusion values such as fractional anisotropy (FA) and mean diffusivity (MD) is currently not well understood. Simulation studies suggest that head motion may introduce either a positive or negative bias, but this has not been quantified in clinical studies. Moreover, alternative measures for removing bias as result of head motion, such as the removal of problematic gradients, has been suggested but not carefully evaluated. The current study examined the impact of head motion on FA and MD across three common pipelines (tract-based spatial statistics, voxelwise, and region of interest analyses) and determined the impact of removing diffusion weighted images. Our findings from a large cohort of healthy controls indicate that while head motion was associated with a positive bias for both FA and MD, the effect was greater for MD. The positive bias was observed across all three analysis pipelines and was present following established protocols for data processing, suggesting that current techniques (i.e., correction of both image and gradient table) for removing motion bias are likely insufficient. However, the removal of images with gross artifacts did not fundamentally change the relationship between motion and DTI scalar values. In addition, Monte Carlo simulations suggested that the random removal of images increases the bias and reduces the precision of both FA and MD. Finally, we provide an example of how head motion can be quantified across different neuropsychiatric populations, which should be implemented as part of any diffusion tensor imaging quality assurance protocol.

  18. Apparent diffusive motion of centrin foci in living cells: implications for diffusion-based motion in centriole duplication

    NASA Astrophysics Data System (ADS)

    Rafelski, Susanne M.; Keller, Lani C.; Alberts, Jonathan B.; Marshall, Wallace F.

    2011-04-01

    The degree to which diffusion contributes to positioning cellular structures is an open question. Here we investigate the question of whether diffusive motion of centrin granules would allow them to interact with the mother centriole. The role of centrin granules in centriole duplication remains unclear, but some proposed functions of these granules, for example, in providing pre-assembled centriole subunits, or by acting as unstable 'pre-centrioles' that need to be captured by the mother centriole (La Terra et al 2005 J. Cell Biol. 168 713-22), require the centrin foci to reach the mother. To test whether diffusive motion could permit such interactions in the necessary time scale, we measured the motion of centrin-containing foci in living human U2OS cells. We found that these centrin foci display apparently diffusive undirected motion. Using the apparent diffusion constant obtained from these measurements, we calculated the time scale required for diffusion to capture by the mother centrioles and found that it would greatly exceed the time available in the cell cycle. We conclude that mechanisms invoking centrin foci capture by the mother, whether as a pre-centriole or as a source of components to support later assembly, would require a form of directed motility of centrin foci that has not yet been observed.

  19. Apparent diffusive motion of centrin foci in living cells: implications for diffusion-based motion in centriole duplication.

    PubMed

    Rafelski, Susanne M; Keller, Lani C; Alberts, Jonathan B; Marshall, Wallace F

    2011-04-01

    The degree to which diffusion contributes to positioning cellular structures is an open question. Here we investigate the question of whether diffusive motion of centrin granules would allow them to interact with the mother centriole. The role of centrin granules in centriole duplication remains unclear, but some proposed functions of these granules, for example, in providing pre-assembled centriole subunits, or by acting as unstable 'pre-centrioles' that need to be captured by the mother centriole (La Terra et al 2005 J. Cell Biol. 168 713-22), require the centrin foci to reach the mother. To test whether diffusive motion could permit such interactions in the necessary time scale, we measured the motion of centrin-containing foci in living human U2OS cells. We found that these centrin foci display apparently diffusive undirected motion. Using the apparent diffusion constant obtained from these measurements, we calculated the time scale required for diffusion to capture by the mother centrioles and found that it would greatly exceed the time available in the cell cycle. We conclude that mechanisms invoking centrin foci capture by the mother, whether as a pre-centriole or as a source of components to support later assembly, would require a form of directed motility of centrin foci that has not yet been observed.

  20. Apparent diffusive motion of centrin foci in living cells: implications for diffusion-based motion in centriole duplication

    PubMed Central

    Rafelski, Susanne M.; Keller, Lani C.; Alberts, Jonathan B.; Marshall, Wallace F.

    2011-01-01

    The degree to which diffusion contributes to positioning cellular structures is an open question. Here we investigate the question of whether diffusive motion of centrin granules would allow them to interact with the mother centriole. The role of centrin granules in centriole duplication remains unclear, but some proposed functions of these granules, for example in providing pre-assembled centriole subunits, or by acting as unstable “pre-centrioles” that need to be captured by the mother centriole (La Terra et al., 2005), require the centrin foci to reach the mother. To test whether diffusive motion could permit such interactions in the necessary time scale, we measured the motion of centrin-containing foci in living human U2OS cells. We found that these centrin foci display apparently diffusive undirected motion. Using the apparent diffusion constant obtained from these measurements, we calculated the time scale required for diffusion to capture by the mother centrioles and found that it would greatly exceed the time available in the cell cycle. We conclude that mechanisms invoking centrin foci capture by the mother, whether as a pre-centriole or as a source of components to support later assembly, would require a form of directed motility of centrin foci that has not yet been observed. PMID:21378439

  1. Relating Brownian motion to diffusion with superparamagnetic colloids

    NASA Astrophysics Data System (ADS)

    Darras, A.; Fiscina, J.; Vandewalle, N.; Lumay, G.

    2017-04-01

    An original experiment is introduced that allows students to relate the Brownian motion of a set of superparamagnetic colloidal particles to their macroscopic diffusion. An external and constant magnetic field is first applied to the colloidal suspension so that the particles self-organize into chains. When the magnetic field is removed, the particles then freely diffuse from their positions in the chain, starting from the same coordinate on the axis perpendicular to the initial chain. This configuration thus enables an observer to study the one dimensional diffusion process, while also observing the underlying Brownian motion of the microscopic particles. Moreover, by studying the evolution of the particle distribution, a measurement of the diffusion coefficient can be obtained. In addition, by repeating this measurement with fluids of various viscosities, the Stokes-Einstein relation may be illustrated.

  2. Ion Motion in Electrolytic Cells: Anomalous Diffusion Evidences.

    PubMed

    Lenzi, E K; Zola, R S; Ribeiro, H V; Vieira, Denner S; Ciuchi, F; Mazzulla, A; Scaramuzza, N; Evangelista, L R

    2017-04-06

    In this study, we argue that ion motion in electrolytic cells containing Milli-Q water, weak electrolytes, or liquid crystals may exhibit unusual diffusive regimes that deviate from the expected behavior, leading the system to present an anomalous diffusion. Our arguments lie on the investigation of the electrical conductivity and its relationship with the mean square displacement, which may be used to characterize the ionic motion. In our analysis, the Poisson-Nernst-Planck diffusional model is used with extended boundary conditions to simulate the charge transfer, accumulation, and/or adsorption-desorption at the electrode surfaces.

  3. An Efficient and Accurate Formalism for the Treatment of Large Amplitude Intramolecular Motion

    PubMed Central

    2012-01-01

    We propose a general approach to describe large amplitude motions (LAM) with multiple degrees of freedom (DOF) in molecules or reaction intermediates, which is useful for the computation of thermochemical or kinetic data. The kinetic part of the LAM Lagrangian is derived using a Z-matrix internal coordinate representation within a new numerical procedure. This derivation is exact for a classical system, and the uncertainties on the prediction of observable quantities largely arise from uncertainties on the LAM potential energy surface (PES) itself. In order to rigorously account for these uncertainties, we present an approach based on Bayesian theory to infer a parametrized physical model of the PES using ab initio calculations. This framework allows for quantification of uncertainties associated with a PES model as well as the forward propagation of these uncertainties to the quantity of interest. A selection and generalization of some treatments accounting for the coupling of the LAM with other internal or external DOF are also presented. Finally, we discuss and validate the approach with two applications: the calculation of the partition function of 1,3-butadiene and the calculation of the high-pressure reaction rate of the CH3 + H → CH4 recombination. PMID:22904694

  4. Ultrafast intramolecular relaxation and wave-packet motion in a ruthenium-based supramolecular photocatalyst.

    PubMed

    Wächtler, Maria; Guthmuller, Julien; Kupfer, Stephan; Maiuri, Margherita; Brida, Daniele; Popp, Jürgen; Rau, Sven; Cerullo, Giulio; Dietzek, Benjamin

    2015-05-18

    The hydrogen-evolving photocatalyst [(tbbpy)2 Ru(tpphz)Pd(Cl)2 ](2+) (tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine, tpphz=tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine) shows excitation-wavelength-dependent catalytic activity, which has been correlated to the localization of the initial excitation within the coordination sphere. In this contribution the excitation-wavelength dependence of the early excited-state relaxation and the occurrence of vibrational coherences are investigated by sub-20 fs transient absorption spectroscopy and DFT/TDDFT calculations. The comparison with the mononuclear precursor [(tbbpy)2 Ru(tpphz)](2+) highlights the influence of the catalytic center on these ultrafast processes. Only in the presence of the second metal center, does the excitation of a (1) MLCT state localized on the central part of the tpphz bridge lead to coherent wave-packet motion in the excited state. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. An Efficient and Accurate Formalism for the Treatment of Large Amplitude Intramolecular Motion.

    PubMed

    Reinisch, Guillaume; Miki, Kenji; Vignoles, Gérard L; Wong, Bryan M; Simmons, Chris S

    2012-08-14

    We propose a general approach to describe large amplitude motions (LAM) with multiple degrees of freedom (DOF) in molecules or reaction intermediates, which is useful for the computation of thermochemical or kinetic data. The kinetic part of the LAM Lagrangian is derived using a Z-matrix internal coordinate representation within a new numerical procedure. This derivation is exact for a classical system, and the uncertainties on the prediction of observable quantities largely arise from uncertainties on the LAM potential energy surface (PES) itself. In order to rigorously account for these uncertainties, we present an approach based on Bayesian theory to infer a parametrized physical model of the PES using ab initio calculations. This framework allows for quantification of uncertainties associated with a PES model as well as the forward propagation of these uncertainties to the quantity of interest. A selection and generalization of some treatments accounting for the coupling of the LAM with other internal or external DOF are also presented. Finally, we discuss and validate the approach with two applications: the calculation of the partition function of 1,3-butadiene and the calculation of the high-pressure reaction rate of the CH(3) + H → CH(4) recombination.

  6. Diffusion in different models of active Brownian motion

    NASA Astrophysics Data System (ADS)

    Lindner, B.; Nicola, E. M.

    2008-04-01

    Active Brownian particles (ABP) have served as phenomenological models of self-propelled motion in biology. We study the effective diffusion coefficient of two one-dimensional ABP models (simplified depot model and Rayleigh-Helmholtz model) differing in their nonlinear friction functions. Depending on the choice of the friction function the diffusion coefficient does or does not attain a minimum as a function of noise intensity. We furthermore discuss the case of an additional bias breaking the left-right symmetry of the system. We show that this bias induces a drift and that it generally reduces the diffusion coefficient. For a finite range of values of the bias, both models can exhibit a maximum in the diffusion coefficient vs. noise intensity.

  7. Analytical correlation functions for motion through diffusivity landscapes.

    PubMed

    Roosen-Runge, Felix; Bicout, Dominique J; Barrat, Jean-Louis

    2016-05-28

    Diffusion of a particle through an energy and diffusivity landscape is a very general phenomenon in numerous systems of soft and condensed matter. On the one hand, theoretical frameworks such as Langevin and Fokker-Planck equations present valuable accounts to understand these motions in great detail, and numerous studies have exploited these approaches. On the other hand, analytical solutions for correlation functions, as, e.g., desired by experimentalists for data fitting, are only available for special cases. We explore the possibility to use different theoretical methods in the specific picture of time-dependent switching between diffusive states to derive analytical functions that allow to link experimental and simulation results to theoretical calculations. In particular, we present a closed formula for diffusion switching between two states, as well as a general recipe of how to generalize the formula to multiple states.

  8. Anomalous Diffusion Index for Lévy Motions

    NASA Astrophysics Data System (ADS)

    Dorea, Chang C. Y.; Medino, Ary V.

    2006-05-01

    In modelling complex systems as real diffusion processes it is common to analyse its diffusive regime through the study of approximating sequences of random walks. For the partial sums S_n=ξ_1 + ξ_2 + ldots + ξ_n one considers the approximating sequence of processes X^{(n)}(t)= a_n (S_{[k_nt]}-b_n). Then, under sufficient smoothness requirements we have the convergence to the desired diffusion, X^{(n)}(t) to X(t). A key assumption usually presumed is the finiteness of the second moment, and, hence the validity of the Central Limit Theorem. Under anomalous diffusive regime the asymptotic behavior of S n may well be non-Gaussian and n^{-1}E(S^2_n) toinfty. Such random walks have been referred by physicists as Lévy motions or Lévy flights. In this work, we introduce an alternative notion to classify these regimes, the diffusion index γ_X. For some γ^0_X properly chosen let γ_X=inf \\{ γ:0 < γ≤γ^0_X,limsup_{tto infty}t^{-1}E|X(t)|^{1/γ} < infty \\}. Relationship between γ_X, the infinitesimal diffusion coefficients and the diffusion constant will be explored. Illustrative examples as well as estimates, based on extreme order statistics, for γ_X will also be presented.

  9. Motion Detection in Diffusion MRI via Online ODF Estimation

    PubMed Central

    Caruyer, Emmanuel; Aganj, Iman; Lenglet, Christophe; Sapiro, Guillermo; Deriche, Rachid

    2013-01-01

    The acquisition of high angular resolution diffusion MRI is particularly long and subject motion can become an issue. The orientation distribution function (ODF) can be reconstructed online incrementally from diffusion-weighted MRI with a Kalman filtering framework. This online reconstruction provides real-time feedback throughout the acquisition process. In this article, the Kalman filter is first adapted to the reconstruction of the ODF in constant solid angle. Then, a method called STAR (STatistical Analysis of Residuals) is presented and applied to the online detection of motion in high angular resolution diffusion images. Compared to existing techniques, this method is image based and is built on top of a Kalman filter. Therefore, it introduces no additional scan time and does not require additional hardware. The performance of STAR is tested on simulated and real data and compared to the classical generalized likelihood ratio test. Successful detection of small motion is reported (rotation under 2°) with no delay and robustness to noise. PMID:23509445

  10. Fractional Brownian motions: memory, diffusion velocity, and correlation functions

    NASA Astrophysics Data System (ADS)

    Fuliński, A.

    2017-02-01

    Fractional Brownian motions (FBMs) have been observed recently in the measured trajectories of individual molecules or small particles in the cytoplasm of living cells and in other dense composite systems, among others. Various types of FBMs differ in a number of ways, including the strength, range and type of damping of the memory encoded in their definitions, but share several basic characteristics: distributions, non-ergodic properties, and scaling of the second moment, which makes it difficult to determine which type of Brownian motion (fractional or normal) the measured trajectory belongs to. Here, we show, by introducing FBMs with regulated range and strength of memory, that it is the structure of memory which determines their physical properties, including mean velocity of diffusion; therefore, the course and kinetics of several processes (including coagulation and some chemical reactions). We also show that autocorrelation functions possess characteristic features which enable identification of an observed FBM, and of the type of memory governing its trajectory. In memoriam Marian Smoluchowski, on the 100th anniversary of the publication of his seminal papers on Brownian motion and diffusion-limited kinetics.

  11. Motion immune diffusion imaging using augmented MUSE for high-resolution multi-shot EPI.

    PubMed

    Guhaniyogi, Shayan; Chu, Mei-Lan; Chang, Hing-Chiu; Song, Allen W; Chen, Nan-Kuei

    2016-02-01

    To develop new techniques for reducing the effects of microscopic and macroscopic patient motion in diffusion imaging acquired with high-resolution multishot echo-planar imaging. The previously reported multiplexed sensitivity encoding (MUSE) algorithm is extended to account for macroscopic pixel misregistrations, as well as motion-induced phase errors in a technique called augmented MUSE (AMUSE). Furthermore, to obtain more accurate quantitative diffusion-tensor imaging measures in the presence of subject motion, we also account for the altered diffusion encoding among shots arising from macroscopic motion. MUSE and AMUSE were evaluated on simulated and in vivo motion-corrupted multishot diffusion data. Evaluations were made both on the resulting imaging quality and estimated diffusion tensor metrics. AMUSE was found to reduce image blurring resulting from macroscopic subject motion compared to MUSE but yielded inaccurate tensor estimations when neglecting the altered diffusion encoding. Including the altered diffusion encoding in AMUSE produced better estimations of diffusion tensors. The use of AMUSE allows for improved image quality and diffusion tensor accuracy in the presence of macroscopic subject motion during multishot diffusion imaging. These techniques should facilitate future high-resolution diffusion imaging. © 2015 Wiley Periodicals, Inc.

  12. Intramolecular vibrational energy redistribution from a high frequency mode in the presence of an internal rotor: Classical thick-layer diffusion and quantum localization

    NASA Astrophysics Data System (ADS)

    Manikandan, Paranjothy; Keshavamurthy, Srihari

    2007-08-01

    We study the effect of an internal rotor on the classical and quantum intramolecular vibrational energy redistribution (IVR) dynamics of a model system with three degrees of freedom. The system is based on a Hamiltonian proposed by Martens and Reinhardt [J. Chem. Phys. 93, 5621 (1990)] to study IVR in the excited electronic state of para-fluorotoluene. We explicitly construct the state space and show, confirming the mechanism proposed by Martens and Reinhardt, that an excited high frequency mode relaxes via diffusion along a thick layer of chaos created by the low frequency-rotor interactions. However, the corresponding quantum dynamics exhibits no appreciable relaxation of the high frequency mode. We attribute the quantum suppression of the classical thick-layer diffusion to the rotor selection rules and, possibly, dynamical localization effects.

  13. Motion immune diffusion imaging using augmented MUSE (AMUSE) for high-resolution multi-shot EPI

    PubMed Central

    Guhaniyogi, Shayan; Chu, Mei-Lan; Chang, Hing-Chiu; Song, Allen W.; Chen, Nan-kuei

    2015-01-01

    Purpose To develop new techniques for reducing the effects of microscopic and macroscopic patient motion in diffusion imaging acquired with high-resolution multi-shot EPI. Theory The previously reported Multiplexed Sensitivity Encoding (MUSE) algorithm is extended to account for macroscopic pixel misregistrations as well as motion-induced phase errors in a technique called Augmented MUSE (AMUSE). Furthermore, to obtain more accurate quantitative DTI measures in the presence of subject motion, we also account for the altered diffusion encoding among shots arising from macroscopic motion. Methods MUSE and AMUSE were evaluated on simulated and in vivo motion-corrupted multi-shot diffusion data. Evaluations were made both on the resulting imaging quality and estimated diffusion tensor metrics. Results AMUSE was found to reduce image blurring resulting from macroscopic subject motion compared to MUSE, but yielded inaccurate tensor estimations when neglecting the altered diffusion encoding. Including the altered diffusion encoding in AMUSE produced better estimations of diffusion tensors. Conclusion The use of AMUSE allows for improved image quality and diffusion tensor accuracy in the presence of macroscopic subject motion during multi-shot diffusion imaging. These techniques should facilitate future high-resolution diffusion imaging. PMID:25762216

  14. From diffusion to anomalous diffusion: A century after Einstein's Brownian motion

    NASA Astrophysics Data System (ADS)

    Sokolov, I. M.; Klafter, J.

    2005-06-01

    Einstein's explanation of Brownian motion provided one of the cornerstones which underlie the modern approaches to stochastic processes. His approach is based on a random walk picture and is valid for Markovian processes lacking long-term memory. The coarse-grained behavior of such processes is described by the diffusion equation. However, many natural processes do not possess the Markovian property and exhibit anomalous diffusion. We consider here the case of subdiffusive processes, which correspond to continuous-time random walks in which the waiting time for a step is given by a probability distribution with a diverging mean value. Such a process can be considered as a process subordinated to normal diffusion under operational time which depends on this pathological waiting-time distribution. We derive two different but equivalent forms of kinetic equations, which reduce to known fractional diffusion or Fokker-Planck equations for waiting-time distributions following a power law. For waiting time distributions which are not pure power laws one or the other form of the kinetic equation is advantageous, depending on whether the process slows down or accelerates in the course of time.

  15. Prospective and retrospective motion correction in diffusion magnetic resonance imaging of the human brain.

    PubMed

    Kober, Tobias; Gruetter, Rolf; Krueger, Gunnar

    2012-01-02

    Diffusion-weighting in magnetic resonance imaging (MRI) increases the sensitivity to molecular Brownian motion, providing insight in the micro-environment of the underlying tissue types and structures. At the same time, the diffusion weighting renders the scans sensitive to other motion, including bulk patient motion. Typically, several image volumes are needed to extract diffusion information, inducing also inter-volume motion susceptibility. Bulk motion is more likely during long acquisitions, as they appear in diffusion tensor, diffusion spectrum and q-ball imaging. Image registration methods are successfully used to correct for bulk motion in other MRI time series, but their performance in diffusion-weighted MRI is limited since diffusion weighting introduces strong signal and contrast changes between serial image volumes. In this work, we combine the capability of free induction decay (FID) navigators, providing information on object motion, with image registration methodology to prospectively--or optionally retrospectively--correct for motion in diffusion imaging of the human brain. Eight healthy subjects were instructed to perform small-scale voluntary head motion during clinical diffusion tensor imaging acquisitions. The implemented motion detection based on FID navigator signals is processed in real-time and provided an excellent detection performance of voluntary motion patterns even at a sub-millimetre scale (sensitivity≥92%, specificity>98%). Motion detection triggered an additional image volume acquisition with b=0 s/mm2 which was subsequently co-registered to a reference volume. In the prospective correction scenario, the calculated motion-parameters were applied to perform a real-time update of the gradient coordinate system to correct for the head movement. Quantitative analysis revealed that the motion correction implementation is capable to correct head motion in diffusion-weighted MRI to a level comparable to scans without voluntary head motion

  16. Quantum Brownian motion with inhomogeneous damping and diffusion

    NASA Astrophysics Data System (ADS)

    Massignan, Pietro; Lampo, Aniello; Wehr, Jan; Lewenstein, Maciej

    2015-03-01

    We analyze the microscopic model of quantum Brownian motion, describing a Brownian particle interacting with a bosonic bath through a coupling which is linear in the creation and annihilation operators of the bath, but may be a nonlinear function of the position of the particle. Physically, this corresponds to a configuration in which damping and diffusion are spatially inhomogeneous. We derive systematically the quantum master equation for the Brownian particle in the Born-Markov approximation and we discuss the appearance of additional terms, for various polynomials forms of the coupling. We discuss the cases of linear and quadratic coupling in great detail and we derive, using Wigner function techniques, the stationary solutions of the master equation for a Brownian particle in a harmonic trapping potential. We predict quite generally Gaussian stationary states, and we compute the aspect ratio and the spread of the distributions. In particular, we find that these solutions may be squeezed (superlocalized) with respect to the position of the Brownian particle. We analyze various restrictions to the validity of our theory posed by non-Markovian effects and by the Heisenberg principle. We further study the dynamical stability of the system, by applying a Gaussian approximation to the time-dependent Wigner function, and we compute the decoherence rates of coherent quantum superpositions in position space. Finally, we propose a possible experimental realization of the physics discussed here, by considering an impurity particle embedded in a degenerate quantum gas.

  17. Proton-bridge motions in amine conjugate acid ions having intramolecular hydrogen bonds to hydroxyl and amine groups.

    PubMed

    Ung, Hou U; Moehlig, Aaron R; Khodagholian, Sevana; Berden, Giel; Oomens, Jos; Morton, Thomas Hellman

    2013-02-14

    Vibrational spectra of two gaseous cations having NH···O intramolecular ionic hydrogen bonds and of nine protonated di- and polyamines having NH···N internal proton bridges, recorded using IR Multiple Photon Dissociation (IRMPD) of mass-selected ions, are reported. The band positions of hydroxyl stretching frequencies do not shift when a protonated amine becomes hydrogen bonded to oxygen. In three protonated diamines, lower frequency bands (550-650 cm(-1)) disappear upon isotopic substitution, as well as several bands in the 1100-1350 cm(-1) region. By treating the internal proton bridge as a linear triatomic, theory assigns the lowest frequency bands to N-H···N asymmetric stretches. A 2-dimensional model, based on quantization on a surface fit to points calculated using a double hybrid functional B2-P3LYP/cc-pVTZ//B3LYP/6-31G**, predicts their positions accurately. In at least one case, the conjugate acid of 1,5-cis-bis(dimethylamino)cyclooctane, a N-H···N bend shows up in the domain predicted by DFT normal mode calculations, but in most other cases the observed bands have frequencies 20-25% lower than expected for bending vibrations. Protonated Me(2)NCH(2)CMe(2)CH(2)CH(2)CH(2)NMe(2) shows three well-resolved bands at 620, 1200, and 1320 cm(-1), of which the lowest can be assigned to the asymmetric stretch. Other ions observed include doubly protonated 1,2,4,5-(Me(2)NCH(2))(4)-benzene and 1,2,4-(Me(2)NCH(2))(3)-benzene-5-CH(2)OH. Apart from the aforementioned rigid ion derived from the alicyclic diamine, the other ions enjoy greater conformational mobility, and coupling to low-frequency C-C bond torsions may account for the shift of vibrations with N-H···N character to lower frequencies. Low-barrier hydrogen bonding (LBHB) accounts for the fact that N-H···N asymmetric stretching vibrations of near linear proton bridges occur at frequencies below 650 cm(-1).

  18. Brownian motion of 2D vacancy islands by adatom terrace diffusion.

    PubMed

    Morgenstern, K; Laegsgaard, E; Besenbacher, F

    2001-06-18

    We have studied the Brownian motion of two-dimensional (2D) vacancy islands on Ag(110) at temperatures between 175 and 215 K. While the detachment of adatoms from the island and their diffusion on the terrace are permitted in this temperature range, the periphery diffusion of single adatoms is prohibited. The present scanning tunneling microscopy results provide the first direct experimental proof that the Brownian motion of the islands follows a simple scaling law with terrace diffusion being the rate limiting process. The activation energy of the vacancy island motion is determined to 0.41 eV.

  19. Resolving High Amplitude Surface Motion with Diffusing Light

    NASA Technical Reports Server (NTRS)

    Wright, W.; Budakian, R.; Putterman, Seth J.

    1996-01-01

    A new technique has been developed for the purpose of imaging high amplitude surface motion. With this method one can quantitatively measure the transition to ripple wave turbulence. In addition, one can measure the phase of the turbulent state. These experiments reveal strong coherent structures in turbulent range of motion.

  20. Single-Step Nonlinear Diffusion Tensor Estimation in the Presence of Microscopic and Macroscopic Motion

    PubMed Central

    Aksoy, Murat; Liu, Chunlei; Moseley, Michael E.; Bammer, Roland

    2012-01-01

    Patient motion can cause serious artifacts in diffusion tensor imaging (DTI), diminishing the reliability of the estimated diffusion tensor information. Studies in this field have so far been limited mainly to the correction of miniscule physiological motion. In order to correct for gross patient motion it is not sufficient to correct for misregistration between successive shots; the change in the diffusion-encoding direction must also be accounted for. This becomes particularly important for multishot sequences, whereby—in the presence of motion—each shot is encoded with a different diffusion weighting. In this study a general mathematical framework to correct for gross patient motion present in a multishot and multicoil DTI scan is presented. A signal model is presented that includes the effect of rotational and translational motion in the patient frame of reference. This model was used to create a nonlinear least-squares formulation, from which the diffusion tensors were obtained using a nonlinear conjugate gradient algorithm. Applications to both phantom simulations and in vivo studies showed that in the case of gross motion the proposed algorithm performs superiorly compared to conventional methods used for tensor estimation. PMID:18429035

  1. Microstructural Evolution and interfacial motion in systems with diffusion barriers

    SciTech Connect

    Perry H. Leo

    2009-03-05

    This research program was designed to model and simulate phase transformations in systems containing diffusion barriers. The modeling work included mass flow, phase formation, and microstructural evolution in interdiffusing systems. Simulation work was done by developing Cahn-Hilliard and phase field equations governing both the temporal and spatial evolution of the composition and deformation fields and other important phase variables.

  2. Onset of anomalous diffusion from local motion rules

    NASA Astrophysics Data System (ADS)

    de Nigris, Sarah; Carletti, Timoteo; Lambiotte, Renaud

    2017-02-01

    Anomalous diffusion processes, in particular superdiffusive ones, are known to be efficient strategies for searching and navigation in animals and also in human mobility. One way to create such regimes are Lévy flights, where the walkers are allowed to perform jumps, the "flights," that can eventually be very long as their length distribution is asymptotically power-law distributed. In our work, we present a model in which walkers are allowed to perform, on a one-dimensional lattice, "cascades" of n unitary steps instead of one jump of a randomly generated length, as in the Lévy case, where n is drawn from a cascade distribution pn. We show that this local mechanism may give rise to superdiffusion or normal diffusion when pn is distributed as a power law. We also introduce waiting times that are power-law distributed as well and therefore the probability distribution scaling is steered by the two local distributions power-law exponents. As a perspective, our approach may engender a possible generalization of anomalous diffusion in context where distances are difficult to define, as in the case of complex networks, and also provide an interesting model for diffusion in temporal networks.

  3. Motion Artifact Reduction in Pediatric Diffusion Tensor Imaging Using Fast Prospective Correction

    PubMed Central

    Alhamud, A.; Taylor, Paul A.; Laughton, Barbara; van der Kouwe, André J.W.; Meintjes, Ernesta M.

    2014-01-01

    Purpose To evaluate the patterns of head motion in scans of young children and to examine the influence of corrective techniques, both qualitatively and quantitatively. We investigate changes that both retrospective (with and without diffusion table reorientation) and prospective (implemented with a short navigator sequence) motion correction induce in the resulting diffusion tensor measures. Materials and Methods Eighteen pediatric subjects (aged 5–6 years) were scanned using 1) a twice-refocused, 2D diffusion pulse sequence, 2) a prospectively motion-corrected, navigated diffusion sequence with reacquisition of a maximum of five corrupted diffusion volumes, and 3) a T1-weighted structural image. Mean fractional anisotropy (FA) values in white and gray matter regions, as well as tractography in the brainstem and projection fibers, were evaluated to assess differences arising from retrospective (via FLIRT in FSL) and prospective motion correction. In addition to human scans, a stationary phantom was also used for further evaluation. Results In several white and gray matter regions retrospective correction led to significantly (P < 0.05) reduced FA means and altered distributions compared to the navigated sequence. Spurious tractographic changes in the retrospectively corrected data were also observed in subject data, as well as in phantom and simulated data. Conclusion Due to the heterogeneity of brain structures and the comparatively low resolution (~2 mm) of diffusion data using 2D single shot sequencing, retrospective motion correction is susceptible to distortion from partial voluming. These changes often negatively bias diffusion tensor imaging parameters. Prospective motion correction was shown to produce smaller changes. PMID:24935904

  4. Persistent super-diffusive motion of Escherichia coli chromosomal loci.

    PubMed

    Javer, Avelino; Kuwada, Nathan J; Long, Zhicheng; Benza, Vincenzo G; Dorfman, Kevin D; Wiggins, Paul A; Cicuta, Pietro; Lagomarsino, Marco Cosentino

    2014-05-30

    The physical nature of the bacterial chromosome has important implications for its function. Using high-resolution dynamic tracking, we observe the existence of rare but ubiquitous 'rapid movements' of chromosomal loci exhibiting near-ballistic dynamics. This suggests that these movements are either driven by an active machinery or part of stress-relaxation mechanisms. Comparison with a null physical model for subdiffusive chromosomal dynamics shows that rapid movements are excursions from a basal subdiffusive dynamics, likely due to driven and/or stress-relaxation motion. Additionally, rapid movements are in some cases coupled with known transitions of chromosomal segregation. They do not co-occur strictly with replication, their frequency varies with growth condition and chromosomal coordinate, and they show a preference for longitudinal motion. These findings support an emerging picture of the bacterial chromosome as off-equilibrium active matter and help developing a correct physical model of its in vivo dynamic structure.

  5. Thermal diffusion by Brownian-motion-induced fluid stress.

    PubMed

    Kreft, Jennifer; Chen, Yeng-Long

    2007-08-01

    The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles subjected to a thermal gradient using a combination of Brownian dynamics and the lattice Boltzmann method. We observe that the DNA molecules will migrate to colder regions of the channel, an observation also made in experiments. In fact, the thermal diffusion coefficient found agrees quantitatively with the experimentally measured value. We also observe that the thermal diffusion coefficient decreases as the radius of the studied spherical particles increases. Furthermore, we observe that the thermal-fluctuation-fluid-momentum-flux coupling induces a gradient in the stress which leads to thermal migration in both systems.

  6. Thermal diffusion by Brownian-motion-induced fluid stress

    NASA Astrophysics Data System (ADS)

    Kreft, Jennifer; Chen, Yeng-Long

    2007-08-01

    The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles subjected to a thermal gradient using a combination of Brownian dynamics and the lattice Boltzmann method. We observe that the DNA molecules will migrate to colder regions of the channel, an observation also made in experiments. In fact, the thermal diffusion coefficient found agrees quantitatively with the experimentally measured value. We also observe that the thermal diffusion coefficient decreases as the radius of the studied spherical particles increases. Furthermore, we observe that the thermal-fluctuation-fluid-momentum-flux coupling induces a gradient in the stress which leads to thermal migration in both systems.

  7. Microstructural Evolution and Interfacial Motion in Systems with Diffusion Barriers

    SciTech Connect

    William C. Johnson

    2007-06-30

    The initial goal of this research program was to model and to simulate phase transformations in systems containing diffusion barriers. The modeling work included the development and testing of code to describe mass flow, the kinetics of phase formation, elastic deformation, and subsequent microstructural evolution occurring during interdiffusion. The primary simulation tools to be used were a class of diffuse interface methods described by the Cahn-Hilliard and phase field equations for the temporal and spatial evolution of the composition and deformation fields and other relevant phase variables. One-dimensional analytical solutions were also to be developed both to test the numerical methods and to establish connections to physical systems. During the early stages of the research program, two new areas of research related to systems with diffusion barriers were identified. The first area concerned phase formation and diffusional phase transformations in reacting systems subject to high electric current densities. Such high-current environments are common in lead-free solders, for example, and have important technological applications. The second area was an offshoot of the present work, and concerned theoretical modeling of phase evolution and cyclical amorphization of metallic alloys during ball milling.

  8. Diffusive-to-ballistic transition in grain boundary motion studied by atomistic simulations

    SciTech Connect

    Deng Chuang; Schuh, Christopher A.

    2011-12-01

    An adapted simulation method is used to systematically study grain boundary motion at velocities and driving forces across more than five orders of magnitude. This analysis reveals that grain boundary migration can occur in two modes, depending upon the temperature (T) and applied driving force (P). At low P and T, grain boundary motion is diffusional, exhibiting the kinetics of a thermally activated system controlled by grain boundary self-diffusion. At high P and T, grain boundary migration exhibits the characteristic kinetic scaling behavior of a ballistic process. A rather broad transition range in both P and T lies between the regimes of diffusive and ballistic grain boundary motion, and is charted here in detail. The recognition and delineation of these two distinct modes of grain boundary migration also leads to the suggestion that many prior atomistic simulations might have probed a different kinetic regime of grain boundary motion (ballistic) as compared to that revealed in most experimental studies (diffusional).

  9. Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry

    NASA Astrophysics Data System (ADS)

    Marino, Raffaele; Aurell, Erik

    2016-06-01

    We consider coupled diffusions in n -dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H. Brenner [J. Colloid Interface Sci. 80, 548 (1981), 10.1016/0021-9797(81)90214-9]. We show in detail how the analysis can be conveniently carried out using local charts and invariance arguments. As a further example, we consider coupled diffusions in two-dimensional complex space and on the group manifold SU(2). We show that although the local operators may be the same as for SO(3), due to the global nature of the solvability conditions the resulting diffusion will differ and generally be more isotropic.

  10. Charge polarization with large amplitude hydrogen motion of pyrazinyl radical: implication for the diffusion dynamics

    NASA Astrophysics Data System (ADS)

    Morita, Akihiro; Kato, Shigeki

    2001-11-01

    In this Letter we discuss in the case of pyrazinyl radical the effect of the large amplitude motion on the charge polarization. The extra hydrogen of pyrazinyl radical is nonplanar at the equilibrium geometry, whereas it is delocalized in the vibrational ground state along the wagging direction. The large amplitude motion of the hydrogen triply enhances the effective out-of-plane polarizability of the ground state. This augmented charge polarization could play a considerable role in the diffusion dynamics in solutions.

  11. Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion.

    PubMed

    Jeon, Jae-Hyung; Chechkin, Aleksei V; Metzler, Ralf

    2014-08-14

    Anomalous diffusion is frequently described by scaled Brownian motion (SBM), a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is 〈x(2)(t)〉 ≃ 2K(t)t with K(t) ≃ t(α-1) for 0 < α < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion, for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely, we demonstrate that under confinement, the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments, in particular, under confinement inside cellular compartments or when optical tweezers tracking methods are used.

  12. Diffusion of Echo 7 electron beams during bounce motion

    SciTech Connect

    Nemzek, R.J.

    1992-01-01

    The Echo 7 sounding rocket experiment injected electron beams into the magnetosphere and detected them after one or more bounces along field lines near L = 6.5. Waves with equatorial amplitudes of a few mV/m diffused the beams so that only {approx}2O% of the initial current returned to the rocket altitude in the northern hemisphere. On successive bounces the electron flux continued to drop at the same rate. These results imply a lifetime of {approx}1.7 for 20 kev electrons just outside of the loss cone. comparison with other Echo flights shows that the beam return is dependent upon geomagnetic conditions: low activity causes there to be less scattering, while high activity can actually prevent detection of the returning beam.

  13. Diffusion of Echo 7 electron beams during bounce motion

    SciTech Connect

    Nemzek, R.J.

    1992-08-01

    The Echo 7 sounding rocket experiment injected electron beams into the magnetosphere and detected them after one or more bounces along field lines near L = 6.5. Waves with equatorial amplitudes of a few mV/m diffused the beams so that only {approx}2O% of the initial current returned to the rocket altitude in the northern hemisphere. On successive bounces the electron flux continued to drop at the same rate. These results imply a lifetime of {approx}1.7 for 20 kev electrons just outside of the loss cone. comparison with other Echo flights shows that the beam return is dependent upon geomagnetic conditions: low activity causes there to be less scattering, while high activity can actually prevent detection of the returning beam.

  14. Solvent gating of intramolecular electron transfer

    SciTech Connect

    Miller, R.M. ); Spears, K.G.; Gong, J.H.; Wach, M. )

    1994-02-03

    The rates for ionic photodissociation of malachite green leucocyanide to form cyanide ion and a malachite green carbonium ion were measured as a function of solvent and temperature. The observed rates in mixtures of polar and nonpolar solvents all had an activation energy of about 1 kcal/mol for a wide range of dielectric constants. This dissociative intramolecular electron transfer (DIET) is unusual because it is the first example where solvent configurational entropy changes are required to enable a large amplitude molecular distortion leading to a nonadiabatic electron transfer and ionic dissociation. This solvent gated intramolecular electron-transfer mechanism is supported by analysis of the preexponential and activation energy trends in dipolar aprotic solven mixtures and alcohol solvents. The large amplitude motion is not separately measurable due to the slow gating rates, but viscosity effects on both the preexponential and the activation energy are analyzed to demonstrate consistency with a barrierless diffusion model having a structural dependence on electron-transfer rate. The rate has an inverse dependence on viscosity raised to the 0.53 power. 36 refs., 6 figs., 4 tabs.

  15. Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

    NASA Astrophysics Data System (ADS)

    Chen, Yao; Wang, Xudong; Deng, Weihua

    2017-10-01

    This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

  16. Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

    NASA Astrophysics Data System (ADS)

    Chen, Yao; Wang, Xudong; Deng, Weihua

    2017-08-01

    This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

  17. Directional sensitivity of anomalous diffusion in human brain assessed by tensorial fractional motion model.

    PubMed

    Xu, Boyan; Gong, Gaolang; Fan, Yang; Wu, Bing; Gao, Jia-Hong

    2017-10-01

    Anisotropic diffusion in the nervous system is most commonly modeled by apparent diffusion tensor, which is based on regular diffusion theory. However, the departure of diffusion-induced signal attenuation from a mono-exponential form implies that there is anomalous diffusion. Recently, a novel diffusion NMR theory based on the fractional motion (FM) model, which is an anomalous diffusion model, has been proposed. While the FM model has been applied to both healthy subjects and tumor patients, its anisotropy in the nervous system remains elusive. In this study, this issue was addressed by measuring the FM-related parameters in 12 non-collinear directions. A metric to quantify the directional deviation was derived. Furthermore, the FM-related parameters were modeled as tensors and analyzed in analogy with the conventional diffusion tensor imaging (DTI). Experimental results, which were obtained for 15 healthy subjects at 3T, exhibited pronounced anisotropy of the FM-related parameters, although the effects were smaller than the apparent diffusion coefficient (ADC). The tensorial nature for α, which is the Noah exponent in the FM model, showed behavior similar to the ADC, especially the principal eigenvector for α aligned with the dominant white matter fiber directions. The Hurst exponent H in the FM model, however, showed no correlation with the major fiber directions. The anisotropy of the FM model may provide complementary information to DTI and may have potential for tractography and detecting brain abnormalities. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Quantum fluctuations increase the self-diffusive motion of para-hydrogen in narrow carbon nanotubes.

    PubMed

    Kowalczyk, Piotr; Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester

    2011-05-28

    Quantum fluctuations significantly increase the self-diffusive motion of para-hydrogen adsorbed in narrow carbon nanotubes at 30 K comparing to its classical counterpart. Rigorous Feynman's path integral calculations reveal that self-diffusive motion of para-hydrogen in a narrow (6,6) carbon nanotube at 30 K and pore densities below ∼29 mmol cm(-3) is one order of magnitude faster than the classical counterpart. We find that the zero-point energy and tunneling significantly smoothed out the free energy landscape of para-hydrogen molecules adsorbed in a narrow (6,6) carbon nanotube. This promotes a delocalization of the confined para-hydrogen at 30 K (i.e., population of unclassical paths due to quantum effects). Contrary the self-diffusive motion of classical para-hydrogen molecules in a narrow (6,6) carbon nanotube at 30 K is very slow. This is because classical para-hydrogen molecules undergo highly correlated movement when their collision diameter approached the carbon nanotube size (i.e., anomalous diffusion in quasi-one dimensional pores). On the basis of current results we predict that narrow single-walled carbon nanotubes are promising nanoporous molecular sieves being able to separate para-hydrogen molecules from mixtures of classical particles at cryogenic temperatures.

  19. Fractional motion model for characterization of anomalous diffusion from NMR signals.

    PubMed

    Fan, Yang; Gao, Jia-Hong

    2015-07-01

    Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

  20. Fractional motion model for characterization of anomalous diffusion from NMR signals

    NASA Astrophysics Data System (ADS)

    Fan, Yang; Gao, Jia-Hong

    2015-07-01

    Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

  1. The influence of spin diffusion and internal motions on NOE intensities in proteins

    NASA Astrophysics Data System (ADS)

    Lane, Andrew N.

    An algorithm has been coded for calculating NOE time courses for an arbitrary number of protons. Simulations were made on three proteins: myoglobin, bovine pancreatic trypsin inhibitor, and the toxic domain of Escherichia coli heat-stable enterotoxin. The calculations were carried out to simulate several conditions under which NOE measurements are commonly made, namely variation of the overall tumbling time and solvent ( 1H 2O, and 2H 2O). The influence of spin diffusion and internal motions on NOE intensities in secondary structures was studied. It was found that spin diffusion is unlikely to lead to false identification of secondary structure elements, but does lead to considerable underestimation of distances longer than about 4 Å, which are used for determination of tertiary structures. Internal motions were simulated using truncated, anisotropic three-dimensional harmonic oscillation. For motions slower than the Larmor frequency, the oscillation has significant effects on the long-range NOEs, whereas faster motions tend to yield distance estimates similar to those of the rigid body calculation, because of counteracting effects of the motion on the correlation time and the average distance. These considerations have significance for the refinement of structures generated by distance geometry or other algorithms.

  2. Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion

    PubMed Central

    Bodrova, Anna S.; Chechkin, Aleksei V.; Cherstvy, Andrey G.; Safdari, Hadiseh; Sokolov, Igor M.; Metzler, Ralf

    2016-01-01

    It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases. PMID:27462008

  3. Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion.

    PubMed

    Bodrova, Anna S; Chechkin, Aleksei V; Cherstvy, Andrey G; Safdari, Hadiseh; Sokolov, Igor M; Metzler, Ralf

    2016-07-27

    It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases.

  4. Quantum dot single molecule tracking reveals a wide range of diffusive motions of membrane transport proteins

    NASA Astrophysics Data System (ADS)

    Crane, Jonathan M.; Haggie, Peter M.; Verkman, A. S.

    2009-02-01

    Single particle tracking (SPT) provides information about the microscopic motions of individual particles in live cells. We applied SPT to study the diffusion of membrane transport proteins in cell plasma membranes in which individual proteins are labeled with quantum dots at engineered extracellular epitopes. Software was created to deduce particle diffusive modes from quantum dot trajectories. SPT of aquaporin (AQP) water channels and cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels revealed several types of diffusion. AQP1 was freely mobile in cell membranes, showing rapid, Brownian-type diffusion. The full-length (M1) isoform of AQP4 also diffused rapidly, though the diffusion of a shorter (M23) isoform of AQP4 was highly restricted due to its supermolecular assembly in raft-like orthogonal arrays. CFTR mobility was also highly restricted, in a spring-like potential, due to its tethering to the actin cytoskeleton through PDZ-domain C-terminus interactions. The biological significance of regulated diffusion of membrane transport proteins is a subject of active investigation.

  5. Brownian Motion in a Speckle Light Field: Tunable Anomalous Diffusion and Selective Optical Manipulation

    PubMed Central

    Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain

    2014-01-01

    The motion of particles in random potentials occurs in several natural phenomena ranging from the mobility of organelles within a biological cell to the diffusion of stars within a galaxy. A Brownian particle moving in the random optical potential associated to a speckle pattern, i.e., a complex interference pattern generated by the scattering of coherent light by a random medium, provides an ideal model system to study such phenomena. Here, we derive a theory for the motion of a Brownian particle in a speckle field and, in particular, we identify its universal characteristic timescale. Based on this theoretical insight, we show how speckle light fields can be used to control the anomalous diffusion of a Brownian particle and to perform some basic optical manipulation tasks such as guiding and sorting. Our results might broaden the perspectives of optical manipulation for real-life applications. PMID:24496461

  6. Meeting Review: Diffuse X-Ray Scattering to Model Protein Motions

    PubMed Central

    Wall, Michael E.; Adams, Paul D.; Fraser, James S.; Sautter, Nicholas K.

    2014-01-01

    Problems in biology increasingly need models of protein flexibility to understand and control protein function. At the same time, as they improve, crystallographic methods are marching closer to the limits of what can be learned from Bragg data in isolation. It is thus inevitable that mainstream protein crystallography will turn to diffuse scattering to model protein motions and improve crystallographic models. The time is ripe to make it happen. PMID:24507780

  7. Driven diffusion in a periodically compartmentalized tube: homogeneity versus intermittency of particle motion.

    PubMed

    Makhnovskii, Yu A; Berezhkovskii, A M; Bogachev, L V; Zitserman, V Yu

    2011-04-14

    We study the effect of a driving force F on drift and diffusion of a point Brownian particle in a tube formed by identical cylindrical compartments, which create periodic entropy barriers for the particle motion along the tube axis. The particle transport exhibits striking features: the effective mobility monotonically decreases with increasing F, and the effective diffusivity diverges as F→∞, which indicates that the entropic effects in diffusive transport are enhanced by the driving force. Our consideration is based on two different scenarios of the particle motion at small and large F, homogeneous and intermittent, respectively. The scenarios are deduced from the careful analysis of statistics of the particle transition times between neighboring openings. From this qualitative picture, the limiting small-F and large-F behaviors of the effective mobility and diffusivity are derived analytically. Brownian dynamics simulations are used to find these quantities at intermediate values of the driving force for various compartment lengths and opening radii. This work shows that the driving force may lead to qualitatively different anomalous transport features, depending on the geometry design.

  8. Collective concerted motion in a molecular adlayer visualized through the surface diffusion of isolated vacancies.

    PubMed

    Urban, Christian; Otero, Roberto; Écija, David; Trelka, Marta; Martín, Nazario; Gallego, José M; Miranda, Rodolfo

    2016-10-21

    We have measured STM movies to study the diffusion of individual vacancies in a self-assembled layer of a tetrathiafulvalene derivative (exTTF) on Au(111) at room temperature. The diffusion is anisotropic, being faster along the compact direction of the molecular lattice. A detailed analysis of the anisotropic displacement distribution of the single vacancies shows that the relative abundance of double jumps (that is, the collective motion of molecular dimers) with respect to single jumps is rather large, the number of double jumps being more than 20% of the diffusion events. We conjecture that the relative abundances of long jumps might be related to the strength of the intermolecular bonding and the misfit of the molecular overlayer with the substrate lattice.

  9. Collective concerted motion in a molecular adlayer visualized through the surface diffusion of isolated vacancies

    NASA Astrophysics Data System (ADS)

    Urban, Christian; Otero, Roberto; Écija, David; Trelka, Marta; Martín, Nazario; Gallego, José M.; Miranda, Rodolfo

    2016-10-01

    We have measured STM movies to study the diffusion of individual vacancies in a self-assembled layer of a tetrathiafulvalene derivative (exTTF) on Au(111) at room temperature. The diffusion is anisotropic, being faster along the compact direction of the molecular lattice. A detailed analysis of the anisotropic displacement distribution of the single vacancies shows that the relative abundance of double jumps (that is, the collective motion of molecular dimers) with respect to single jumps is rather large, the number of double jumps being more than 20% of the diffusion events. We conjecture that the relative abundances of long jumps might be related to the strength of the intermolecular bonding and the misfit of the molecular overlayer with the substrate lattice.

  10. Intravoxel incoherent motion diffusion-weighted MR imaging in assessing and characterizing solitary pulmonary lesions

    PubMed Central

    Wan, Qi; Deng, Ying-Shi; Zhou, Jia-Xuan; Yu, Yu-Dong; Bao, Ying-Ying; Lei, Qiang; Chen, Hou-Jin; Peng, Ya-Hui; Mei, Ying-Jie; Zeng, Qing-Si; Li, Xin-Chun

    2017-01-01

    This study aimed to investigate the potential of intravoxel incoherent motion (IVIM) diffusion-weighted MR imaging in assessing solitary pulmonary lesions (SPLs). Sixty-two patients with pathologically confirmed SPLs, including 51 and 11 cases of malignant and benign lesions, respectively, were assessed. Diffusion weighted imaging (DWI) with 13 b values was used to derive apparent diffusion coefficient (ADC) and IVIM parameters, including true diffusion coefficient (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f). Our results showed that, there was an excellent inter-observer agreement on the measurements of D and ADC between observers (inter-class correlation coefficient, ICC = 0.902 and 0.884, respectively). Meanwhile, f and D* showed good and substantial reproducibility (ICC = 0.787 and 0.623, respectively). D and ADC of malignant lesions were significantly lower than those of benign lesions (both P ≤ 0.001), while similar values were obtained in both groups for D* and f (both P > 0.05). In receiver operating characteristic (ROC) analysis, D showed the highest area under curve (AUC) for distinguishing malignant from benign lesions, followed by ADC. Accompanying signs of SPLs have specific features on IVIM maps. In conclusion, IVIM provides functional information in characterizing SPLs which is helpful to differential diagnosis. D and ADC have a significantly higher diagnostic value than f and D*. PMID:28225064

  11. Intravoxel incoherent motion diffusion-weighted MR imaging in assessing and characterizing solitary pulmonary lesions.

    PubMed

    Wan, Qi; Deng, Ying-Shi; Zhou, Jia-Xuan; Yu, Yu-Dong; Bao, Ying-Ying; Lei, Qiang; Chen, Hou-Jin; Peng, Ya-Hui; Mei, Ying-Jie; Zeng, Qing-Si; Li, Xin-Chun

    2017-02-22

    This study aimed to investigate the potential of intravoxel incoherent motion (IVIM) diffusion-weighted MR imaging in assessing solitary pulmonary lesions (SPLs). Sixty-two patients with pathologically confirmed SPLs, including 51 and 11 cases of malignant and benign lesions, respectively, were assessed. Diffusion weighted imaging (DWI) with 13 b values was used to derive apparent diffusion coefficient (ADC) and IVIM parameters, including true diffusion coefficient (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f). Our results showed that, there was an excellent inter-observer agreement on the measurements of D and ADC between observers (inter-class correlation coefficient, ICC = 0.902 and 0.884, respectively). Meanwhile, f and D* showed good and substantial reproducibility (ICC = 0.787 and 0.623, respectively). D and ADC of malignant lesions were significantly lower than those of benign lesions (both P ≤ 0.001), while similar values were obtained in both groups for D* and f (both P > 0.05). In receiver operating characteristic (ROC) analysis, D showed the highest area under curve (AUC) for distinguishing malignant from benign lesions, followed by ADC. Accompanying signs of SPLs have specific features on IVIM maps. In conclusion, IVIM provides functional information in characterizing SPLs which is helpful to differential diagnosis. D and ADC have a significantly higher diagnostic value than f and D*.

  12. A robust post-processing workflow for datasets with motion artifacts in diffusion kurtosis imaging.

    PubMed

    Li, Xianjun; Yang, Jian; Gao, Jie; Luo, Xue; Zhou, Zhenyu; Hu, Yajie; Wu, Ed X; Wan, Mingxi

    2014-01-01

    The aim of this study was to develop a robust post-processing workflow for motion-corrupted datasets in diffusion kurtosis imaging (DKI). The proposed workflow consisted of brain extraction, rigid registration, distortion correction, artifacts rejection, spatial smoothing and tensor estimation. Rigid registration was utilized to correct misalignments. Motion artifacts were rejected by using local Pearson correlation coefficient (LPCC). The performance of LPCC in characterizing relative differences between artifacts and artifact-free images was compared with that of the conventional correlation coefficient in 10 randomly selected DKI datasets. The influence of rejected artifacts with information of gradient directions and b values for the parameter estimation was investigated by using mean square error (MSE). The variance of noise was used as the criterion for MSEs. The clinical practicality of the proposed workflow was evaluated by the image quality and measurements in regions of interest on 36 DKI datasets, including 18 artifact-free (18 pediatric subjects) and 18 motion-corrupted datasets (15 pediatric subjects and 3 essential tremor patients). The relative difference between artifacts and artifact-free images calculated by LPCC was larger than that of the conventional correlation coefficient (p<0.05). It indicated that LPCC was more sensitive in detecting motion artifacts. MSEs of all derived parameters from the reserved data after the artifacts rejection were smaller than the variance of the noise. It suggested that influence of rejected artifacts was less than influence of noise on the precision of derived parameters. The proposed workflow improved the image quality and reduced the measurement biases significantly on motion-corrupted datasets (p<0.05). The proposed post-processing workflow was reliable to improve the image quality and the measurement precision of the derived parameters on motion-corrupted DKI datasets. The workflow provided an effective post

  13. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.

    PubMed

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J; Weik, Martin

    2015-03-16

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  14. Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra.

    PubMed

    Ryabov, Yaroslav

    2015-09-01

    In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  15. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    PubMed Central

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. PMID:25774711

  16. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    NASA Astrophysics Data System (ADS)

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-03-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  17. Anomalous diffusion as modeled by a nonstationary extension of Brownian motion.

    PubMed

    Cushman, John H; O'Malley, Daniel; Park, Moongyu

    2009-03-01

    If the mean-square displacement of a stochastic process is proportional to t;{beta} , beta not equal1 , then it is said to be anomalous. We construct a family of Markovian stochastic processes with independent nonstationary increments and arbitrary but a priori specified mean-square displacement. We label the family as an extended Brownian motion and show that they satisfy a Langevin equation with time-dependent diffusion coefficient. If the time derivative of the variance of the process is homogeneous, then by computing the fractal dimension it can be shown that the complexity of the family is the same as that of the Brownian motion. For two particles initially separated by a distance x , the finite-size Lyapunov exponent (FSLE) measures the average rate of exponential separation to a distance ax . An analytical expression is developed for the FSLEs of the extended Brownian processes and numerical examples presented. The explicit construction of these processes illustrates that contrary to what has been stated in the literature, a power-law mean-square displacement is not necessarily related to a breakdown in the classical central limit theorem (CLT) caused by, for example, correlation (fractional Brownian motion or correlated continuous-time random-walk schemes) or infinite variance (Levy motion). The classical CLT, coupled with nonstationary increments, can and often does give rise to power-law moments such as the mean-square displacement.

  18. Anomalous diffusion as modeled by a nonstationary extension of Brownian motion

    NASA Astrophysics Data System (ADS)

    Cushman, John H.; O'Malley, Daniel; Park, Moongyu

    2009-03-01

    If the mean-square displacement of a stochastic process is proportional to tβ , β≠1 , then it is said to be anomalous. We construct a family of Markovian stochastic processes with independent nonstationary increments and arbitrary but a priori specified mean-square displacement. We label the family as an extended Brownian motion and show that they satisfy a Langevin equation with time-dependent diffusion coefficient. If the time derivative of the variance of the process is homogeneous, then by computing the fractal dimension it can be shown that the complexity of the family is the same as that of the Brownian motion. For two particles initially separated by a distance x , the finite-size Lyapunov exponent (FSLE) measures the average rate of exponential separation to a distance ax . An analytical expression is developed for the FSLEs of the extended Brownian processes and numerical examples presented. The explicit construction of these processes illustrates that contrary to what has been stated in the literature, a power-law mean-square displacement is not necessarily related to a breakdown in the classical central limit theorem (CLT) caused by, for example, correlation (fractional Brownian motion or correlated continuous-time random-walk schemes) or infinite variance (Levy motion). The classical CLT, coupled with nonstationary increments, can and often does give rise to power-law moments such as the mean-square displacement.

  19. Weak Ergodicity Breaking of Receptor Motion in Living Cells Stemming from Random Diffusivity

    NASA Astrophysics Data System (ADS)

    Manzo, Carlo; Torreno-Pina, Juan A.; Massignan, Pietro; Lapeyre, Gerald J.; Lewenstein, Maciej; Garcia Parajo, Maria F.

    2015-01-01

    Molecular transport in living systems regulates numerous processes underlying biological function. Although many cellular components exhibit anomalous diffusion, only recently has the subdiffusive motion been associated with nonergodic behavior. These findings have stimulated new questions for their implications in statistical mechanics and cell biology. Is nonergodicity a common strategy shared by living systems? Which physical mechanisms generate it? What are its implications for biological function? Here, we use single-particle tracking to demonstrate that the motion of dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN), a receptor with unique pathogen-recognition capabilities, reveals nonergodic subdiffusion on living-cell membranes In contrast to previous studies, this behavior is incompatible with transient immobilization, and, therefore, it cannot be interpreted according to continuous-time random-walk theory. We show that the receptor undergoes changes of diffusivity, consistent with the current view of the cell membrane as a highly dynamic and diverse environment. Simulations based on a model of an ordinary random walk in complex media quantitatively reproduce all our observations, pointing toward diffusion heterogeneity as the cause of DC-SIGN behavior. By studying different receptor mutants, we further correlate receptor motion to its molecular structure, thus establishing a strong link between nonergodicity and biological function. These results underscore the role of disorder in cell membranes and its connection with function regulation. Because of its generality, our approach offers a framework to interpret anomalous transport in other complex media where dynamic heterogeneity might play a major role, such as those found, e.g., in soft condensed matter, geology, and ecology.

  20. A second-order Markov process for modeling diffusive motion through spatial discretization.

    PubMed

    Sant, Marco; Papadopoulos, George K; Theodorou, Doros N

    2008-01-14

    A new "mesoscopic" stochastic model has been developed to describe the diffusive behavior of a system of particles at equilibrium. The model is based on discretizing space into slabs by drawing equispaced parallel planes along a coordinate direction. A central role is played by the probability that a particle exits a slab via the face opposite to the one through which it entered (transmission probability), as opposed to exiting via the same face through which it entered (reflection probability). A simple second-order Markov process invoking this probability is developed, leading to an expression for the self-diffusivity, applicable for large slab widths, consistent with a continuous formulation of diffusional motion. This model is validated via molecular dynamics simulations in a bulk system of soft spheres across a wide range of densities.

  1. In vivo measurement of proton diffusion in the presence of coherent motion

    SciTech Connect

    Johnson, G.A.; Maki, J.H. )

    1991-06-01

    Measurement of the self-diffusion coefficient D of water in tissue has been performed traditionally using the technique proposed by Stejskal and Tanner. A variant of that technique is shown here, employing flow-compensated gradients that significantly reduce the sensitivity to small coherent motions that are common in body imaging. An interleaved sequence with four values of diffusion-sensitizing gradient (b) minimizes registration errors. Eddy currents and other systematic errors are reduced, permitting the measurement of standards in an imaging context within 5% of nonimaging values in the literature. The flow-compensated sequence permits the measure of D for tissues in the abdominal cavity of the rat. The authors present in vivo measurements of D for the following rat tissues; liver, kidney (cortex), kidney (medulla) muscle, brain, fat.

  2. Motion Compensated Abdominal Diffusion Weighted MRI by Simultaneous Image Registration and Model Estimation (SIR-ME).

    PubMed

    Kurugol, Sila; Freiman, Moti; Afacan, Onur; Domachevsky, Liran; Perez-Rossello, Jeannette M; Callahan, Michael J; Warfield, Simon K

    2015-01-01

    Non-invasive characterization of water molecule's mobility variations by quantitative analysis of diffusion-weighted MRI (DW-MRI) signal decay in the abdomen has the potential to serve as a biomarker in gastrointestinal and oncological applications. Accurate and reproducible estimation of the signal decay model parameters is challenging due to the presence of respiratory, cardiac, and peristalsis motion. Independent registration of each b-value image to the b-value=0 s/mm(2) image prior to parameter estimation might be sub-optimal because of the low SNR and contrast difference between images of varying b-value. In this work, we introduce a motion-compensated parameter estimation framework that simultaneously solves image registration and model estimation (SIR-ME) problems by utilizing the interdependence of acquired volumes along the diffusion weighting dimension. We evaluated the improvement in model parameters estimation accuracy using 16 in-vivo DW-MRI data sets of Crohn's disease patients by comparing parameter estimates obtained using the SIR-ME model to the parameter estimates obtained by fitting the signal decay model to the acquired DW-MRI images. The proposed SIR-ME model reduced the average root-mean-square error between the observed signal and the fitted model by more than 50%. Moreover, the SIR-ME model estimates discriminate between normal and abnormal bowel loops better than the standard parameter estimates.

  3. Pattern formation, social forces, and diffusion instability in games with success-driven motion

    NASA Astrophysics Data System (ADS)

    Helbing, Dirk

    2009-02-01

    A local agglomeration of cooperators can support the survival or spreading of cooperation, even when cooperation is predicted to die out according to the replicator equation, which is often used in evolutionary game theory to study the spreading and disappearance of strategies. In this paper, it is shown that success-driven motion can trigger such local agglomeration and may, therefore, be used to supplement other mechanisms supporting cooperation, like reputation or punishment. Success-driven motion is formulated here as a function of the game-theoretical payoffs. It can change the outcome and dynamics of spatial games dramatically, in particular as it causes attractive or repulsive interaction forces. These forces act when the spatial distributions of strategies are inhomogeneous. However, even when starting with homogeneous initial conditions, small perturbations can trigger large inhomogeneities by a pattern-formation instability, when certain conditions are fulfilled. Here, these instability conditions are studied for the prisoner’s dilemma and the snowdrift game. Furthermore, it is demonstrated that asymmetrical diffusion can drive social, economic, and biological systems into the unstable regime, if these would be stable without diffusion.

  4. Femtochemistry of Intramolecular Charge and Proton Transfer Reactions in Solution

    SciTech Connect

    Douhal, Abderrazzak; Sanz, Mikel; Carranza, Maria Angeles; Organero, Juan Angel; Tormo, Laura

    2005-03-17

    We report on the first observation of ultrafast intramolecular charge- and proton-transfer reactions in 4'-dimethylaminoflavonol (DAMF) in solution. Upon femtosecond excitation of a non-planar structure of DMAF in apolar medium, the intramolecular charge transfer (ICT) does not occur, and a slow (2 ps) proton motion takes place. However, in polar solvents, the ICT is very fast (100-200 fs) and the produced structure is stabilized that proton motion takes place in few or tens of ps.

  5. Steady motion of skyrmions and domains walls under diffusive spin torques

    NASA Astrophysics Data System (ADS)

    Elías, Ricardo Gabriel; Vidal-Silva, Nicolas; Manchon, Aurélien

    2017-03-01

    We explore the role of the spin diffusion of conducting electrons in two-dimensional magnetic textures (domain walls and skyrmions) with spatial variation of the order of the spin precession length λex. The effect of diffusion reflects in four additional torques that are third order in spatial derivatives of magnetization and bilinear in λex and in the nonadiabatic parameter β'. In order to study the dynamics of the solitons when these diffusive torques are present, we derive the Thiele equation in the limit of steady motion and we compare the results with the nondiffusive limit. When considering a homogenous current these torques increase the longitudinal velocity of transverse domain walls of width Δ by a factor (λex/Δ)2(α/3), α being the magnetic damping constant. In the case of single skyrmions with core radius r0these new contributions tend to increase the Magnus effect in an amount proportional to (λex/r0) 2(1 +2 α β') .

  6. Coherent nuclear wavepacket motions in ultrafast excited-state intramolecular proton transfer: sub-30-fs resolved pump-probe absorption spectroscopy of 10-hydroxybenzo[h]quinoline in solution.

    PubMed

    Takeuchi, Satoshi; Tahara, Tahei

    2005-11-17

    The dynamics of the excited-state intramolecular proton transfer of 10-hydroxybenzo[h]quinoline (10-HBQ) and the associated coherent nuclear motion were investigated in solution by femtosecond absorption spectroscopy. Sub-picosecond transient absorption measurements revealed spectral features of the stimulated emission and absorption of the keto excited state (the product of the reaction). The stimulated emission band appeared in the 600-800-nm region, corresponding to the wavelength region of the steady-state keto fluorescence. It showed successive temporal changes with time constants of 350 fs and 8.3 ps and then disappeared with the lifetime of the keto excited state (260 ps). The spectral feature of the stimulated emission changed in the 350-fs dynamics, which was likely assignable to the intramolecular vibrational energy redistribution in the keto excited state. The 8.3-ps change caused a spectral blue shift and was attributed to the vibrational cooling process. The excited-state absorption was observed in the 400-600-nm region, and it also showed temporal changes characterized by the 350-fs and 8.3-ps components. To examine the coherent nuclear dynamics (nuclear wavepacket motion) in excited-state 10-HBQ, we carried out pump-probe measurements of the stimulated emission and absorption signals with time resolution as good as 27 fs. The obtained data showed substantially modulated signals due to the excited-state vibrational coherence up to a delay time of several picoseconds after photoexcitation. This means that the vibrational coherence created by photoexcitation in the enol excited state is transferred to the product. Fourier transform analysis indicated that four frequency components in the 200-700-cm(-1) region contribute to the oscillatory signal, corresponding to the coherent nuclear motions in excited-state 10-HBQ. Especially, the lowest-frequency mode at 242 cm(-1) is dephased significantly faster than the other three modes. This observation was

  7. Intravoxel incoherent motion diffusion-weighted MR imaging of gliomas: efficacy in preoperative grading.

    PubMed

    Hu, Yu-Chuan; Yan, Lin-Feng; Wu, Lang; Du, Pang; Chen, Bao-Ying; Wang, Liang; Wang, Shu-Mei; Han, Yu; Tian, Qiang; Yu, Ying; Xu, Tian-Yong; Wang, Wen; Cui, Guang-Bin

    2014-12-01

    The preoperative grading of gliomas, which is critical for guiding therapeutic strategies, remains unsatisfactory. We aimed to retrospectively assess the efficacy of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) in the grading of gliomas. Forty-two newly diagnosed glioma patients underwent conventional MR imaging, DWI, and contrast-enhanced MR imaging. Parameters of apparent diffusion coefficient (ADC), slow diffusion coefficient (D), fast diffusion coefficient (D*), and fraction of fast ADC (f) were generated. They were tested for differences between low- and high-grade gliomas based on one-way ANOVA. Receiver-operating characteristic (ROC) analyses were conducted to determine the optimal thresholds as well as the sensitivity and specificity for grading. ADC, D, and f were higher in the low-grade gliomas, whereas D* tended to be lower (all P<0.05). The AUC, sensitivity, specificity and the cutoff value, respectively, for differentiating low- from high-grade gliomas for ADC, D and f, and differentiating high- from low-grade gliomas for D* were as follows: ADC, 0.926, 100%, 82.8%, and 0.7 × 10(-3) mm(2)/sec; D, 0.942, 92.3%, 86.2%, and 0.623 × 10(-3) mm(2)/sec; f, 0.902, 92.3%, 86.2%, and 35.3%; D*, 0.798, 79.3%, 84.6%, and 0.303 × 10(-3) mm(2)/sec. The IVIM DWI demonstrates efficacy in differentiating the low- from high-grade gliomas.

  8. Coriolis coupling as a source of non-RRKM effects in triatomic near-symmetric top molecules: Diffusive intramolecular energy exchange between rotational and vibrational degrees of freedom.

    PubMed

    Kryvohuz, M; Marcus, R A

    2010-06-14

    A classical theory is proposed to describe the non-RRKM effects in activated asymmetric top triatomic molecules observed numerically in classical molecular dynamics simulations of ozone. The Coriolis coupling is shown to result in an effective diffusive energy exchange between the rotational and vibrational degrees of freedom. A stochastic differential equation is obtained for the K-component of the rotational angular momentum that governs the diffusion.

  9. Electron motion and distribution functions in the diffusion region of asymmetric reconnection

    NASA Astrophysics Data System (ADS)

    Bessho, N.; Chen, L. J.; Hesse, M.

    2015-12-01

    We study electron motion and electron distribution functions in the diffusion region in asymmetric reconnection with negligible guide field by means of two-dimensional particle-in-cell (PIC) simulations and theoretical analysis. Near the stagnation point of the electron inflows, which is located in the magnetospheric side in the diffusion region, electron distribution functions show two populations: A crescent-shaped component in the vy-vz plane (y is the out-of-plane direction, and z is the inflow direction), and the magnetospheric component that has been accelerated in the direction parallel to the magnetic field. Particle tracing in a PIC simulation shows that a population of electrons from the magnetosheath travels along crescent-shaped orbits in the velocity space during meandering motion across the neutral line. Those electrons are mainly accelerated by the in-plane electric field Ez, which is strong only in the magnetospheric side and plays a more significant role to energize electrons than the reconnection electric field. We theoretically predict the shape of the distribution functions near the stagnation point. The crescent-shaped distribution is formed because only a part of electrons from the magnetosheath can access a particular location in the magnetospheric side of the X-line. The penetration length of magnetosheath electrons into the magnetosphere is analytically derived. Theoretical predictions on the distribution shape and the penetration length agree well with simulation results. The crescent-shaped electron distributions are expected to be observed in dayside magnetopause reconnection by satellites, such as the NASA Magnetospheric Multi-scale (MMS) mission. We will discuss comparison between numerical and analytical results with data obtained by MMS as well as Cluster.

  10. Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level.

    PubMed

    Habuchi, Satoshi; Yamamoto, Takuya; Tezuka, Yasuyuki

    2016-09-26

    We demonstrate a method for the synthesis of cyclic polymers and a protocol for characterizing their diffusive motion in a melt state at the single molecule level. An electrostatic self-assembly and covalent fixation (ESA-CF) process is used for the synthesis of the cyclic poly(tetrahydrofuran) (poly(THF)). The diffusive motion of individual cyclic polymer chains in a melt state is visualized using single molecule fluorescence imaging by incorporating a fluorophore unit in the cyclic chains. The diffusive motion of the chains is quantitatively characterized by means of a combination of mean-squared displacement (MSD) analysis and a cumulative distribution function (CDF) analysis. The cyclic polymer exhibits multiple-mode diffusion which is distinct from its linear counterpart. The results demonstrate that the diffusional heterogeneity of polymers that is often hidden behind ensemble averaging can be revealed by the efficient synthesis of the cyclic polymers using the ESA-CF process and the quantitative analysis of the diffusive motion at the single molecule level using the MSD and CDF analyses.

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

    NASA Astrophysics Data System (ADS)

    Silva, Antonio

    2005-03-01

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

  12. Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

    NASA Astrophysics Data System (ADS)

    Marshall, Wallace F.; Fung, Jennifer C.

    2016-04-01

    The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.

  13. Laser filamentation induced air-flow motion in a diffusion cloud chamber.

    PubMed

    Sun, Haiyi; Liu, Jiansheng; Wang, Cheng; Ju, Jingjing; Wang, Zhanxin; Wang, Wentao; Ge, Xiaochun; Li, Chuang; Chin, See Leang; Li, Ruxin; Xu, Zhizhan

    2013-04-22

    We numerically simulated the air-flow motion in a diffusion cloud chamber induced by femtosecond laser filaments for different chopping rates. A two dimensional model was employed, where the laser filaments were treated as a heat flux source. The simulated patterns of flow fields and maximum velocity of updraft compare well with the experimental results for the chopping rates of 1, 5, 15 and 150 Hz. A quantitative inconsistency appears between simulated and experimental maximum velocity of updraft for 1 kHz repetition rate although a similar pattern of flow field is obtained, and the possible reasons were analyzed. Based on the present simulated results, the experimental observation of more water condensation/snow at higher chopping rate can be explained. These results indicate that the specific way of laser filament heating plays a significant role in the laser-induced motion of air flow, and at the same time, our previous conclusion of air flow having an important effect on water condensation/snow is confirmed.

  14. Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

    PubMed Central

    Marshall, Wallace F.; Fung, Jennifer C.

    2016-01-01

    The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by un-attached chromosomes, but that randomly-directed active forces applied to the telomeres speeds up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions. PMID:27046097

  15. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    SciTech Connect

    Berdiyorov, G. Tabet, N.; Harrabi, K.; Mehmood, U.; Hussein, I. A.; Peeters, F. M.; Zhang, J.; McLachlan, M. A.

    2015-07-14

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.

  16. Comparing nonrigid registration techniques for motion corrected MR prostate diffusion imaging

    SciTech Connect

    Buerger, C. Sénégas, J.; Kabus, S.; Carolus, H.; Schulz, H.; Renisch, S.; Agarwal, H.; Turkbey, B.; Choyke, P. L.

    2015-01-15

    Purpose: T{sub 2}-weighted magnetic resonance imaging (MRI) is commonly used for anatomical visualization in the pelvis area, such as the prostate, with high soft-tissue contrast. MRI can also provide functional information such as diffusion-weighted imaging (DWI) which depicts the molecular diffusion processes in biological tissues. The combination of anatomical and functional imaging techniques is widely used in oncology, e.g., for prostate cancer diagnosis and staging. However, acquisition-specific distortions as well as physiological motion lead to misalignments between T{sub 2} and DWI and consequently to a reduced diagnostic value. Image registration algorithms are commonly employed to correct for such misalignment. Methods: The authors compare the performance of five state-of-the-art nonrigid image registration techniques for accurate image fusion of DWI with T{sub 2}. Results: Image data of 20 prostate patients with cancerous lesions or cysts were acquired. All registration algorithms were validated using intensity-based as well as landmark-based techniques. Conclusions: The authors’ results show that the “fast elastic image registration” provides most accurate results with a target registration error of 1.07 ± 0.41 mm at minimum execution times of 11 ± 1 s.

  17. Coarse analysis of multiscale systems: Diffuser flows, charged particle motion, and connections to averaging theory

    NASA Astrophysics Data System (ADS)

    Fung, Jimmy

    We describe a technique for the efficient computation of the dominant-scale dynamics of a fluid system when only a high-fidelity simulation is available. Such a technique is desirable when governing equations for the dominant scales are unavailable, when model reduction is impractical, or when the original high-fidelity computation is expensive. We adopt the coarse analysis framework proposed by I. G. Kevrekidis (Comm. Math. Sci. 2003), where a computational superstructure is designed to use short-time, high-fidelity simulations to extract the dominant features for a multiscale system. We apply this technique to compute the dominant features of the compressible flow through a planar diffuser. We apply the proper orthogonal decomposition to classify the dominant and subdominant scales of diffuser flows. We derive a coarse projective Adams-Bashforth time integration routine and compute averaged diffuser flows. The results include accurate tracking of the dominant-scale dynamics for a range of parameter values for the computational superstructure. These results demonstrate that coarse analysis methods are useful for solving fluid flow problems of a multiscale nature. In order to elucidate the behavior of coarse analysis techniques, we make comparisons to averaging theory. To this end, we derive governing equations for the average motion of charged particles in a magnetic field in a number of different settings. First, we apply a novel procedure, inspired by WKB theory and Whitham averaging, to average the variational principle. The resulting equations are equivalent to the guiding center equations for charged particle motion; this marks an instance where averaging and variational principles commute. Secondly, we apply Lagrangian averaging techniques, previously applied in fluid mechanics, to derive averaged equations. Making comparisons to the WKB/Whitham derivation allows for the necessary closure of the Lagrangian averaging formulation. We also discuss the

  18. Review of observations of ground diffusion in space and in time and fractal model of ground motion

    NASA Astrophysics Data System (ADS)

    Shiltsev, Vladimir

    2010-09-01

    We present numerous observations of the diffusive motion of the ground and tunnels for scientific instruments and show that if systematic movements are excluded the remaining uncorrelated component of the motion obeys a characteristic fractal law with the displacement variance dY2 scaling with time and spatial intervals T and L as dY2∝TαLγ with both exponents close to 1 (α≈γ≈1). We briefly describe experimental methods of the mesoscopic and microscopic ground motion detection used in measurements at physics research facilities sensitive to ground motion, particularly large high energy elementary particle accelerators. A simple mathematical model of the fractal motion demonstrating the observed scaling law is also presented and discussed. This paper is a subsequent full detail publication to [V. Shiltsev, Phys. Rev. Lett. 104, 238501 (2010)PRLTAO0031-900710.1103/PhysRevLett.104.238501].

  19. Chronic kidney disease: Pathological and functional evaluation with intravoxel incoherent motion diffusion-weighted imaging.

    PubMed

    Mao, Wei; Zhou, Jianjun; Zeng, Mengsu; Ding, Yuqin; Qu, Lijie; Chen, Caizhong; Ding, Xiaoqiang; Wang, Yaqiong; Fu, Caixia

    2017-09-21

    Because chronic kidney disease (CKD) is a worldwide problem, accurate pathological and functional evaluation is required for planning treatment and follow-up. Intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can assess both capillary perfusion and tissue diffusion and may be helpful in evaluating renal function and pathology. To evaluate functional and pathological alterations in CKD by applying IVIM-DWI. Prospective study. In all, 72 CKD patients who required renal biopsy and 20 healthy volunteers. 1.5T. All subjects underwent IVIM-DWI of the kidneys, and image analysis was performed by two radiologists. The mean values of true diffusion coefficient (D), pseudo diffusion coefficient (D*), and perfusion fraction (f) were acquired from renal parenchyma. Correlation between IVIM-DWI parameters and estimated glomerular filtration rate (eGFR), as well as pathological damage, were assessed. One-way analysis of variance (ANOVA), paired sample t-test and Spearman correlation analysis. The paired sample t-test revealed that IVIM-DWI parameters were significantly lower in medulla than cortex for both patients and controls (P < 0.01). Regardless of whether eGFR was reduced, ANOVA revealed that f values of renal parenchyma were significantly lower in patients than controls (P < 0.05). Spearman correlation analysis revealed that there were positive correlations between eGFR and D (cortex, r = 0.466, P < 0.001; medulla, r = 0.491, P < 0.001), and between eGFR and f (cortex, r = 0.713, P < 0.001; medulla, r = 0.512, P < 0.001). Negative correlations were found between f and glomerular injury (cortex, r = -0.773, P < 0.001; medulla, r = -0.629, P < 0.001), and between f and tubulointerstitial lesion (cortex, r = -0.728, P < 0.001; medulla, r = -0.547, P < 0.001). IVIM-DWI might be feasible for noninvasive evaluation of renal function and pathology of CKD, especially in detection of renal insufficiency at an early stage. 1

  20. First passage times for a tracer particle in single file diffusion and fractional Brownian motion.

    PubMed

    Sanders, Lloyd P; Ambjörnsson, Tobias

    2012-05-07

    We investigate the full functional form of the first passage time density (FPTD) of a tracer particle in a single-file diffusion (SFD) system whose population is: (i) homogeneous, i.e., all particles having the same diffusion constant and (ii) heterogeneous, with diffusion constants drawn from a heavy-tailed power-law distribution. In parallel, the full FPTD for fractional Brownian motion [fBm-defined by the Hurst parameter, H ∈ (0, 1)] is studied, of interest here as fBm and SFD systems belong to the same universality class. Extensive stochastic (non-Markovian) SFD and fBm simulations are performed and compared to two analytical Markovian techniques: the method of images approximation (MIA) and the Willemski-Fixman approximation (WFA). We find that the MIA cannot approximate well any temporal scale of the SFD FPTD. Our exact inversion of the Willemski-Fixman integral equation captures the long-time power-law exponent, when H ≥ 1/3, as predicted by Molchan [Commun. Math. Phys. 205, 97 (1999)] for fBm. When H < 1/3, which includes homogeneous SFD (H = 1/4), and heterogeneous SFD (H < 1/4), the WFA fails to agree with any temporal scale of the simulations and Molchan's long-time result. SFD systems are compared to their fBm counter parts; and in the homogeneous system both scaled FPTDs agree on all temporal scales including also, the result by Molchan, thus affirming that SFD and fBm dynamics belong to the same universality class. In the heterogeneous case SFD and fBm results for heterogeneity-averaged FPTDs agree in the asymptotic time limit. The non-averaged heterogeneous SFD systems display a lack of self-averaging. An exponential with a power-law argument, multiplied by a power-law pre-factor is shown to describe well the FPTD for all times for homogeneous SFD and sub-diffusive fBm systems.

  1. Diffusion-weighted MR neurography of extremity nerves with unidirectional motion-probing gradients at 3 T: feasibility study.

    PubMed

    Zhao, Lianxin; Wang, Guangbin; Yang, Linlin; Wu, Lebin; Lin, Xiangtao; Chhabra, Avneesh

    2013-05-01

    The objective of our study was to show the feasibility and performance of diffusion-weighted MR neurography (MRN) of extremity nerves with unidirectional motion-probing gradients at 3 T. Forty-seven healthy volunteers and 10 patients underwent diffusion-weighted MRN of extremity nerves with unidirectional motion-probing gradients (anterior-posterior direction only) on a 3-T unit. Images were displayed using a maximum-intensity-projection technique. Two radiologists blindly and independently evaluated the imaging quality of extremity nerves on diffusion-weighted MRN images using a 4-point grading scale, with 4 indicating excellent quality and 1 indicating poor quality, and evaluated the relation of the lesion to adjacent nerves in patients. In volunteers, the long trajectories of major extremity nerves, including the radial, median, ulnar, sciatic, tibial, and common peroneal nerves, could be visualized 3D on diffusion-weighted MRN images. The mean imaging quality scores of all nerves for observers 1 and 2 were 3.68 ± 0.70 (SD) and 3.70 ± 0.66, respectively. Interobserver agreement was good (κ = 0.774). In patients, there was no discrepancy in imaging quality scores between observers. Scores of all nerves were 2-4 except in two patients with neurofibromatosis and one patient who underwent imaging soon after surgery. The extent of the lesions and the relationship of the lesions to the adjacent nerves were clearly depicted on diffusion-weighted MRN images of all patients. This preliminary study shows that 3-T diffusion-weighted MRN with unidirectional motion-probing gradients is feasible for 3D visualization of major extremity nerves. Diffusion-weighted MRN may enable nerve depiction and allow assessment of the anatomic relationship between lesions with diffusion restriction and adjacent nerves.

  2. The crossover from collective motion to periphery diffusion for two-dimensional adatom-islands on Cu(111).

    PubMed

    Karim, Altaf; Kara, Abdelkader; Trushin, Oleg; Rahman, Talat S

    2011-11-23

    The diffusion of two-dimensional adatom-islands (up to 100 atoms) on Cu(111) has been studied, using the self-learning kinetic Monte Carlo method (Trushin et al 2005 Phys. Rev. B 72 115401). A variety of multiple- and single-atom processes are revealed in the simulations, and the size dependences of the diffusion coefficients and effective diffusion barriers are calculated for each. From the tabulated frequencies of events found in the simulation, we show a crossover from diffusion due to the collective motion of the island to a regime in which the island diffuses through periphery-dominated mass transport. This crossover occurs for island sizes between 13 and 19 atoms. For islands containing 19-100 atoms the scaling exponent is 1.5, which is in good agreement with previous work. The diffusion of islands containing 2-13 atoms can be explained primarily on the basis of a linear increase of the barrier for the collective motion with the size of the island.

  3. Intramolecular and nonlinear dynamics

    SciTech Connect

    Davis, M.J.

    1993-12-01

    Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

  4. [Application of diffusion-weighted intravoxel incoherent motion imaging in diagnosis of renal cell carcinoma subtypes].

    PubMed

    Cong, X Y; Chen, Y; Zhang, J; Yu, X D; Ye, F; Yu, W J; Zhang, M M; Ouyang, H; Zhao, X M

    2016-06-23

    To evaluate the value of parameters derived from intravoxel incoherent motion diffusion-weighted magnetic resonance imaging in differentiating histopathological subtypes of renal cell carcinoma (RCC). Between May 2014 and December 2015, a total of 69 patients who were surgically and pathologically diagnosed as renal cell carcinoma were recruited for the study. We examined 61 clear cell RCC (ccRCC), and 8 non-clear cell carcinoma (non-ccRCC, including 7 chromophobe RCC and 1 papillary RCC). All the ccRCC were divided into well differentiated group (n=46), moderately differentiated group (n=8), and poorly differentiated group (n=7). In addition to routine renal magnetic resonance imaging examination performed on a 3.0-Tesla MR system, all patients were imaged with axial intravoxel incoherent motion diffusion-weighted imaging. Using biexponential model, we calculated the diffusion coefficient (D), pseudodiffusion coefficient (D(*)), and perfusion fraction (f). The D and f values of the ccRCC were higher (each P<0.05) than that for non-ccRCC [D (1.29±0.30)×10(-3)mm(2)/s, D(*) (42.92±20.21)×10(-3)mm(2)/s, and f (35.71±6.61)% versus D (0.78±0.23)×10(-3)mm(2)/s, D(*) (32.60±11.33)×10(-3)mm(2)/s, and f (21.52±8.44)% ]. In the well differentiated group of ccRCC, we found D of (1.36±0.29)×10(-3)mm(2)/s, D(*) (38.39±18.51)×10(-3)mm(2)/s, and f (36.40±6.96)%. The D, D(*,) f values of moderately differentiated lesions were (1.10±0.24)×10(-3)mm(2)/s, (59.90±20.23)×10(-3) mm(2)/s, and (32.88±4.02)%, respectively, those of the poorly differentiated group were (1.03±0.16)×10(-3)mm(2)/s, (53.28±18.74)×10(-3)mm(2)/s, and (34.42±6.21)%. The well differentiated group of ccRCC showed a higher D value than the moderately differentiated and poorly differentiated groups (each P<0.05). D(*) values were significantly lower for the well differentiated group than for the moderately differentiated group (P<0.05). The sensitivity and specificity of D values were 90

  5. Predicting diffusion paths and interface motion in gamma/gamma + beta, Ni-Cr-Al diffusion couples

    NASA Technical Reports Server (NTRS)

    Nesbitt, J. A.; Heckel, R. W.

    1987-01-01

    A simplified model has been developed to predict Beta recession and diffusion paths in ternary gamma/gamma + beta diffusion couples (gamma:fcc, beta: NiAl structure). The model was tested by predicting beta recession and diffusion paths for four gamma/gamma + beta, Ni-Cr-Al couples annealed for 100 hours at 1200 C. The model predicted beta recession within 20 percent of that measured for each of the couples. The model also predicted shifts in the concentration of the gamma phase at the gamma/gamma + beta interface within 2 at. pct Al and 6 at. pct Cr of that measured in each of the couples. A qualitative explanation based on simple kinetic and mass balance arguments has been given which demonstrates the necessity for diffusion in the two-phase region of certain gamma/gamma + beta, Ni-Cr-Al couples.

  6. Retrospective head motion correction approaches for diffusion tensor imaging: Effects of preprocessing choices on biases and reproducibility of scalar diffusion metrics.

    PubMed

    Kreilkamp, Barbara A K; Zacà, Domenico; Papinutto, Nico; Jovicich, Jorge

    2016-01-01

    To evaluate how retrospective head motion correction strategies affect the estimation of scalar metrics commonly used in clinical diffusion tensor imaging (DTI) studies along with their across-session reproducibility errors. Fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD) and their respective across-session reproducibility errors were measured on a 4T test-retest dataset of healthy participants using five processing pipelines. These differed in: 1) the number of b0 volumes used for motion correction reference (one or five); 2) the estimations of the gradient matrix rotation (based on 6 or 12 degrees of freedom derived from coregistration); and 3) the software packages used (FSL or DTIPrep). Biases and reproducibility were evaluated in three regions of interest (ROIs) (bilateral arcuate fasciculi, cingula, and the corpus callosum) and also at the full brain level with tract based skeleton images. Preprocessing choices affected DTI measures and their reproducibility. The DTIPrep pipeline exhibited higher DTI metrics: FA/MD and AD (P < 0.05) relative to FSL pipelines both at the ROI and full brain level, and lower RD estimates (P < 0.05) at the ROI level. Within FSL pipelines no such effects were found (P-values ranging between 0.25 and 0.97). The DTIPrep pipeline showed the highest number of white matter skeleton voxels, with significantly higher reproducibility (P < 0.001) relative to the other pipelines (tested on P < 0.01 uncorrected maps). The use of an iteratively averaged b0 image as motion correction reference (as performed by DTIPrep) affects both scalar values and improves test-retest reliability relative to the other tested pipelines. These considerations are potentially relevant for data analysis in longitudinal DTI studies. © 2015 Wiley Periodicals, Inc.

  7. Diffusion tensor imaging studies of attention-deficit/hyperactivity disorder: meta-analyses and reflections on head motion.

    PubMed

    Aoki, Yuta; Cortese, Samuele; Castellanos, Francisco Xavier

    2017-07-03

    Diffusion tensor imaging studies have shown atypical fractional anisotropy (FA) in individuals with attention-deficit/hyperactivity disorder (ADHD), albeit with conflicting results. We performed meta-analyses of whole-brain voxel-based analyses (WBVBA) and tract-based spatial statistics (TBSS) studies in ADHD, along with a qualitative review of TBSS studies addressing the issue of head motion, which may bias results. We conducted a systematic literature search (last search on April 1st, 2016) to identify studies comparing FA values between individuals with ADHD and typically developing (TD) participants. Signed differential mapping was used to compute effect sizes and integrate WBVBA and TBSS studies, respectively. TBSS datasets reporting no between-group motion differences were identified. We identified 14 WBVBA (ADHDn = 314, TDn = 278) and 13 TBSS datasets (ADHDn = 557, TDn = 568). WBVBA meta-analysis showed both significantly lower and higher FA values in individuals with ADHD; TBSS meta-analysis showed significantly lower FA in ADHD compared with TD in four clusters: two in the corpus callosum (isthmus and posterior midbody), one in right inferior fronto-occipital fasciculus, and one in left inferior longitudinal fasciculus. However, four of six datasets confirming no group-differences in motion showed no significant between-group FA differences. A growing diffusion tensor imaging (DTI) literature (total N = 1,717) and a plethora of apparent findings suggest atypical interhemispheric connection in ADHD. However, FA results in ADHD should be considered with caution, since many studies did not examine potential group differences in head motion, and most of the studies reporting no difference in motion showed no significant results. Future studies should address head motion as a priority and assure that groups do not differ in head motion. © 2017 Association for Child and Adolescent Mental Health.

  8. Cellular automaton simulation of the diffusive motion of bacteria and their adhesion to nanostructures on a solid surface.

    PubMed

    Yamamoto, Takehiro; Emura, Chie; Oya, Masashi

    2016-12-01

    The growth of a biofilm begins with the adhesion of bacteria to a solid surface. Consequently, biofilm growth can be managed by the control of bacterial adhesion. Recent experimental studies have suggested that bacterial adhesion can be controlled by modifying a solid surface using nanostructures. Computational prediction and analysis of bacterial adhesion behavior are expected to be useful for the design of effective arrangements of nanostructures for controlling bacterial adhesion. The present study developed a cellular automaton (CA) model for bacterial adhesion simulation that could describe both the diffusive motion of bacteria and dependence of their adhesion patterns on the distance between nanostructures observed in experimental studies. The diffusive motion was analyzed by the moment scaling spectrum theory, and the present model was confirmed to describe subdiffusion behavior due to obstacles. Adhesion patterns observed in experimental studies can be successfully simulated by introducing CA rules to describe a mechanism by which bacteria tend to move to increase the area of contact with nanostructures.

  9. Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle

    PubMed Central

    Kinsey, Stephen T.; Locke, Bruce R.; Dillaman, Richard M.

    2011-01-01

    Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction–diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction–diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle. PMID:21177946

  10. High-Resolution Multi-Shot Spiral Diffusion Tensor Imaging with Inherent Correction of Motion-Induced Phase Errors

    PubMed Central

    Truong, Trong-Kha; Guidon, Arnaud

    2014-01-01

    Purpose To develop and compare three novel reconstruction methods designed to inherently correct for motion-induced phase errors in multi-shot spiral diffusion tensor imaging (DTI) without requiring a variable-density spiral trajectory or a navigator echo. Theory and Methods The first method simply averages magnitude images reconstructed with sensitivity encoding (SENSE) from each shot, whereas the second and third methods rely on SENSE to estimate the motion-induced phase error for each shot, and subsequently use either a direct phase subtraction or an iterative conjugate gradient (CG) algorithm, respectively, to correct for the resulting artifacts. Numerical simulations and in vivo experiments on healthy volunteers were performed to assess the performance of these methods. Results The first two methods suffer from a low signal-to-noise ratio (SNR) or from residual artifacts in the reconstructed diffusion-weighted images and fractional anisotropy maps. In contrast, the third method provides high-quality, high-resolution DTI results, revealing fine anatomical details such as a radial diffusion anisotropy in cortical gray matter. Conclusion The proposed SENSE+CG method can inherently and effectively correct for phase errors, signal loss, and aliasing artifacts caused by both rigid and nonrigid motion in multi-shot spiral DTI, without increasing the scan time or reducing the SNR. PMID:23450457

  11. [Joint correction for motion artifacts and off-resonance artifacts in multi-shot diffusion magnetic resonance imaging].

    PubMed

    Wu, Wenchuan; Fang, Sheng; Guo, Hua

    2014-06-01

    Aiming at motion artifacts and off-resonance artifacts in multi-shot diffusion magnetic resonance imaging (MRI), we proposed a joint correction method in this paper to correct the two kinds of artifacts simultaneously without additional acquisition of navigation data and field map. We utilized the proposed method using multi-shot variable density spiral sequence to acquire MRI data and used auto-focusing technique for image deblurring. We also used direct method or iterative method to correct motion induced phase errors in the process of deblurring. In vivo MRI experiments demonstrated that the proposed method could effectively suppress motion artifacts and off-resonance artifacts and achieve images with fine structures. In addition, the scan time was not increased in applying the proposed method.

  12. MRI-based staging of hepatic fibrosis: Comparison of intravoxel incoherent motion diffusion-weighted imaging with magnetic resonance elastography.

    PubMed

    Ichikawa, Shintaro; Motosugi, Utaroh; Morisaka, Hiroyuki; Sano, Katsuhiro; Ichikawa, Tomoaki; Enomoto, Nobuyuki; Matsuda, Masanori; Fujii, Hideki; Onishi, Hiroshi

    2015-07-01

    To evaluate the use of intravoxel incoherent motion (IVIM) imaging for staging hepatic fibrosis, and compare its staging ability with that of magnetic resonance elastography (MRE). This study included 129 patients with pathologically staged liver fibrosis, and 53 patients with healthy livers. All patients underwent both MRE and IVIM imaging. Four diffusivity indices were calculated with 11 b-values; slow diffusion coefficient related to molecular diffusion (D), fast diffusion coefficient related to perfusion in micro-vessels (D*), perfusion-related diffusion fraction (f), and apparent diffusion coefficient (ADC). Receiver operating characteristic curve analysis was performed to determine the accuracy of IVIM imaging and MRE for staging hepatic fibrosis. D*, f, and ADC values decreased significantly with fibrosis stage (P < 0.0124), and liver stiffness increased (P < 0.0001). The Az value of MRE was significantly higher than that of D* for all fibrosis stages (D* vs. MRE for ≥ F1, 0.851 vs. 0.992 [P < 0.0001]; ≥ F2, 0.898 vs. 0.998 [P = 0.0003]; ≥ F3, 0.904 vs. 0.995 [P = 0.0004]; F4, 0.885 vs. 0.996 [P < 0.0001]). IVIM imaging is a useful technique for evaluating hepatic fibrosis, but MRE is better able to discriminate fibrosis stages than IVIM imaging. © 2014 Wiley Periodicals, Inc.

  13. Motion blur filtering: A statistical approach for extracting confinement forces and diffusivity from a single blurred trajectory.

    PubMed

    Calderon, Christopher P

    2016-05-01

    Single particle tracking (SPT) can aid in understanding a variety of complex spatiotemporal processes. However, quantifying diffusivity and confinement forces from individual live cell trajectories is complicated by inter- and intratrajectory kinetic heterogeneity, thermal fluctuations, and (experimentally resolvable) statistical temporal dependence inherent to the underlying molecule's time correlated confined dynamics experienced in the cell. The problem is further complicated by experimental artifacts such as localization uncertainty and motion blur. The latter is caused by the tagged molecule emitting photons at different spatial positions during the exposure time of a single frame. The aforementioned experimental artifacts induce spurious time correlations in measured SPT time series that obscure the information of interest (e.g., confinement forces and diffusivity). We develop a maximum likelihood estimation (MLE) technique that decouples the above noise sources and systematically treats temporal correlation via time series methods. This ultimately permits a reliable algorithm for extracting diffusivity and effective forces in confined or unconfined environments. We illustrate how our approach avoids complications inherent to mean square displacement or autocorrelation techniques. Our algorithm modifies the established Kalman filter (which does not handle motion blur artifacts) to provide a likelihood based time series estimation procedure. The result extends A. J. Berglund's motion blur model [Phys. Rev. E 82, 011917 (2010)PLEEE81539-375510.1103/PhysRevE.82.011917] to handle confined dynamics. The approach can also systematically utilize (possibly time dependent) localization uncertainty estimates afforded by image analysis if available. This technique, which explicitly treats confinement and motion blur within a time domain MLE framework, uses an exact likelihood (time domain methods facilitate analyzing nonstationary signals). Our estimator is demonstrated

  14. Motion blur filtering: A statistical approach for extracting confinement forces and diffusivity from a single blurred trajectory

    NASA Astrophysics Data System (ADS)

    Calderon, Christopher P.

    2016-05-01

    Single particle tracking (SPT) can aid in understanding a variety of complex spatiotemporal processes. However, quantifying diffusivity and confinement forces from individual live cell trajectories is complicated by inter- and intratrajectory kinetic heterogeneity, thermal fluctuations, and (experimentally resolvable) statistical temporal dependence inherent to the underlying molecule's time correlated confined dynamics experienced in the cell. The problem is further complicated by experimental artifacts such as localization uncertainty and motion blur. The latter is caused by the tagged molecule emitting photons at different spatial positions during the exposure time of a single frame. The aforementioned experimental artifacts induce spurious time correlations in measured SPT time series that obscure the information of interest (e.g., confinement forces and diffusivity). We develop a maximum likelihood estimation (MLE) technique that decouples the above noise sources and systematically treats temporal correlation via time series methods. This ultimately permits a reliable algorithm for extracting diffusivity and effective forces in confined or unconfined environments. We illustrate how our approach avoids complications inherent to mean square displacement or autocorrelation techniques. Our algorithm modifies the established Kalman filter (which does not handle motion blur artifacts) to provide a likelihood based time series estimation procedure. The result extends A. J. Berglund's motion blur model [Phys. Rev. E 82, 011917 (2010), 10.1103/PhysRevE.82.011917] to handle confined dynamics. The approach can also systematically utilize (possibly time dependent) localization uncertainty estimates afforded by image analysis if available. This technique, which explicitly treats confinement and motion blur within a time domain MLE framework, uses an exact likelihood (time domain methods facilitate analyzing nonstationary signals). Our estimator is demonstrated to be

  15. Motion.

    ERIC Educational Resources Information Center

    Brand, Judith, Ed.

    2002-01-01

    This issue of Exploratorium Magazine focuses on the topic of motion. Contents include: (1) "First Word" (Zach Tobias); (2) "Cosmic Collisions" (Robert Irion); (3) "The Mobile Cell" (Karen E. Kalumuck); (4) "The Paths of Paths" (Steven Vogel); (5) "Fragments" (Pearl Tesler); (6) "Moving Pictures" (Amy Snyder); (7) "Plants on the Go" (Katharine…

  16. Motion.

    ERIC Educational Resources Information Center

    Gerhart, James B.; Nussbaum, Rudi H.

    This monograph was written for the Conference on the New Instructional Materials in Physics held at the University of Washington in summer, 1965. It is intended for use in an introductory course in college physics. It consists of an extensive qualitative discussion of motion followed by a detailed development of the quantitative methods needed to…

  17. Motion.

    ERIC Educational Resources Information Center

    Brand, Judith, Ed.

    2002-01-01

    This issue of Exploratorium Magazine focuses on the topic of motion. Contents include: (1) "First Word" (Zach Tobias); (2) "Cosmic Collisions" (Robert Irion); (3) "The Mobile Cell" (Karen E. Kalumuck); (4) "The Paths of Paths" (Steven Vogel); (5) "Fragments" (Pearl Tesler); (6) "Moving Pictures" (Amy Snyder); (7) "Plants on the Go" (Katharine…

  18. Decreases in Molecular Diffusion, Perfusion Fraction and Perfusion-Related Diffusion in Fibrotic Livers: A Prospective Clinical Intravoxel Incoherent Motion MR Imaging Study

    PubMed Central

    Lu, Pu-Xuan; Huang, Hua; Yuan, Jing; Zhao, Feng; Chen, Zhi-Yi; Zhang, Qinwei; Ahuja, Anil T.; Zhou, Bo-Ping; Wáng, Yì-Xiáng J.

    2014-01-01

    Purpose This study was aimed to determine whether pure molecular-based diffusion coefficient (D) and perfusion-related diffusion parameters (perfusion fraction f, perfusion-related diffusion coefficient D*) differ in healthy livers and fibrotic livers through intra-voxel incoherent motion (IVIM) MR imaging. Material and Methods 17 healthy volunteers and 34 patients with histopathologically confirmed liver fibrosis patients (stage 1 = 14, stage 2 = 8, stage 3& 4 = 12, METAVIR grading) were included. Liver MR imaging was performed at 1.5-T. IVIM diffusion weighted imaging sequence was based on standard single-shot DW spin echo-planar imaging, with ten b values of 10, 20, 40, 60, 80, 100, 150, 200, 400, 800 sec/mm2 respectively. Pixel-wise realization and regions-of-interest based quantification of IVIM parameters were performed. Results D, f, and D* in healthy volunteer livers and patient livers were 1.096±0.155 vs 0.917±0.152 (10−3 mm2/s, p = 0.0015), 0.164±0.021 vs 0.123±0.029 (p<0.0001), and 13.085±2.943 vs 9.423±1.737 (10−3 mm2/s, p<0.0001) respectively, all significantly lower in fibrotic livers. As the fibrosis severity progressed, D, f, and D* values decreased, with a trend significant for f and D*. Conclusion Fibrotic liver is associated with lower pure molecular diffusion, lower perfusion volume fraction, and lower perfusion-related diffusion. The decrease of f and D* in the liver is significantly associated liver fibrosis severity. PMID:25436458

  19. Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls.

    PubMed

    Wilms, Dorothea; Virnau, Peter; Snook, Ian K; Binder, Kurt

    2012-11-01

    The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensurate with the ideal triangular lattice is also studied, where (due to a transition in the number of rows, n → n-1) the confined crystal is incommensurate with the confining boundaries, and a soliton staircase forms along the walls. It is shown that mean-square displacements (MSDs) of particles as a function of time show an overshoot and then saturate at a horizontal plateau in the commensurate case, the value of the plateau being largest in the center of the strip. Conversely, when solitons are present, MSDs are largest in the rows containing the solitons, and all MSDs do not settle down at well-defined plateaus in the direction parallel to the boundaries, due to the lack of positional long-range order in ideal two-dimensional crystals. The MSDs of the solitons (which can be treated like quasiparticles at very low temperature) have also been studied and their dynamics are found to be about an order of magnitude slower than that of the colloidal particles themselves. Finally, transport of individual colloidal particles by diffusion processes is studied: both standard vacancy-interstitial pair formation and cooperative ring rotation processes are identified. These processes require thermal activation, with activation energies of the order of 10T(m) (T(m) being the melting

  20. Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls

    NASA Astrophysics Data System (ADS)

    Wilms, Dorothea; Virnau, Peter; Snook, Ian K.; Binder, Kurt

    2012-11-01

    The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensurate with the ideal triangular lattice is also studied, where (due to a transition in the number of rows, n→n-1) the confined crystal is incommensurate with the confining boundaries, and a soliton staircase forms along the walls. It is shown that mean-square displacements (MSDs) of particles as a function of time show an overshoot and then saturate at a horizontal plateau in the commensurate case, the value of the plateau being largest in the center of the strip. Conversely, when solitons are present, MSDs are largest in the rows containing the solitons, and all MSDs do not settle down at well-defined plateaus in the direction parallel to the boundaries, due to the lack of positional long-range order in ideal two-dimensional crystals. The MSDs of the solitons (which can be treated like quasiparticles at very low temperature) have also been studied and their dynamics are found to be about an order of magnitude slower than that of the colloidal particles themselves. Finally, transport of individual colloidal particles by diffusion processes is studied: both standard vacancy-interstitial pair formation and cooperative ring rotation processes are identified. These processes require thermal activation, with activation energies of the order of 10Tm (Tm being the melting temperature of

  1. A novel measure of reliability in Diffusion Tensor Imaging after data rejections due to subject motion.

    PubMed

    Sairanen, V; Kuusela, L; Sipilä, O; Savolainen, S; Vanhatalo, S

    2017-02-15

    Diffusion Tensor Imaging (DTI) is commonly challenged by subject motion during data acquisition, which often leads to corrupted image data. Currently used procedure in DTI analysis is to correct or completely reject such data before tensor estimations, however assessing the reliability and accuracy of the estimated tensor in such situations has evaded previous studies. This work aims to define the loss of data accuracy with increasing image rejections, and to define a robust method for assessing reliability of the result at voxel level. We carried out simulations of every possible sub-scheme (N=1,073,567,387) of Jones30 gradient scheme, followed by confirming the idea with MRI data from four newborn and three adult subjects. We assessed the relative error of the most commonly used tensor estimates for DTI and tractography studies, fractional anisotropy (FA) and the major orientation vector (V1), respectively. The error was estimated using two measures, the widely used electric potential (EP) criteria as well as the rotationally variant condition number (CN). Our results show that CN and EP are comparable in situations with very few rejections, but CN becomes clearly more sensitive to depicting errors when more gradient vectors and images were rejected. The error in FA and V1 was also found depend on the actual FA level in the given voxel; low actual FA levels were related to high relative errors in the FA and V1 estimates. Finally, the results were confirmed with clinical MRI data. This showed that the errors after rejections are, indeed, inhomogeneous across brain regions. The FA and V1 errors become progressively larger when moving from the thick white matter bundles towards more superficial subcortical structures. Our findings suggest that i) CN is a useful estimator of data reliability at voxel level, and ii) DTI preprocessing with data rejections leads to major challenges when assessing brain tissue with lower FA levels, such as all newborn brain, as well as

  2. Intravoxel incoherent motion diffusion-weighted imaging for monitoring chemotherapeutic efficacy in gastric cancer

    PubMed Central

    Song, Xiao-Li; Kang, Heoung Keun; Jeong, Gwang Woo; Ahn, Kyu Youn; Jeong, Yong Yeon; Kang, Yang Joon; Cho, Hye Jung; Moon, Chung Man

    2016-01-01

    AIM: To assess intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) for monitoring early efficacy of chemotherapy in a human gastric cancer mouse model. METHODS: IVIM-DWI was performed with 12 b-values (0-800 s/mm2) in 25 human gastric cancer-bearing nude mice at baseline (day 0), and then they were randomly divided into control and 1-, 3-, 5- and 7-d treatment groups (n = 5 per group). The control group underwent longitudinal MRI scans at days 1, 3, 5 and 7, and the treatment groups underwent subsequent MRI scans after a specified 5-fluorouracil/calcium folinate treatment. Together with tumor volumes (TV), the apparent diffusion coefficient (ADC) and IVIM parameters [true water molecular diffusion coefficient (D), perfusion fraction (f) and pseudo-related diffusion coefficient (D*)] were measured. The differences in those parameters from baseline to each measurement (ΔTV%, ΔADC%, ΔD%, Δf% and ΔD*%) were calculated. After image acquisition, tumor necrosis, microvessel density (MVD) and cellular apoptosis were evaluated by hematoxylin-eosin (HE), CD31 and terminal-deoxynucleotidyl transferase mediated nick end labeling (TUNEL) staining respectively, to confirm the imaging findings. Mann-Whitney test and Spearman's correlation coefficient analysis were performed. RESULTS: The observed relative volume increase (ΔTV%) in the treatment group were significantly smaller than those in the control group at day 5 (ΔTVtreatment% = 19.63% ± 3.01% and ΔTVcontrol% = 83.60% ± 14.87%, P = 0.008) and day 7 (ΔTVtreatment% = 29.07% ± 10.01% and ΔTVcontrol% = 177.06% ± 63.00%, P = 0.008). The difference in ΔTV% between the treatment and the control groups was not significant at days 1 and 3 after a short duration of treatment. Increases in ADC in the treatment group (ΔADC%treatment, median, 30.10% ± 18.32%, 36.11% ± 21.82%, 45.22% ± 24.36%) were significantly higher compared with the control group (ΔADC%control, median, 4.98% ± 3.39%, 6.26% ± 3

  3. Intravoxel incoherent motion diffusion-weighted MR imaging of breast cancer: association with histopathological features and subtypes.

    PubMed

    Kim, Yunju; Ko, Kyounglan; Kim, Daehong; Min, Changki; Kim, Sungheon G; Joo, Jungnam; Park, Boram

    2016-07-01

    To evaluate the associations between intravoxel incoherent motion (IVIM)-derived parameters and histopathological features and subtypes of breast cancer. Pre-operative MRI from 275 patients with unilateral breast cancer was analyzed. The apparent diffusion coefficient (ADC) and IVIM parameters [tissue diffusion coefficient (Dt), perfusion fraction (fp) and pseudodiffusion coefficient] were obtained from cancer and normal tissue using diffusion-weighted imaging with b-values of 0, 30, 70, 100, 150, 200, 300, 400, 500 and 800 s mm(-2). We then compared the IVIM parameters of tumours with different histopathological features and subtypes. The ADC and Dt were lower and fp was higher in cancers than in normal tissues (p < 0.001). The Dt was lower in high Ki-67 cancer than in low Ki-67 cancer (p = 0.019), whereas ADC showed no significant difference (p = 0.309). Luminal B [human epidermal growth factor receptor 2 (HER2)-negative] cancer showed lower ADC (p = 0.003) and Dt (p = 0.001) than other types. We found low tissue diffusivity in high Ki-67 cancer and luminal B (HER2-negative) cancer using IVIM imaging. Low tissue diffusivity is more clearly shown in high Ki-67 tumours and luminal B (HER2-negative) tumours with the IVIM model.

  4. Spatially constrained incoherent motion method improves diffusion-weighted MRI signal decay analysis in the liver and spleen

    PubMed Central

    Taimouri, Vahid; Afacan, Onur; Perez-Rossello, Jeannette M.; Callahan, Michael J.; Mulkern, Robert V.; Warfield, Simon K.; Freiman, Moti

    2015-01-01

    Purpose: To evaluate the effect of the spatially constrained incoherent motion (SCIM) method on improving the precision and robustness of fast and slow diffusion parameter estimates from diffusion-weighted MRI in liver and spleen in comparison to the independent voxel-wise intravoxel incoherent motion (IVIM) model. Methods: We collected diffusion-weighted MRI (DW-MRI) data of 29 subjects (5 healthy subjects and 24 patients with Crohn’s disease in the ileum). We evaluated parameters estimates’ robustness against different combinations of b-values (i.e., 4 b-values and 7 b-values) by comparing the variance of the estimates obtained with the SCIM and the independent voxel-wise IVIM model. We also evaluated the improvement in the precision of parameter estimates by comparing the coefficient of variation (CV) of the SCIM parameter estimates to that of the IVIM. Results: The SCIM method was more robust compared to IVIM (up to 70% in liver and spleen) for different combinations of b-values. Also, the CV values of the parameter estimations using the SCIM method were significantly lower compared to repeated acquisition and signal averaging estimated using IVIM, especially for the fast diffusion parameter in liver (CVIV IM = 46.61 ± 11.22, CVSCIM = 16.85 ± 2.160, p < 0.001) and spleen (CVIV IM = 95.15 ± 19.82, CVSCIM = 52.55 ± 1.91, p < 0.001). Conclusions: The SCIM method characterizes fast and slow diffusion more precisely compared to the independent voxel-wise IVIM model fitting in the liver and spleen. PMID:25832079

  5. Dissecting diffusive and advective motion in colloidal sedimentation by multi-speckle Ultra-Small-Angle XPCS

    NASA Astrophysics Data System (ADS)

    Möller, Johannes; Narayanan, Theyencheri

    In colloidal suspensions internal or external fields can induce directed motions of particles in addition to Brownian diffusion. Here, gradients in temperature or chemical potential, shear flow as well as gravity can act as an external field. Examples for internal motions can be found in synthetic self-propelling particles and microorganisms, generally coined as active matter. We present multi-speckle X-ray photon correlation spectroscopy measurements in the Ultra-Small-Angle scattering range which probes an expanded length scale comparable to DLS and optical microscopy. To demonstrate the advanced capabilities, we show measurements probing the motions within a settling suspension of sub-micron sized silica particles. A global fitting procedure has been applied to separate the diffusive and advective contributions to the particle dynamics. With this, macroscopic parameters such as the sedimentation velocity can be probed on a microscopic level in highly opaque and concentrated systems, which are in general difficult to access for optical investigations. This procedure may prove its value for investigating various kinds of non-equilibrium systems.

  6. In vivo cardiac diffusion-weighted magnetic resonance imaging: quantification of normal perfusion and diffusion coefficients with intravoxel incoherent motion imaging.

    PubMed

    Delattre, Benedicte M A; Viallon, Magalie; Wei, Hongjiang; Zhu, Yuemin M; Feiweier, Thorsten; Pai, Vinay M; Wen, Han; Croisille, Pierre

    2012-11-01

    Diffusion-weighted imaging (DWI) and the introduction of the intravoxel incoherent motion (IVIM) model have provided a unique method for evaluating perfusion and diffusion within a tissue without the need for a contrast agent. Despite its relevance, cardiac DWI has thus far been limited by low b values because of signal loss induced by physiological motion. The goal of this study was to develop a methodology for estimating IVIM parameters of in vivo cardiac magnetic resonance imaging using an efficient DWI acquisition framework. This was achieved by investigating various acquisition strategies (principal component analysis [PCA] filtering and temporal maximum intensity projection [PCATMIP] and single trigger delay [TD]) and fitting methods. Simulations were performed on a synthetic dataset of diffusion-weighted signal intensity (SI) to determine the fitting method that would yield IVIM parameters with the greatest accuracy. The required number of b values to correctly estimate IVIM parameters was also investigated. Breath-hold DWI scans were performed for 12 volunteers to collect several TD values during diastole. Thirteen b values ranging from 0 to 550 s/mm were used. The IVIM parameters derived using the data from all the acquired TDs (PCATMIP technique) were compared with those derived using a single acquisition performed at an optimized diastolic time point (1TD). The main result of this study was that PCATMIP, when combined with a fitting model that accounted for T1 and T2 relaxation, provided IVIM parameters with less variability. However, an acquisition performed with 1 optimized diastolic TD provided results that were as good as those provided using PCATMIP if the R-R variability during the acquisition was sufficiently low (± 5%). Furthermore, the use of only 9 b values (that could be acquired in 2 breath-holds), instead of 13 b values (requiring 3 breath-holds), was sufficient to determine the IVIM parameters. This study demonstrates that IVIM is

  7. Intravoxel Incoherent Motion Diffusion Weighted Magnetic Resonance Imaging for Differentiation Between Nasopharyngeal Carcinoma and Lymphoma at the Primary Site

    PubMed Central

    Yu, Xiao-Ping; Hou, Jing; Li, Fei-Ping; Wang, Hui; Hu, Ping-Sheng; Bi, Feng; Wang, Wei

    2016-01-01

    Objective The aim of the study was to investigate the utility of intravoxel incoherent motion (IVIM) diffusion-weighted magnetic resonance imaging (DWI) for differentiating nasopharyngeal carcinoma (NPC) from lymphoma. Methods Intravoxel incoherent motion–based parameters including the apparent diffusion coefficient (ADC), pure diffusion coefficient (D), pseudodiffusion coefficient (D*), perfusion fraction (f), and fD* (the product of D* and f) were retrospectively compared between 102 patients (82 with NPC, 20 with lymphoma) who received pretreatment IVIM DWI. Results Compared with lymphoma, NPC exhibited higher ADC, D, D*, fD* values (P < 0.001) and f value (P = 0.047). The optimal cutoff values (area under the curve, sensitivity, and specificity, respectively) for distinguishing the 2 tumors were as follows: ADC value of 0.761 × 10−3 mm2/s (0.781, 93.90%, 55.00%); D, 0.66 × 10−3 mm2/s (0.802, 54.88%, 100.00%); D*, 7.89 × 10−3 mm2/s (0.898, 82.93%, 85.00%); f, 0.29 (0.644, 41.46%, 95.00%); and fD*, 1.99 × 10−3 mm2/s (0.960, 85.37%, 100.00%). Conclusions Nasopharyngeal carcinoma exhibits different IVIM-based imaging features from lymphoma. Intravoxel incoherent motion DWI is useful for differentiating lymphoma from NPC. PMID:26953769

  8. Clinical Intravoxel Incoherent Motion and Diffusion MR Imaging: Past, Present, and Future.

    PubMed

    Iima, Mami; Le Bihan, Denis

    2016-01-01

    The concept of diffusion magnetic resonance (MR) imaging emerged in the mid-1980s, together with the first images of water diffusion in the human brain, as a way to probe tissue structure at a microscopic scale, although the images were acquired at a millimetric scale. Since then, diffusion MR imaging has become a pillar of modern clinical imaging. Diffusion MR imaging has mainly been used to investigate neurologic disorders. A dramatic application of diffusion MR imaging has been acute brain ischemia, providing patients with the opportunity to receive suitable treatment at a stage when brain tissue might still be salvageable, thus avoiding terrible handicaps. On the other hand, it was found that water diffusion is anisotropic in white matter, because axon membranes limit molecular movement perpendicularly to the nerve fibers. This feature can be exploited to produce stunning maps of the orientation in space of the white matter tracts and brain connections in just a few minutes. Diffusion MR imaging is now also rapidly expanding in oncology, for the detection of malignant lesions and metastases, as well as monitoring. Water diffusion is usually largely decreased in malignant tissues, and body diffusion MR imaging, which does not require any tracer injection, is rapidly becoming a modality of choice to detect, characterize, or even stage malignant lesions, especially for breast or prostate cancer. After a brief summary of the key methodological concepts beyond diffusion MR imaging, this article will give a review of the clinical literature, mainly focusing on current outstanding issues, followed by some innovative proposals for future improvements. © RSNA, 2016

  9. Femtosecond laser studies of ultrafast intramolecular processes

    SciTech Connect

    Hayden, C.

    1993-12-01

    The goal of this research is to better understand the detailed mechanisms of chemical reactions by observing, directly in time, the dynamics of fundamental chemical processes. In this work femtosecond laser pulses are used to initiate chemical processes and follow the progress of these processes in time. The authors are currently studying ultrafast internal conversion and subsequent intramolecular relaxation in unsaturated hydrocarbons. In addition, the authors are developing nonlinear optical techniques to prepare and monitor the time evolution of specific vibrational motions in ground electronic state molecules.

  10. Quantitative non-Gaussian diffusion and intravoxel incoherent motion magnetic resonance imaging: differentiation of malignant and benign breast lesions.

    PubMed

    Iima, Mami; Yano, Kojiro; Kataoka, Masako; Umehana, Masaki; Murata, Katsutoshi; Kanao, Shotaro; Togashi, Kaori; Le Bihan, Denis

    2015-04-01

    The purpose of this study was to explore the potential of non-Gaussian diffusion and perfusion magnetic resonance imaging (MRI) using intravoxel incoherent motion (IVIM) MRI for the diagnosis of breast lesions. This study included 26 women with breast lesions. Diffusion-weighted images were acquired using 16 b values up to 2500 s/mm and analyzed using a kurtosis diffusion model (apparent diffusion coefficient [ADC0] and kurtosis [K]) for the diffusion component and IVIM model (perfusion fraction [fIVIM] and pseudodiffusion coefficient [D*]) for the perfusion component. Diagnostic performance of diffusion and perfusion parameters was evaluated from receiver operating characteristic analyses. The ADC0 in malignant lesions was significantly lower than that in benign lesions and normal tissue (P < 0.001, P < 0.001), whereas K was significantly higher (P < 0.05, P < 0.001), as well as fIVIM (P < 0.05, P < 0.01). No significant difference was found in D*. The receiver operating characteristic analysis gave high area under the curve values for ADC0, K, and fIVIM for distinguishing malignant from benign lesions (0.99, 0.85, and 0.82, respectively). The ADC0 allowed benign tumors to be identified with 100% negative predictive value and malignant tumors with 100% sensitivity. The malignant/benign diagnosis thresholds were 1.4 × 10 mm/s as well as 0.6 and 7%, respectively, for ADC0, K, and fIVIM. With a proper methodological framework, IVIM MRI can provide valuable information on tissue structure and microvasculature beneficial for the diagnosis of breast cancer lesions.

  11. Coarse-graining Brownian motion: from particles to a discrete diffusion equation.

    PubMed

    de la Torre, J A; Español, Pep

    2011-09-21

    We study the process of coarse-graining in a simple model of diffusion of Brownian particles. At a detailed level of description, the system is governed by a Brownian dynamics of non-interacting particles. The coarse-level is described by discrete concentration variables defined in terms of Delaunay cells. These coarse variables obey a stochastic differential equation that can be understood as a discrete version of a diffusion equation. We study different models for the two basic building blocks of this equation which are the free energy function and the diffusion matrix. The free energy function is shown to be non-additive due to the overlapping of cells in the Delaunay construction. The diffusion matrix is state dependent in principle, but for near-equilibrium situations it is shown that it may be safely evaluated at the equilibrium value of the concentration field.

  12. Intravoxel incoherent motion (IVIM) in diffusion-weighted imaging (DWI) for Hepatocellular carcinoma: correlation with histologic grade

    PubMed Central

    Granata, Vincenza; Fusco, Roberta; Catalano, Orlando; Guarino, Benedetta; Granata, Francesco; Tatangelo, Fabiana; Avallone, Antonio; Piccirillo, Mauro; Palaia, Raffaele; Izzo, Francesco; Petrillo, Antonella

    2016-01-01

    Purpose To assess the correlation between DWI diffusion parameters obtained using Intravoxel Incoherent Motion Method (IVIM) and histological grade of Hepatocellular carcinoma (HCC). Results According to Edmondson-Steiner grade lesions were classified with grade 1 (14), grade 2 (30), grade 3 (18), and grade 4 (0). Apparent Diffusion Coefficient (ADC), perfusion fraction (fp), tissue diffusion coefficient (Dt) median values were statistically different in HCC groups with 1, 2, 3 histological grade (p<0.001). A significant correlation was reported between ADC, fp, Dt and histologic grade respectively of 0.687, 0.737 and 0.674. Receiver operating characteristic (ROC) analysis demonstrated that an ADC of 2.11×10-3 mm2/sec, an fp of 47.33% and an Dt of 0.94×10-3 mm2/sec were the optimal cutoff values to differentiate high histological grade (3) versus low histological grade (1-2), with a sensitivity and specificity for ADC of 100% and 100%, for fp of 100% and 89%, for Dt of 100% and 74%, respectively. Material and Methods A retrospective approved study was performed including 34 patients with 62 HCCs. IVIM was performed to obtain ADC, fp, pseudo-diffusion coefficient (Dp), Dt coefficients. Kruskal Wallis, Spearman Correlation Coefficient, ROC analysis were performed. Conclusions ADC and IVIM-derived fp showed significantly better diagnostic performance in differentiating high-grade from low-grade HCC, and significant correlation was observed between ADC, fp, Dt and histological grade. PMID:27764817

  13. Intramolecular carbonickelation of alkenes

    PubMed Central

    Lhermet, Rudy

    2013-01-01

    Summary The efficiency of the intramolecular carbonickelation of substituted allylic ethers and amines has been studied to evaluate the influence of the groups borne by the double bond on this cyclization. The results show that when this reaction takes place, it affords only the 5-exo-trig cyclization products, viz. dihydrobenzofurans or indoles. Depending on the tethered heteroatom (O or N), the outcome of the cyclization differs. While allylic ethers are relatively poor substrates that undergo a side elimination and need an intracyclic double bond to proceed, allylic amines react well and afford indoline and indole derivatives. Finally, the synthesis of the trinuclear ACE core of a morphine-like skeleton was achieved by using NiBr2bipy catalysis. PMID:23766783

  14. Hepatocellular carcinoma: short-term reproducibility of apparent diffusion coefficient and intravoxel incoherent motion parameters at 3.0T.

    PubMed

    Kakite, Suguru; Dyvorne, Hadrien; Besa, Cecilia; Cooper, Nancy; Facciuto, Marcelo; Donnerhack, Claudia; Taouli, Bachir

    2015-01-01

    To evaluate short-term test-retest and interobserver reproducibility of IVIM (intravoxel incoherent motion) diffusion parameters and ADC (apparent diffusion coefficient) of hepatocellular carcinoma (HCC) and liver parenchyma at 3.0T. In this prospective Institutional Review Board (IRB)-approved study, 11 patients were scanned twice using a free-breathing single-shot echo-planar-imaging, diffusion-weighted imaging (DWI) sequence using 4 b values (b = 0, 50, 500, 1000 s/mm(2)) and IVIM DWI using 16 b values (0-800 s/mm(2)) at 3.0T. IVIM parameters (D: true diffusion coefficient, D*: pseudodiffusion coefficient, PF: perfusion fraction) and ADC (using 4 b and 16 b) were calculated. Short-term test-retest and interobserver reproducibility of IVIM parameters and ADC were assessed by measuring correlation coefficient, coefficient of variation (CV), and Bland-Altman limits of agreements (BA-LA). Fifteen HCCs were assessed in 10 patients. Reproducibility of IVIM metrics in HCC was poor for D* and PF (mean CV 60.6% and 37.3%, BA-LA: -161.6% to 135.3% and -66.2% to 101.0%, for D* and PF, respectively), good for D and ADC (CV 19.7% and <16%, BA-LA -57.4% to 36.3% and -38.2 to 34.1%, for D and ADC, respectively). Interobserver reproducibility was on the same order of test-retest reproducibility except for PF in HCC. Reproducibility of diffusion parameters was better in liver parenchyma compared to HCC. Poor reproducibility of D*/PF and good reproducibility for D/ADC were observed in HCC and liver parenchyma. These findings may have implications for trials using DWI in HCC. © 2014 Wiley Periodicals, Inc.

  15. Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature Factors, Correlated Motions, and Diffuse X-Ray Scattering

    PubMed Central

    Riccardi, Demian; Cui, Qiang; Phillips, George N.

    2010-01-01

    In this study, the variance-covariance matrix of protein motions is used to compare several elastic network models within the theoretical framework of x-ray scattering from crystals. A set of 33 ultra-high resolution structures is used to characterize the average scaling behavior of the vibrational density of states and make comparisons between experimental and theoretical temperature factors. Detailed investigations of the vibrational density of states, correlations, and predicted diffuse x-ray scatter are carried out for crystalline Staphylococcal nuclease; correlations and diffuse x-ray scatter are also compared to predictions from the translation, libration, screw model and a liquid-like dynamics model. We show that elastic network models developed to best predict temperature factors without regard for the crystal environment have relatively strong long-range interactions that yield very short-ranged atom-atom correlations. Further, we find that the low-frequency modes dominate the variance-covariance matrix only for those models with a physically reasonable vibrational density of states, and the fraction of modes required to converge the correlations is higher than that typically used for elastic network model studies. The practical implications are explored using computed diffuse x-ray scatter, which can be measured experimentally. PMID:20959103

  16. Real-Time Correction of Rigid-Body-Motion-Induced Phase Errors for Diffusion-Weighted Steady State Free Precession Imaging

    PubMed Central

    O’Halloran, R; Aksoy, M; Aboussouan, E; Peterson, E; Van, A; Bammer, R

    2014-01-01

    Purpose Diffusion contrast in diffusion-weighted steady state free precession MRI is generated through the constructive addition of signal from many coherence pathways. Motion-induced phase causes destructive interference which results in loss of signal magnitude and diffusion contrast. In this work, a 3D navigator-based real-time correction of the rigid-body-motion-induced phase errors is developed for diffusion-weighted steady state free precession MRI. Methods The efficacy of the real-time prospective correction method in preserving phase coherence of the steady-state is tested in 3D phantom experiments and 3D scans of healthy human subjects. Results In nearly all experiments, the signal magnitude in images obtained with proposed prospective correction was higher than the signal magnitude in images obtained with no correction. In the human subjects the mean magnitude signal in the data was up to 30 percent higher with prospective motion correction than without. Prospective correction never resulted in a decrease in mean signal magnitude in either the data or in the images. Conclusions The proposed prospective motion correction method is shown to preserve the phase coherence of the steady state in diffusion-weighted steady state free precession MRI, thus mitigating signal magnitude losses that would confound the desired diffusion contrast. PMID:24715414

  17. Real-time correction of rigid body motion-induced phase errors for diffusion-weighted steady-state free precession imaging.

    PubMed

    O'Halloran, Rafael; Aksoy, Murat; Aboussouan, Eric; Peterson, Eric; Van, Anh; Bammer, Roland

    2015-02-01

    Diffusion contrast in diffusion-weighted steady-state free precession magnetic resonance imaging (MRI) is generated through the constructive addition of signal from many coherence pathways. Motion-induced phase causes destructive interference which results in loss of signal magnitude and diffusion contrast. In this work, a three-dimensional (3D) navigator-based real-time correction of the rigid body motion-induced phase errors is developed for diffusion-weighted steady-state free precession MRI. The efficacy of the real-time prospective correction method in preserving phase coherence of the steady state is tested in 3D phantom experiments and 3D scans of healthy human subjects. In nearly all experiments, the signal magnitude in images obtained with proposed prospective correction was higher than the signal magnitude in images obtained with no correction. In the human subjects, the mean magnitude signal in the data was up to 30% higher with prospective motion correction than without. Prospective correction never resulted in a decrease in mean signal magnitude in either the data or in the images. The proposed prospective motion correction method is shown to preserve the phase coherence of the steady state in diffusion-weighted steady-state free precession MRI, thus mitigating signal magnitude losses that would confound the desired diffusion contrast. © 2014 Wiley Periodicals, Inc.

  18. Model-based motion correction of reduced field of view diffusion MRI data

    NASA Astrophysics Data System (ADS)

    Hering, Jan; Wolf, Ivo; Meinzer, Hans-Peter; Maier-Hein, Klaus H.

    2014-03-01

    In clinical settings, application of the most recent modelling techniques is usually unfeasible due to the limited acquisition time. Localised acquisitions enclosing only the object of interest by reducing the field-of-view (FOV) counteract the time limitation but pose new challenges to the subsequent processing steps like motion correction. We use datasets from the Human Connectome Project (HCP) to simulate head motion distorted reduced FOV acquisitions and present an evaluation of head motion correction approaches: the commonly used affine regis- tration onto an unweighted reference image guided by the mutual information (MI) metric and a model-based approach, which uses reference images computed from approximated tensor data to improve the performance of the MI metric. While the standard approach using the MI metric yields up to 15% outliers (error>5 mm) and a mean spatial error above 1.5 mm, the model-based approach reduces the number of outliers (1%) and the spatial error significantly (p<0.01). The behavior is also reflected by the visual analysis of the MI metric. The evaluation shows that the MI metric is of very limited use for reduced FOV data post-processing. The model-based approach has proven more suitable in this context.

  19. Wetting Layer Super-Diffusive Motion and QSE Growth in Pb/Si

    NASA Astrophysics Data System (ADS)

    Tringides, M. C.; Hupalo, M.; Man, K. L.; Loy, M. M. T.; Altman, M. S.

    The unusual growth mode of uniform height islands discovered in Pb/Si was related to the electronic energy modulation with island height due to quantum size effects (QSEs). In addition to these energetic reasons provided by QSE, there is also the question of kinetics, i.e., how atoms move at relatively low temperatures (as low as 150 K) to build the islands in the short time of minutes. Controlled experiments with different techniques have shown the intriguing role of the dense wetting layer in transporting mass. STM experiments monitoring how unstable islands transform into stable islands have shown that the wetting layer between the islands moves selectively to the unstable islands, climbs over their sides, forms quickly rings of constant width ˜ 20 nm, and finally it completes the island top, but at a slower rate than the ring completion. This growth is independent of the starting interface, whether it is the amorphous wetting layer on the Si(111) (7 × 7) or the well-ordered Si(111)-Pb α (surd 3× surd 3) surface (except Pb diffusion on the latter interface is faster by a factor of ˜ 5). Real-time low-energy electron microscopy (LEEM) observations of mass transport phenomena have confirmed the fast mobility of the wetting layer in Pb/Si and in addition have revealed some unusual features that are unexpected from classical diffusion behavior. The experiment monitors the refilling of a circular vacant area generated by a laser pulse. The concentration profile does not disperse as in normal diffusion, the refilling speed Δ x/Δ t is constant (instead of Δ x/surd Δ t = constant), and the equilibration time diverges below a critical coverage, θ c, as 1/tau ˜ (θ c - θ)^{-kappa}. The absolute value of the refilling speed 0.05 nm/s at 190 K is orders of magnitude higher than what is expected from Pb diffusion on Pb crystals at higher temperatures. These results are compared with predictions of three candidate models: (i) a conventional diffusion model with a

  20. The Measurement of the Diffusive Motion of Protons in Biological Systems.

    DTIC Science & Technology

    1983-06-02

    the diffusion coefficient being reduced from that of pure water by .20%. The properties of the water in the Artemia cysts differ greatly from those of...of agarose and polyox, and the cysts of the brine shrimp ( Artemia ) gave an affirmative answer to these questions. Our first experiments were on pure...were obtained on the Artemia cysts. This system is an important biological model, and is especially suited for QNS studies, since the hydration of the

  1. Differentiation of high-grade and low-grade diffuse gliomas by intravoxel incoherent motion MR imaging

    PubMed Central

    Togao, Osamu; Hiwatashi, Akio; Yamashita, Koji; Kikuchi, Kazufumi; Mizoguchi, Masahiro; Yoshimoto, Koji; Suzuki, Satoshi O.; Iwaki, Toru; Obara, Makoto; Van Cauteren, Marc; Honda, Hiroshi

    2016-01-01

    Background Our aim was to assess the diagnostic performance of intravoxel incoherent motion (IVIM) MR imaging for differentiating high-grade gliomas (HGGs) from low-grade gliomas (LGGs). Methods Forty-five patients with diffuse glioma (age 50.9 ± 20.4 y; 26 males, 19 females) were assessed with IVIM imaging using 13 b-values (0–1000 s/mm2) at 3T. The perfusion fraction (f), true diffusion coefficient (D), and pseudo-diffusion coefficient (D*) were calculated by fitting the bi-exponential model. The apparent diffusion coefficient (ADC) was obtained with 2 b-values (0 and 1000 s/mm2). Relative cerebral blood volume was measured by the dynamic susceptibility contrast method. Two observers independently measured D, ADC, D*, and f, and these measurements were compared between the LGG group (n = 16) and the HGG group (n = 29). Results Both D (1.26 ± 0.37 mm2/s in LGG, 0.94 ± 0.19 mm2/s in HGG; P < .001) and ADC (1.28 ± 0.35 mm2/s in LGG, 1.03 ± 0.19 mm2/s in HGG; P < .01) were lower in the HGG group. D was lower than ADC in the LGG (P < .05) and HGG groups (P < .0001). D* was not different between the groups. The f-values were significantly larger in HGG (17.5 ± 6.3%) than in LGG (5.8 ± 3.8%; P < .0001) and correlated with relative cerebral blood volume (r = 0.85; P < .0001). Receiver operating characteristic analyses showed areas under curve of 0.95 with f, 0.78 with D, 0.73 with ADC, and 0.60 with D*. Conclusion IVIM imaging is useful in differentiating HGGs from LGGs. PMID:26243792

  2. Chemotherapy response evaluation in a mouse model of gastric cancer using intravoxel incoherent motion diffusion-weighted MRI and histopathology

    PubMed Central

    Cheng, Jin; Wang, Yi; Zhang, Chun-Fang; Wang, He; Wu, Wei-Zhen; Pan, Feng; Hong, Nan; Deng, Jie

    2017-01-01

    AIM To determine the role of intravoxel incoherent motion (IVIM) diffusion-weighted (DW) magnetic resonance imaging (MRI) using a bi-exponential model in chemotherapy response evaluation in a gastric cancer mouse model. METHODS Mice bearing MKN-45 human gastric adenocarcinoma xenografts were divided into four treated groups (TG1, 2, 3 and 4, n = 5 in each group) which received Fluorouracil and Calcium Folinate and a control group (CG, n = 7). DW-MRI scans with 14 b-values (0-1500 s/mm2) were performed before and after treatment on days 3, 7, 14 and 21. Fast diffusion component (presumably pseudo-perfusion) parameters including the fast diffusion coefficient (D*) and fraction volume (fp), slow diffusion coefficient (D) and the conventional apparent diffusion coefficients (ADC) were calculated by fitting the IVIM model to the measured DW signals. The median changes from the baseline to each post-treatment time point for each measurement (ΔADC, ΔD* and Δfp) were calculated. The differences in the median changes between the two groups were compared using the mixed linear regression model by the restricted maximum likelihood method shown as z values. Histopathological analyses including Ki-67, CD31, TUNEL and H&E were conducted in conjunction with the MRI scans. The median percentage changes were compared with the histopathological analyses between the pre- and post-treatment for each measurement. RESULTS Compared with the control group, D* in the treated group decreased significantly (ΔD*treated% = -30%, -34% and -20%, with z = -5.40, -4.18 and -1.95. P = 0.0001, 0.0001 and 0.0244) and fp increased significantly (Δfptreated% = 93%, 113% and 181%, with z = 4.63, 5.52, and 2.12, P = 0.001, 0.0001 and 0.0336) on day 3, 7 and 14, respectively. Increases in ADC in the treated group were higher than those in the control group on days 3 and 14 (z = 2.44 and 2.40, P = 0.0147 and P = 0.0164). CONCLUSION Fast diffusion measurements derived from the bi-exponential IVIM model

  3. Asymptotic analysis of reaction-diffusion-advection problems: Fronts with periodic motion and blow-up

    NASA Astrophysics Data System (ADS)

    Nefedov, Nikolay

    2017-02-01

    This is an extended variant of the paper presented at MURPHYS-HSFS 2016 conference in Barcelona. We discuss further development of the asymptotic method of differential inequalities to investigate existence and stability of sharp internal layers (fronts) for nonlinear singularly perturbed periodic parabolic problems and initial boundary value problems with blow-up of fronts for reaction-diffusion-advection equations. In particular, we consider periodic solutions with internal layer in the case of balanced reaction. For the initial boundary value problems we prove the existence of fronts and give their asymptotic approximation including the new case of blowing-up fronts. This case we illustrate by the generalised Burgers equation.

  4. Fractional Diffusion, Low Exponent Lévy Stable Laws, and 'Slow Motion' Denoising of Helium Ion Microscope Nanoscale Imagery.

    PubMed

    Carasso, Alfred S; Vladár, András E

    2012-01-01

    Helium ion microscopes (HIM) are capable of acquiring images with better than 1 nm resolution, and HIM images are particularly rich in morphological surface details. However, such images are generally quite noisy. A major challenge is to denoise these images while preserving delicate surface information. This paper presents a powerful slow motion denoising technique, based on solving linear fractional diffusion equations forward in time. The method is easily implemented computationally, using fast Fourier transform (FFT) algorithms. When applied to actual HIM images, the method is found to reproduce the essential surface morphology of the sample with high fidelity. In contrast, such highly sophisticated methodologies as Curvelet Transform denoising, and Total Variation denoising using split Bregman iterations, are found to eliminate vital fine scale information, along with the noise. Image Lipschitz exponents are a useful image metrology tool for quantifying the fine structure content in an image. In this paper, this tool is applied to rank order the above three distinct denoising approaches, in terms of their texture preserving properties. In several denoising experiments on actual HIM images, it was found that fractional diffusion smoothing performed noticeably better than split Bregman TV, which in turn, performed slightly better than Curvelet denoising.

  5. Swing motion as a diffusion mechanism of lipid bilayers in a gel phase

    NASA Astrophysics Data System (ADS)

    Oh, Younghoon; Kim, Jeongmin; Yethiraj, Arun; Sung, Bong June

    2016-01-01

    Lipid bilayers are a model system for studying the properties of cell membranes. For lipid bilayers of a single lipid component, there is a phase transition from a fluid phase to a gel phase as the temperature is decreased. The dynamic behavior of lipids in the gel phase is interesting: some models show dynamic heterogeneity with a large disparity in timescales between fast and slow molecules, and a spatial segregation of the slow molecules. In this paper we study the dynamics of coarse-grained models of lipid bilayers using the dry Martini, Lennard-Jones Martini, polarizable Martini, and BMW models. All four models show similar dynamical behaviors in the gel phase although the transition temperature is model-dependent. We find that the primary mode of transport in the gel phase is a hopping of the lipid molecules. Hopping is seen in both the translational and rotational dynamics, which are correlated, i.e., the lipid molecules display a swing-like motion in the gel phase.

  6. Swing motion as a diffusion mechanism of lipid bilayers in a gel phase.

    PubMed

    Oh, Younghoon; Kim, Jeongmin; Yethiraj, Arun; Sung, Bong June

    2016-01-01

    Lipid bilayers are a model system for studying the properties of cell membranes. For lipid bilayers of a single lipid component, there is a phase transition from a fluid phase to a gel phase as the temperature is decreased. The dynamic behavior of lipids in the gel phase is interesting: some models show dynamic heterogeneity with a large disparity in timescales between fast and slow molecules, and a spatial segregation of the slow molecules. In this paper we study the dynamics of coarse-grained models of lipid bilayers using the dry Martini, Lennard-Jones Martini, polarizable Martini, and BMW models. All four models show similar dynamical behaviors in the gel phase although the transition temperature is model-dependent. We find that the primary mode of transport in the gel phase is a hopping of the lipid molecules. Hopping is seen in both the translational and rotational dynamics, which are correlated, i.e., the lipid molecules display a swing-like motion in the gel phase.

  7. From Random Walks to Brownian Motion, from Diffusion to Entropy: Statistical Principles in Introductory Physics

    NASA Astrophysics Data System (ADS)

    Reeves, Mark

    2014-03-01

    Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is dominant contribution of the entropy in driving important biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy) that enable students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce seemingly complex biological processes and structures to be described by tractable models that include deterministic processes and simple probabilistic inference. The students test these models in simulations and in laboratory experiments that are biologically relevant. The students are challenged to bridge the gap between statistical parameterization of their data (mean and standard deviation) and simple model-building by inference. This allows the students to quantitatively describe realistic cellular processes such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront ``random'' forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk

  8. A hydrodynamic/Brownian motion model of thermal diffusion in liquids

    NASA Astrophysics Data System (ADS)

    Bielenberg, James R.; Brenner, Howard

    2005-10-01

    A recently modified formulation of fluid-mechanical transport processes, which has been shown to correctly predict the thermophoretic force on a rigid isolated particle in a single-component fluid continuum (gas or liquid), is combined with steady-state Stokes-Einstein-type sedimentation-equilibrium/Boltzmann distribution-like arguments appropriate to a dilute suspension of such particles, each regarded as Brownian, so as to furnish an elementary hydrodynamic theory for thermal diffusion separation phenomena in dilute binary liquid-phase mixtures (the Ludwig/Soret effect) for the case of a disparate solute/solvent molecular size ratio. The results of the theory are shown to accord well with experiments on polymer solutions in regard to both the magnitude and algebraic sign of the Soret coefficient, as well as with respect to the effects of temperature and mixture composition on this coefficient. An extension (albeit less rigorous) of the preceding theory to the case of nondilute, thermodynamically ideal, binary solutions of miscible liquids of comparable molecular size also yields results in reasonable accord with experiments.

  9. Averaging Horizontal-to-Vertical (H/V) Spectral Ratios of Earthquake Motions for Velocity Inversions Based on Diffuse Field Theory for Plane Waves

    NASA Astrophysics Data System (ADS)

    Matsushima, S.; Sanchez-Sesma, F. J.; Kawase, H.

    2010-12-01

    In this work we explore the application of diffuse field concepts to analyze strong motion records at a site in which site effects can be described using a one dimensional (1D) model. For this case we derived a corollary of Claerbout (1968) result for 1D layered medium. We found that the imaginary part of Green function at the free surface is proportional to the square of the absolute value of the corresponding transfer function for a plane, vertically incident wave with unit amplitude. Average strong ground motion in a "sufficiently" flat layered site will be statistically equivalent. We may conceive the illumination as produced by incident plane waves. They represent the most important part of earthquake ground motions. Their associated motions, being multiple scattered, are formed of waves that sample significant portions of the considered area. This is a distinctive feature of earthquake motions, for which the excited domain is large, basically from the source to the receiver. For a set of incoming plane waves (of P, SV, and SH types) with varying azimuths and incidence angles we assume that the ground motion will be spatially homogeneous in a statistical sense. In other words, the average of normalized ground motion spectral densities will depend only on depth. Therefore, we can apply a 1D description of wave propagation for a diffuse (average) field of ground motions. To prove the above hypothesis for H/V ratios of earthquake ground motions, we first show a comparison of averaged synthetics of 1D underground structures with a corresponding simple theoretical prediction from 1D transfer functions. After summing up a few hundreds of synthetics with different angles of incidences, azimuths, and polarizations, we can obtain identical H/V ratios that the simple theory of diffuse field predicts. Then we show several examples of H/V ratios for actual seismic motions observed in Japan. We found that the earthquake H/V ratios are quite stable (and converging rapidly

  10. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Zhong, Cheng; Douglas, Jack F.; Wang, Xiaodong; Cao, Qingping; Zhang, Dongxian; Jiang, Jian-Zhong

    2015-04-01

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

  11. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

    SciTech Connect

    Zhang, Hao; Zhong, Cheng; Wang, Xiaodong; Cao, Qingping; Jiang, Jian-Zhong E-mail: jack.douglas@nist.gov; Douglas, Jack F. E-mail: jack.douglas@nist.gov; Zhang, Dongxian

    2015-04-28

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by “dynamic heterogeneity” in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔG{sub a} with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τ{sub α} can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract “cooperatively rearranging regions” of AG. We also find coexisting clusters of relatively “immobile” atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of “mobile” atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized (“immobile”) and wandering (“mobile”) particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

  12. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys.

    PubMed

    Zhang, Hao; Zhong, Cheng; Douglas, Jack F; Wang, Xiaodong; Cao, Qingping; Zhang, Dongxian; Jiang, Jian-Zhong

    2015-04-28

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

  13. A theoretical study of rotational diffusion models for rod-shaped viruses. The influence of motion on 31P nuclear magnetic resonance lineshapes and transversal relaxation.

    PubMed Central

    Magusin, P C; Hemminga, M A

    1993-01-01

    Information about the interaction between nucleic acids and coat proteins in intact virus particles may be obtained by studying the restricted backbone dynamics of the incapsulated nucleic acids using 31P nuclear magnetic resonance (NMR) spectroscopy. In this article, simulations are carried out to investigate how reorientation of a rod-shaped virus particle as a whole and isolated nucleic acid motions within the virion influence the 31P NMR lineshape and transversal relaxation dominated by the phosphorus chemical shift anisotropy. Two opposite cases are considered on a theoretical level. First, isotropic rotational diffusion is used as a model for mobile nucleic acids that are loosely or partially bound to the protein coat. The effect of this type of diffusion on lineshape and transversal relaxation is calculated by solving the stochastic Liouville equation by an expansion in spherical functions. Next, uniaxial rotational diffusion is assumed to represent the mobility of phosphorus in a virion that rotates as a rigid rod about its length axis. This type of diffusion is approximated by an exchange process among discrete sites. As turns out from these simulations, the amplitude and the frequency of the motion can only be unequivocally determined from experimental data by a combined analysis of the lineshape and the transversal relaxation. In the fast motional region both the isotropic and the uniaxial diffusion model predict the same transversal relaxation as the Redfield theory. For very slow motion, transversal relaxation resembles the nonexponential relaxation as observed for water molecules undergoing translational diffusion in a magnetic field gradient. In this frequency region T2e is inversely proportional to the cube root of the diffusion coefficient. In addition to the isotropic and uniaxial diffusion models, a third model is presented, in which fast restricted nucleic acid backbone motions dominating the lineshape are superimposed on a slow rotation of the

  14. A comparative simulation study of bayesian fitting approaches to intravoxel incoherent motion modeling in diffusion-weighted MRI.

    PubMed

    While, Peter T

    2017-03-31

    To assess the performance of various least squares and Bayesian modeling approaches to parameter estimation in intravoxel incoherent motion (IVIM) modeling of diffusion-weighted MRI data. Simulated tissue models of different type (breast/liver) and morphology (discrete/continuous) were used to generate noisy data according to the IVIM model at several signal-to-noise ratios. IVIM parameter maps were generated using six different approaches, including full nonlinear least squares (LSQ), segmented least squares (SEG), Bayesian modeling with a Gaussian shrinkage prior (BSP) and Bayesian modeling with a spatial homogeneity prior (FBM), plus two modified approaches. Estimators were compared by calculating the median absolute percentage error and deviation, and median percentage bias. The Bayesian modeling approaches consistently outperformed the least squares approaches, with lower relative error and deviation, and provided cleaner parameter maps with reduced erroneous heterogeneity. However, a weakness of the Bayesian approaches was exposed, whereby certain tissue features disappeared completely in regions of high parameter uncertainty. Lower error and deviation were generally afforded by FBM compared with BSP, at the cost of higher bias. Bayesian modeling is capable of producing more visually pleasing IVIM parameter maps than least squares approaches, but their potential to mask certain tissue features demands caution during implementation. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  15. Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics [The Day the Water Stood Still: Intramolecular Hydrogen Bonding to Restrict Gd-Aqua Ligand Dynamics

    DOE PAGES

    Boros, Eszter; Srinivas, Raja; Kim, Hee -Kyung; ...

    2017-04-11

    Aqua ligands can undergo rapid internal rotation about the M-O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivitymore » were systematically ruled out. Finally, intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.« less

  16. Real-Time Measurement and Correction of Both B0 Changes and Subject Motion in Diffusion Tensor Imaging Using a Double Volumetric Navigated (DvNav) Sequence

    PubMed Central

    Alhamud, A.; Taylor, Paul A.; van der Kouwe, A.J.W.; Meintjes, E. M.

    2015-01-01

    Diffusion tensor imaging (DTI) requires a set of diffusion weighted measurements in order to acquire enough information to characterize local structure. The MRI scanner automatically performs a shimming process by acquiring a field map before the start of a DTI scan. Changes in B0, which can occur throughout the DTI acquisition due to several factors (including heating of the iron shim coils or subject motion), cause significant signal distortions that result in warped diffusion tensor (DT) parameter estimates. In this work we introduce a novel technique to simultaneously measure, report and correct in real time subject motion and changes in B0 field homogeneity, both in and through the imaging plane. This is achieved using double volumetric navigators (DvNav), i.e. a pair of 3D EPI acquisitions, interleaved with the DTI pulse sequence. Changes in the B0 field are evaluated in terms of zero-order (frequency) and first-order (linear gradients) shim. The ability of the DvNav to accurately estimate the shim parameters was first validated in a water phantom. Two healthy subjects were scanned both in the presence and absence of motion using standard, motion corrected (single navigator, vNav), and DvNav DTI sequences. The difference in performance between the proposed 3D EPI field maps and the standard 3D gradient echo field maps of the MRI scanner was also evaluated in a phantom and two healthy subjects. The DvNav sequence was shown to accurately measure and correct changes in B0 following manual adjustments of the scanner’s central frequency and the linear shim gradients. Compared to other methods, the DvNav produced DTI results that showed greater spatial overlap with anatomical references, particularly in scans with subject motion. This is largely due to the ability of the DvNav system to correct shim changes and subject motion between each volume acquisition, thus reducing shear distortion. PMID:26584865

  17. Investigating the effect of poly-l-lactic acid nanoparticles carrying hypericin on the flow-biased diffusive motion of HeLa cell organelles.

    PubMed

    Penjweini, Rozhin; Deville, Sarah; Haji Maghsoudi, Omid; Notelaers, Kristof; Ethirajan, Anitha; Ameloot, Marcel

    2017-07-19

    In this study, we investigate in human cervical epithelial HeLa cells the intracellular dynamics and the mutual interaction with the organelles of the poly-l-lactic acid nanoparticles (PLLA NPs) carrying the naturally occurring hydrophobic photosensitizer hypericin. Temporal and spatiotemporal image correlation spectroscopy was used for the assessment of the intracellular diffusion and directed motion of the nanocarriers by tracking the hypericin fluorescence. Using image cross-correlation spectroscopy and specific fluorescent labelling of endosomes, lysosomes and mitochondria, the NPs dynamics in association with the cell organelles was studied. Static colocalization experiments were interpreted according to the Manders' overlap coefficient. Nanoparticles associate with a small fraction of the whole-organelle population. The organelles moving with NPs exhibit higher directed motion compared to those moving without them. The rate of the directed motion drops substantially after the application of nocodazole. The random component of the organelle motions is not influenced by the NPs. Image correlation and cross-correlation spectroscopy are most appropriate to unravel the motion of the PLLA nanocarrier and to demonstrate that the rate of the directed motion of organelles is influenced by their interaction with the nanocarriers. Not all PLLA-hypericin NPs are associated with organelles. © 2017 Royal Pharmaceutical Society.

  18. Plate motion

    SciTech Connect

    Gordon, R.G. )

    1991-01-01

    The motion of tectonic plates on the earth is characterized in a critical review of U.S. research from the period 1987-1990. Topics addressed include the NUVEL-1 global model of current plate motions, diffuse plate boundaries and the oceanic lithosphere, the relation between plate motions and distributed deformations, accelerations and the steadiness of plate motions, the distribution of current Pacific-North America motion across western North America and its margin, plate reconstructions and their uncertainties, hotspots, and plate dynamics. A comprehensive bibliography is provided. 126 refs.

  19. Intravoxel Incoherent Motion MR Imaging in the Head and Neck: Correlation with Dynamic Contrast-Enhanced MR Imaging and Diffusion-Weighted Imaging.

    PubMed

    Xu, Xiao Quan; Choi, Young Jun; Sung, Yu Sub; Yoon, Ra Gyoung; Jang, Seung Won; Park, Ji Eun; Heo, Young Jin; Baek, Jung Hwan; Lee, Jeong Hyun

    2016-01-01

    To investigate the correlation between perfusion- and diffusion-related parameters from intravoxel incoherent motion (IVIM) and those from dynamic contrast-enhanced MR imaging (DCE-MRI) and diffusion-weighted imaging in tumors and normal muscles of the head and neck. We retrospectively enrolled 20 consecutive patients with head and neck tumors with MR imaging performed using a 3T MR scanner. Tissue diffusivity (D), pseudo-diffusion coefficient (D(*)), and perfusion fraction (f) were derived from bi-exponential fitting of IVIM data obtained with 14 different b-values in three orthogonal directions. We investigated the correlation between D, f, and D(*) and model-free parameters from the DCE-MRI (wash-in, Tmax, Emax, initial AUC60, whole AUC) and the apparent diffusion coefficient (ADC) value in the tumor and normal masseter muscle using a whole volume-of-interest approach. Pearson's correlation test was used for statistical analysis. No correlation was found between f or D(*) and any of the parameters from the DCE-MRI in all patients or in patients with squamous cell carcinoma (p > 0.05). The ADC was significantly correlated with D values in the tumors (p < 0.001, r = 0.980) and muscles (p = 0.013, r = 0.542), despite its significantly higher value than D. The difference between ADC and D showed significant correlation with f values in the tumors (p = 0.017, r = 0.528) and muscles (p = 0.003, r = 0.630), but no correlation with D(*) (p > 0.05, respectively). Intravoxel incoherent motion shows no significant correlation with model-free perfusion parameters derived from the DCE-MRI but is feasible for the analysis of diffusivity in both tumors and normal muscles of the head and neck.

  20. Intravoxel Incoherent Motion MR Imaging in the Head and Neck: Correlation with Dynamic Contrast-Enhanced MR Imaging and Diffusion-Weighted Imaging

    PubMed Central

    Xu, Xiao Quan; Choi, Young Jun; Sung, Yu Sub; Yoon, Ra Gyoung; Jang, Seung Won; Park, Ji Eun; Heo, Young Jin; Baek, Jung Hwan

    2016-01-01

    Objective To investigate the correlation between perfusion- and diffusion-related parameters from intravoxel incoherent motion (IVIM) and those from dynamic contrast-enhanced MR imaging (DCE-MRI) and diffusion-weighted imaging in tumors and normal muscles of the head and neck. Materials and Methods We retrospectively enrolled 20 consecutive patients with head and neck tumors with MR imaging performed using a 3T MR scanner. Tissue diffusivity (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f) were derived from bi-exponential fitting of IVIM data obtained with 14 different b-values in three orthogonal directions. We investigated the correlation between D, f, and D* and model-free parameters from the DCE-MRI (wash-in, Tmax, Emax, initial AUC60, whole AUC) and the apparent diffusion coefficient (ADC) value in the tumor and normal masseter muscle using a whole volume-of-interest approach. Pearson's correlation test was used for statistical analysis. Results No correlation was found between f or D* and any of the parameters from the DCE-MRI in all patients or in patients with squamous cell carcinoma (p > 0.05). The ADC was significantly correlated with D values in the tumors (p < 0.001, r = 0.980) and muscles (p = 0.013, r = 0.542), despite its significantly higher value than D. The difference between ADC and D showed significant correlation with f values in the tumors (p = 0.017, r = 0.528) and muscles (p = 0.003, r = 0.630), but no correlation with D* (p > 0.05, respectively). Conclusion Intravoxel incoherent motion shows no significant correlation with model-free perfusion parameters derived from the DCE-MRI but is feasible for the analysis of diffusivity in both tumors and normal muscles of the head and neck. PMID:27587952

  1. Mathematical Development and Computational Analysis of Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) Based on Bloch Nuclear Magnetic Resonance (NMR) Diffusion Model for Myocardial Motion.

    PubMed

    Dada, Michael O; Jayeoba, Babatunde; Awojoyogbe, Bamidele O; Uno, Uno E; Awe, Oluseyi E

    2017-09-13

    Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) is a tagged image analysis method that can measure myocardial motion and strain in near real-time and is considered a potential candidate to make magnetic resonance tagging clinically viable. However, analytical expressions of radially tagged transverse magnetization in polar coordinates (which is required to appropriately describe the shape of the heart) have not been explored because the physics required to directly connect myocardial deformation of tagged Nuclear Magnetic Resonance (NMR) transverse magnetization in polar geometry and the appropriate harmonic phase parameters are not yet available. The analytical solution of Bloch NMR diffusion equation in spherical geometry with appropriate spherical wave tagging function is important for proper analysis and monitoring of heart systolic and diastolic deformation with relevant boundary conditions. In this study, we applied Harmonic Phase MRI method to compute the difference between tagged and untagged NMR transverse magnetization based on the Bloch NMR diffusion equation and obtained radial wave tagging function for analysis of myocardial motion. The analytical solution of the Bloch NMR equations and the computational simulation of myocardial motion as developed in this study are intended to significantly improve healthcare for accurate diagnosis, prognosis and treatment of cardiovascular related deceases at the lowest cost because MRI scan is still one of the most expensive anywhere. The analysis is fundamental and significant because all Magnetic Resonance Imaging techniques are based on the Bloch NMR flow equations.

  2. Brownian motion

    NASA Astrophysics Data System (ADS)

    Lavenda, B. H.

    1985-02-01

    Brownian motion, the doubly random motion of small particles suspended in a liquid due to molecular collisions, and its implications and applications in the history of modern science are discussed. Topics examined include probabilistic phenomena, the kinetic theory of gases, Einstein's atomic theory of Brownian motion, particle displacement, diffusion measurements, the determination of the mass of the atom and of Avogadro's number, the statistical mechanics of thermodynamics, nonequilibrium systems, Langevin's equation of motion, time-reversed evolution, mathematical analogies, and applications in economics and radio navigation. Diagrams and drawings are provided.

  3. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    DOE PAGES

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  4. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    SciTech Connect

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  5. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

    PubMed

    Van Benschoten, Andrew H; Afonine, Pavel V; Terwilliger, Thomas C; Wall, Michael E; Jackson, Colin J; Sauter, Nicholas K; Adams, Paul D; Urzhumtsev, Alexandre; Fraser, James S

    2015-08-01

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation-libration-screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  6. WE-G-18C-09: Separating Perfusion and Diffusion Components From Diffusion Weighted MRI of Rectum Tumors Based On Intravoxel Incoherent Motion (IVIM) Analysis

    SciTech Connect

    Tyagi, N; Wengler, K; Mazaheri, Y; Hunt, M; Deasy, J; Gollub, M

    2014-06-15

    Purpose: Pseudodiffusion arises from the microcirculation of blood in the randomly oriented capillary network and contributes to the signal decay acquired using a multi-b value diffusion weighted (DW)-MRI sequence. This effect is more significant at low b-values and should be properly accounted for in apparent diffusion coefficient (ADC) calculations. The purpose of this study was to separate perfusion and diffusion component based on a biexponential and a segmented monoexponential model using IVIM analysis Methods. The signal attenuation is modeled as S(b) = S0[(1−f)exp(−bD) + fexp(−bD*)]. Fitting the biexponetial decay leads to the quantification of D, the true diffusion coefficient, D*, the pseudodiffusion coefficient, and f, the perfusion fraction. A nonlinear least squares fit and two segmented monoexponential models were used to derive the values for D, D*,‘and f. In the segmented approach b = 200 s/mm{sup 2} was used as the cut-off value for calculation of D. DW-MRI's of a rectum cancer patient were acquired before chemotherapy, before radiation therapy (RT), and 4 weeks into RT and were investigated as an example case. Results: Mean ADC for the tumor drawn on the DWI cases was 0.93, 1.0 and 1.13 10{sup −3}×mm{sup 2}/s before chemotherapy, before RT and 4 weeks into RT. The mean (D.10{sup −3} × mm{sup 2}/s, D* 10{sup −3} × mm{sup 2}/s, and f %) based on biexponential fit was (0.67, 18.6, and 27.2%), (0.72, 17.7, and 28.9%) and (0.83,15.1, and 30.7%) at these time points. The mean (D, D* f) based on segmented fit was (0.72, 10.5, and 12.1%), (0.72, 8.2, and 17.4%) and (.82, 8.1, 16.5%) Conclusion: ADC values are typically higher than true diffusion coefficients. For tumors with significant perfusion effect, ADC should be analyzed at higher b-values or separated from the perfusion component. Biexponential fit overestimates the perfusion fraction because of increased sensitivity to noise at low b-values.

  7. Coherent-state path integral versus coarse-grained effective stochastic equation of motion: From reaction diffusion to stochastic sandpiles.

    PubMed

    Wiese, Kay Jörg

    2016-04-01

    We derive and study two different formalisms used for nonequilibrium processes: the coherent-state path integral, and an effective, coarse-grained stochastic equation of motion. We first study the coherent-state path integral and the corresponding field theory, using the annihilation process A+A→A as an example. The field theory contains counterintuitive quartic vertices. We show how they can be interpreted in terms of a first-passage problem. Reformulating the coherent-state path integral as a stochastic equation of motion, the noise generically becomes imaginary. This renders it not only difficult to interpret, but leads to convergence problems at finite times. We then show how alternatively an effective coarse-grained stochastic equation of motion with real noise can be constructed. The procedure is similar in spirit to the derivation of the mean-field approximation for the Ising model, and the ensuing construction of its effective field theory. We finally apply our findings to stochastic Manna sandpiles. We show that the coherent-state path integral is inappropriate, or at least inconvenient. As an alternative, we derive and solve its mean-field approximation, which we then use to construct a coarse-grained stochastic equation of motion with real noise.

  8. POCS-enhanced inherent correction of motion-induced phase errors (POCS-ICE) for high-resolution multishot diffusion MRI.

    PubMed

    Guo, Hua; Ma, Xiaodong; Zhang, Zhe; Zhang, Bida; Yuan, Chun; Huang, Feng

    2016-01-01

    For multishot diffusion weighted imaging (DWI), one of the challenges is to remove phase variations induced by physiological motion among different shots. In this study, a new method is proposed to iteratively solve the phase errors and DWI images simultaneously, for navigator-free acquisitions. Instead of solving phase errors and the image sequentially in the two-step parallel imaging, the proposed method, named POCS-enhanced Inherent Correction of motion-induced phase Errors (POCS-ICE), treats both the phase and DWI image as unknowns and solves them simultaneously. Multishot DWI with constant density spiral trajectory served as a specific example. Simulation and in vivo experiments were performed to evaluate the proposed method. POCS-ICE shows improved image quality in terms of higher SNR and fewer artifacts than the compared method, SENSE+CG. The improvement becomes more conspicuous as the number of shots increases. The convergence behavior of POCS-ICE was also shown to be more stable. POCS-ICE can inherently and reliably correct motion-induced phase errors in navigator-free multishot DWI, and it is easier to determine the stopping criterion without manual interventions. The improved spatial resolution and image resolvability are beneficial to study of brain microstructures and physiological features for neuroscience. © 2015 Wiley Periodicals, Inc.

  9. Quantification and analysis of intramolecular interactions.

    PubMed

    Gonthier, Jérôme F; Corminboeuf, Clémence

    2014-01-01

    Non-covalent interactions play a prominent role in chemistry and biology. While a myriad of theoretical methods have been devised to quantify and analyze intermolecular interactions, the theoretical toolbox for the intramolecular analogues is much scarcer. Yet interactions within molecules govern fundamental phenomena as illustrated by the energetic differences between structural isomers. Their accurate quantification is of utmost importance. This paper gives an overview of the most common approaches able to probe intramolecular interactions and stresses both their characteristics and limitations. We finally introduce our recent theoretical approach, which represents the first step towards the development of an intramolecular version of Symmetry-Adapted Perturbation Theory (SAPT).

  10. Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion.

    PubMed

    Malyarenko, Dariya I; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K; Ross, Brian D; Chenevert, Thomas L

    2015-12-01

    Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b-maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction.

  11. A new extended diffusion model for rotational motion of symmetric-top molecules in the liquid phase

    NASA Astrophysics Data System (ADS)

    Lascombe, J.; Besnard, M.; Maraval, P.

    1982-11-01

    In this paper, we present first a model called partially relaxed rotation model (PRR), to treat the reorientation motion of a symmetric top which rotates freely around its molecular axis with a tumbling motion relaxed according to a characteristic time τ 1. We show that this model can easily be extended to develop a 2τ model where both tumbling and spinning motion around the molecular axis are relaxed with a second characteristic time τ 2. As limiting cases one can obtain from the 2τ model, the Gordon-McClung and PRR models. Next, we illustrate the PPR and 2τ models by calculating Raman and infrared rotational spectral densities of liquid cyclopropane at room temperature. We also discuss in the PRR model the influence of the characteristic relaxation time τ 1, on the Raman rotational profile Î21( overlineν) Finally, we emphasize on the example of room-temperature liquid cyclopropane, the advantage of the PRR model to treat a E″ degenerated Raman profile with negligible Coriolis vibrational-rotational interaction. bl

  12. Relationship between diffusion parameters derived from intravoxel incoherent motion MRI and perfusion measured by dynamic contrast-enhanced MRI of soft tissue tumors.

    PubMed

    Marzi, Simona; Stefanetti, Linda; Sperati, Francesca; Anelli, Vincenzo

    2016-01-01

    Our aim was to evaluate the link between diffusion parameters measured by intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) and the perfusion metrics obtained with dynamic contrast-enhanced (DCE) MRI in soft tissue tumors (STTs). Twenty-eight patients affected by histopathologically confirmed STT were included in a prospective study. All patients underwent both DCE MRI and IVIM DWI. The perfusion fraction f, diffusion coefficient D and perfusion-related diffusion coefficient D* were estimated using a bi-exponential function to fit the DWI data. DCE MRI was acquired with a temporal resolution of 3-5 s. Maps of the initial area under the gadolinium concentration curve (IAUGC), time to peak (TTP) and maximum slope of increase (MSI) were derived using commercial software. The relationships between the DCE MRI and IVIM DWI measurements were assessed by Spearman's test. To exclude false positive results under multiple testing, the false discovery rate (FDR) procedure was applied. The Mann-Whitney test was used to evaluate the differences between all variables in patients with non-myxoid and myxoid STT. No significant relationship was found between IVIM parameters and any DCE MRI parameters. Higher f and D*f values were found in non-myxoid tumors compared with myxoid tumors (p = 0.004 and p = 0.003, respectively). MSI was significantly higher in non-myxoid tumors than in myxoid tumors (p = 0.029). From the visual assessments of single clinical cases, both f and D*f maps were in satisfactory agreement with DCE maps in the extreme cases of an avascular mass and a highly vascularized mass, whereas, for tumors with slight vascularity or with a highly heterogeneous perfusion pattern, this association was not straightforward. Although IVIM DWI was demonstrated to be feasible in STT, our data did not support evident relationships between perfusion-related IVIM parameters and perfusion measured by DCE MRI.

  13. Intravoxel incoherent motion model–based analysis of diffusion-weighted magnetic resonance imaging with 3 b-values for response assessment in locoregional therapy of hepatocellular carcinoma

    PubMed Central

    Mürtz, Petra; Penner, Arndt-Hendrik; Pfeiffer, Anne-Kristina; Sprinkart, Alois M; Pieper, Claus C; König, Roy; Block, Wolfgang; Schild, Hans H; Willinek, Winfried A; Kukuk, Guido M

    2016-01-01

    Purpose The aim of this study was to evaluate an intravoxel incoherent motion (IVIM) model–based analysis of diffusion-weighted imaging (DWI) for assessing the response of hepatocellular carcinoma (HCC) to locoregional therapy. Patients and methods Respiratory-gated DWI (b=0, 50, and 800 s/mm2) was retrospectively analyzed in 25 patients who underwent magnetic resonance imaging at 1.5 T before and 6 weeks following the first cycle of transarterial chemoembolization therapy, transarterial ethanol-lipiodol embolization therapy, and transarterial radioembolization therapy. In addition to the determination of apparent diffusion coefficient, ADC(0,800), an estimation of the diffusion coefficient, D′, and the perfusion fraction, f′, was performed by using a simplified IVIM approach. Parameters were analyzed voxel-wise. Tumor response was assessed in a central slice by using a region of interest (ROI) covering the whole tumor. HCCs were categorized into two groups, responders and nonresponders, according to tumor size changes on first and second follow ups (if available) and changes of contrast-enhanced region on the first follow up. Results In total, 31 HCCs were analyzed: 17 lesions were assigned to responders and 14 were to nonresponders. In responders, ADC(0,800) and D′ were increased after therapy by ~30% (P=0.00004) and ~42% (P=0.00001), respectively, whereas f′ was decreased by ~37% (P=0.00094). No significant changes were found in nonresponders. Responders and nonresponders were better differentiated by changes in D′ than by changes in ADC(0,800) (area under the curve =0.878 vs 0.819 or 0.714, respectively). Conclusion In patients with HCCs undergoing embolization therapy, diffusion changes were better reflected by D′ than by conventional ADC(0,800), which is influenced by counteracting perfusion changes as assessed by f′. PMID:27799790

  14. Diffusion parameter mapping with the combined intravoxel incoherent motion and kurtosis model using artificial neural networks at 3 T.

    PubMed

    Bertleff, Marco; Domsch, Sebastian; Weingärtner, Sebastian; Zapp, Jascha; O'Brien, Kieran; Barth, Markus; Schad, Lothar R

    2017-09-28

    Artificial neural networks (ANNs) were used for voxel-wise parameter estimation with the combined intravoxel incoherent motion (IVIM) and kurtosis model facilitating robust diffusion parameter mapping in the human brain. The proposed ANN approach was compared with conventional least-squares regression (LSR) and state-of-the-art multi-step fitting (LSR-MS) in Monte-Carlo simulations and in vivo in terms of estimation accuracy and precision, number of outliers and sensitivity in the distinction between grey (GM) and white (WM) matter. Both the proposed ANN approach and LSR-MS yielded visually increased parameter map quality. Estimations of all parameters (perfusion fraction f, diffusion coefficient D, pseudo-diffusion coefficient D*, kurtosis K) were in good agreement with the literature using ANN, whereas LSR-MS resulted in D* overestimation and LSR yielded increased values for f and D*, as well as decreased values for K. Using ANN, outliers were reduced for the parameters f (ANN, 1%; LSR-MS, 19%; LSR, 8%), D* (ANN, 21%; LSR-MS, 25%; LSR, 23%) and K (ANN, 0%; LSR-MS, 0%; LSR, 15%). Moreover, ANN enabled significant distinction between GM and WM based on all parameters, whereas LSR facilitated this distinction only based on D and LSR-MS on f, D and K. Overall, the proposed ANN approach was found to be superior to conventional LSR, posing a powerful alternative to the state-of-the-art method LSR-MS with several advantages in the estimation of IVIM-kurtosis parameters, which might facilitate increased applicability of enhanced diffusion models at clinical scan times. Copyright © 2017 John Wiley & Sons, Ltd.

  15. Translational and Rotational Diffusion of Two Differently Charged Solutes in Ethylammonium Nitrate-Methanol Mixture: Does the Nanostructure of the Amphiphiles Influence the Motion of the Solute?

    PubMed

    Kundu, Niloy; Roy, Arpita; Dutta, Rupam; Sarkar, Nilmoni

    2016-06-23

    In this Article, we have investigated the translational and rotational diffusion of two structurally similar but differently charged solutes (rhodamine 6G perchlorate and fluorescein sodium salt) in ethylammonium nitrate (EAN)-methanol (CH3OH) mixture to understand the effect of added ionic liquid on the motion of the solutes. EAN and CH3OH both are amphiphilic molecules and characterized by an extended hydrogen bonding network. Recently, Russina et al. found that a wide distribution of clusters exist in the CH3OH rich region (0.10 ≤ χEAN ≤ 0.15) and EAN molecules preserve their bulk-sponge-like morphology (Russina, O.; Sferrazza, A.; Caminiti, R.; Triolo, A. J. Phys. Chem. Lett. 2014, 5, 1738-1742). The effect of this microheterogeneous mixture on the solute's motion shows some interesting results compared to other PIL (protic ionic liquid)-cosolvent mixtures. Analysis of the time-resolved anisotropy data with the aid of Stokes-Einstein-Debye (SED) hydrodynamic theory predicts that the reorientation time of both of the solutes appears close to the stick hydrodynamic line in the methanol rich region. The hydrogen bond accepting solutes experience specific interaction with CH3OH, and with increasing concentration of EAN, the specific interaction between the solute and solvent molecules is decreased while the decrease is more prominent in the low mole fraction of EAN due to the large size of cluster formation. The temperature dependent anisotropy measurements show that the hydrogen bonding interaction between EAN and CH3OH is increased with increasing temperature. Moreover, fluorescence correlation spectroscopy (FCS) shows the dynamic heterogeneity of the mixture which is due to the segregation of the alkyl chain of the PIL. Formation of a large cluster at a low mole fraction of IL (0.10 ≤ χEAN ≤ 0.15) can be proved by the insensitivity of the translational diffusion and rotational activation energy of the solutes to the concentration of EAN. Thus, the

  16. Visual information and expert's idea in Hurst index estimation of the fractional Brownian motion using a diffusion type approximation.

    PubMed

    Taheriyoun, Ali R; Moghimbeygi, Meisam

    2017-02-14

    An approximation of the fractional Brownian motion based on the Ornstein-Uhlenbeck process is used to obtain an asymptotic likelihood function. Two estimators of the Hurst index are then presented in the likelihood approach. The first estimator is produced according to the observed values of the sample path; while the second one employs the likelihood function of the incremental process. We also employ visual roughness of realization to restrict the parameter space and to obtain prior information in Bayesian approach. The methods are then compared with three contemporary estimators and an experimental data set is studied.

  17. Experimental verification of near-wall hindered diffusion for the Brownian motion of nanoparticles using evanescent wave microscopy

    NASA Astrophysics Data System (ADS)

    Banerjee, Arindam; Kihm, Kenneth D.

    2005-10-01

    A total internal reflection fluorescence microscopy technique coupled with three-dimensional tracking of nanoparticles is used to experimentally verify the theory on near-wall hindered Brownian motion [Goldman , Chem. Eng. Sci. 22, 637 (1967); Brenner, Chem. Eng. Sci. 16, 242 (1967)] very close to the solid surface (within ˜1μm ). The measured mean square displacements (MSDs) in the lateral x-y directions show good agreement with the theory for all tested nanoparticles of radii 50, 100, 250, and 500 nm. However, the measured MSDs in the z direction deviate substantially from the theory particularly for the case of smaller particles of 50 and 100 nm radius. Since the theory considers only the hydrodynamic interaction of moving particles with a stationary solid wall, additionally possible interaction forces like gravitational forces, van der Waals forces, and electro-osmotic forces have been examined to delineate the physical reasons for the discrepancy.

  18. Intravoxel incoherent motion diffusion-weighted imaging in the liver: comparison of mono-, bi- and tri-exponential modelling at 3.0-T.

    PubMed

    Cercueil, Jean-Pierre; Petit, Jean-Michel; Nougaret, Stéphanie; Soyer, Philippe; Fohlen, Audrey; Pierredon-Foulongne, Marie-Ange; Schembri, Valentina; Delhom, Elisabeth; Schmidt, Sabine; Denys, Alban; Aho, Serge; Guiu, Boris

    2015-06-01

    To determine whether a mono-, bi- or tri-exponential model best fits the intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) signal of normal livers. The pilot and validation studies were conducted in 38 and 36 patients with normal livers, respectively. The DWI sequence was performed using single-shot echoplanar imaging with 11 (pilot study) and 16 (validation study) b values. In each study, data from all patients were used to model the IVIM signal of normal liver. Diffusion coefficients (Di ± standard deviations) and their fractions (fi ± standard deviations) were determined from each model. The models were compared using the extra sum-of-squares test and information criteria. The tri-exponential model provided a better fit than both the bi- and mono-exponential models. The tri-exponential IVIM model determined three diffusion compartments: a slow (D1 = 1.35 ± 0.03 × 10(-3) mm(2)/s; f1 = 72.7 ± 0.9 %), a fast (D2 = 26.50 ± 2.49 × 10(-3) mm(2)/s; f2 = 13.7 ± 0.6 %) and a very fast (D3 = 404.00 ± 43.7 × 10(-3) mm(2)/s; f3 = 13.5 ± 0.8 %) diffusion compartment [results from the validation study]. The very fast compartment contributed to the IVIM signal only for b values ≤15 s/mm(2) CONCLUSION: The tri-exponential model provided the best fit for IVIM signal decay in the liver over the 0-800 s/mm(2) range. In IVIM analysis of normal liver, a third very fast (pseudo)diffusion component might be relevant. • For normal liver, tri-exponential IVIM model might be superior to bi-exponential • A very fast compartment (D = 404.00 ± 43.7 × 10 (-3) mm (2) /s; f = 13.5 ± 0.8 %) is determined from the tri-exponential model • The compartment contributes to the IVIM signal only for b ≤ 15 s/mm(2).

  19. Intravoxel incoherent motion diffusion-weighted MRI at 3.0 T differentiates malignant breast lesions from benign lesions and breast parenchyma.

    PubMed

    Bokacheva, Louisa; Kaplan, Jennifer B; Giri, Dilip D; Patil, Sujata; Gnanasigamani, Merlin; Nyman, C Gregory; Deasy, Joseph O; Morris, Elizabeth A; Thakur, Sunitha B

    2014-10-01

    To study the differentiation of malignant breast lesions from benign lesions and fibroglandular tissue (FGT) using apparent diffusion coefficient (ADC) and intravoxel incoherent motion (IVIM) parameters. This retrospective study included 26 malignant and 14 benign breast lesions in 35 patients who underwent diffusion-weighted MRI at 3.0T and nine b-values (0-1000 s/mm(2) ). ADC and IVIM parameters (perfusion fraction fp , pseudodiffusion coefficient Dp , and true diffusion coefficient Dd ) were determined in lesions and FGT. For comparison, IVIM was also measured in 16 high-risk normal patients. A predictive model was constructed using linear discriminant analysis. Lesion discrimination based on ADC and IVIM parameters was assessed using receiver operating characteristic (ROC) and area under the ROC curve (AUC). In FGT of normal subjects, fp was 1.1 ± 1.1%. In malignant lesions, fp (6.4 ± 3.1%) was significantly higher than in benign lesions (3.1 ± 3.3%, P = 0.0025) or FGT (1.5 ± 1.2%, P < 0.001), and Dd ((1.29 ± 0.28) × 10(-3) mm(2) /s) was lower than in benign lesions ((1.56 ± 0.28) × 10(-3) mm(2) /s, P = 0.011) or FGT ((1.86 ± 0.34) × 10(-3) mm(2) /s, P < 0.001). A combination of Dd and fp provided higher AUC for discrimination between malignant and benign lesions (0.84) or FGT (0.97) than ADC (0.72 and 0.86, respectively). The IVIM parameters provide accurate identification of malignant lesions. © 2013 Wiley Periodicals, Inc.

  20. The Therapeutic Response of Gastrointestinal Stromal Tumors to Imatinib Treatment Assessed by Intravoxel Incoherent Motion Diffusion-Weighted Magnetic Resonance Imaging with Histopathological Correlation

    PubMed Central

    Zhang, Chunfang; Wang, He; Cheng, Jin; Wu, Weizhen; Hong, Nan; Wang, Yi

    2016-01-01

    Purpose To exploit the intravoxel incoherent motion (IVIM) diffusion-weighted (DW) MRI when evaluating the therapeutic response of gastrointestinal stromal tumors (GIST) to Imatinib in a mouse model. Materials and Methods Mice with xenografts bearing cells from the GIST-T1 cell line were randomly divided into a treated group receiving Imatinib and a control group. DWMRI scans with 14 b-values (0–1500 s/mm2) were performed before and after treatment (days 1, 3 and 7). IVIM related parameters perfusion fractions (fp) and perfusion-related diffusion coefficients (D*) and the conventional apparent diffusion coefficients (ADC) were calculated by fitting the DWMRI signal decay. The mean changes from baseline to each post-treatment time point for each measurement (ΔADC, Δfp and ΔD*) were calculated. The differences of mean changes between the two groups were tested for statistical significance. Histopathological analyses including Ki-67, CD31, TUNEL and H&E were conducted in conjunction with the MRI scans. Results Increases in ADC of the treated group were higher than those of the control group after treatment, whereas statistical significances were not observed. Compared to the control group, D* in the treated group decreased significantly (ΔD*treated = -41%, -49%, and -49% with P = 0.0001, 0.0001 and 0.0001), and fp increased significantly (Δfptreated = 79%, 82% and 110%, with P = 0.001, 0.0001 and P = 0.0007) on days 1, 3 and 7 after treatment. Histopathological analyses demonstrated different tumor tissue characteristics between the treated and control groups. Conclusion IVIM measurements may serve as more sensitive imaging biomarkers than ADC when assessing GIST response to Imatinib as early as one day after treatment. PMID:27911930

  1. Use of diffusion-weighted magnetic resonance imaging to distinguish between lung cancer and focal inflammatory lesions: a comparison of intravoxel incoherent motion derived parameters and apparent diffusion coefficient.

    PubMed

    Deng, Yu; Li, Xinchun; Lei, Yongxia; Liang, Changhong; Liu, Zaiyi

    2016-11-01

    Background Using imaging techniques to diagnose malignant and inflammatory lesions in the lung can be challenging. Purpose To compare intravoxel incoherent motion (IVIM) and apparent diffusion coefficient (ADC) magnetic resonance imaging (MRI) analysis in their ability to discriminate lung cancer from focal inflammatory lung lesions. Material and Methods Thirty-eight patients with lung masses were included: 30 lung cancers and eight inflammatory lesions. Patients were imaged with 3.0T MRI diffusion weighted imaging (DWI) using 10 b values (range, 0-1000 s/mm(2)). Tissue diffusivity ( D), pseudo-diffusion coefficient ( D*), and perfusion fraction ( f) were calculated using segmented biexponential analysis. ADC (total) was calculated with monoexponential fitting of the DWI data. D, D*, f, and ADC were compared between lung cancer and inflammatory lung lesions. Receiver operating characteristic analysis was performed for all DWI parameters. Results The ADC was significantly higher for inflammatory lesions than for lung cancer ([1.21 ± 0.20] × 10(-3) mm(2)/s vs. [0.97 ± 0.15] × 10(-3) mm(2)/s; P = 0.004). By IVIM, f was found to be significantly higher in inflammatory lesions than lung cancer ([46.10 ± 12.92] % vs. [29.29 ± 10.89] %; P = 0.005). There was no difference in D and D* between lung cancer and inflammatory lesions ( P = 0.747 and 0.124, respectively). f showed comparable diagnostic performance with ADC in differentiating lung cancer from inflammatory lung lesions, with areas under the curve of 0.833 and 0.826, sensitivity 80.0% and 73.3%, and specificity 75.0% and 87.5%, respectively. Conclusion The IVIM parameter f value provides comparable diagnostic performance with ADC and could be used as a surrogate marker for differentiating lung cancer from inflammatory lesions.

  2. Measurement of electromagnetic pulse emitted during rapid intramolecular electron transfer

    NASA Astrophysics Data System (ADS)

    Beard, Matthew C.; Turner, Gordon M.; Schmuttenmaer, Charles A.

    2001-03-01

    We have measured the electromagnetic radiation emitted during intramolecular electron transfer using a method does not rely on secondary processes.^1 The motion of the electrons themselves generates the measured signal (as understood by Maxwell's equations). If the electron transfer occurs on a timescale of 0.1 to 10 picoseconds, the emitted radiation will fall in the THz or far-infrared region of the spectrum (1 THz = 33.33 wavenumbers), which is the region covered by our detector. We photoexcite a sample of partially oriented molecules and measure the emitted waveform. The polarity of the emitted field determines the direction of charge transfer unambiguously, and the shape of the field encodes the dynamics of the charge transfer -- a slower transfer rate produces a broader temporal pulse. Future work will extend this method to systems that are difficult to study by traditional means. 1. M. C. Beard, G. M. Turner, and C. A. Schmuttenmaer, J. Am. Chem. Soc. 122, 11541 (2000).

  3. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    SciTech Connect

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-07-28

    A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  4. Intramolecular association within the SAFT framework

    NASA Astrophysics Data System (ADS)

    Avlund, Ane S.; Kontogeorgis, Georgios M.; Chapman, Walter G.

    2011-07-01

    A general theory for modelling intramolecular association within the SAFT framework is proposed. Sear and Jackson [Phys. Rev. E. 50 (1), 386 (1994)] and Ghonasgi and Chapman [J. Chem. Phys. 102 (6), 2585 (1995)] have previously extended SAFT to include intramolecular association for chains with two sites. We show that the resulting equations from the two approaches are equivalent, and use their work as a basis for developing a new general theory. The approach used by Ghonasgi and Chapman is based on mass balances and an infinite dilution result and provides the equations needed to determine the contribution to the Helmholtz free energy from association (inter- as well as intramolecularly) at equilibrium. Sear and Jackson rederived the contribution to the Helmholtz free energy from association from the theory by Wertheim [J. Stat. Phys. 42 (3-4), 459 (1986)] with inclusion of intramolecular association, and using this approach we obtain an expression for the Helmholtz free energy that is valid also at non-equilibrium states (with respect to hydrogen bonds), which is very useful when calculating derivatives.

  5. Organocatalyzed Intramolecular Carbonyl-Ene Reactions.

    PubMed

    Dahlmann, Heidi A; McKinney, Amanda J; Santos, Maria P; Davis, Lindsey O

    2016-05-31

    An organocatalyzed intramolecular carbonyl-ene reaction was developed to produce carbocyclic and heterocyclic 5- and 6-membered rings from a citronellal-derived trifluoroketone and a variety of aldehydes. A phosphoramide derivative was found to promote the cyclization of the trifluoroketone, whereas a less acidic phosphoric acid proved to be a superior catalyst for the aldehyde substrates.

  6. Plasma Motions and Turbulent Magnetic Diffusivity of Active Region AR 12158 Using a Minimum Energy Functional and Non-Force-Free Reconstructions of Vector Magnetograms

    NASA Astrophysics Data System (ADS)

    Tremblay, Benoit; Vincent, Alain

    2017-01-01

    We present a generalization of the resistive minimum-energy fit (MEF-R: Tremblay and Vincent, Solar Phys. 290, 437, 2015) for non-force-free (NFF) magnetic fields. In MEF-R, an extremum principle is used to infer two-dimensional maps of plasma motions [boldsymbol{v}(x,y)] and magnetic eddy diffusivity [η _{eddy}(x,y)] at the photosphere. These reconstructions could be used as boundary conditions in data-driven simulations or in data assimilation. The algorithm is validated using the analytical model of a resistive expanding spheromak by Rakowski, Laming, and Lyutikov ( Astrophys. J. 730, 30, 2011). We study the flaring Active Region AR 12158 using a series of magnetograms and Dopplergrams provided by the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). The results are discussed for a non-force-free magnetic-field reconstruction [boldsymbol{B}_{NFF}] (Hu and Dasgupta in Solar Phys. 247, 87, 2008). We found that the vertical plasma velocities [vz(x,y)] inferred using MEF-R are very similar to the observed Doppler velocities [vr(x,y)]. Finally, we study the potential spatial correlation between microturbulent velocities and significant values of η_{eddy}(x,y).

  7. Orthogonally combined motion- and diffusion-sensitized driven equilibrium (OC-MDSDE) preparation for vessel signal suppression in 3D turbo spin echo imaging of peripheral nerves in the extremities.

    PubMed

    Cervantes, Barbara; Kirschke, Jan S; Klupp, Elizabeth; Kooijman, Hendrik; Börnert, Peter; Haase, Axel; Rummeny, Ernst J; Karampinos, Dimitrios C

    2017-03-05

    To design a preparation module for vessel signal suppression in MR neurography of the extremities, which causes minimal attenuation of nerve signal and is highly insensitive to eddy currents and motion. The orthogonally combined motion- and diffusion-sensitized driven equilibrium (OC-MDSDE) preparation was proposed, based on the improved motion- and diffusion-sensitized driven equilibrium methods (iMSDE and FC-DSDE, respectively), with specific gradient design and orientation. OC-MDSDE was desensitized against eddy currents using appropriately designed gradient prepulses. The motion sensitivity and vessel signal suppression capability of OC-MDSDE and its components were assessed in vivo in the knee using 3D turbo spin echo (TSE). Nerve-to-vessel signal ratios were measured for iMSDE and OC-MDSDE in 7 subjects. iMSDE was shown to be highly sensitive to motion with increasing flow sensitization. FC-DSDE showed robustness against motion, but resulted in strong nerve signal loss with diffusion gradients oriented parallel to the nerve. OC-MDSDE showed superior vessel suppression compared to iMSDE and FC-DSDE and maintained high nerve signal. Mean nerve-to-vessel signal ratios in 7 subjects were 0.40 ± 0.17 for iMSDE and 0.63 ± 0.37 for OC-MDSDE. OC-MDSDE combined with 3D TSE in the extremities allows high-near-isotropic-resolution imaging of peripheral nerves with reduced vessel contamination and high nerve signal. Magn Reson Med, 2017. © 2017 Wiley Periodicals, Inc. © 2017 International Society for Magnetic Resonance in Medicine.

  8. The Limit of Intramolecular H-Bonding.

    PubMed

    Hubbard, Thomas A; Brown, Alisdair J; Bell, Ian A W; Cockroft, Scott L

    2016-11-23

    Hydrogen bonds are ubiquitous interactions in molecular recognition. The energetics of such processes are governed by the competing influences of pre-organization and flexibility that are often hard to predict. Here we have measured the strength of intramolecular interactions between H-bond donor and acceptor sites separated by a variable linker. A striking distance-dependent threshold was observed in the intramolecular interaction energies. H-bonds were worth less than -1 kJ mol(-1) when the interacting groups were separated by ≥6 rotating bonds, but ranged between -5 and -9 kJ mol(-1) for ≤5 rotors. Thus, only very strong external H-bond acceptors were able to compete with the stronger internal H-bonds. In addition, a constant energetic penalty per rotor of ∼5-6 kJ mol(-1) was observed in less strained situations where the molecule contained ≥4 rotatable bonds.

  9. 3T multiparametric MRI of the prostate: Does intravoxel incoherent motion diffusion imaging have a role in the detection and stratification of prostate cancer in the peripheral zone?

    PubMed

    Valerio, Mariacristina; Zini, Chiara; Fierro, Davide; Giura, Francesca; Colarieti, Anna; Giuliani, Alessandro; Laghi, Andrea; Catalano, Carlo; Panebianco, Valeria

    2016-04-01

    To evaluate the potential added value of the intravoxel incoherent motion model to conventional multiparametric magnetic resonance protocol in order to differentiate between healthy and neoplastic prostate tissue in the peripheral zone. Mono-exponential and bi-exponential fits were used to calculate ADC and IVIM parameters in 53 patients with peripheral zone biopsy proved tumor. Inferential statistics analysis was performed on T2, ADC and IVIM parameters (D, D*, f) comparing healthy and neoplastic tissues. Linear discriminant analysis was performed for the conventional parameters (T2 and ADC), the IVIM parameters (molecular diffusion coefficient (D), perfusion-related diffusion coefficient (D*), and perfusion fraction (f) and the combined T2-weighted imaging/DWI and IVIM parameters (T2, ADC, D, D* and f). A correlation with Gleason scores was achieved. The values of T2, ADC and D were significantly lower in cancerous tissues (2749.82 ± 1324.67 ms, 0.76 ± 0.27 × 10(-3)mm(2)/s and 0.99 ± 0.38 × 10(-3)mm(2)/s respectively) compared to those found in the healthy tissues (3750.70 ± 1735.37 ms, 1.39 ± 0.48 × 10(-3)mm(2)/s and 1.77 ± 0.36 × 10(-3)mm(2)/s respectively); D* parameter was significantly increased in neoplastic compared to healthy tissue (15.56 ± 12.91 × 10(-3)mm(2)/s and 10.25 ± 10.52 × 10(-3)mm(2)/s respectively). The specificity, sensitivity and accuracy of the T2-weighted imaging/DWI and IVIM parameters were 100, 96 and 98%, respectively, compare to 88, 92 and 90% and 96, 92 and 94 for T2-weighted imaging/ADC and IVIM alone. IVIM parameters increase the specificity and sensitivity in the evaluation of peripheral zone prostate cancer. A statistical difference between low grade tumors and high grade tumors has been demostrated in that ADC, D and D* dataset; in particular, D has been found to have the highest significativity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  10. An unusual intramolecular trans-amidation.

    PubMed

    Rivera, Heriberto; Dhar, Sachin; La Clair, James J; Tsai, Shiou-Chuan; Burkart, Michael D

    2016-06-23

    Polyketide biosynthesis engages a series of well-timed biosynthetic operations to generate elaborate natural products from simple building blocks. Mimicry of these processes has offered practical means for total synthesis and provided a foundation for reaction discovery. We now report an unusual intramolecular trans-amidation reaction discovered while preparing stabilized probes for the study of actinorhodin biosynthesis. This rapid cyclization event offers insight into the natural cyclization process inherent to the biosynthesis of type II polyketide antibiotics.

  11. Quantification of intramolecular nonbonding interactions in organochalcogens.

    PubMed

    Roy, Dipankar; Sunoj, Raghavan B

    2006-05-04

    Intramolecular nonbonding interactions between chalcogen atoms in a series of ortho substituted arylselenides (S/O...Se-Y, with Y = -Me, -CN, -Cl, and -F) are quantified using the coupled cluster CCSD(T)/cc-pVDZ level of theory. A homodesmic reaction method as well as an ortho-para approach are employed in evaluating the strength of intramolecular interactions. Comparison of the results obtained using the ab initio MP2 method and pure and hybrid density functional theories are performed with that of the coupled cluster values to assess the quality of different density functionals in evaluating the strength of nonbonding interactions. The interaction energies are found to be higher when the thioformyl group acts as the donor and the Se-F bond acts as the acceptor. In a given series with the same donor atom, the strength of the interaction follows the order Me < CN < Cl < F, exhibiting fairly high sensitivity to the group attached to selenium (Se-Y). Analysis of electron density at the S/O...Se bond critical point within the Atoms in Molecule framework shows a very good correlation with the computed intramolecular interaction energies.

  12. Intramolecular hydrogen bonding in medicinal chemistry.

    PubMed

    Kuhn, Bernd; Mohr, Peter; Stahl, Martin

    2010-03-25

    The formation of intramolecular hydrogen bonds has a very pronounced effect on molecular structure and properties. We study both aspects in detail with the aim of enabling a more rational use of this class of interactions in medicinal chemistry. On the basis of exhaustive searches in crystal structure databases, we derive propensities for intramolecular hydrogen bond formation of five- to eight-membered ring systems of relevance in drug discovery. A number of motifs, several of which are clearly underutilized in drug discovery, are analyzed in more detail by comparing small molecule and protein-ligand X-ray structures. To investigate effects on physicochemical properties, sets of closely related structures with and without the ability to form intramolecular hydrogen bonds were designed, synthesized, and characterized with respect to membrane permeability, water solubility, and lipophilicity. We find that changes in these properties depend on a subtle balance between the strength of the hydrogen bond interaction, geometry of the newly formed ring system, and the relative energies of the open and closed conformations in polar and unpolar environments. A number of general guidelines for medicinal chemists emerge from this study.

  13. Intravoxel Incoherent Motion Diffusion Weighted MR Imaging at 3.0 T: Assessment of Steatohepatitis and Fibrosis Compared with Liver Biopsy in Type 2 Diabetic Patients

    PubMed Central

    Parente, Daniella Braz; Paiva, Fernando Fernandes; Oliveira Neto, Jaime Araújo; Machado-Silva, Lilian; Figueiredo, Fatima Aparecida Ferreira; Lanzoni, Valeria; Campos, Carlos Frederico Ferreira; do Brasil, Pedro Emmanuel Alvarenga Americano; Gomes, Marilia de Brito; Perez, Renata de Mello; Rodrigues, Rosana Souza

    2015-01-01

    Objective To evaluate the capability of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) to assess steatohepatitis and fibrosis determined by histopathology in type 2 diabetic patients. Methods Fifty-nine type 2 diabetic patients (49 women, 10 men; mean age, 54 ± 9 years) were submitted to liver biopsy for the evaluation of non-alcoholic fatty liver disease (NAFLD) and underwent DWI on a 3.0T MR system using 10 b values. Institutional approval and patient consent were obtained. Pure molecular-based (D), perfusion-related (D*), and vascular fraction (f) were calculated using a double exponential model and least squares curve fitting. D, D*, and f were compared between patients with and without steatohepatitis and between patients with and without fibrosis. The variables were compared by using the Ranksum test and Student t-test. Results Steatohepatitis was observed in 22 patients and fibrosis in 16 patients. A lower D median (0.70 s/mm2 vs. 0.83 s/mm2, p<0.05) and a lower D* median (34.39 s/mm2 vs. 45.23 s/mm2, p<0.05) were observed among those with steatohepatitis. A lower D median (0.70 s/mm2 vs. 0.82 s/mm2, p<0.05) and a lower D* median (35.01 s/mm2 vs. 44.76 s/mm2, p=0.05) were also observed among those with fibrosis. Conclusion IVIM-DWI has the potential to aid in the characterization of steatohepatitis and fibrosis. PMID:25961735

  14. Intramolecular vibrations in low-frequency normal modes of amino acids: L-alanine in the neat solid state.

    PubMed

    Zhang, Feng; Wang, Houng-Wei; Tominaga, Keisuke; Hayashi, Michitoshi

    2015-03-26

    This paper presents a theoretical analysis of the low-frequency phonons of L-alanine by using the solid-state density functional theory at the Γ point. We are particularly interested in the intramolecular vibrations accessing low-frequency phonons via harmonic coupling with intermolecular vibrations. A new mode-analysis method is introduced to quantify the vibrational characteristics of such intramolecular vibrations. We find that the torsional motions of COO(-) are involved in low-frequency phonons, although COO(-) is conventionally assumed to undergo localized torsion. We also find the broad distributions of intramolecular vibrations relevant to important functional groups of amino acids, e.g., the COO(-) and NH3(+) torsions, in the low-frequency phonons. The latter finding is illustrated by the concept of frequency distribution of vibrations. These findings may lead to immediate implications in other amino acid systems.

  15. The value of intravoxel incoherent motion model-based diffusion-weighted imaging for outcome prediction in resin-based radioembolization of breast cancer liver metastases

    PubMed Central

    Pieper, Claus Christian; Meyer, Carsten; Sprinkart, Alois Martin; Block, Wolfgang; Ahmadzadehfar, Hojjat; Schild, Hans Heinz; Mürtz, Petra; Kukuk, Guido Matthias

    2016-01-01

    Purpose To evaluate prognostic values of clinical and diffusion-weighted magnetic resonance imaging-derived intravoxel incoherent motion (IVIM) parameters in patients undergoing primary radioembolization for metastatic breast cancer liver metastases. Subjects and methods A total of 21 females (mean age 54 years, range 43–72 years) with liver-dominant metastatic breast cancer underwent standard liver magnetic resonance imaging (1.5 T, diffusion-weighted imaging with b-values of 0, 50, and 800 s/mm2) before and 4–6 weeks after radioembolization. The IVIM model-derived estimated diffusion coefficient D’ and the perfusion fraction f’ were evaluated by averaging the values of the two largest treated metastases in each patient. Kaplan–Meier and Cox regression analyses for overall survival (OS) were performed. Investigated parameters were changes in f’- and D’-values after therapy, age, sex, Eastern Cooperative Oncology Group (ECOG) status, grading of primary tumor, hepatic tumor burden, presence of extrahepatic disease, baseline bilirubin, previous bevacizumab therapy, early stasis during radioembolization, chemotherapy after radioembolization, repeated radioembolization and Response Evaluation Criteria in Solid Tumors (RECIST) response at 6-week follow-up. Results Median OS after radioembolization was 6 (range 1.5–54.9) months. In patients with therapy-induced decreasing or stable f’-values, median OS was significantly longer than in those with increased f’-values (7.6 [range 2.6–54.9] vs 2.6 [range 1.5–17.4] months, P<0.0001). Longer median OS was also seen in patients with increased D’-values (6 [range 1.6–54.9] vs 2.8 [range 1.5–17.4] months, P=0.008). Patients with remission or stable disease (responders) according to RECIST survived longer than nonresponders (7.2 [range 2.6–54.9] vs 2.6 [range 1.5–17.4] months, P<0.0001). An ECOG status ≤1 resulted in longer median OS than >1 (7.6 [range 2.6–54.9] vs 1.7 [range 1.5–4

  16. Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration.

    PubMed Central

    Sprous, D; Harvey, S C

    1996-01-01

    We report a computer modeling study of DNA supercoiling in model plasmids over the size range of 140-1260 bp. We used a computer model with basepair resolution. Molecular dynamics was used to produce ensembles at 300 K and to investigate intramolecular motions. The plasmid models varied by their sequence. The sequence types employed for comparison included a curve-bearing plasmid, a heterogenous sequence plasmid, and a homogenous sequence. Within the three sequence types tested at the 1260-bp plasmid size, we observed several sequence-dependent phenomena. Writhe, radius of gyration, slither motion, and branching probability were seen to be sequence dependent. Branching probability was the least in the homogenous plasmid and the greatest in the curve-bearing plasmid. The curve imposed a symmetry on the plasmid that was absent in the heterogenous sequence. Significant localizations and enhancements of intramolecular concentration were seen to a persistence length. Molecular dynamics allowed us to observe the mechanism of branch formation and reabsorption. We observed a size-dependent change in the types of motion observed in plasmids. Slither motion predominated in plasmids up to 600 bp in size, whereas global rearrangements were more important in the 1260 mer. Images FIGURE 1 FIGURE 5 FIGURE 10 PMID:8785349

  17. Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration.

    PubMed

    Sprous, D; Harvey, S C

    1996-04-01

    We report a computer modeling study of DNA supercoiling in model plasmids over the size range of 140-1260 bp. We used a computer model with basepair resolution. Molecular dynamics was used to produce ensembles at 300 K and to investigate intramolecular motions. The plasmid models varied by their sequence. The sequence types employed for comparison included a curve-bearing plasmid, a heterogenous sequence plasmid, and a homogenous sequence. Within the three sequence types tested at the 1260-bp plasmid size, we observed several sequence-dependent phenomena. Writhe, radius of gyration, slither motion, and branching probability were seen to be sequence dependent. Branching probability was the least in the homogenous plasmid and the greatest in the curve-bearing plasmid. The curve imposed a symmetry on the plasmid that was absent in the heterogenous sequence. Significant localizations and enhancements of intramolecular concentration were seen to a persistence length. Molecular dynamics allowed us to observe the mechanism of branch formation and reabsorption. We observed a size-dependent change in the types of motion observed in plasmids. Slither motion predominated in plasmids up to 600 bp in size, whereas global rearrangements were more important in the 1260 mer.

  18. Multifaceted ultrafast intramolecular charge transfer dynamics of 4-(dimethylamino)benzonitrile (DMABN).

    PubMed

    Park, Myeongkee; Kim, Chul Hoon; Joo, Taiha

    2013-01-17

    Intramolecular charge transfer (ICT) of DMABN has been the subject of extensive investigations. Through the measurements of highly time-resolved fluorescence spectra (TRFS) over the whole emission region, we have examined the ICT dynamics of DMABN in acetonitrile free from the solvation dynamics and vibronic relaxation. The ICT dynamics was found to be characterized by a broad range of time scales; nearly instantaneous (<30 fs), 160 fs, and 3.3 ps. TRFS revealed that an ICT state with partially twisted geometry, ICT(P), is formed within a few hundred femtoseconds either directly from the initial photoexcited state or via the locally excited (LE) state. The ICT(P) state undergoes further relaxation along the intramolecular nuclear coordinate to reach the twisted ICT (TICT) state with the time constant of 4.8 ps. A conformational diversity along the rotation of the dimethylamino group was speculated to account for the observed diffusive dynamics.

  19. Intramolecular Isotopic Studies: Chemical Enhancements and Alternatives

    NASA Astrophysics Data System (ADS)

    Hayes, J. M.

    2016-12-01

    As mass spectroscopic and NMR-based methods now appropriately flourish, chemical techniques should not be forgotten. First, the methods developed by pioneering intramolecular analysts can be reapplied to new samples. Second, they can be extended. The synthesis of intramolecular isotopic standards is particularly important and straightforward. It requires only that a chemical reaction has no secondary products. An example is provided by the addition of carbon dioxide to a Grignard reagent. The reaction proceeds with an isotope effect. The isotopic composition of the carboxyl group in the acid which is produced is thus not equal to that of the starting carbon dioxide but the unconsumed CO2 can be recovered and analyzed. A simple titration can show that all the rest of the CO2 is in the product acid. The isotopic composition of the carboxyl group can then be calculated by difference. The product is an intramolecular isotopic standard, an organic molecule in which the isotopic composition of a specific carbon position is known accurately. Both analysts and reviewers can thus gain invaluable confidence in the accuracy of instrumental results. A second example: the haloform reaction quantitatively degrades methyl ketones, producing a carboxylic acid which can be decarboxylated to determine the isotopic composition of the parent carbonyl and a haloform (CHI3, for example) that can be combusted to determine the isotopic composition of the methyl group. Ketones thus analyzed can be combined with Grignard reagents to yield carbon skeletons in which the isotopic compositions of internal and terminal -CH2- and -CH3 groups are known accurately. In general, analysts accustomed to demanding quantitative reactions should remember the power of mass balances and recognize that many organic-chemical reactions, while not quantitative, lack side products and can be driven to the total consumption of at least one reactant.

  20. Intramolecular energy transfer reactions in polymetallic

    SciTech Connect

    Petersen, J.

    1990-11-01

    This report is concerned with intramolecular, energy-transfer reactions. The concept of preparing synthetically a complex molecular species, capable of absorbing a photon at one metal center (antenna fragment), transferring that energy to a second metal center (reactive fragment) via a bridging ligand was first reported by our group in 1979. It is now apparent that a major emphasis in inorganic chemistry in the future will involve these types of molecular ensembles. Complexes discussed include Rh, Ru, and Cu complexes. 23 refs., 14 tabs.

  1. The stereochemical course of intramolecular Michael reactions.

    PubMed

    Kwan, Eugene E; Scheerer, Jonathan R; Evans, David A

    2013-01-04

    We present a general model for understanding the stereochemical course of intramolecular Michael reactions. We show that the addition of β-ketoester enolates to α,β-unsaturated esters and imides bearing adjacent stereocenters (X, Y = H, Me, OR) leads to high levels of asymmetric induction. Reinforcing and nonreinforcing stereochemical relationships are evaluated from the syn and anti reactant diastereomers. On the basis of synthetic, spectroscopic, and computational studies, we propose that the outcomes of these reactions can be rationalized by a dipole-minimized chair transition-state model.

  2. Electrochemical intramolecular aminooxygenation of unactivated alkenes.

    PubMed

    Xu, Fan; Zhu, Lin; Zhu, Shaobin; Yan, Xiaomei; Xu, Hai-Chao

    2014-09-26

    An electrochemical approach to the intramolecular aminooxygenation of unactivated alkenes has been developed. This process is based on the addition of nitrogen-centered radicals, generated through electrochemical oxidation, to alkenes followed by trapping of the cyclized radical intermediate with 2,2,6,6-tetramethylpiperidine-N-oxyl radical (TEMPO). Difunctionalization of a variety of alkenes with easily available carbamates/amides and TEMPO affords aminooxygenation products in high yields and with excellent trans selectivity for cyclic systems (d.r. up to>20:1). The approach provides a much-needed complementary route to existing cis-selective methods.

  3. Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum.

    PubMed

    Liu, Jian; Miller, William H; Paesani, Francesco; Zhang, Wei; Case, David A

    2009-10-28

    The important role of liquid water in many areas of science from chemistry, physics, biology, geology to climate research, etc., has motivated numerous theoretical studies of its structure and dynamics. The significance of quantum effects on the properties of water, however, has not yet been fully resolved. In this paper we focus on quantum dynamical effects in liquid water based on the linearized semiclassical initial value representation (LSC-IVR) with a quantum version of the simple point charge/flexible (q-SPC/fw) model [Paesani et al., J. Chem. Phys. 125, 184507 (2006)] for the potential energy function. The infrared (IR) absorption spectrum and the translational diffusion constants have been obtained from the corresponding thermal correlation functions, and the effects of intermolecular and intramolecular correlations have been studied. The LSC-IVR simulation results are compared with those predicted by the centroid molecular dynamics (CMD) approach. Although the LSC-IVR and CMD results agree well for the broadband for hindered motions in liquid water, the intramolecular bending and O-H stretching peaks predicted by the LSC-IVR are blueshifted from those given by CMD; reasons for this are discussed. We also suggest that the broadband in the IR spectrum corresponding to restricted translation and libration gives more information than the diffusion constant on the nature of quantum effects on translational and rotational motions and should thus receive more attention in this regard.

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

    PubMed

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

    2011-11-08

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

  5. Thiol dependent intramolecular locking of Orai1 channels

    PubMed Central

    Alansary, Dalia; Schmidt, Barbara; Dörr, Kathrin; Bogeski, Ivan; Rieger, Heiko; Kless, Achim; Niemeyer, Barbara A.

    2016-01-01

    Store-operated Ca2+ entry mediated by STIM1-gated Orai1 channels is essential to activate immune cells and its inhibition or gain-of-function can lead to immune dysfunction and other pathologies. Reactive oxygen species interacting with cysteine residues can alter protein function. Pretreatment of the Ca2+ selective Orai1 with the oxidant H2O2 reduces ICRAC with C195, distant to the pore, being its major redox sensor. However, the mechanism of inhibition remained elusive. Here we combine experimental and theoretical approaches and show that oxidation of Orai1 leads to reduced subunit interaction, slows diffusion and that either oxidized C195 or its oxidomimetic mutation C195D located at the exit of transmembrane helix 3 virtually eliminates channel activation by intramolecular interaction with S239 of transmembrane helix 4, thereby locking the channel in a closed conformation. Our results demonstrate a novel mechanistic model for ROS-mediated inhibition of Orai1 and identify a candidate residue for pharmaceutical intervention. PMID:27624281

  6. Diffusing diffusivity: Rotational diffusion in two and three dimensions

    NASA Astrophysics Data System (ADS)

    Jain, Rohit; Sebastian, K. L.

    2017-06-01

    We consider the problem of calculating the probability distribution function (pdf) of angular displacement for rotational diffusion in a crowded, rearranging medium. We use the diffusing diffusivity model and following our previous work on translational diffusion [R. Jain and K. L. Sebastian, J. Phys. Chem. B 120, 3988 (2016)], we show that the problem can be reduced to that of calculating the survival probability of a particle undergoing Brownian motion, in the presence of a sink. We use the approach to calculate the pdf for the rotational motion in two and three dimensions. We also propose new dimensionless, time dependent parameters, αr o t ,2 D and αr o t ,3 D, which can be used to analyze the experimental/simulation data to find the extent of deviation from the normal behavior, i.e., constant diffusivity, and obtain explicit analytical expressions for them, within our model.

  7. Intramolecular interactions in the polar headgroup of sphingosine: serinol.

    PubMed

    Loru, Donatella; Peña, Isabel; Alonso, José L; Sanz, M Eugenia

    2016-03-04

    The intramolecular interactions in the lipid sphingosine have been elucidated through the investigation of the amino alcohol serinol which mimics its polar headgroup. Intricate networks of intramolecular hydrogen bonds involving the hydroxyl groups and the amino group contribute to the stabilisation of five different conformations observed in the broadband rotational spectrum.

  8. Helical polymers based on intramolecularly hydrogen-bonded aromatic polyamides.

    PubMed

    Lu, Yi-Xuan; Shi, Zhu-Ming; Li, Zhan-Ting; Guan, Zhibin

    2010-12-21

    Inspired by arylamide-based oligomeric foldermers that are stabilized by intramolecular hydrogen bonding, a series of polyamides with intramolecular hydrogen-bonding motifs were synthesized via polycondensation reactions. These polymers can fold into helical conformation different from their linear control. The chirality of helical conformation can further be tuned via acid-base complexation using chiral residues.

  9. Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution

    SciTech Connect

    Bellucci, Michael A.; Coker, David F.

    2012-05-21

    The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

  10. The intramolecular click reaction using 'carbocontiguous' precursors.

    PubMed

    Patil, Pravin C; Luzzio, Frederick A

    2017-07-20

    The synthesis and utilization of all carbon-chain 'carbocontiguous' azidoalkynyl precursors for an intramolecular click reaction is described. The substrates contain both azidoalkyl and ethynylmethyl groups which are conjoined by a 2-(phenylsulfonylmethyl)-4,5-diphenyloxazole lynchpin and are suitably disposed for ring closure. On promotion by copper salts, a number of cyclic click products having the 1,4-disubstituted endo-fused triazole component and the 4,5-diphenyloxazole component are obtained. In one case, removal of the phenylsulfonylmethyl group from the substrate prior to cyclization gave the 1,5-disubstituted exo-fused triazole. The utilization of CuSO4/sodium ascorbate system appears to be the optimal conditions for closure/cyclization and afforded the cyclized products in yields of 84-95%.

  11. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines.

    PubMed

    Bártová, Kateřina; Čechová, Lucie; Procházková, Eliška; Socha, Ondřej; Janeba, Zlatko; Dračínský, Martin

    2017-10-06

    Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in (15)N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

  12. Intramolecular Rovibrational Dynamics of Hydrocarbons and Argon

    NASA Astrophysics Data System (ADS)

    McIlroy, Andrew

    This dissertation describes investigations of the intramolecular dynamics of two types of systems: isolated hydrocarbon molecules, and clusters of Ar atoms with an HF molecule. Both are studied via high resolution (0.001 cm^{-1}) infrared (IR) laser spectroscopy in a slit supersonic expansion. The slit expansion provides a cold (T = 3-15 K) source of isolated gas phase molecules or complexes with sufficient pathlength to carry out IR laser absorption experiments. Furthermore, probing the expansion parallel to the slit produces Doppler broadening up to a factor of ten below that found at room temperature facilitating high resolution, state specific experiments. In the hydrocarbon v = 1 >=ts 0 CH stretch spectra, the vibrational mixing ultimately responsible for intramolecular vibrational energy redistribution (IVR) is elucidated from the observation of splitting of the individual rovibrational transitions; this is due to coupling of the CH stretch to the bath of combination and overtone states. The repetition of qualitative patterns in these data suggest that in some cases individual functional groups within a molecule may control IVR rates largely independent of the specific details of the molecule. For example, vibrational coupling of acetylenic CH stretches is shown to produce similar relaxation rates in molecules whose vibrational state densities vary by almost three orders of magnitude. The studies of Ar_{rm n}HF complexes, n = 1-4, focus on the transition from a free, gas phase HF molecule to a "solvated" HF in an Ar matrix. Models describing the observed red shifting of the HF vibration with the sequential addition of Ar atoms are investigated. Furthermore, these multibody clusters provide the opportunity to test the approximation of the potential energy surfaces (PES) of weakly bound (< 1000 cm^{-1}) systems with sums of two-body potentials. Initial calculations and experiments suggest that significant discrepancies exist between the true PES and the

  13. Molecular motion and ion diffusion in choline chloride based deep eutectic solvents studied by 1H pulsed field gradient NMR spectroscopy.

    PubMed

    D'Agostino, Carmine; Harris, Robert C; Abbott, Andrew P; Gladden, Lynn F; Mantle, Mick D

    2011-12-28

    Deep Eutectic Solvents (DESs) are a novel class of solvents with potential industrial applications in separation processes, chemical reactions, metal recovery and metal finishing processes such as electrodeposition and electropolishing. Macroscopic physical properties such as viscosity, conductivity, eutectic composition and surface tension are already available for several DESs, but the microscopic transport properties for this class of compounds are not well understood and the literature lacks experimental data that could give a better insight into the understanding of such properties. This paper presents the first pulsed field gradient nuclear magnetic resonance (PFG-NMR) study of DESs. Several choline chloride based DESs were chosen as experimental samples, each of them with a different associated hydrogen bond donor. The molecular equilibrium self-diffusion coefficient of both the choline cation and hydrogen bond donor was probed using a standard stimulated echo PFG-NMR pulse sequence. It is shown that the increasing temperature leads to a weaker interaction between the choline cation and the correspondent hydrogen bond donor. The self-diffusion coefficients of the samples obey an Arrhenius law temperature-dependence, with values of self-diffusivity in the range of [10(-10)-10(-13) m(2) s(-1)]. In addition, the results also highlight that the molecular structure of the hydrogen bond donor can greatly affect the mobility of the whole system. While for ethaline, glyceline and reline the choline cation diffuses slower than the associated hydrogen bond donor, reflecting the trend of molecular size and molecular weight, the opposite behaviour is observed for maline, in which the hydrogen bond donor, i.e. malonic acid, diffuses slower than the choline cation, with self-diffusion coefficients values of the order of 10(-13) m(2) s(-1) at room temperature, which are remarkably low values for a liquid. This is believed to be due to the formation of extensive dimer

  14. Protein Motions and Folding Investigated by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2002-03-01

    NMR spin relaxation spectroscopy is a powerful experimental approach for globally characterizing conformational dynamics of proteins in solution. Laboratory frame relaxation measurements are sensitive to overall rotational diffusion and internal motions on picosecond-nanosecond time scales, while rotating frame relaxation measurements are sensitive to chemical exchange processes on microsecond-millisecond time scales. The former approach is illustrated by ^15N laboratory-frame relaxation experiments as a function of temperature for the helical subdomain HP36 of the F-actin-binding headpiece domain of chicken villin. The data are analyzed using the model-free formalism to characterize order parameters and effective correlation times for intramolecular motions of individual ^15N sites. The latter approach is illustrated by ^13C Carr-Purcell-Meiboom-Gill relaxation measurements for the de novo designed α_2D protein and by ^15N rotating-frame relaxation measurements for the peripheral subunit-binding domain (PSBD) from the dihydrolopoamide acetyltransferase component of the pyruvate dehydrogenase multienzyme complex from Bacillus stearothermophilus. These experiments are used to determine the folding and unfolding kinetic rate constants for the two proteins. The results for HP36, α_2D, and PSBD illustrate the capability of current NMR methods for characterizing dynamic processes on multiple time scales in proteins.

  15. Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

    PubMed Central

    Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

    2008-01-01

    Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

  16. Ultrastructural evidence for intramolecular double stranding in iota-carrageenan.

    PubMed

    Abeysekera, R M; Bergström, E T; Goodall, D M; Norton, I T; Robards, A W

    1993-10-04

    Kinetic studies of primary processes of conformational ordering in gel-forming biopolymers have suggested that a change in mechanism from intermolecular to intramolecular multistrand formation occurs on lowering the concentration of biopolymer. We report here ultrastructural observations consistent with intramolecular double stranding in a carbohydrate polymer, iota-carrageenan, by arresting this process of primary conformational ordering by an ultra-rapid freeze fixation technique. High-resolution transmission electron microscopy (TEM) revealed isolated iota-carrageenan chains showing a range of morphologies (linear, circular, and hairpin) consistent with intramolecular stranding. Control experiments in which iota-carrageenan was frozen in the disordered form revealed longer and thinner strands.

  17. Anatomy of Particle Diffusion

    ERIC Educational Resources Information Center

    Bringuier, E.

    2009-01-01

    The paper analyses particle diffusion from a thermodynamic standpoint. The main goal of the paper is to highlight the conceptual connection between particle diffusion, which belongs to non-equilibrium statistical physics, and mechanics, which deals with particle motion, at the level of third-year university courses. We start out from the fact…

  18. Anatomy of Particle Diffusion

    ERIC Educational Resources Information Center

    Bringuier, E.

    2009-01-01

    The paper analyses particle diffusion from a thermodynamic standpoint. The main goal of the paper is to highlight the conceptual connection between particle diffusion, which belongs to non-equilibrium statistical physics, and mechanics, which deals with particle motion, at the level of third-year university courses. We start out from the fact…

  19. TU-F-CAMPUS-I-01: Head and Neck Squamous Cell Carcinoma: Short-Term Repeatability of Apparent Diffusion Coefficient and Intravoxel Incoherent Motion Parameters at 3.0T

    SciTech Connect

    Ding, Y; Fuller, C; Mohamed, A; Wang, J; Hazle, J

    2015-06-15

    Purpose: Many published studies have recently demonstrated the potential value of intravoxel incoherent motion (IVIM) analysis for disease evaluation. However, few have questioned its measurement repeatability/reproducibility when applied. The purpose of this study was to determine the short-term measurement repeatability of apparent diffusion coefficient ADC, true diffusion coefficient D, pseudodiffusion coefficient D* and perfusion fraction f, in head and neck squamous cell carcinoma (HNSCC) primary tumors and metastatic nodes. Methods: Ten patients with known HNSCC were examined twice using echo-planar DW-MRI with 12 b values (0 to 800 s/mm2) 1hour to 24 hours apart before radiation treatment. All patients were scanned with the customized radiation treatment immobilization devices to reduce motion artifacts and to improve image registration in repeat scans. Regions of interests were drawn in primary tumor and metastases node in each patient (Fig. 1). ADC and IVIM parameters D, D* and f were calculated by least squares data fitting. Short-term test–retest repeatability of ADC and IVIM parameters were assessed by measuring Bland–Altman limits of agreements (BA-LA). Results: Sixteen HNSCC lesions were assessed in 10 patients. Repeatability of perfusion-sensitive parameters, D* and f, in HNSCC lesions was poor (BA-LA: -144% to 88% and −57% to 96% for D* and f, respectively); a lesser extent was observed for the diffusion-sensitive parameters of ADC and D (BA-LA: −34% to 39% and −37% to 40%, for ADC and D, respectively) (Fig. 2). Conclusion: Poor repeatability of D*/f and good repeatability for ADC/D were observed in HNSCC primary tumors and metastatic nodes. Efforts should be made to improve the measurement repeatability of perfusion-sensitive IVIM parameters.

  20. Intramolecular epitope spreading in Heymann nephritis.

    PubMed

    Shah, Pallavi; Tramontano, Alfonso; Makker, Sudesh P

    2007-12-01

    Immunization with megalin induces active Heymann nephritis, which reproduces features of human idiopathic membranous glomerulonephritis. Megalin is a complex immunological target with four discrete ligand-binding domains (LBDs) that may contain epitopes to which pathogenic autoantibodies are directed. Recently, a 236-residue N-terminal fragment, termed "L6," that spans the first LBD was shown to induce autoantibodies and severe disease. We used this model to examine epitope-specific contributions to pathogenesis. Sera obtained from rats 4 weeks after immunization with L6 demonstrated reactivity only with the L6 fragment on Western blot, whereas sera obtained after 8 weeks demonstrated reactivity with all four recombinant fragments of interest (L6 and LBDs II, III, and IV). We demonstrated that the L6 immunogen does not contain the epitopes responsible for the reactivity to the LBD fragments. Therefore, the appearance of antibodies directed at LBD fragments several weeks after the primary immune response suggests intramolecular epitope spreading. In vivo, we observed a temporal association between increased proteinuria and the appearance of antibodies to LBD fragments. These data implicate B cell epitope spreading in antibody-mediated pathogenesis of active Heymann nephritis, a model that should prove valuable for further study of autoimmune dysregulation.

  1. Intramolecular photoelectron diffraction in the gas phase

    NASA Astrophysics Data System (ADS)

    Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Ayuso, D.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2013-09-01

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  2. Intramolecular photoelectron diffraction in the gas phase.

    PubMed

    Ueda, K; Miron, C; Plésiat, E; Argenti, L; Patanen, M; Kooser, K; Ayuso, D; Mondal, S; Kimura, M; Sakai, K; Travnikova, O; Palacios, A; Decleva, P; Kukk, E; Martín, F

    2013-09-28

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  3. Exciton Correlations in Intramolecular Singlet Fission

    SciTech Connect

    Sanders, Samuel N.; Kumarasamy, Elango; Pun, Andrew B.; Appavoo, Kannatassen; Steigerwald, Michael L.; Campos, Luis M.; Sfeir, Matthew Y.

    2016-05-16

    We have synthesized a series of asymmetric pentacene-tetracene heterodimers with a variable-length conjugated bridge that undergo fast and efficient intramolecular singlet fission (iSF). These compounds have distinct singlet and triplet energies, which allow us to study the spatial dynamics of excitons during the iSF process, including the significant role of exciton correlations in promoting triplet pair generation and recombination. We demonstrate that the primary photoexcitations in conjugated dimers are delocalized singlets that enable fast and efficient iSF. However, in these asymmetric dimers, the singlet becomes more localized on the lower energy unit as the length of the bridge is increased, slowing down iSF relative to analogous symmetric dimers. We resolve the recombination kinetics of the inequivalent triplets produced via iSF, and find that they primarily decay via concerted processes. By identifying different decay channels, including delayed fluorescence via triplet-triplet annihilation, we can separate transient species corresponding to both correlated triplet pairs and uncorrelated triplets. Recombination of the triplet pair proceeds rapidly despite our experimental and theoretical demonstration that individual triplets are highly localized and unable to be transported across the conjugated linker. In this class of compounds, the rate of formation and yield of uncorrelated triplets increases with bridge length. Overall, these constrained, asymmetric systems provide a unique platform to isolate and study transient species essential for singlet fission, which are otherwise difficult to observe in symmetric dimers or condensed phases.

  4. Exciton Correlations in Intramolecular Singlet Fission

    DOE PAGES

    Sanders, Samuel N.; Kumarasamy, Elango; Pun, Andrew B.; ...

    2016-05-16

    We have synthesized a series of asymmetric pentacene-tetracene heterodimers with a variable-length conjugated bridge that undergo fast and efficient intramolecular singlet fission (iSF). These compounds have distinct singlet and triplet energies, which allow us to study the spatial dynamics of excitons during the iSF process, including the significant role of exciton correlations in promoting triplet pair generation and recombination. We demonstrate that the primary photoexcitations in conjugated dimers are delocalized singlets that enable fast and efficient iSF. However, in these asymmetric dimers, the singlet becomes more localized on the lower energy unit as the length of the bridge is increased,more » slowing down iSF relative to analogous symmetric dimers. We resolve the recombination kinetics of the inequivalent triplets produced via iSF, and find that they primarily decay via concerted processes. By identifying different decay channels, including delayed fluorescence via triplet-triplet annihilation, we can separate transient species corresponding to both correlated triplet pairs and uncorrelated triplets. Recombination of the triplet pair proceeds rapidly despite our experimental and theoretical demonstration that individual triplets are highly localized and unable to be transported across the conjugated linker. In this class of compounds, the rate of formation and yield of uncorrelated triplets increases with bridge length. Overall, these constrained, asymmetric systems provide a unique platform to isolate and study transient species essential for singlet fission, which are otherwise difficult to observe in symmetric dimers or condensed phases.« less

  5. Exciton Correlations in Intramolecular Singlet Fission

    SciTech Connect

    Sanders, Samuel N.; Kumarasamy, Elango; Pun, Andrew B.; Appavoo, Kannatassen; Steigerwald, Michael L.; Campos, Luis M.; Sfeir, Matthew Y.

    2016-05-16

    We have synthesized a series of asymmetric pentacene-tetracene heterodimers with a variable-length conjugated bridge that undergo fast and efficient intramolecular singlet fission (iSF). These compounds have distinct singlet and triplet energies, which allow us to study the spatial dynamics of excitons during the iSF process, including the significant role of exciton correlations in promoting triplet pair generation and recombination. We demonstrate that the primary photoexcitations in conjugated dimers are delocalized singlets that enable fast and efficient iSF. However, in these asymmetric dimers, the singlet becomes more localized on the lower energy unit as the length of the bridge is increased, slowing down iSF relative to analogous symmetric dimers. We resolve the recombination kinetics of the inequivalent triplets produced via iSF, and find that they primarily decay via concerted processes. By identifying different decay channels, including delayed fluorescence via triplet-triplet annihilation, we can separate transient species corresponding to both correlated triplet pairs and uncorrelated triplets. Recombination of the triplet pair proceeds rapidly despite our experimental and theoretical demonstration that individual triplets are highly localized and unable to be transported across the conjugated linker. In this class of compounds, the rate of formation and yield of uncorrelated triplets increases with bridge length. Overall, these constrained, asymmetric systems provide a unique platform to isolate and study transient species essential for singlet fission, which are otherwise difficult to observe in symmetric dimers or condensed phases.

  6. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  7. Amino acid salt catalyzed intramolecular Robinson annulation†‡

    PubMed Central

    Li, Pingfan; Yamamoto, Hisashi

    2009-01-01

    The silica gel absorbed amino acid salt catalyzed asymmetric intramolecular Robinson annulation reaction has been developed; up to 97% ee was obtained with this readily recoverable organocatalyst. PMID:19724802

  8. Nuclear spin relaxation due to motion on inequivalent sites: H diffusion on O and T sites in the face-centred cubic structure

    NASA Astrophysics Data System (ADS)

    Luo, Xinjun; Sholl, C. A.

    2003-02-01

    Magnetization recoveries for nuclear spin relaxation of like spins due to magnetic dipolar coupling and diffusion on inequivalent sites involve a sum of exponentials. The theory is applied to diffusion on octahedral and tetrahedral interstitial sites in the face-centred cubic structure. Monte Carlo simulations have been used to generate relaxation data for parameters typical for H in metals. It is found that only a single exponential would be observable in the high- and low-temperature limits, but that two-exponential recoveries could be observable in the vicinity of the maximum in the relaxation rate as a function of temperature. The Monte Carlo relaxation data has been fitted using a Bloembergen-Pound-Purcell (BPP) model to assess the accuracy of the BPP model.

  9. All-optical evaluation of spin-orbit interaction based on diffusive spin motion in a two-dimensional electron gas

    SciTech Connect

    Kohda, M.; Altmann, P.; Salis, G.; Schuh, D.; Ganichev, S. D.; Wegscheider, W.

    2015-10-26

    A method is presented that enables the measurement of spin-orbit coefficients in a diffusive two-dimensional electron gas without the need for processing the sample structure, applying electrical currents or resolving the spatial pattern of the spin mode. It is based on the dependence of the average electron velocity on the spatial distance between local excitation and detection of spin polarization, resulting in a variation of spin precession frequency that in an external magnetic field is linear in the spatial separation. By scanning the relative positions of the exciting and probing spots in a time-resolved Kerr rotation microscope, frequency gradients along the [100] and [010] crystal axes of GaAs/AlGaAs QWs are measured to obtain the Rashba and Dresselhaus spin-orbit coefficients, α and β. This simple method can be applied in a variety of materials with electron diffusion for evaluating spin-orbit coefficients.

  10. Classifying Motion.

    ERIC Educational Resources Information Center

    Duzen, Carl; And Others

    1992-01-01

    Presents a series of activities that utilizes a leveling device to classify constant and accelerated motion. Applies this classification system to uniform circular motion and motion produced by gravitational force. (MDH)

  11. Classifying Motion.

    ERIC Educational Resources Information Center

    Duzen, Carl; And Others

    1992-01-01

    Presents a series of activities that utilizes a leveling device to classify constant and accelerated motion. Applies this classification system to uniform circular motion and motion produced by gravitational force. (MDH)

  12. A numerical study of primary production related to vertical turbulent diffusion with special reference to vertical motions of the phytoplankton cells in nutrient and light fields

    NASA Astrophysics Data System (ADS)

    Zakardjian, Bruno; Prieur, Louis

    1994-08-01

    Assuming stationary physical processes, in particular the light field and turbulent activity [ K( z)], we described steady-state and convergent solutions obtained from a simple time-dependent vertical model of phytoplankton dynamics. Simulations included vertical turbulent motions experienced by the cells in the light and nutrient fields. Parallel simulations made with a classical formulation of phytoplankton growth, i.e., neglecting vertical turbulent motions, are discussed. From two typical situations of stratification in the Western Mediterranean, we identified two distinct systems of new production, as the consequence of Low (LTR) and High Turbulent Regime (HTR) in the photic zone respectively. Data from the Prolig-II (1985) and Almofront-I (1991) cruises supported the LTR system of new production. The results of the second part of the Mediprod-I (1969) cruise show several patterns that specifically appeared in the HTR simulation. Regenerated production was not influenced by the turbulent activity situation. In natural conditions, regenerated production depends on the specific phytoplankton-grazers system that develops according to the level of new production; such ecological dynamics were not considered in our model. Differences with the reference model changed the relationships between the vertical distributions of biomass and new production. Particularly, the HTR simulation led to distinct vertical distribution of biomass and new production. Such a pattern did not occur with the reference model. Although the vertical turbulent motions affected both the level and vertical distribution of new production, a significant effect on the depth-integrated production finally depends on how the phytoplankton biomass interacts with its environmental conditions. It is shown that the minimum of K( z) in the euphotic zone determined the system of new production, whereas its values below the euphotic zone scaled the production and biomass levels. The two distinct systems of

  13. Visual information and expert’s idea in Hurst index estimation of the fractional Brownian motion using a diffusion type approximation

    NASA Astrophysics Data System (ADS)

    Taheriyoun, Ali R.; Moghimbeygi, Meisam

    2017-02-01

    An approximation of the fractional Brownian motion based on the Ornstein-Uhlenbeck process is used to obtain an asymptotic likelihood function. Two estimators of the Hurst index are then presented in the likelihood approach. The first estimator is produced according to the observed values of the sample path; while the second one employs the likelihood function of the incremental process. We also employ visual roughness of realization to restrict the parameter space and to obtain prior information in Bayesian approach. The methods are then compared with three contemporary estimators and an experimental data set is studied.

  14. Visual information and expert’s idea in Hurst index estimation of the fractional Brownian motion using a diffusion type approximation

    PubMed Central

    Taheriyoun, Ali R.; Moghimbeygi, Meisam

    2017-01-01

    An approximation of the fractional Brownian motion based on the Ornstein-Uhlenbeck process is used to obtain an asymptotic likelihood function. Two estimators of the Hurst index are then presented in the likelihood approach. The first estimator is produced according to the observed values of the sample path; while the second one employs the likelihood function of the incremental process. We also employ visual roughness of realization to restrict the parameter space and to obtain prior information in Bayesian approach. The methods are then compared with three contemporary estimators and an experimental data set is studied. PMID:28195153

  15. 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.

  16. Intramolecular electron arrangement with a rotative trigger.

    PubMed

    Kume, Shoko; Nomoto, Kuniharu; Kusamoto, Tetsuro; Nishihara, Hiroshi

    2009-10-14

    We have constructed a single molecule system, consisting of a ferrocene-tethered copper complex, in which electron transfer between redox centers is triggered by molecular rotational motion. In the compound, an asymmetric methyl-substituted 2,2'-pyridylpyrimidine ligand, tethered to the ferrocene moiety, has two isomeric ring-inversion coordination conformations around the copper center. Both isomeric structures were characterized by X-ray crystallography. (1)H NMR and electrochemical measurements revealed that these isomers interconvert through rotation of the pyrimidine at room temperature, but the process is frozen below 233 K in the solution state. The two isomers undergo different redox processes, and the identity of the first oxidation center alternates between the copper center and ferrocene, as confirmed by chemical oxidation monitored by EPR and UV-vis absorption spectroscopy. Oxidation of the compound causes spontaneous isomerization of the pyrimidine due to the different relative stabilities of the isomers in the monovalent and divalent states. Oxidation in the motionless state at low temperatures extracts the first electron from the ferrocene center. When molecular motion is released by warming, the electron moves from the copper center to the ferrocene, leading to an enhancement of the copper(II) signal in the EPR spectrum. The synchronized motion/electron migration process was observed as a one-step UV-vis absorption spectral conversion.

  17. Vibrational pseudo-diffusive motion of the oxygen octahedra in La{sub 2}CuO{sub 4} and Sr doped La{sub 2}CuO{sub 4} from anelastic and {sup 139}La NQR relaxation

    SciTech Connect

    Cordero, F.; Campana, A.; Corti, M.; Rigamonti, A.; Cantelli, R.; Ferretti, M.

    1999-04-20

    The vibrational dynamics in nearly stoichiometric La{sub 2}CuO{sub 4+{delta}} has been studied by means of anelastic relaxation and by {sup 139}La NQR relaxation. Evidence of dynamical tilting of the octahedra in a double well local potential is obtained with both the experimental techniques. Anelastic relaxation at the quadrupole frequency {nu}{sub Q} {approximately} 19 MHz occurs at T {approximately} 330 K. The data are analyzed in terms of a model of pseudo-diffusive cooperative motion. The measured effective barrier is 2800 K, higher than the one of the local potential because of the cooperative character of the motion. Upon Sr doping the {sup 139}La relaxation is still dominated by the octahedra tilting waves for T > 100 K, while at low temperatures the magnetic relaxation mechanism related to Cu{sup 2+} spin fluctuation dominates. It is argued how the freezing of the tilts (occurring below 100 K in the undoped La{sub 2}CuO{sub 4}) might correspond to the formation of static stripes.

  18. Phase singularity diffusion.

    PubMed

    Cheng, Xiaojun; Lockerman, Yitzchak; Genack, Azriel Z

    2014-06-01

    We follow the trajectories of phase singularities at nulls of intensity in the speckle pattern of waves transmitted through random media as the frequency of the incident radiation is scanned in microwave experiments and numerical simulations. Phase singularities are observed to diffuse with a linear increase of the square displacement 〈R2〉 with frequency shift. The product of the diffusion coefficient of phase singularities in the transmitted speckle pattern and the photon diffusion coefficient through the random medium is proportional to the square of the effective sample length. This provides the photon diffusion coefficient and a method for characterizing the motion of dynamic material systems.

  19. Intramolecular energy transfer in fullerene pyrazine dyads

    SciTech Connect

    Guldi, D.M.; Torres-Garcia, G.; Mattay, J.

    1998-11-26

    Excited-state properties of three different pyrazine derivatives 4--6 were probed by emission and transient absorption spectroscopy. They display emission maxima at 464 (4), 417 (5), and 515 nm (6) that are red-shifted with respect to their strong UV ground-state absorption and formed with overall quantum yields ({Phi}) of 0.156, 0.22, and 0.13, respectively. Once photoexcited, these triplet excited pyrazines undergo rapid intermolecular energy transfer to a monofunctionalized fullerene derivative (7) with bimolecular rate constants ranging from 3.64 {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1} (6) to 1.1 {times} 10{sup 10} M{sup {minus}1} s{sup {minus}1} (4). The product of these bimolecular energy-transfer reactions is in all cases the fullerene triplet excited state. Functionalization of pristine C{sub 60} with the investigated pyrazine derivatives promotes the UV-vis absorption characteristics and, in turn, improves the light-harvesting efficiency of the resulting dyads 1--3 relative to pristine C{sub 60}. Photoexcitation of the pyrazine moieties in dyads 1--3 leads to the formation of their singlet excited states. In contrast to the pyrazine models, photoexcitation of dyad 1--3 is followed by rapid intramolecular deactivation processes of the latter via energy transfer to the fullerene ground state with half-lives between 37 and 100 ps. In turn, energy transfer transforms the short-lived and moderately redox-active singlet excited states of pyrazine into the highly reactive fullerene triplet excited state. The latter is found to produce effectively singlet oxygen ({sup 1}O{sub 2}) with quenching rate constants for 1--3 of (1--1.5) {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1}. Similarly, reductive quenching of the triplet excited states in dyads 1--3 via electron transfer with diazabicyclooctane (DABCO) occurs with rate constants of 5.2--9.4 {times} 10{sup 7} M{sup {minus}1} s{sup {minus}1}.

  20. Photochemical Dynamics of Intramolecular Singlet Fission

    NASA Astrophysics Data System (ADS)

    Lin, Zhou; Iwasaki, Hikari; Van Voorhis, Troy

    2017-06-01

    Singlet fission (SF) converts a singlet exciton (S_1) into a pair of triplet ones (T_1) via a ``multi-exciton'' (ME) intermediate: S_1 \\longleftrightarrow ^1ME \\longleftrightarrow ^1(T_1T_1) \\longrightarrow 2T_1. In exothermic cases, e.g., crystalline pentacene or its derivatives, the quantum yield of SF can reach 200%. With SF doubling the electric current generated by an incident high-energy photon, the solar conversion efficiency in pentacene-based organic photovoltaics (OPVs) can exceed the Shockley-Queisser limit of 33.7%. The ME state is popularly considered to be a dimeric state with significant charge transfer (CT) character that is strongly coupled to both S_1 and ^1(T_1T_1), while this local model lacks strong support from full quantum dynamics studies. Intramolecular SF (ISF) occurring to covalently-bound dimers in the solution phase is an excellent model for a straightforward dynamics simulation of local excitons. In the present study, we investigate the ISF mechanisms for three covalently-bound dimers of pentacene derivatives, including ortho-, meta-, and para-bis(6,13-bis(triisopropylsilylethynyl)pentacene)benzene, in non-protic solvents. Specifically, we propagate the real-time, non-adiabatic quantum mechanical/molecular mechanical (QM/MM) dynamics on the potential energy surfaces associated with the states of S_1, ^1(T_1T_1) and CT. We explore how the energies of these ISF-relevant states and the non-adiabatic couplings between each other fluctuate with time and the instantaneous molecular configuration (e.g., intermonomer distance and orientation). We also quantitatively compare Condon and non-Condon ISF dynamics with solution-phase spectroscopic data. Our results allow us to understand the roles of CT energy levels in the ISF mechanism and propose a design strategy to maximize ISF efficiency. M. B. Smith and J. Michl, Chem. Rev. 110, 6891 (2010). W. Shockley and H. J. Queisser, J. Appl. Phys. 32, 510 (1961). T. C. Berkelbach, M. S. Hybertsen

  1. Racing Carbon Atoms. Atomic Motion Reaction Coordinates and Structural Effects on Newtonian Kinetic Isotope Effects

    PubMed Central

    Andujar-De Sanctis, Ivonne L.

    2012-01-01

    Intramolecular 13C kinetic isotope effects were determined for the dimerization of methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newton’s second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity. PMID:23025278

  2. Racing carbon atoms. Atomic motion reaction coordinates and structural effects on Newtonian kinetic isotope effects.

    PubMed

    Andujar-De Sanctis, Ivonne L; Singleton, Daniel A

    2012-10-19

    Intramolecular (13)C kinetic isotope effects were determined for the dimerization of methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newton's second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity.

  3. The role of intramolecular scattering in K-shell photoionization

    NASA Astrophysics Data System (ADS)

    Ayuso, D.; Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2014-04-01

    We report evidence of intramolecular scattering occurring in inner shell photoionization of small molecules. Pronounced oscillations of the ratios between vibrationally resolved cross sections (v-ratios) as a function of photon energy have been observed theoretically and experimentally. Qualitative agreement with a 1st Born model confirms that they are due to intramolecular scattering: when an electron is ejected from a very localized region in the center of a polyatomic molecule, such as the C(1s) orbital in a CF4 molecule, it is diffracted by the surrounding atomic centers, encoding the geometry of the molecule [1, 2].

  4. Intramolecular donor-acceptor cyclopropane ring-opening cyclizations.

    PubMed

    Cavitt, Marchello A; Phun, Lien H; France, Stefan

    2014-02-07

    Cyclization reactions of donor-acceptor (D-A) cyclopropanes are recognized as versatile methods for construction of carbocyclic and heterocyclic scaffolds. In the literature, many examples of these polarized cyclopropanes' reactivity with nucleophiles, electrophiles, and radicals are prevalent. Although intermolecular reactivity of donor-acceptor cyclopropanes is widely reported, reviews that center on their intramolecular chemistry are rare. Thereupon, this tutorial review focalizes on new intramolecular transformations of donor-acceptor cyclopropanes for cycloisomerizations, formal cycloadditions, umpolung reactions, rearrangements and ring-opening lactonizations/lactamizations from 2009 to 2013. Furthermore, the role of D-A acceptor cyclopropanes as reactive subunits in natural product synthesis is underscored.

  5. Intramolecular nonbonded S...N interaction in rabeprazole.

    PubMed

    Hayashi, Kazuhiko; Ogawa, Shiho; Sano, Shigeki; Shiro, Motoo; Yamaguchi, Kentaro; Sei, Yoshihisa; Nagao, Yoshimitsu

    2008-06-01

    Intramolecular nonbonded S...N interactions in the crystal structures of the derivatives (7a-d) of sodium rabeprazole (1) and an intermolecular nonbonded S...N interaction between ethylmethylsulfoxide and pyridine in a solution were recognized. These results made us estimate that the intramolecular nonbonded S...N interaction existed in 1 and its derivatives in a solution, and formed the 4-membered quasi-ring in 2 (Fig. 1) followed by the increase of the reactivity of 2 to give the putative spiro sulfoxide 3, which is the key intermediate in the reaction cascade of 1 (Chart 1).

  6. Rational Design for Rotaxane Synthesis through Intramolecular Slippage: Control of Activation Energy by Rigid Axle Length.

    PubMed

    Masai, Hiroshi; Terao, Jun; Fujihara, Tetsuaki; Tsuji, Yasushi

    2016-05-04

    We describe a new concept for rotaxane synthesis through intramolecular slippage using π-conjugated molecules as rigid axles linked with organic soluble and flexible permethylated α-cyclodextrins (PM α-CDs) as macrocycles. Through hydrophilic-hydrophobic interactions and flipping of PM α-CDs, successful quantitative conversion into rotaxanes was achieved without covalent bond formation. The rotaxanes had high activation barrier for their de-threading, so that they were kinetically isolated and derivatized even under conditions unfavorable for maintaining the rotaxane structures. (1) H NMR spectroscopy experiments clearly revealed that the restricted motion of the linked macrocycle with the rigid axle made it possible to control the kinetic stability by adjusting the length of the rigid axle in the precursor structure rather than the steric bulkiness of the stopper unit.

  7. Motion Sickness

    MedlinePlus

    Motion sickness is a common problem in people traveling by car, train, airplanes, and especially boats. Anyone ... children, pregnant women, and people taking certain medicines. Motion sickness can start suddenly, with a queasy feeling ...

  8. Oxacycle synthesis via intramolecular reaction of carbanions and peroxides.

    PubMed

    Willand-Charnley, Rachel; Puffer, Benjamin W; Dussault, Patrick H

    2014-04-23

    The intramolecular reaction of dialkyl peroxides with carbanions, generated via chemoselective metal-heteroatom exchange or deprotonation, provides a new approach to cyclic ethers. Applied in tandem with C-C bond formation, the strategy enables a one-step annelation to form oxaospirocycles.

  9. Oxacycle Synthesis via Intramolecular Reaction of Carbanions and Peroxides

    PubMed Central

    2015-01-01

    The intramolecular reaction of dialkyl peroxides with carbanions, generated via chemoselective metal-heteroatom exchange or deprotonation, provides a new approach to cyclic ethers. Applied in tandem with C–C bond formation, the strategy enables a one-step annelation to form oxaospirocycles. PMID:24702123

  10. Synthesis of Antitumor Lycorines by Intramolecular Diels-Alder Reaction.

    PubMed

    Pérez, Dolores; Burés, Gema; Guitián, Enrique; Castedo, Luis

    1996-03-08

    Pharmacologically interesting lycorines were obtained by a short, efficient method based on an intramolecular Diels-Alder reaction between an alpha-pyrone and an alkyne, followed by loss of CO(2) in a retro Diels-Alder reaction. The cyclization precursors (pyrones 9) were obtained in good yields in two or three steps from the corresponding homophthalic acid or anhydride.

  11. Diffusion in monodisperse ferrofluids

    NASA Astrophysics Data System (ADS)

    Peredo-Ortíz, R.; Hernández-Contreras, M.; Hernández Gómez, R.

    2017-01-01

    The diffusion coefficients characterizing the translational and rotational Brownian motion of a particle in a concentrated suspension were determined in the long time diffusive regime for a ferrofluid suspension with the use of a Langevin equation approach. These dynamical properties depend on the equilibrium micro-structural information of the suspension and take into account the effect of direct anisotropic inter-particle's interactions on self-diffusion. The comparison of this theory with Brownian dynamic simulations results is made in terms of colloid density and dipole interaction strength.

  12. Fractional Levy motion through path integrals

    SciTech Connect

    Calvo, Ivan; Sanchez, Raul; Carreras, Benjamin A

    2009-01-01

    Fractional Levy motion (fLm) is the natural generalization of fractional Brownian motion in the context of self-similar stochastic processes and stable probability distributions. In this paper we give an explicit derivation of the propagator of fLm by using path integral methods. The propagators of Brownian motion and fractional Brownian motion are recovered as particular cases. The fractional diffusion equation corresponding to fLm is also obtained.

  13. Diffusion in Coulomb crystals.

    PubMed

    Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

    2011-07-01

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  14. Diffusion in Coulomb crystals

    SciTech Connect

    Hughto, J.; Schneider, A. S.; Horowitz, C. J.; Berry, D. K.

    2011-07-15

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions ''hop'' in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter {Gamma}=175 to Coulomb parameters up to {Gamma}=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  15. Teaching Diffusion with a Coin

    ERIC Educational Resources Information Center

    Haddad, Hamilton; Baldo, Marcus Vinicius Chrysostomo

    2010-01-01

    In this article, the authors describe an inexpensive and simple way to make students intuitively experience the probabilistic nature and nonorientated motion of diffusing particles. This understanding allows students to realize why diffusion works so well over short distances and becomes increasingly and rapidly less effective as the distances…

  16. Recent insights into intramolecular 13C isotope composition of biomolecules

    NASA Astrophysics Data System (ADS)

    Gilbert, A.; Yamada, K.; Julien, M.; Yoshida, N.; Remaud, G.; Robins, R.

    2016-12-01

    In 1961 Abelson & Hoering shown that the intramolecular 13C distribution in amino acids was not homogeneous, namely the carboxylic acid positions were 13C-enriched compared with the mean of the remaining C-atoms in the molecule [1]. Nearly 20 years later, Monson & Hayes were able to demonstrate that even and odd positions in acetogenic fatty acids also showed non-statistical 13C isotope distributions, and that the pattern varied depending on the organism [2]. It took a further decade for the intramolecular 13C distribution in the key metabolite, glucose, to be defined [3]. Although informative, much of this work was incomplete, a number of positions having to be deduced by difference. This limitation arose mainly due to the lack of techniques enabling the separation and quantification of 13C isotopomers of the target molecule. In the past decade, quantitative 13C NMR has been developed for the determination of the intramolecular isotope composition of a given molecule with a precision of 1‰ or better [4]. This breakthrough has made possible a comprehensive view of the determinants governing intramolecular isotope composition of biological molecules. In particular, it can be shown that intramolecular pattern in sugars is influenced by the C-assimilation pathway and by post-photosynthetic fractionation associated with carbohydrate metabolism [5]. In addition, analysis by NMR of the alkyl chain of acetogenic lipids (fatty acids, n-alkanes) shows an alternation between odd and even C-atom positions, as observed by Monson& Hayes [2], throughout the molecule [6]. Overall, it is becoming apparent that this pattern is influenced by two principal metabolic factors: (i) the 13C pattern extant in the starting compounds; (ii) isotope fractionation associated with the enzymes involved in the biosynthetic pathway. On the whole, the determination of intramolecular isotope patterns in biomolecules allows better insights into the conditions and pathways by which they are formed

  17. Dendrimer light-harvesting: intramolecular electrodynamics and mechanisms.

    PubMed

    Andrews, David L; Bradshaw, David S; Jenkins, Robert D; Rodríguez, Justo

    2009-12-07

    In the development of highly efficient materials for harvesting solar energy, there is an increasing focus on purpose-built dendrimers and allied multi-chromophore systems. A proliferation of antenna chromophores is not the only factor determining the sought light-harvesting efficiency; the internal geometry and photophysics of these molecules are also crucially important. In particular, the mechanisms by means of which radiant energy is ultimately trapped depends on an intricate interplay of electronic, structural, energetic and symmetry properties. To better understand these processes a sound theoretical representation of the intramolecular electrodynamics is required. A suitable formalism, based on quantum electrodynamics, readily delivers physical insights into the necessary excitation channelling processes, and it affords a rigorous basis for modelling the intramolecular flow of energy.

  18. Proximity vs. strain in intramolecular ring-closing reactions

    NASA Astrophysics Data System (ADS)

    Karaman, Rafik

    2010-07-01

    The DFT and ab initio calculation results for ring-closing reactions of eight different ω-bromoalkanecarboxylate anions (1-8) reveal that the activation energy (ΔG ‡) for the intramolecular cyclization process is strongly correlated with both (i) the experimental intramolecular cyclization rate (log k intra) and (ii) the distance between the two reactive centres, whereas the slope values of the change in enthalpy (ΔH) vs. the attack angle (α) and the distance between the two reacting centres (r) were found to correlate strongly with the experimental strain energy of the cycle being formed (E s Exp). These results assist in designing pro-prodrug systems that can be utilized to improve the overall biopharmaceutical profile of current medications in order to enhance their effectiveness and ease their utility.

  19. Intramolecular Aminocyanation of Alkenes via N–CN Bond Cleavage**

    PubMed Central

    Pan, Zhongda; Pound, Sarah M.; Rondla, Naveen R.; Douglas, Christopher J.

    2014-01-01

    A metal-free, Lewis acid-promoted intramolecular aminocyanation of alkenes was developed. B(C6F5)3 activates N-sulfonyl cyanamides, leading an formal cleavage of the N-CN bonds in conjunction with vicinal addition of sulfonamide and nitrile groups across an alkene. This method enables atom-economical access to indolines and tetrahydroquinolines in excellent yields, and provides a complementary strategy for regioselective alkene difunctionalizations with sulfonamide and nitrile groups. Labeling experiments with 13C suggest a fully intramolecular cyclization pattern due to lack of label scrambling in double crossover experiments. Catalysis with Lewis acid is realized and the reaction can be conducted under air. PMID:24719371

  20. Intramolecular aminocyanation of alkenes by N-CN bond cleavage.

    PubMed

    Pan, Zhongda; Pound, Sarah M; Rondla, Naveen R; Douglas, Christopher J

    2014-05-12

    A metal-free, Lewis acid promoted intramolecular aminocyanation of alkenes was developed. B(C6F5)3 activates N-sulfonyl cyanamides, thus leading to a formal cleavage of the N-CN bonds in conjunction with vicinal addition of sulfonamide and nitrile groups across an alkene. This method enables atom-economical access to indolines and tetrahydroquinolines in excellent yields, and provides a complementary strategy for regioselective alkene difunctionalizations with sulfonamide and nitrile groups. Labeling experiments with (13)C suggest a fully intramolecular cyclization pattern due to the lack of label scrambling in double crossover experiments. Catalysis with Lewis acid is realized and the reaction can be conducted under air. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Intramolecular amide bonds stabilize pili on the surface of bacilli

    SciTech Connect

    Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.; Whitelegge, Julian P.; He, Chuan; Schneewind, Olaf

    2010-01-12

    Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.

  2. Fractal model of anomalous diffusion.

    PubMed

    Gmachowski, Lech

    2015-12-01

    An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.

  3. Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin

    PubMed Central

    Krishnan, V. V.; Lau, Edmond Y.; Yamada, Justin; Denning, Daniel P.; Patel, Samir S.; Colvin, Michael E.; Rexach, Michael F.

    2008-01-01

    The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine–glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin–cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion. PMID:18688269

  4. The Physical Chemistry of the Intramolecular Cyclodehydration Reactions of Prepolymers

    NASA Astrophysics Data System (ADS)

    Rabinovich, I. B.; Karyakin, Nikolai V.; Rusanov, Aleksandr L.; Korshak, V. V.

    1986-07-01

    The experimental data on the thermodynamics of the intramolecular cyclodehydration reactions of prepolymers in the solid phase are examined and treated systematically. The changes in the thermodynamic functions of the above processes have been analysed in detail over a wide temperature range. The temperature ranges corresponding to the formation of polyheteroarylenes which are "defect-free" to the maximum extent have been estimated. The bibliography includes 65 references.

  5. Overcoming product inhibition in catalysis of the intramolecular Schmidt reaction.

    PubMed

    Motiwala, Hashim F; Fehl, Charlie; Li, Sze-Wan; Hirt, Erin; Porubsky, Patrick; Aubé, Jeffrey

    2013-06-19

    A method for carrying out the intramolecular Schmidt reaction of alkyl azides and ketones using a substoichiometric amount of catalyst is reported. Following extensive screening, the use of the strong hydrogen-bond-donating solvent hexafluoro-2-propanol was found to be consistent with low catalyst loadings, which ranged from 2.5 mol % for favorable substrates to 25 mol % for more difficult cases. Reaction optimization, broad substrate scope, and preliminary mechanistic studies of this improved version of the reaction are described.

  6. Overcoming Product Inhibition in Catalysis of the Intramolecular Schmidt Reaction

    PubMed Central

    Motiwala, Hashim F.; Fehl, Charlie; Li, Sze-Wan; Hirt, Erin; Porubsky, Patrick; Aubé, Jeffrey

    2014-01-01

    A method for carrying out the intramolecular Schmidt reaction of alkyl azides and ketones using a substoichiometric amount of catalyst is reported. Following extensive screening, the use of the strong hydrogen bond donating solvent hexafluoro-2-propanol was found to be consistent with low catalyst loadings, which range from 2.5 mol% for favorable substrates to 25 mol% for more difficult cases. Reaction optimization, broad substrate scope, and preliminary mechanistic studies of this improved version of the reaction are described. PMID:23687993

  7. Short intramolecular hydrogen bonds: derivatives of malonaldehyde with symmetrical substituents.

    PubMed

    Hargis, Jacqueline C; Evangelista, Francesco A; Ingels, Justin B; Schaefer, Henry F

    2008-12-24

    A systematic study of various derivatives of malonaldehyde has been carried out to explore very short hydrogen bonds (r(OO) < 2.450 A). Various electron-withdrawing groups, including CN, NO(2), and BH(2), have been attached to the central carbon atom, C(2). To C(1) and C(3), strong electron donors and/or sterically hindered substituents were used to strengthen the intramolecular hydrogen bond, including but not limited to NH(2), N(CH(3))(2), and C(CH(3))(3). Seven molecules (Figure 2 ) were found to have extremely short intramolecular hydrogen bonds. The chemical systems investigated are intriguing due to their low energetic barriers for the intramolecular hydrogen atom transfers. Classical barriers were predicted using correlated methods including second-order perturbation theory and coupled cluster theory in conjunction with the Dunning hierarchy of correlation consistent basis sets, cc-pVXZ (X = D, T, Q, 5). Focal point analyses allowed for the barriers to be evaluated at the CBS limit including core correlation and zero-point vibrational energy corrections. B3LYP energies are benchmarked against highly accurate correlated energies for intramolecular hydrogen bonded systems. The focal point extrapolated method, including coupled cluster full triple excitation contributions, gives a hydrogen transfer barrier for malonaldehyde of approximately 4 kcal mol(-1). We describe two compounds with extremely low classical barriers, nitromalonamide (0.43 kcal mol(-1)) and 2-borylmalonamide (0.60 kcal mol(-1)). An empirical relationship was drawn between the B3LYP energetic barriers and the predicted coupled cluster barriers at the CBS limit. By relating these two quantities, barrier heights may be estimated for systems too large to presently use highly correlated electronic structure methods.

  8. Communication: Pseudoisomorphs in liquids with intramolecular degrees of freedom

    NASA Astrophysics Data System (ADS)

    Olsen, Andreas Elmerdahl; Dyre, Jeppe C.; Schrøder, Thomas B.

    2016-12-01

    Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be identified by requiring scale invariance of the inherent-structure reduced-unit low-frequency vibrational spectrum evaluated for a single equilibrium configuration. This rationalizes why generalized excess-entropy scaling, density scaling, and isochronal superposition apply for many liquids with internal degrees of freedom.

  9. Bimorpholine-mediated enantioselective intramolecular and intermolecular aldol condensation.

    PubMed

    Kanger, Tõnis; Kriis, Kadri; Laars, Marju; Kailas, Tiiu; Müürisepp, Aleksander-Mati; Pehk, Tõnis; Lopp, Margus

    2007-07-06

    Monosalts of N-substituted bimorpholine derivatives are efficient organocatalysts in intramolecular and intermolecular aldol reactions. The properties of the catalysts can be tuned either by the selection of an appropriate acid for the salt formation or by the change of a substituent at the nitrogen atom. In aldol condensation, i-Pr-substituted bimorpholine is the most stereoselective catalyst affording products in high yield with enantioselectivities up to 95% ee.

  10. Ultrafast excited-state intramolecular proton transfer of aloesaponarin I.

    PubMed

    Nagaoka, Shin-ichi; Uno, Hidemitsu; Huppert, Dan

    2013-04-25

    Time-resolved emission of aloesaponarin I was studied with the fluorescence up-conversion and time-correlated single-photon-counting techniques. The rates of the excited-state intramolecular proton transfer, of the solvent and molecular rearrangements, and of the decay from the excited proton-transferred species were determined and interpreted in the light of time-dependent density functional calculations. These results were discussed in conjunction with UV protection and singlet-oxygen quenching activity of aloe.

  11. Visible-Light Photocatalytic Intramolecular Cyclopropane Ring Expansion.

    PubMed

    Luis-Barrera, Javier; Laina-Martín, Víctor; Rigotti, Thomas; Peccati, Francesca; Solans-Monfort, Xavier; Sodupe, Mariona; Mas-Ballesté, Rubén; Liras, Marta; Alemán, José

    2017-06-26

    Described herein is a new visible-light photocatalytic strategy for the synthesis of enantioenriched dihydrofurans and cyclopentenes by an intramolecular nitro cyclopropane ring expansion reaction. Mechanistic studies and DFT calculations are used to elucidate the key factors in this new ring expansion reaction, and the need for the nitro group on the cyclopropane. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Correlated diffusion imaging

    PubMed Central

    2013-01-01

    Background Prostate cancer is one of the leading causes of cancer death in the male population. Fortunately, the prognosis is excellent if detected at an early stage. Hence, the detection and localization of prostate cancer is crucial for diagnosis, as well as treatment via targeted focal therapy. New imaging techniques can potentially be invaluable tools for improving prostate cancer detection and localization. Methods In this study, we introduce a new form of diffusion magnetic resonance imaging called correlated diffusion imaging, where the tissue being imaged is characterized by the joint correlation of diffusion signal attenuation across multiple gradient pulse strengths and timings. By taking into account signal attenuation at different water diffusion motion sensitivities, correlated diffusion imaging can provide improved delineation between cancerous tissue and healthy tissue when compared to existing diffusion imaging modalities. Results Quantitative evaluation using receiver operating characteristic (ROC) curve analysis, tissue class separability analysis, and visual assessment by an expert radiologist were performed to study correlated diffusion imaging for the task of prostate cancer diagnosis. These results are compared with that obtained using T2-weighted imaging and standard diffusion imaging (via the apparent diffusion coefficient (ADC)). Experimental results suggest that correlated diffusion imaging provide improved delineation between healthy and cancerous tissue and may have potential as a diagnostic tool for cancer detection and localization in the prostate gland. Conclusions A new form of diffusion magnetic resonance imaging called correlated diffusion imaging (CDI) was developed for the purpose of aiding radiologists in cancer detection and localization in the prostate gland. Preliminary results show CDI shows considerable promise as a diagnostic aid for radiologists in the detection and localization of prostate cancer. PMID:23924150

  13. Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores.

    PubMed

    van der Velde, Jasper H M; Ploetz, Evelyn; Hiermaier, Matthias; Oelerich, Jens; de Vries, Jan Willem; Roelfes, Gerard; Cordes, Thorben

    2013-12-16

    Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark-states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self-healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet-related dark-states, which is a mechanism that appears to be common for both triplet-state quenchers (cyclooctatetraene) and redox-active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution-additives, such as cysteamine and procatechuic acid, on the self-healing process are studied. The results suggest the potential applicability of self-healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super-resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self-healing fluorophores, including their applications in various research fields.

  14. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  15. Intramolecular bridges formed by photoswitchable click amino acids.

    PubMed

    Hoppmann, Christian; Kühne, Ronald; Beyermann, Michael

    2012-01-01

    Photoswitchable click amino acids (PSCaa) are amino acids bearing a side chain consisting of a photoswitchable unit elongated with a functional group that allows for a specific click reaction, such as an alkene that can react with the thiol group of a cysteine residue. An intramolecular click reaction results in the formation of a photoswitchable bridge, which can be used for controlling conformational domains in peptides and proteins. The ability to control conformations as well as the efficiency of the intramolecular bridging depends on the length of the PSCaa side chain and the distance to the cysteine residue to be clicked with. On comparing i,i+4 and i,i+7 spacings of PSCaa and cysteine in a model peptide without a preferred conformation, it was seen that the thiol-ene click reaction takes place efficiently in both cases. Upon induction of an α-helical structure by the addition of trifluoroethanol, the thiol click reaction occurs preferentially with the i,i+4 spacing. Even in the presence of glutathione as an additional thiol the click reaction of the PSCaa occurs intramolecularly with the cysteine rather than with the glutathione, indicating that the click reaction may be used even under reducing conditions occurring in living cells.

  16. Stereocontrolled intramolecular iron-mediated diene/olefin cyclocoupling

    NASA Astrophysics Data System (ADS)

    Dorange, Ismet B.

    A methodology for stereocontrol during the intramolecular coupling between cyclohexadiene-Fe(CO)3 complexes and pendant alkenes is presented. Introduction of a methoxy group at the C(3) position of the diene moiety controls pre- and post-cyclization rearrangements of the diene Fe(CO)3 unit, allowing the preparation of spirolactams with defined relative stereochemistry and with a cyclohexenone framework, thus making this reaction a potentially valuable tool for the construction of quaternary carbon centers.* A new methodology for the formation of tricarbonyl(cyclohexadienyl)ketone iron complexes was also developed. This method involves the coupling of a Grignard reagent with an acyl mesylate iron complex, giving rise to ketone derivatives in excellent yields. The possibility of intramolecular coupling between diene-Fe(CO)3 complexes and homoallylic olefin was demonstrated. The stereospecific formation of spiroketones occurred in excellent yields under thermal conditions, but appeared to be limited to the simpler, less substituted pendant alkenes. The control of the stereochemical outcome of these spirocyclization was achieved using the "C(3) substitution method" previously described. The same trends were observed in these series. Also illustrated in these studies is the extension of this spirocoupling to the formation of a spiro[5.5]undecane framework. It is the first time that this framework has been accessed using this intramolecular coupling.* *Please refer to dissertation for diagram.

  17. Ultraslow scaled Brownian motion

    NASA Astrophysics Data System (ADS)

    Bodrova, Anna S.; Chechkin, Aleksei V.; Cherstvy, Andrey G.; Metzler, Ralf

    2015-06-01

    We define and study in detail utraslow scaled Brownian motion (USBM) characterized by a time dependent diffusion coefficient of the form D(t)≃ 1/t. For unconfined motion the mean squared displacement (MSD) of USBM exhibits an ultraslow, logarithmic growth as function of time, in contrast to the conventional scaled Brownian motion. In a harmonic potential the MSD of USBM does not saturate but asymptotically decays inverse-proportionally to time, reflecting the highly non-stationary character of the process. We show that the process is weakly non-ergodic in the sense that the time averaged MSD does not converge to the regular MSD even at long times, and for unconfined motion combines a linear lag time dependence with a logarithmic term. The weakly non-ergodic behaviour is quantified in terms of the ergodicity breaking parameter. The USBM process is also shown to be ageing: observables of the system depend on the time gap between initiation of the test particle and start of the measurement of its motion. Our analytical results are shown to agree excellently with extensive computer simulations.

  18. Solution conformation of peptides by the intramolecular nuclear Overhauser effect experiment. Study of valinomycin-K+.

    PubMed Central

    Krishna, N R; Agresti, D G; Glickson, J D; Walter, R

    1978-01-01

    This study demonstrates how the intramolecular nuclear Overhauser effect (NOE) experiment can be employed quantitatively to select from a set of possible conformations for a peptide or a protein the particular conformation (or a group of conformations) most consistent with the data. This procedure is demonstrated on a model depsipeptide system--valinomycin K+ in CDCl3--for which the solution conformation has been inferred by other methods. The NOE enhancements are very sensitive to the conformations assumed by this antibiotic. It is shown that the set of conformations, collectively labeled as A2 (including the X-ray crystallographic structure) gives a very good description of the NOE enhancements. The structure proposed by Bystrov et al. (1977. Eur. J. Biochem. 78:63) for the uncomplexed valinomycin in nonpolar solvents is also consistent with the experimental data on the potassium complex. Using statistical hypothesis testing involving the Hamilton R-factor ratio criterion, all the other models have been rejected as inconsistent with the experimental data. A general formalism is presented for describing the NOE effects in isotropically reorienting molecules. The formalism is not restricted to the extreme narrowing limit of the rotational correlation times and hence applies to both small and large molecules. Some of the factors that can influence the NOE measurements, viz. anisotropic rotational diffusion, conformational averaging, and nuclear spin diffusion, have been considered in this study. PMID:737287

  19. Evaluation of a Simplified Intravoxel Incoherent Motion (IVIM) Analysis of Diffusion-Weighted Imaging for Prediction of Tumor Size Changes and Imaging Response in Breast Cancer Liver Metastases Undergoing Radioembolization: A Retrospective Single Center Analysis.

    PubMed

    Pieper, Claus C; Sprinkart, Alois M; Meyer, Carsten; König, Roy; Schild, Hans H; Kukuk, Guido M; Mürtz, Petra

    2016-04-01

    To investigate the value of a simplified intravoxel incoherent motion (IVIM) analysis for evaluation of therapy-induced tumor changes and response of breast cancer liver metastases (mBRC) undergoing radioembolization.In 21 females (mean age 54 years, range 43-72) with mBRC tumor size changes and response evaluation criteria in solid tumors (RECIST) response to 26 primary radioembolization procedures were analyzed. Standard 1.5-T liver magnetic resonance imaging including respiratory-gated diffusion-weighted imaging (DWI) with b0 = 0 s/mm, b1 = 50 s/mm, b2 = 800 s/mm before and 6 weeks after each treatment was performed. In addition to the apparent diffusion coefficient (ADC)(0,800), the estimated diffusion coefficient D' and the perfusion fraction f' were determined using a simplified IVIM approach. For each radioembolization, the 2 largest treated metastases (if available) were analyzed. Lesions were categorized according to size changes into group A (reduction of longest diameter [LD]) and group B (LD increase) after 3 months. Radioembolization procedures were further categorized into "response" (partial response and stable disease) and "nonresponse" (progressive disease) according to RECIST after 3 months. ADC and D' are given in 10 mm/s.Forty-five metastases were analyzed. Thirty-two lesions were categorized as A; 13 as B. Before therapy, group A lesions showed significantly larger f'-values than B (P = 0.001), but ADC(0,800) and D' did not differ. After therapy, in group A lesions the ADC(0,800)- and D'-values increased and f' decreased (P < 0.0001); in contrast in group B lesions f' increased (P = 0.001). Groups could be differentiated by preinterventional f' and by changes of D' and f' between pre and postinterventional imaging (area under the curve [AUC] of 0.903, 0.747 and 1.0, respectively).Preinterventional parameters did not differ between responders and nonresponders according to RECIST. ADC(0,800)- and D'-values showed a

  20. Evaluation of a Simplified Intravoxel Incoherent Motion (IVIM) Analysis of Diffusion-Weighted Imaging for Prediction of Tumor Size Changes and Imaging Response in Breast Cancer Liver Metastases Undergoing Radioembolization

    PubMed Central

    Pieper, Claus C.; Sprinkart, Alois M.; Meyer, Carsten; König, Roy; Schild, Hans H.; Kukuk, Guido M.; Mürtz, Petra

    2016-01-01

    Abstract To investigate the value of a simplified intravoxel incoherent motion (IVIM) analysis for evaluation of therapy-induced tumor changes and response of breast cancer liver metastases (mBRC) undergoing radioembolization. In 21 females (mean age 54 years, range 43–72) with mBRC tumor size changes and response evaluation criteria in solid tumors (RECIST) response to 26 primary radioembolization procedures were analyzed. Standard 1.5-T liver magnetic resonance imaging including respiratory-gated diffusion-weighted imaging (DWI) with b0 = 0 s/mm2, b1 = 50 s/mm2, b2 = 800 s/mm2 before and 6 weeks after each treatment was performed. In addition to the apparent diffusion coefficient (ADC)(0,800), the estimated diffusion coefficient D′ and the perfusion fraction f′ were determined using a simplified IVIM approach. For each radioembolization, the 2 largest treated metastases (if available) were analyzed. Lesions were categorized according to size changes into group A (reduction of longest diameter [LD]) and group B (LD increase) after 3 months. Radioembolization procedures were further categorized into “response” (partial response and stable disease) and “nonresponse” (progressive disease) according to RECIST after 3 months. ADC and D′ are given in 10−6 mm2/s. Forty-five metastases were analyzed. Thirty-two lesions were categorized as A; 13 as B. Before therapy, group A lesions showed significantly larger f′-values than B (P = 0.001), but ADC(0,800) and D′ did not differ. After therapy, in group A lesions the ADC(0,800)- and D′-values increased and f′ decreased (P < 0.0001); in contrast in group B lesions f′ increased (P = 0.001). Groups could be differentiated by preinterventional f′ and by changes of D′ and f′ between pre and postinterventional imaging (area under the curve [AUC] of 0.903, 0.747 and 1.0, respectively). Preinterventional parameters did not differ between responders and nonresponders

  1. Intramolecular Interactions and Regulation of Cofactor Binding by the Four Repressive Elements in the Caspase Recruitment Domain-containing Protein 11 (CARD11) Inhibitory Domain*♦

    PubMed Central

    Jattani, Rakhi P.; Tritapoe, Julia M.

    2016-01-01

    The CARD11 signaling scaffold transmits signaling between antigen receptors on B and T lymphocytes and the transcription factor NF-κB during the adaptive immune response. CARD11 activity is controlled by an inhibitory domain (ID), which participates in intramolecular interactions and prevents cofactor binding prior to receptor triggering. Oncogenic CARD11 mutations associated with the activated B cell-like subtype of diffuse large B cell lymphoma somehow perturb ID-mediated autoinhibition to confer CARD11 with the dysregulated spontaneous signaling to NF-κB that is required for the proliferation and survival of the lymphoma. Here, we investigate how the four repressive elements (REs) we have discovered in the CARD11 ID function to inhibit CARD11 activity with cooperativity and redundancy. We find that each RE contributes to the maintenance of the closed inactive state of CARD11 that predominates in the absence of receptor engagement. Each RE also contributes to the prevention of Bcl10 binding in the basal unstimulated state. RE1, RE2, and RE3 participate in intramolecular interactions with other CARD11 domains and share domain targets for binding. Remarkably, diffuse large B cell lymphoma-associated gain-of-function mutations in the caspase recruitment domain, LATCH, or coiled coil can perturb intramolecular interactions mediated by multiple REs, suggesting how single amino acid oncogenic CARD11 mutations can perturb or bypass the action of redundant inhibitory REs to achieve the level of hyperactive CARD11 signaling required to support lymphoma growth. PMID:26884334

  2. Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.

    PubMed

    Ryu, Kyoung-Seok; Tugarinov, Vitali; Clore, G Marius

    2014-10-15

    The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by (15)Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5-1 s) is many orders of magnitude larger than the calculated transfer time (1-100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.

  3. Diffusion on ruffled membrane surfaces.

    PubMed

    Naji, Ali; Brown, Frank L H

    2007-06-21

    We present a position Langevin equation for overdamped particle motion on rough two-dimensional surfaces. A Brownian dynamics algorithm is suggested to evolve this equation numerically, allowing for the prediction of effective (projected) diffusion coefficients over corrugated surfaces. In the case of static surface roughness, we find that a simple area-scaling prediction for the projected diffusion coefficient leads to seemingly quantitative agreement with numerical results. To study the effect of dynamic surface evolution on the diffusive process, we consider particle diffusion over a thermally fluctuating elastic membrane. Surface fluctuation has the effect of increasing the effective diffusivity toward a limiting annealed-surface value discussed previously. We argue that protein motion over cell surfaces spans a variety of physical regimes, making it impossible to identify a single approximation scheme appropriate to all measurements of interest.

  4. Circular Motion.

    ERIC Educational Resources Information Center

    Lee, Paul D.

    1995-01-01

    Provides a period-long activity using battery powered cars rolling in a circular motion on a tile floor. Students measure the time and distance as the car moves to derive the equation for centripetal acceleration. (MVL)

  5. Circular Motion.

    ERIC Educational Resources Information Center

    Lee, Paul D.

    1995-01-01

    Provides a period-long activity using battery powered cars rolling in a circular motion on a tile floor. Students measure the time and distance as the car moves to derive the equation for centripetal acceleration. (MVL)

  6. Chaotic ion motion in magnetosonic plasma waves

    NASA Technical Reports Server (NTRS)

    Varvoglis, H.

    1984-01-01

    The motion of test ions in a magnetosonic plasma wave is considered, and the 'stochasticity threshold' of the wave's amplitude for the onset of chaotic motion is estimated. It is shown that for wave amplitudes above the stochasticity threshold, the evolution of an ion distribution can be described by a diffusion equation with a diffusion coefficient D approximately equal to 1/v. Possible applications of this process to ion acceleration in flares and ion beam thermalization are discussed.

  7. Recent experimental advances on excited-state intramolecular proton coupled electron transfer reaction.

    PubMed

    Hsieh, Cheng-Chih; Jiang, Chang-Ming; Chou, Pi-Tai

    2010-10-19

    Proton-coupled electron transfer reactions form the basis of many important chemical processes including much of the energy conversion that occurs within living cells. However, much of the physical chemistry that underlies these reaction mechanisms remains poorly understood. In this Account, we report on recent progress in the understanding of excited-state intramolecular proton-coupled electron transfer (PCET) reactions. The strategic design and synthesis of various types of PCET molecules, along with steady-state and femtosecond time-resolved spectroscopy, have uncovered the mechanisms of several excited-state PCET reactions in solution. These experimental advancements correlate well with current theoretical models, in which the proton has quantum motion with a high probability of tunneling. In addition, the rate of proton transfer is commonly incorporated within the rate of rearrangement of solvent molecules. As a result, the reaction activation free energy is essentially governed by the solvent reorganization because the charge redistribution is considered based on a solvent polarity-induced barrier instead of the height of the proton migration barrier. In accord with this theoretical basis, we can rationalize the observation that the proton transfer for many excited-state PCET systems occurs during the solvent relaxation time scale of 1-10 ps: the highly exergonic reaction takes place before the system reaches its equilibrium polarization. Also, we have used various derivatives of proton transfer molecules, especially those of 3-hydroxyflavone to clearly demonstrate how researchers can tune the dynamics of excited-state PCET through changes in the magnitude or direction of the dipole vector within the reaction. Subsequently, using 2-(2'-hydroxyphenyl)benzoxazole as the parent model, we then report on methods for the development of an ideal system for probing PCET reaction. Because future biomedical applications of such systems will likely occur in aqueous

  8. Conserved linear dynamics of single-molecule Brownian motion

    NASA Astrophysics Data System (ADS)

    Serag, Maged F.; Habuchi, Satoshi

    2017-06-01

    Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

  9. Gas-Phase Intramolecular Cyclization of Argentinated N-Allylbenzamides

    NASA Astrophysics Data System (ADS)

    Sun, Hezhi; Chai, Yunfeng; Jin, Zhe; Sun, Cuirong; Pan, Yuanjiang

    2015-05-01

    The fragmentations of argentinated N-allylbenzamides have been exhaustively studied through collision-induced dissociation and through deuterium labeling. The intriguing elimination of AgOH is certified as the consequence of intramolecular cyclization between terminal olefin and carbonyl carbon following proton transfer to carbonyl oxygen, rather than simple enolization of amide. Linear free energy correlations and density functional theory (DFT) calculations were performed to understand the competitive relationship between AgOH loss and AgH loss, which results from the 1,2-elimination of α-hydrogen (to the amido nitrogen) with the silver.

  10. Intramolecular charge transfer in donor-acceptor molecules

    SciTech Connect

    Slama-Schwok, A.; Blanchard-Desce, M.; Lehn, J.M. )

    1990-05-17

    The photophysical properties of donor-acceptor molecules, push-pull polyenes and carotenoids, have been studied by absorption and fluorescence spectroscopy. The compounds bear various acceptor and donor groups, linked together by chains of different length and structure. The position of the absorption and fluorescence maxima and their variation in solvents of increasing polarity are in agreement with long-distance intramolecular charge-transfer processes, the linker acting as a molecular wire. The effects of the linker length and structure and of the nature of acceptor and donor are presented.

  11. Recording intramolecular mechanics during the manipulation of a large molecule.

    PubMed

    Moresco, F; Meyer, G; Rieder, K H; Tang, H; Gourdon, A; Joachim, C

    2001-08-20

    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  12. Recording Intramolecular Mechanics during the Manipulation of a Large Molecule

    NASA Astrophysics Data System (ADS)

    Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Tang, Hao; Gourdon, André; Joachim, Christian

    2001-08-01

    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  13. Catalytic Intramolecular Ketone Alkylation with Olefins by Dual Activation.

    PubMed

    Lim, Hee Nam; Dong, Guangbin

    2015-12-07

    Two complementary methods for catalytic intramolecular ketone alkylation reactions with unactivated olefins, resulting in Conia-ene-type reactions, are reported. The transformations are enabled by dual activation of both the ketone and the olefin and are atom-economical as stoichiometric oxidants or reductants are not required. Assisted by Kool's aniline catalyst, the reaction conditions can be both pH- and redox-neutral. A broad range of functional groups are thus tolerated. Whereas the rhodium catalysts are effective for the formation of five-membered rings, a ruthenium-based system that affords the six-membered ring products was also developed.

  14. C1-Cx revisited: intramolecular synergism in a cellulase.

    PubMed Central

    Din, N; Damude, H G; Gilkes, N R; Miller, R C; Warren, R A; Kilburn, D G

    1994-01-01

    Endoglucanase A (CenA) from the bacterium Cellulomonas fimi is composed of a catalytic domain and a nonhydrolytic cellulose-binding domain that can function independently. The individual domains interact synergistically in the disruption and hydrolysis of cellulose fibers. This intramolecular synergism is distinct from the well-known intermolecular synergism between individual cellulases. The catalytic domain corresponds to the hydrolytic Cx system and the cellulose-binding domain corresponds to the nonhydrolytic C1 system postulated by Reese et al. [Reese, E. T., Sui, R. G. H. & Levinson, H. S. (1950) J. Bacteriol. 59, 485-497] to be required for the hydrolysis of cellulose. PMID:7972069

  15. Intravoxel incoherent motion diffusion-weighted imaging as an adjunct to dynamic contrast-enhanced MRI to improve accuracy of the differential diagnosis of benign and malignant breast lesions.

    PubMed

    Ma, Dejing; Lu, Feng; Zou, Xuexue; Zhang, Hu; Li, Yangyang; Zhang, Lin; Chen, Liang; Qin, Dongjing; Wang, Bin

    2017-02-01

    To investigate the value of use of intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) as an adjunct to dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) to distinguish benign from malignant breast lesions. Retrospective analysis of data pertaining to 117 patients with breast lesions who underwent DCE-MRI and IVIM-DWI examination with 3.0T MRI was conducted. A total of 128 lesions were pathologically confirmed (47 benign and 81 malignant). Between-group differences in DCE-MRI parameters (Morphology, enhancement pattern, maximum slope of increase (MSI) and time-signal curve (TIC) type) and IVIM-DWI parameters (f value, D value and D* value) were assessed. Multivariate logistic regression was performed to identify variables that distinguished benign from malignant breast lesions. The diagnostic performance of DCE-MRI and DCE-MRI plus IVIM-DWI, to distinguish benign from malignant breast lesions, was evaluated using pathology results as the gold standard. Lesion morphology, MSI, and TIC type (P<0.05), but not the enhancement pattern (P>0.05), were significantly different between the benign and malignant groups. The f (8.53±2.14) and D* (7.64±2.07) values in the malignant group were significantly higher than those in the benign group (7.68±1.97 and 6.83±2.13, respectively), while the D value (0.99±0.22) was significantly lower than that (1.34±0.17) in the benign group (P<0.05 for all). On logistic regression analysis, the sensitivity, specificity and accuracy of DCE-MRI were 90.1%, 70.2% and 82.8% respectively; the corresponding figures for the combination of IVIM-DWI and DCE-MRI were 88.8%, 85.1%, and 87.5%respectively. IVIM-DWI method as an adjunct to DCE-MRI can improve the specificity and accuracy in differential diagnosis of benign and malignant lesions of breast. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Collective motion of dimers.

    PubMed

    Penington, Catherine J; Korvasová, Karolína; Hughes, Barry D; Landman, Kerry A

    2012-11-01

    We consider a discrete agent-based model on a one-dimensional lattice and a two-dimensional square lattice, where each agent is a dimer occupying two sites. Agents move by vacating one occupied site in favor of a nearest-neighbor site and obey either a strict simple exclusion rule or a weaker constraint that permits partial overlaps between dimers. Using indicator variables and careful probability arguments, a discrete-time master equation for these processes is derived systematically within a mean-field approximation. In the continuum limit, nonlinear diffusion equations that describe the average agent occupancy of the dimer population are obtained. In addition, we show that multiple species of interacting subpopulations give rise to advection-diffusion equations. Averaged discrete simulation data compares very well with the solution to the continuum partial differential equation models. Since many cell types are elongated rather than circular, this work offers insight into population-level behavior of collective cellular motion.

  17. Fluorescence spectroscopic properties of nitro-substituted diphenylpolyenes: effects of intramolecular planarization and intermolecular interactions in crystals.

    PubMed

    Sonoda, Yoriko; Tsuzuki, Seiji; Goto, Midori; Tohnai, Norimitsu; Yoshida, Masaru

    2010-01-14

    The steady-state absorption and fluorescence properties of (E,E,E)-1,6-diaryl-1,3,5-hexatrienes (2, aryl = 2-nitrophenyl; 3, aryl = 3-nitrophenyl; 4, aryl = 4-nitrophenyl) have been investigated in solution and in the crystalline state. The solid-state absorption spectra of 2-4 shifted to longer wavelengths than those in solution. A combination of theoretical calculations and single-crystal X-ray structure analyses shows considerable planarization of molecules in the solid state, which is mainly responsible for the spectral red shifts. The effects of intermolecular interactions on the absorption spectra appeared to be relatively small in these crystals. This is consistent with the monomeric origin of the solid-state emission. Molecule 2 was nonfluorescent in all solvents studied, probably due to the efficient nonradiative deactivation from ionic species produced by excited-state intramolecular proton transfer (ESIPT) along the C-H...O-type hydrogen bonds. The fluorescence of 3, observed only in medium polar solvents, originated from an intramolecular charge transfer (ICT*) state, while that of 4 derived from locally excited (LE*) and/or ICT* states depending on the solvent polarity. All three molecules exhibited LE* fluorescence in the solid state. No observation of ICT* emission in crystals strongly suggests the twisted geometries for ICT* (TICT) of 3 and 4 in solution. The measurable fluorescence from crystal 2 can be attributed to the restricted torsional motions in the solid excited state.

  18. Relativistic Brownian motion

    NASA Astrophysics Data System (ADS)

    Dunkel, Jörn; Hänggi, Peter

    2009-02-01

    Over the past one hundred years, Brownian motion theory has contributed substantially to our understanding of various microscopic phenomena. Originally proposed as a phenomenological paradigm for atomistic matter interactions, the theory has since evolved into a broad and vivid research area, with an ever increasing number of applications in biology, chemistry, finance, and physics. The mathematical description of stochastic processes has led to new approaches in other fields, culminating in the path integral formulation of modern quantum theory. Stimulated by experimental progress in high energy physics and astrophysics, the unification of relativistic and stochastic concepts has re-attracted considerable interest during the past decade. Focusing on the framework of special relativity, we review, here, recent progress in the phenomenological description of relativistic diffusion processes. After a brief historical overview, we will summarize basic concepts from the Langevin theory of nonrelativistic Brownian motions and discuss relevant aspects of relativistic equilibrium thermostatistics. The introductory parts are followed by a detailed discussion of relativistic Langevin equations in phase space. We address the choice of time parameters, discretization rules, relativistic fluctuation-dissipation theorems, and Lorentz transformations of stochastic differential equations. The general theory is illustrated through analytical and numerical results for the diffusion of free relativistic Brownian particles. Subsequently, we discuss how Langevin-type equations can be obtained as approximations to microscopic models. The final part of the article is dedicated to relativistic diffusion processes in Minkowski spacetime. Since the velocities of relativistic particles are bounded by the speed of light, nontrivial relativistic Markov processes in spacetime do not exist; i.e., relativistic generalizations of the nonrelativistic diffusion equation and its Gaussian solutions

  19. Semirubin. A novel dipyrrinone strapped by intramolecular hydrogen bonds.

    PubMed

    Huggins, M T; Lightner, D A

    2000-09-22

    (4Z)-9-(5-Carboxypentyl)-2,3,7,8-tetramethyl-(10H)-dipyrrin- 1-one (1, semirubin), a new dipyrrinone model for one-half of bilirubin, the yellow-orange neurotoxic pigment of jaundice, was synthesized following Friedel-Crafts acylation of 2,3,7, 8-tetramethyl-(10H)-dipyrrin-1-one (5) with the half-ester acid chloride of adipic acid. Unlike other dipyrrinone models for bilirubin, such as the xanthobilirubic acids, which engage only in intermolecular hydrogen bonding, 1 is unique in having been designed and found to engage in intramolecular hydrogen bonding, between the carboxylic acid and the dipyrrinone lactam and pyrrole. This important conformation-determining structural characteristic, shared by 1 and bilirubin, renders them less polar than their methyl esters and leaves them monomeric in nonpolar solvents, where their esters are dimeric. The corresponding 10-oxo analogue (3) of 1 serves as a model for 10-oxo-bilirubin, a presumed bilirubin metabolite in alternate pathways for bilirubin excretion. Like 1, 3 is found to engage in intramolecular hydrogen bonding. Unlike the methyl ester of 1, the ethyl ester of 3 is not intermolecularly hydrogen bonded in nonpolar solvents.

  20. A Study of Intramolecular Hydrogen Bonding in Levoglucosan Derivatives.

    PubMed

    Quiquempoix, Lucas; Bogdan, Elena; Wells, Neil J; Le Questel, Jean-Yves; Graton, Jérôme; Linclau, Bruno

    2017-03-24

    Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.

  1. Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins

    PubMed Central

    Sperschneider, Jana; Datta, Amitava; Wise, Michael J.

    2011-01-01

    Pseudoknots are an essential feature of RNA tertiary structures. Simple H-type pseudoknots have been studied extensively in terms of biological functions, computational prediction, and energy models. Intramolecular kissing hairpins are a more complex and biologically important type of pseudoknot in which two hairpin loops form base pairs. They are hard to predict using free energy minimization due to high computational requirements. Heuristic methods that allow arbitrary pseudoknots strongly depend on the quality of energy parameters, which are not yet available for complex pseudoknots. We present an extension of the heuristic pseudoknot prediction algorithm DotKnot, which covers H-type pseudoknots and intramolecular kissing hairpins. Our framework allows for easy integration of advanced H-type pseudoknot energy models. For a test set of RNA sequences containing kissing hairpins and other types of pseudoknot structures, DotKnot outperforms competing methods from the literature. DotKnot is available as a web server under http://dotknot.csse.uwa.edu.au. PMID:21098139

  2. A Study about Regioisomeric Hydroquinones with Multiple Intramolecular Hydrogen Bonding.

    PubMed

    Martínez-Cifuentes, Maximiliano; Cardona, Wilson; Saitz, Claudio; Weiss-López, Boris; Araya-Maturana, Ramiro

    2017-04-07

    A theoretical exploration about hydrogen bonding in a series of synthetic regioisomeric antitumor tricyclic hydroquinones is presented. The stabilization energy for the intramolecular hydrogen bond (IHB) formation in four structurally different situations were evaluated: (a) IHB between the proton of a phenolic hydroxyl group and an ortho-carbonyl group (forming a six-membered ring); (b) between the oxygen atom of a phenolic hydroxyl group and the proton of an hydroxyalkyl group (seven membered ring); (c) between the proton of a phenolic hydroxyl group with the oxygen atom of the hydroxyl group of a hydroxyalkyl moiety (seven-membered ring); and (d) between the proton of a phenolic hydroxyl group and an oxygen atom directly bonded to the aromatic ring in ortho position (five-membered ring). A conformational analysis for the rotation around the hydroxyalkyl substituent is also performed. It is observed that there is a correspondence between the conformational energies and the IHB. The strongest intramolecular hydrogen bonds are those involving a phenolic proton and a carbonyl oxygen atom, forming a six-membered ring, and the weakest are those involving a phenolic proton with the oxygen atom of the chromenone, forming five-membered rings. Additionally, the synthesis and structural assignment of two pairs of regioisomeric hydroquinones, by 2D-NMR experiments, are reported. These results can be useful in the design of biologically-active molecules.

  3. Intramolecular carbon isotope distribution of acetic acid in vinegar.

    PubMed

    Hattori, Ryota; Yamada, Keita; Kikuchi, Makiko; Hirano, Satoshi; Yoshida, Naohiro

    2011-09-14

    Compound-specific carbon isotope analysis of acetic acid is useful for origin discrimination and quality control of vinegar. Intramolecular carbon isotope distributions, which are each carbon isotope ratios of the methyl and carboxyl carbons in the acetic acid molecule, may be required to obtain more detailed information to discriminate such origin. In this study, improved gas chromatography-pyrolysis-gas chromatography-combustion-isotope ratio mass spectrometry (GC-Py-GC-C-IRMS) combined with headspace solid-phase microextraction (HS-SPME) was used to measure the intramolecular carbon isotope distributions of acetic acid in 14 Japanese vinegars. The results demonstrated that the methyl carbons of acetic acid molecules in vinegars produced from plants were mostly isotopically depleted in (13)C relative to the carboxyl carbon. Moreover, isotopic differences (δ(13)C(carboxyl) - δ(13)C(methyl)) had a wide range from -0.3 to 18.2‰, and these values differed among botanical origins, C3, C4, and CAM plants.

  4. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-03-01

    The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

  5. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics of H2CCO + and D2CCO +

    NASA Astrophysics Data System (ADS)

    Niu, Baohua; Bai, Ying; Shirley, David A.

    1993-08-01

    High resolution helium Iα (584 Å) photoelectron spectra of H2CCO and D2CCO are reported. The present spectra of the ground states of ketene cations show more vibrational fine structure than previously reported. The adiabatic ionization energies (AIEs) of the cations' first, second, and fifth excited states are determined unambiguously. The doubletlike fine structures present in the first excited states of ketene cations imply the excitation of a ``soft'' mode that was not observed before. It was assigned to the ν5 mode, which is characterized by the CH2 (CD2) group out-of-plane wagging motion. The complexity of the photoelectron spectra obtained for the ionic first excited states is attributed to the possible dissociation and predissociation of this state. Strong isotope effects are observed in the vibronic (vibrational) couplings in most of the ionic states. Vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra for four of the six ionic states observed. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum of the upper potential energy surfaces (PES). The decay dynamics of the ionic first and fifth excited states of ketene are characterized by ultrafast intramolecular processes such as dissociation and predissociation.

  6. Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study

    NASA Astrophysics Data System (ADS)

    Omidyan, Reza; Iravani, Maryam

    2016-11-01

    The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH2) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S1/S0), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

  7. Using Thz Spectroscopy to Probe Intramolecular Electron Transfer and Solvent Dynamics

    NASA Astrophysics Data System (ADS)

    Schmuttenmaer, Charles

    2002-03-01

    We have measured the electromagnetic radiation emitted during intramolecular electron transfer using a method does not rely on secondary processes.^1 The motion of the electrons themselves generates the measured signal (as understood by Maxwell's equations). If the electron transfer occurs on a timescale of 0.1 to 10 picoseconds, the emitted radiation will fall in the THz or far-infrared region of the spectrum (1 THz = 33.33 wavenumbers). We photoexcite a sample of partially oriented molecules and measure the emitted waveform. The polarity of the emitted field determines the direction of charge transfer unambiguously, and the shape of the field encodes the dynamics of the charge transfer -- a slower transfer rate produces a broader temporal pulse. Solvent repolarization dynamics also contribute to the measured response, and will be discussed. Future work will extend this method to systems that are difficult to study by traditional means. 1. M. C. Beard, G. M. Turner, and C. A. Schmuttenmaer, J. Phys. Chem. A, In Press (2001).

  8. Superdiffusive trajectories in Brownian motion.

    PubMed

    Duplat, Jérôme; Kheifets, Simon; Li, Tongcang; Raizen, Mark G; Villermaux, Emmanuel

    2013-02-01

    The Brownian motion of a microscopic particle in a fluid is one of the cornerstones of statistical physics and the paradigm of a random process. One of the most powerful tools to quantify it was provided by Langevin, who explicitly accounted for a short-time correlated "thermal" force. The Langevin picture predicts ballistic motion, ~t(2) at short-time scales, and diffusive motion ~t at long-time scales, where x is the displacement of the particle during time t, and the average is taken over the thermal distribution of initial conditions. The Langevin equation also predicts a superdiffusive regime, where ~t(3), under the condition that the initial velocity is fixed rather than distributed thermally. We analyze the motion of an optically trapped particle in air and indeed find t(3) dispersion. This observation is a direct proof of the existence of the random, rapidly varying force imagined by Langevin.

  9. Diffusive mixing and Tsallis entropy

    DOE PAGES

    O'Malley, Daniel; Vesselinov, Velimir V.; Cushman, John H.

    2015-04-29

    Brownian motion, the classical diffusive process, maximizes the Boltzmann-Gibbs entropy. The Tsallis q-entropy, which is non-additive, was developed as an alternative to the classical entropy for systems which are non-ergodic. A generalization of Brownian motion is provided that maximizes the Tsallis entropy rather than the Boltzmann-Gibbs entropy. This process is driven by a Brownian measure with a random diffusion coefficient. In addition, the distribution of this coefficient is derived as a function of q for 1 < q < 3. Applications to transport in porous media are considered.

  10. Brownian Motion.

    ERIC Educational Resources Information Center

    Lavenda, Bernard H.

    1985-01-01

    Explains the phenomenon of Brownian motion, which serves as a mathematical model for random processes. Topics addressed include kinetic theory, Einstein's theory, particle displacement, and others. Points out that observations of the random course of a particle suspended in fluid led to the first accurate measurement of atomic mass. (DH)

  11. Brownian Motion.

    ERIC Educational Resources Information Center

    Lavenda, Bernard H.

    1985-01-01

    Explains the phenomenon of Brownian motion, which serves as a mathematical model for random processes. Topics addressed include kinetic theory, Einstein's theory, particle displacement, and others. Points out that observations of the random course of a particle suspended in fluid led to the first accurate measurement of atomic mass. (DH)

  12. Diffusion MRI

    NASA Astrophysics Data System (ADS)

    Fukuyama, Hidenao

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

  13. Intramolecular cyclization of a diruthenium complex: insight into the mechanism of heteroatom-directed intramolecular C-H/olefin coupling reactions.

    PubMed

    Gong, Dawei; Hu, Bowen; Shi, Jing; Chen, Dafa

    2015-07-28

    Complex 2, synthesized by the reaction of {(C5H4N)(μ2-η(5):η(1)-C9H5)}Ru3(CO)9 (1) with 1,5-hexadiene, could further transform to another diruthenium complex 3via intramolecular carbometalation. The results are relevant to the mechanism of transition-metal catalyzed heteroatom-directed intramolecular C-H/olefin coupling reactions.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2014-01-01

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

  16. Plasmapause diffusion

    NASA Technical Reports Server (NTRS)

    Horwitz, J. L.

    1983-01-01

    The Bohm diffusion coefficient and observed electrostatic wave scattering are used as the bases of estimates of the smoothing effect that diffusion may have on steep plasmapause density gradients. The estimate for diffusion resulting from scattering by observed electrostatic waves is found to be much lower than that of the perpendicular Bohm diffusion coefficient for characteristic plasma temperatures and magnetic fields. This diffusion rate estimate may be too small, however, if the wave amplitudes are significantly higher for steep plasmapauses. The effects are therefore negligible for most considerations of macroscopic plasmapause dynamics, but may be significant in limiting drift wave instabilities and similar phenomena driven by the steepness of the plasmapause density gradient.

  17. Muon motion in titanium hydride

    NASA Technical Reports Server (NTRS)

    Kempton, J. R.; Petzinger, K. G.; Kossler, W. J.; Schone, H. E.; Hitti, B. S.; Stronach, C. E.; Adu, N.; Lankford, W. F.; Reilly, J. J.; Seymour, E. F. W.

    1988-01-01

    Motional narrowing of the transverse-field muon spin rotation signal was observed in gamma-TiH(x) for x = 1.83, 1.97, and 1.99. An analysis of the data for TiH1.99 near room temperature indicates that the mechanism responsible for the motion of the muon out of the octahedral site is thermally activated diffusion with an attempt frequency comparable to the optical vibrations of the lattice. Monte Carlo calculations to simulate the effect of muon and proton motion upon the muon field-correlation time were used to interpret the motional narrowing in TiH1.97 near 500 K. The interpretation is dependent upon whether the Bloembergen, Purcell, and Pound (BPP) theory or an independent spin-pair relaxation model is used to obtain the vacancy jump rate from proton NMR T1 measurements. Use of BPP theory shows that the field-correction time can be obtained if the rate of motion of the muon with respect to the rate of the motion for the protons is decreased. An independent spin-pair relaxation model indicates that the field-correlation time can be obtained if the rate of motion for the nearest-neighbor protons is decreased.

  18. Muon motion in titanium hydride

    NASA Technical Reports Server (NTRS)

    Kempton, J. R.; Petzinger, K. G.; Kossler, W. J.; Schone, H. E.; Hitti, B. S.; Stronach, C. E.; Adu, N.; Lankford, W. F.; Reilly, J. J.; Seymour, E. F. W.

    1988-01-01

    Motional narrowing of the transverse-field muon spin rotation signal was observed in gamma-TiH(x) for x = 1.83, 1.97, and 1.99. An analysis of the data for TiH1.99 near room temperature indicates that the mechanism responsible for the motion of the muon out of the octahedral site is thermally activated diffusion with an attempt frequency comparable to the optical vibrations of the lattice. Monte Carlo calculations to simulate the effect of muon and proton motion upon the muon field-correlation time were used to interpret the motional narrowing in TiH1.97 near 500 K. The interpretation is dependent upon whether the Bloembergen, Purcell, and Pound (BPP) theory or an independent spin-pair relaxation model is used to obtain the vacancy jump rate from proton NMR T1 measurements. Use of BPP theory shows that the field-correction time can be obtained if the rate of motion of the muon with respect to the rate of the motion for the protons is decreased. An independent spin-pair relaxation model indicates that the field-correlation time can be obtained if the rate of motion for the nearest-neighbor protons is decreased.

  19. Aging scaled Brownian motion

    NASA Astrophysics Data System (ADS)

    Safdari, Hadiseh; Chechkin, Aleksei V.; Jafari, Gholamreza R.; Metzler, Ralf

    2015-04-01

    Scaled Brownian motion (SBM) is widely used to model anomalous diffusion of passive tracers in complex and biological systems. It is a highly nonstationary process governed by the Langevin equation for Brownian motion, however, with a power-law time dependence of the noise strength. Here we study the aging properties of SBM for both unconfined and confined motion. Specifically, we derive the ensemble and time averaged mean squared displacements and analyze their behavior in the regimes of weak, intermediate, and strong aging. A very rich behavior is revealed for confined aging SBM depending on different aging times and whether the process is sub- or superdiffusive. We demonstrate that the information on the aging factorizes with respect to the lag time and exhibits a functional form that is identical to the aging behavior of scale-free continuous time random walk processes. While SBM exhibits a disparity between ensemble and time averaged observables and is thus weakly nonergodic, strong aging is shown to effect a convergence of the ensemble and time averaged mean squared displacement. Finally, we derive the density of first passage times in the semi-infinite domain that features a crossover defined by the aging time.

  20. Aging scaled Brownian motion.

    PubMed

    Safdari, Hadiseh; Chechkin, Aleksei V; Jafari, Gholamreza R; Metzler, Ralf

    2015-04-01

    Scaled Brownian motion (SBM) is widely used to model anomalous diffusion of passive tracers in complex and biological systems. It is a highly nonstationary process governed by the Langevin equation for Brownian motion, however, with a power-law time dependence of the noise strength. Here we study the aging properties of SBM for both unconfined and confined motion. Specifically, we derive the ensemble and time averaged mean squared displacements and analyze their behavior in the regimes of weak, intermediate, and strong aging. A very rich behavior is revealed for confined aging SBM depending on different aging times and whether the process is sub- or superdiffusive. We demonstrate that the information on the aging factorizes with respect to the lag time and exhibits a functional form that is identical to the aging behavior of scale-free continuous time random walk processes. While SBM exhibits a disparity between ensemble and time averaged observables and is thus weakly nonergodic, strong aging is shown to effect a convergence of the ensemble and time averaged mean squared displacement. Finally, we derive the density of first passage times in the semi-infinite domain that features a crossover defined by the aging time.

  1. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    NASA Astrophysics Data System (ADS)

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  2. Flexible Viologen Cyclophanes: Odd/Even Effects on Intramolecular Interactions.

    PubMed

    Berville, Mathilde; Choua, Sylvie; Gourlaouen, Christophe; Boudon, Corinne; Ruhlmann, Laurent; Bailly, Corinne; Cobo, Saioa; Saint-Aman, Eric; Wytko, Jennifer; Weiss, Jean

    2017-01-04

    The ability of three bis-viologen cyclophanes to act as redox-triggered contractile switches is investigated. Odd/even effects in the formation of cyclic bis-viologens are circumvented by the use of a Zincke salt intermediate and a tetrathiafulvalene template to prepare a flexible cyclophane with hexyl linkers. Comparative spectro-electrochemical studies of this macrocycle with two other pentyl- or heptyl-linked cyclic bis-viologens show that the development of intramolecular interactions in aqueous solution depends on the length of the bridges. This dependence is confirmed by EPR and DFT studies of the magnetic coupling in the diradical dication species. The anti-ferromagnetic or ferromagnetic nature of the coupling depend, respectively, on the odd or even number of methylene groups in the spacer.

  3. Direct Preparation of Carbon Nanotube Intramolecular Junctions on Structured Substrates

    NASA Astrophysics Data System (ADS)

    An, Jianing; Zhan, Zhaoyao; Sun, Gengzhi; Mohan, Hari Krishna Salila Vijayalal; Zhou, Jinyuan; Kim, Young-Jin; Zheng, Lianxi

    2016-12-01

    Leveraging the unique properties of single-walled carbon nanotube (SWNT) intramolecular junctions (IMJs) in innovative nanodevices and next-generation nanoelectronics requires controllable, repeatable, and large-scale preparation, together with rapid identification and comprehensive characterization of such structures. Here we demonstrate SWNT IMJs through directly growing ultralong SWNTs on trenched substrates. It is found that the trench configurations introduce axial strain in partially suspended nanotubes, and promote bending deformation in the vicinity of the trench edges. As a result, the lattice and electronic structure of the nanotubes can be locally modified, to form IMJs in the deformation regions. The trench patterns also enable pre-defining the formation locations of SWNT IMJs, facilitating the rapid identification. Elaborate Raman characterization has verified the formation of SWNT IMJs and identified their types. Rectifying behavior has been observed by electrical measurements on the as-prepared semiconducting-semiconducting (S-S) junction.

  4. Prodrugs design based on inter- and intramolecular chemical processes.

    PubMed

    Karaman, Rafik

    2013-12-01

    This review provides the reader a concise overview of the majority of prodrug approaches with the emphasis on the modern approaches to prodrug design. The chemical approach catalyzed by metabolic enzymes which is considered as widely used among all other approaches to minimize the undesirable drug physicochemical properties is discussed. Part of this review will shed light on the use of molecular orbital methods such as DFT, semiempirical and ab initio for the design of novel prodrugs. This novel prodrug approach implies prodrug design based on enzyme models that were utilized for mimicking enzyme catalysis. The computational approach exploited for the prodrug design involves molecular orbital and molecular mechanics (DFT, ab initio, and MM2) calculations and correlations between experimental and calculated values of intramolecular processes that were experimentally studied to assign the factors determining the reaction rates in certain processes for better understanding on how enzymes might exert their extraordinary catalysis.

  5. Direct Preparation of Carbon Nanotube Intramolecular Junctions on Structured Substrates

    PubMed Central

    An, Jianing; Zhan, Zhaoyao; Sun, Gengzhi; Mohan, Hari Krishna Salila Vijayalal; Zhou, Jinyuan; Kim, Young-Jin; Zheng, Lianxi

    2016-01-01

    Leveraging the unique properties of single-walled carbon nanotube (SWNT) intramolecular junctions (IMJs) in innovative nanodevices and next-generation nanoelectronics requires controllable, repeatable, and large-scale preparation, together with rapid identification and comprehensive characterization of such structures. Here we demonstrate SWNT IMJs through directly growing ultralong SWNTs on trenched substrates. It is found that the trench configurations introduce axial strain in partially suspended nanotubes, and promote bending deformation in the vicinity of the trench edges. As a result, the lattice and electronic structure of the nanotubes can be locally modified, to form IMJs in the deformation regions. The trench patterns also enable pre-defining the formation locations of SWNT IMJs, facilitating the rapid identification. Elaborate Raman characterization has verified the formation of SWNT IMJs and identified their types. Rectifying behavior has been observed by electrical measurements on the as-prepared semiconducting-semiconducting (S-S) junction. PMID:27905564

  6. 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.

  7. Intramolecular transposition by a synthetic IS50 (Tn5) derivative

    SciTech Connect

    Tomcsanyi, T.; Phadnis, S.H.; Berg, D.E. ); Berg, C.M. )

    1990-11-01

    We report the formation of deletions and inversions by intramolecular transposition of Tn5-derived mobile elements. The synthetic transposons used contained the IS50 O and I end segments and the transposase gene, a contraselectable gene encoding sucrose sensitivity (sacB), antibiotic resistance genes, and a plasmid replication origin. Both deletions and inversions were associated with loss of a 300-bp segment that is designated the vector because it is outside of the transposon. Deletions were severalfold more frequent than inversions, perhaps reflecting constraints on DNA twisting or abortive transposition. Restriction and DNA sequence analyses showed that both types of rearrangements extended from one transposon end to many different sites in target DNA. In the case of inversions, transposition generated 9-bp direct repeats of target sequences.

  8. Intramolecular Charge Transfer States in the Condensed Phase

    NASA Astrophysics Data System (ADS)

    Williams, C. F.; Herbert, J. M.

    2009-06-01

    Time-Dependent Density Functional Theory (TDDFT) with long range corrected functionals can give accurate results for the energies of electronically excited states involving Intramolecular Charge Transfer (ICT) in large molecules. If this is combined with a Molecular Mechanics (MM) representation of the surrounding solvent this technique can be used to interpret the results of condensed phase UV-Vis Spectroscopy. Often the MM region is represented by a set of point charges, however this means that the solvent cannot repolarize to adapt to the new charge distribution as a result of ICT and so the excitation energies to ICT states are overestimated. To solve this problem an algorithm that interfaces TDDFT with the polarizable force-field AMOEBA is presented; the effect of solvation on charge transfer in species such as 4,4'dimethylaminobenzonitrile (DMABN) is discussed. M.A. Rohrdanz, K.M. Martins, and J.M. Herbert, J. Chem. Phys. 130 034107 (2008).

  9. Acquisition of accurate data from intramolecular quenched fluorescence protease assays.

    PubMed

    Arachea, Buenafe T; Wiener, Michael C

    2017-04-01

    The Intramolecular Quenched Fluorescence (IQF) protease assay utilizes peptide substrates containing donor-quencher pairs that flank the scissile bond. Following protease cleavage, the dequenched donor emission of the product is subsequently measured. Inspection of the IQF literature indicates that rigorous treatment of systematic errors in observed fluorescence arising from inner-filter absorbance (IF) and non-specific intermolecular quenching (NSQ) is incompletely performed. As substrate and product concentrations vary during the time-course of enzyme activity, iterative solution of the kinetic rate equations is, generally, required to obtain the proper time-dependent correction to the initial velocity fluorescence data. Here, we demonstrate that, if the IQF assay is performed under conditions where IF and NSQ are approximately constant during the measurement of initial velocity for a given initial substrate concentration, then a simple correction as a function of initial substrate concentration can be derived and utilized to obtain accurate initial velocity data for analysis.

  10. Solvent reorganizational red-edge effect in intramolecular electron transfer.

    PubMed Central

    Demchenko, A P; Sytnik, A I

    1991-01-01

    Polar solvents are characterized by statistical distributions of solute-solvent interaction energies that result in inhomogeneous broadening of the solute electronic spectra. This allows photoselection of the high interaction energy part of the distribution by excitation at the red (long-wavelength) edge of the absorption bands. We observe that intramolecular electron transfer in the bianthryl molecule from the locally excited (LE) to the charge-transfer (CT) state, which requires solvent relaxation and does not occur in vitrified polar solutions, is dramatically facilitated in low-temperature propylene glycol glass by the red-edge excitation. This allows one to obtain spectroscopically the pure CT form and observe its dependence upon the relaxational properties of the solvent. A qualitative potential model of this effect is presented. PMID:11607224

  11. Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

    NASA Astrophysics Data System (ADS)

    Mikhailov, G. P.; Lazarev, V. V.

    2016-07-01

    The effect the number of chitosan monomer units CTS n ( n = 1-5), the protonation of chitosan dimers, and the interaction between CTS n ( n = 1-3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS n is 2 n - 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.

  12. Intramolecular strain coordinates kinesin stepping behavior along microtubules

    PubMed Central

    Yildiz, Ahmet; Tomishige, Michio; Gennerich, Arne; Vale, Ronald D.

    2008-01-01

    SUMMARY Kinesin advances 8 nm along a microtubule per ATP hydrolyzed, but the mechanism responsible for coordinating the enzymatic cycles of kinesin’s two identical motor domains remains unresolved. Here, we have tested whether such coordination is mediated by intramolecular tension generated by the “neck linkers”, mechanical elements that span between the motor domains. When tension is reduced by extending the neck linkers with artificial peptides, the coupling between ATP hydrolysis and forward stepping is impaired and motor’s velocity decreases as a consequence. However, speed recovers to nearly normal levels when external tension is applied by an optical trap. Remarkably, external load also induces bidirectional stepping of an immotile kinesin that lacks its mechanical element (neck linker) and fuel (ATP). Our results indicate that the kinesin motor domain senses and responds to strain in a manner that facilitates its plus-end-directed stepping and communication between its two motor domains. PMID:18805095

  13. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    PubMed Central

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-01-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development. PMID:27752093

  14. [Motion sickness].

    PubMed

    Taillemite, J P; Devaulx, P; Bousquet, F

    1997-01-01

    Motion sickness is a general term covering sea-sickness, car-sickness, air-sickness, and space-sickness. Symptoms can occur when a person is exposed to unfamiliar movement whether real or simulated. Despite progress in the technology and comfort of modern transportation (planes, boats, and overland vehicles), a great number of travelers still experience motion sickness. Bouts are characterized by an initial phase of mild discomfort followed by neurologic and gastro-intestinal manifestations. The delay in onset depends on specific circumstances and individual susceptibility. Attacks are precipitated by conflicting sensory, visual, and vestibular signals but the underlying mechanism is unclear. Most medications used for prevention and treatment (e.g. anticholinergics and antihistamines) induce unwanted sedation. Furthermore no one drug is completely effective or preventive under all conditions.

  15. Polymeric photosensitizers: effects of intramolecular energy migration on sensitization efficiences

    SciTech Connect

    Urruti, E.H.; Kilp, T.

    1984-01-01

    The occurrence of intramolecular energy migration was found to have no significant effect on the efficiency of ketyl radical formation via hydrogen abstration from cumene by benzophenone (BP) or poly(vinylbenzophenone) (PVBP). Rate constants were found to be 1.1 x 10/sup 6/ and 0.81 x 10/sup 6/ M/sup -1/ s/sup -1/ for the small molecule and the polymer, respectively. The large difference in rate constants, 9.6 x 10/sup 6/ and 22.2 x 10/sup 6/ M/sup -1/ s/sup -1/ for BP and PVBP, respectively, when tetrahydrofuran was used as a quencher is probably attributable to preferential solvation. Conversely, intramolecular energy migration was found to significantly enhance the overall efficiency of triplet energy transfer to 1-methylnaphthalene (MeN). Rate constants for formation of /sup 3/MeN were found to be 0.94 x 10/sup 9/ and 1.85 x 10/sup 9/ M/sup -1/ s/sup -1/ for BP and PVBP, respectively. An energy migration coefficient, LAMBDA, of 3.28 x 10/sup -5/ cm/sup 2/ s/sup -1/ and a frequency of energy migration, omega, of 7.88 x 10/sup 10/ x/sup -1/ were calculated for PVBP. For a series of copolymers of methyl methacrylate with vinylbenzophenone, values of LAMBDA and omega were strongly dependent on the ketone content of the polymer and decreased sharply at 40 mol % VBP or less.

  16. Asymmetric gear rectifies random robot motion

    NASA Astrophysics Data System (ADS)

    Li, He; Zhang, H. P.

    2013-06-01

    We experimentally study the dynamics of centimetric robots and their interactions with rotary gears through inelastic collisions. Under the impacts of self-propelled robots, a gear with symmetric teeth diffuses with no preferred direction of motion. An asymmetric gear, however, rectifies random motion of nearby robots which, in return, exert a torque on the gear and drive it into unidirectional motion. Rectification efficiency increases with the degree of gear asymmetry. Our work demonstrates that asymmetric environments can be used to rectify and extract energy from random motion of macroscopic self-propelled particles.

  17. Fast diffusion of water nanodroplets on graphene.

    PubMed

    Ma, Ming; Tocci, Gabriele; Michaelides, Angelos; Aeppli, Gabriel

    2016-01-01

    Diffusion across surfaces generally involves motion on a vibrating but otherwise stationary substrate. Here, using molecular dynamics, we show that a layered material such as graphene opens up a new mechanism for surface diffusion whereby adsorbates are carried by propagating ripples in a motion similar to surfing. For water nanodroplets, we demonstrate that the mechanism leads to exceedingly fast diffusion that is 2-3 orders of magnitude faster than the self-diffusion of water molecules in liquid water. We also reveal the underlying principles that regulate this new mechanism for diffusion and show how it also applies to adsorbates other than water, thus opening up the prospect of achieving fast and controllable motion of adsorbates across material surfaces more generally.

  18. Griffith diffusers

    NASA Technical Reports Server (NTRS)

    Yang, T.-T.; Nelson, C. D.

    1979-01-01

    Contoured wall diffusers are designed by using an inverse method. The prescribed wall velocity distribution(s) was taken from the high lift airfoil designed by A. A. Griffith in 1938; therefore, such diffusers are named Griffith diffusers. First the formulation of the inverse problem and the method of solution are outlined. Then the typical contour of a two-dimensional diffuser and velocity distributions across the flow channel at various stations are presented. For a Griffith diffuser to operate as it is designed, boundary layer suction is necessary. Discussion of the percentage of through-flow required to be removed for the purpose of boundary layer control is given. Finally, reference is made to the latest version of a computer program for a two-dimensional diffuser requiring only area ratio, nondimensional length and suction percentage as inputs.

  19. Griffith diffusers

    NASA Technical Reports Server (NTRS)

    Yang, T.-T.; Nelson, C. D.

    1979-01-01

    Contoured wall diffusers are designed by using an inverse method. The prescribed wall velocity distribution(s) was taken from the high lift airfoil designed by A. A. Griffith in 1938; therefore, such diffusers are named Griffith diffusers. First the formulation of the inverse problem and the method of solution are outlined. Then the typical contour of a two-dimensional diffuser and velocity distributions across the flow channel at various stations are presented. For a Griffith diffuser to operate as it is designed, boundary layer suction is necessary. Discussion of the percentage of through-flow required to be removed for the purpose of boundary layer control is given. Finally, reference is made to the latest version of a computer program for a two-dimensional diffuser requiring only area ratio, nondimensional length and suction percentage as inputs.

  20. The role of large-amplitude motions in the spectroscopy and dynamics of H{sub 5}{sup +}

    SciTech Connect

    Lin, Zhou; McCoy, Anne B.

    2014-03-21

    Protonated hydrogen dimer, H{sub 5}{sup +}, is the intermediate in the astrochemically important proton transfer reaction between H{sub 3}{sup +} and H{sub 2}. To understand the mechanism for this process, we focus on how large amplitude motions in H{sub 5}{sup +} result in scrambling of the five hydrogen atoms in the collision complex. To this end, the one-dimensional zero-point corrected potential surfaces were mapped out as functions of reaction coordinates for the H{sub 3}{sup +} + H{sub 2} collision using minimized energy path diffusion Monte Carlo [C. E. Hinkle and A. B. McCoy, J. Phys. Chem. Lett. 1, 562 (2010)]. In this study, the previously developed approach was extended to allow for the investigation of selected excited states that are expected to be involved in the proton scrambling dynamics. Specifically, excited states in the shared proton motion between the two H{sub 2} groups, and in the outer H{sub 2} bending motions were investigated. Of particular interest is the minimum distance between H{sub 3}{sup +} and H{sub 2} at which all five hydrogen atoms become free to exchange. In addition, this diffusion Monte Carlo-based approach was used to determine the zero-point energy E{sub 0}, the dissociation energy D{sub 0}, and excitation energies associated with the vibrational motions that were investigated. The evolution of the wave functions was also studied, with a focus on how the intramolecular vibrations in H{sub 5}{sup +} evolve into motions of H{sub 3}{sup +} or H{sub 2}. In the case of the proton scrambling, we find that the relevant transition states become fully accessible at separations between H{sub 3}{sup +} and H{sub 2} of approximately 2.15 Å, a distance that is accessed by the excited states of H{sub 5}{sup +} with two or more quanta in the shared proton stretch. The implications of this finding on the vibrational spectroscopy of H{sub 5}{sup +} are also discussed.

  1. Neoclassical diffusion in a turbulent plasma

    SciTech Connect

    Yushmanov, P. . Inst. Atomnoj Ehnergii Texas Univ., Austin, TX . Inst. for Fusion Studies)

    1991-11-01

    This work describes a new approach to plasma transport where the toroidal drift motion is considered as a perturbation to the fluctuating velocity. Percolation theory is used to determine the scaling of the diffusion coefficient. Several neoclassical phenomena should persist even when diffusion is enhanced from neoclassical predictions. Numerical simulation results support the theoretical scaling arguments.

  2. Highly enantioselective intramolecular 1,3-dipolar cycloaddition: a route to piperidino-pyrrolizidines.

    PubMed

    Vidadala, Srinivasa Rao; Golz, Christopher; Strohmann, Carsten; Daniliuc, Constantin-G; Waldmann, Herbert

    2015-01-07

    Enantioselective catalytic intermolecular 1,3-dipolar cycloadditions are powerful methods for the synthesis of heterocycles. In contrast, intramolecular enantioselective 1,3-dipolar cycloadditions are virtually unexplored. A highly enantioselective synthesis of natural-product-inspired pyrrolidino-piperidines by means of an intramolecular 1,3-dipolar cycloaddition with azomethine ylides is now reported. The method has a wide scope and yields the desired cycloadducts with four tertiary stereogenic centers with up to 99% ee. Combining the enantioselective catalytic intramolecular 1,3-dipolar cycloaddition with a subsequent diastereoselective intermolecular 1,3-dipolar cycloaddition yielded complex piperidino-pyrrolizidines with very high stereoselectivity in a one-pot tandem reaction.

  3. Branching Reaction in Melanogenesis: The Effect of Intramolecular Cyclization on Thiol Binding

    NASA Astrophysics Data System (ADS)

    Kishida, Ryo; Kasai, Hideaki; Aspera, Susan Meñez; Arevalo, Ryan Lacdao; Nakanishi, Hiroshi

    2017-01-01

    With the aid of density functional theory-based first principles calculations, we investigated energetics and electronic structure changes in reactions involving dopaquinone to give insights into the branching behaviors in melanogenesis. The reactions we investigated are the intramolecular cyclization and thiol binding, which are competing with each other. It was found that, in order to accomplish thiol binding, charge transfer of around one electron from thiol to dopaquinone occurs. Furthermore, intramolecular cyclization of dopaquinone increases the lowest unnoccupied molecular orbital level substantially. This result clearly shows prevention of the binding of thiol by intramolecular cyclization.

  4. DFT and AIM studies of intramolecular hydrogen bonds in dicoumarols

    NASA Astrophysics Data System (ADS)

    Trendafilova, Natasha; Bauer, Günther; Mihaylov, Tzvetan

    2004-07-01

    Density functional calculations with Becke's three parameter hybrid method using the correlation functional of Lee, Yang and Parr (B3LYP) were carried out for 3,3 '-benzylidenebis(4-hydroxycoumarin) (phenyldicoumarol, PhDC), 3,3 '-methylenebis(4-hydroxycoumarin) (dicoumarol, DC) and the parent compound, 4-hydroxycoumarin (4-HC). Different basis sets were tested in the course of the calculations: 6-31G*, 6-31+G** and 6-311G*. In full agreement with available X-ray data, B3LYP/6-31G* calculations of the lowest-energy conformer, PhDC showed two O-H⋯O asymmetrical intramolecular hydrogen bonds with O⋯O distances 2.638 and 2.696 Å. The HB energies in PhDC were estimated of -55.46 and -52.32 kJ/mol, respectively. The values obtained correlated with the calculated and experimental O⋯O distances and predicted difference in the hydrogen bonding strengths in PhDC. The total HB energy in PhDC was calculated of -107.73 kJ/mol. At the same level of theory, both O⋯O intramolecular distances in DC were calculated identical (2.696 Å) and thus two symmetrical hydrogen bondings were obtained. The single HB strength was estimated of -50.89 kJ/mol and the total one of -101.79 kJ/mol. The electron density ( ρb) and Laplacian (∇ 2ρb) properties, estimated by AIM calculations, showed that both O⋯H bonds have low ρb and positive ∇ 2ρb values (consistent with electrostatic character of the HBs), whereas both O-H bonds have covalent character (∇ 2ρb<0). Natural population analysis data for PhDC, DC and 4-HC were used to predict electrostatic interactions in the exocyclic rings. The calculated oxygen natural charges were found to correlate with the O⋯O distances in PhDC and DC. On the basis of the calculated bond ellipticity, the π-delocalization in the exocyclic rings of PhDC and DC was estimated. The results thus obtained helped to describe the nature of the intramolecular O⋯H-O bonds and the forces driving their formation

  5. Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.

    PubMed

    Escudero, Daniel

    2016-09-20

    Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of

  6. Reaction mechanism and isotope effects derived from centroid transition state theory in intramolecular proton transfer reactions

    NASA Astrophysics Data System (ADS)

    Iftimie, Radu; Schofield, Jeremy

    2001-10-01

    In this article the tautomerization reaction of the enol form of malonaldehyde is used to investigate the magnitude and origin of changes in centroid transition state theory proton transfer reaction rate predictions caused by the quantum dispersion of heavy nuclei. Using an empirical valence bond method to construct the potential energy surface, it is found that quantization of the nuclear degrees of freedom of the carbon atoms significantly influences the centroid potential of mean force used to describe the proton transfer reaction. In contrast, an ab initio simulation carried out using a recently developed molecular mechanics based importance sampling method [J. Chem. Phys. 114, 6763 (2001)] in combination with an accurate density functional theory evaluation of the electronic energies shows a substantially smaller influence of the quantum nuclear degrees of freedom of the secondary atoms on the centroid potential of mean force. A detailed analysis of the different influence of quantization of the nuclear degrees of freedom of secondary atoms observed in the ab initio and empirical valence bond centroid potential of mean force was carried out. It is shown that for the empirical valence bond potential, a significant decrease of the centroid potential of mean force arises through the quantum tunneling of carbon atoms in the molecular backbone. Furthermore, it is demonstrated that in molecular mechanics potentials aimed to describe intramolecular proton transfer reactions, the functional form of the potential energy terms coupling the primary and secondary atom motions as the reaction proceeds as well as the mass of the primary particle can significantly influence the centroid transition state theory predictions of secondary kinetic isotope effects. Finally, the dependence of the reaction rate predictions and isotope effects on the choice of reaction coordinate is investigated and the validity of calculating kinetic isotope effects using the centroid transition

  7. Ground and excited state intramolecular proton transfer controlled intramolecular charge separation and recombination: A new type of charge and proton transfer reaction

    NASA Astrophysics Data System (ADS)

    Nie, Daobo; Bian, Zuqiang; Yu, Anchi; Chen, Zhuqi; Liu, Zhiwei; Huang, Chunhui

    2008-06-01

    A novel β-diketone 1-(4-(9-carbazol)phenyl)-3-phenyl-1,3-propanedione (CDBM) has been synthesized. When excited at 380 nm, this molecule shows single fluorescence. However, when excited at 338 nm, it shows dual fluorescence. A Al 3+ complex Al(CDBM) 3 has been synthesized to investigate the dual fluorescence of CDBM. It is found that this complex shows single fluorescence under all excitation. This result indicated that the dual fluorescence of CDBM may relate to the intramolecular proton transfer reaction. Based on the experimental and theoretical studies of CDBM, N-(4-cyanophenyl)carbazole (CBN) and Al(CDBM) 3, a "ground and excited state intramolecular proton transfer controlled intramolecular charge separation and recombination" mechanism is proposed to explain the unusual excitation-dependent dual fluorescence of CDBM.

  8. Motion Simulator

    NASA Technical Reports Server (NTRS)

    1993-01-01

    MOOG, Inc. supplies hydraulic actuators for the Space Shuttle. When MOOG learned NASA was interested in electric actuators for possible future use, the company designed them with assistance from Marshall Space Flight Center. They also decided to pursue the system's commercial potential. This led to partnership with InterActive Simulation, Inc. for production of cabin flight simulators for museums, expositions, etc. The resulting products, the Magic Motion Simulator 30 Series, are the first electric powered simulators. Movements are computer-guided, including free fall to heighten the sense of moving through space. A projection system provides visual effects, and the 11 speakers of a digital laser based sound system add to the realism. The electric actuators are easier to install, have lower operating costs, noise, heat and staff requirements. The U.S. Space & Rocket Center and several other organizations have purchased the simulators.

  9. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces.

    PubMed

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M; Otero, Roberto; Gallego, José M; Ballester, Pablo; Galan-Mascaros, José R; Ecija, David

    2016-03-11

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  10. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    PubMed Central

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M.; Otero, Roberto; Gallego, José M.; Ballester, Pablo; Galan-Mascaros, José R.; Ecija, David

    2016-01-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure. PMID:26964764

  11. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

    We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Intramolecular charge transfer effects on 3-aminobenzoic acid

    NASA Astrophysics Data System (ADS)

    Stalin, T.; Rajendiran, N.

    2006-03-01

    Effect of solvents, buffer solutions of different pH and β-cyclodextrin on the absorption and fluorescence spectra of 3-aminobenzoic acid (3ABA) have been investigated. The solid inclusion complex of 3ABA with β-CD is discussed by UV-Vis, fluorimetry, semiempirical quantum calculations (AM1), FT-IR, 1H NMR and Scanning Electron Microscope (SEM). The thermodynamic parameters (Δ H, Δ G and Δ S) of the inclusion process are also determined. The experimental results indicated that the inclusion processes is an exothermic and spontaneous. The large Stokes shift emission in solvents with 3ABA are correlated with different solvent polarity scales suggest that, 3ABA molecule is more polar in the S 1 state. Solvent, β-CD studies and excited state dipole moment values confirms that the presence of intramolecular charge transfer (ICT) in 3ABA. Acidity constants for different prototropic equilibria of 3ABA in the S 0 and S 1 states are calculated. β-Cyclodextrin studies shows that 3ABA forms a 1:1 inclusion complex with β-CD. β-CD studies suggest COOH group present in non-polar part and amino group present in hydrophilic part of the β-CD cavity. A mechanism is proposed to explain the inclusion process.

  13. In Vivo Measurement of Intramolecular Distances Using Genetically Encoded Reporters

    PubMed Central

    Sandtner, Walter; Bezanilla, Francisco; Correa, Ana M.

    2007-01-01

    The function of membrane proteins occurs in the context of the cell membrane in living cells acting in concert with various cell components such as other proteins, cofactors, etc. The understanding of the function at the molecular level requires structural techniques, but high resolution structural studies are normally obtained in vitro and in artificial membranes or detergent. Ideally the correlation of structure and function should be carried out in the native environment but most of the techniques applicable in vivo lack the high resolution necessary to track conformational changes on a molecular level. Here we report on the successful application of an improved variant of lanthanide-based resonance energy transfer a fluorescent based technique, to Shaker potassium channels expressed in live Xenopus oocytes. Lanthanide-based resonance energy transfer is particularly suitable to measure intramolecular distances with high resolution. The improvements reported in this work are mainly based on the use of two different small genetically encoded tags (the Lanthanide Binding Tag and the hexa-histidine tag), which due to their small size can be encoded at will in many positions of interest without distorting the protein's function. The technique reported here has the additional improvement that the two tags can be placed independently in contrast to previously described techniques that rely on chemical labeling procedures of thiols. PMID:17766346

  14. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    NASA Astrophysics Data System (ADS)

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M.; Otero, Roberto; Gallego, José M.; Ballester, Pablo; Galan-Mascaros, José R.; Ecija, David

    2016-03-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  15. Intramolecular indicator displacement assay for anions: supramolecular sensor for glyphosate.

    PubMed

    Minami, Tsuyoshi; Liu, Yuanli; Akdeniz, Ali; Koutnik, Petr; Esipenko, Nina A; Nishiyabu, Ryuhei; Kubo, Yuji; Anzenbacher, Pavel

    2014-08-13

    One of the well-known strategies for anion sensing is an indicator (dye) displacement assay. However, the disadvantage of the dye displacement assays is the low sensitivity due to the excess of the dye used. To overcome this setback, we have developed an "Intramolecular Indicator Displacement Assay (IIDA)". The IIDAs comprise a receptor and a spacer with an attached anionic chromophore in a single-molecule assembly. In the resting state, the environment-sensitive anionic chromophore is bound by the receptor, while the anionic substrate competes for binding into the receptor. The photophysical properties of the dye exhibit change in fluorescence when displaced by anions, which results in cross-reactive response. To illustrate the concept, we have prepared IID sensors 1 and 2. Here, the characterization of sensors and microtiter arrays comprising the IIDA are reported. The microtiter array including IID sensors 1 and 2 is capable of recognizing biological phosphates in water. The utility of the IIDA approach is demonstrated on sensing of a phosphonate herbicide glyphosate and other biologically important anions such as pyrophosphate in the presence of interferent sodium chloride.

  16. Inversion of experimental data to extract intermolecular and intramolecular potentials

    SciTech Connect

    Ho, T.S.; Rabitz, H. )

    1993-12-23

    We present a general nonlinear inverse method utilizing discrete experimental data to extract inter- and intramolecular potential energy surfaces. The inverse method is formulated in terms of perturbation expansions of the experimental data upon the functional variations of the underlying potential energy surface--a functional sensitivity analysis approach. A distinction is drawn between the inverse method and the conventional parameter fitting procedure in that the former treats the potential energy surfaces as continuous functions of the internuclear coordinates, whereas the latter is based on restricted forms with a small number of parameters. The possible numerical instability of molecular nonlinear inverse problems is examined in detail using singular function expansion analysis and is overcome using the Tikhonov regularization method, which incorporates the a priori smooth properties of the sought-after potential energy surfaces. Numerical studies show that the iterative inversion procedure based on this inverse method is generic, efficient, and stable and is capable of accurately rendering physically acceptable potential energy surfaces for a variety of problems--either spectroscopic or collisional and one-dimensional or multidimensional. An example employing actual laboratory data has been successfully inverted. Application of the method to small polyatomic systems of current interest and improvement of the method by including higher-order sensitivity densities are also discussed. 84 refs., 9 figs.

  17. Intramolecular proton transfer (IPT) in alkoxyamine: a theoretical investigation.

    PubMed

    Parkhomenko, Dmitriy; Bagryanskaya, Elena G; Marque, Sylvain R A; Siri, Didier

    2013-09-07

    The Intramolecular Proton Transfer (IPT) in alkoxyamines is one of the main factors determining the process of Nitroxide Mediated Polymerization (NMP). Recently, we proposed an experimental approach to study IPT and applied it to a series of alkoxyamines. It was found that IPT dramatically depends on the structure of the alkoxyamine, but it was not clear which factors are significant for IPT (M. V. Edeleva et al., J. Polym. Sci., Part A: Polym. Chem. 2009, 47, 6579-6595). To understand the mechanism and the factors determining the IPT process, in this article we investigate the geometrical parameters and thermokinetics of this reaction using the BMK/6-311++G(3df,3pd)//B3LYP/6-31+G(d,p) method. It was found that the thermokinetics and geometrical parameters of the transition state (TS) for IPT do not depend on the alkoxyamine structure. The only factor which determines the occurrence of IPT is the position of the TS energy level of the C-ON bond homolysis.

  18. Intramolecular, oxidatively induced substitution on a coordinated terpyridyl ligand

    SciTech Connect

    Huynh, M.H.V.; Lee, D.G.; White, P.S.; Meyer, T.J.

    1999-11-10

    In recent experiments, the authors demonstrated that in the Os-hydrazido complexes, trans-[Os{sup VI}(L{sub 3})(Cl){sub 2}(NN(CH{sub 2}){sub 4}O)]{sup 2+} (L{sub 3} = 2,2{prime}:6{prime},2{double{underscore}prime}-terpyridine or tris(1-pyrazolyl)-methane and N(CH{sub 2}){sub 4}O{sup {minus}} = morpholide), there are four interconvertible oxidation states with Os(VI), Os(V), Os(IV), and Os(III) accessible within the solvent limit in CH{sub 3}CN. Examples of Os(VI), Os(V), and Os(IV) have been characterized by X-ray crystallography. The authors report here a remarkable reaction between trans-[Os{sup VI}(tpy)(Cl){sub 2}(NN(CH{sub 2}){sub 4}O)]{sup 2+} (2), has been characterized crystallographically. An extraordinary electrophilic substituent effect of Os(VI) on the tpy ligand and the ability of Os(VI) to undergo reversible intramolecular Os(VI {yields} IV) electron transfer appear to play essential roles in these reactions.

  19. Tryptophan synthase: a multienzyme complex with an intramolecular tunnel.

    PubMed

    Miles, E W

    2001-01-01

    Tryptophan synthase is a classic enzyme that channels a metabolic intermediate, indole. The crystal structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium revealed for the first time the architecture of a multienzyme complex and the presence of an intramolecular tunnel. This remarkable hydrophobic tunnel provides a likely passageway for indole from the active site of the alpha subunit, where it is produced, to the active site of the beta subunit, where it reacts with L-serine to form L-tryptophan in a pyridoxal phosphate-dependent reaction. Rapid kinetic studies of the wild type enzyme and of channel-impaired mutant enzymes provide strong evidence for the proposed channeling mechanism. Structures of a series of enzyme-substrate intermediates at the alpha and beta active sites are elucidating enzyme mechanisms and dynamics. These structural results are providing a fascinating picture of loops opening and closing, of domain movements, and of conformational changes in the indole tunnel. Solution studies provide further evidence for ligand-induced conformational changes that send signals between the alpha and beta subunits. The combined results show that the switching of the enzyme between open and closed conformations couples the catalytic reactions at the alpha and beta active sites and prevents the escape of indole.

  20. Catalytic, Enantioselective, Intramolecular Carbosulfenylation of Olefins. Preparative and Stereochemical Aspects

    PubMed Central

    Denmark, Scott E.; Jaunet, Alex

    2014-01-01

    The first catalytic, enantioselective, intramolecular carbosulfenylation of isolated alkenes with aromatic nucleophiles is described. The combination of N-phenylsulfenylphthalimide, a chiral selenophosphoramide derived from BINAM, and ethanesulfonic acid as a co-catalytic Brønsted acid induced an efficient and selective cyclofunctionalization of various alkenes (aliphatic and aromatic) tethered to a 3,4-methylenedioxyphenyl ring. Under these conditions, 6-phenylthio-5,6,7,8-tetrahydronaphthalenes are formed diastereospecifically in good yields (50–92%) and high enantioselectivities (71:29 – 97:3 er). E-Alkenes reacted much more rapidly and with much higher selectivity than Z-alkenes, whereas electron rich alkenes reacted more rapidly but with comparable selectivity to electron-neutral alkenes and electron deficient alkenes. The Brønsted acid played a critical role in effecting reproducible enantioselectivity. A model for the origin of enantioselectivity and the dependence of rate and selectivity on alkene structure is proposed along with a rationale for the site selectivity in reactions with mono-activated arene nucleophiles. PMID:24328051

  1. Mercury(II) 2-aminoethanethiolate clusters: intramolecular transformations and mechanisms.

    PubMed

    Bharara, Mohan S; Parkin, Sean; Atwood, David A

    2006-09-04

    The combination of HgF2 and 2-aminoethanethiol (AET, with some AET.HCl present) yielded a cyclic tetranuclear thiolate, [Hg4Cl4(SCH2CH2NH2)4] (1), with alternating Hg and S atoms. The Cl from the reaction mixture led to the formation of Hg-Cl bonds with no Hg-F in the final product. In contrast, a similar reaction with HgBr2 yielded a nonanuclear cluster, [Hg9Br15(SCH2CH2NH3)15]3+ (2), and the disulfide salt {[HgBr4][(NH3CH2CH2S-)2]} (3). Despite similar reactions, the AET groups in 2 are protonated compared to the nonprotonated amine groups in 1, which allows the ligand to chelate the Hg atom in the latter compound. The reaction with HgI2 yielded a cyclic tetranuclear compound, [Hg4I6(SCH2CH2NH2)2(SCH2CH2NH3)2](H2O/EtOH) (4), containing protonated and nonprotonated AET groups. Compound 4 at room temperature irreversibly rearranges to [Hg4I4(SCH2CH2NH2)4] (5), which is isostructural to 1. A systematic pathway for the formation of 1 along with the intramolecular conversion of 4 to 5 is proposed. These compounds demonstrate that very diverse Hg-S compounds form under similar reaction conditions.

  2. Vibrational spectroscopy and intramolecular dynamics of 1-butyne.

    PubMed

    Portnov, Alexander; Rosenwaks, Salman; Bar, Ilana

    2004-09-22

    Photodissociation of jet-cooled vibrationally excited 1-butyne, C(2)H(5)C[Triple Bond]C[Single Bond]H, coupled with mass spectrometric detection of H photofragments, facilitated measurements of action spectra and Doppler profiles, expressing the yield of the ensuing fragments versus the vibrational excitation and UV probe lasers, respectively. Both the action spectra and the simultaneously measured room temperature photoacoustic spectra in the 2nu(1), 3nu(1), and 4nu(1) C[Single Bond]H acetylenic stretch regions exhibit unresolved rotational envelopes with significant narrowing of the former due to temperature-related change in the rotational structure. The narrowing of the action spectrum in the 3nu(1) region exposed a resonance splitting, implying intramolecular vibrational energy redistribution (IVR) time of approximately 1 ps. Asymmetric rotor simulation of the band contours provided the rotational constants and estimates for the homogeneous broadening arising from IVR to the bath vibrational states. The homogenous linewidth of 4nu(1) is anomalously narrower than that of 2nu(1) and 3nu(1), indicating a longer lived 4nu(1) state despite the increasing background state density, suggestive of a lack of low-order resonances or of mode-specific coupling with the bath states. The Doppler profiles indicate that the H photofragments are released with low average translational energies, pointing to an indirect dissociation process occurring after internal conversion (IC) to the ground electronic state or after IC and isomerization to butadiene.

  3. Intramolecular Alkene Aminocarbonylation Using Concerted Cycloadditions of Amino-Isocyanates.

    PubMed

    Ivanovich, Ryan A; Clavette, Christian; Vincent-Rocan, Jean-François; Roveda, Jean-Grégoire; Gorelsky, Serge I; Beauchemin, André M

    2016-06-01

    The ubiquity of nitrogen heterocycles in biologically active molecules challenges synthetic chemists to develop a variety of tools for their construction. While developing metal-free hydroamination reactions of hydrazine derivatives, it was discovered that carbazates and semicarbazides can also lead to alkene aminocarbonylation products if nitrogen-substituted isocyanates (N-isocyanates) are formed in situ as reactive intermediates. At first this reaction required high temperatures (150-200 °C), and issues included competing hydroamination and N-isocyanate dimerization pathways. Herein, improved conditions for concerted intramolecular alkene aminocarbonylation with N-isocyanates are reported. The use of βN-benzyl carbazate precursors allows the effective minimization of N-isocyanate dimerization. Diminished dimerization leads to higher yields of alkene aminocarbonylation products, to reactivity at lower temperatures, and to an improved scope for a reaction sequence involving alkene aminocarbonylation followed by 1,2-migration of the benzyl group. Furthermore, fine-tuning of the blocking (masking) group on the N-isocyanate precursor, and reaction conditions relying on base catalysis for N-isocyanate formation from simpler precursors resulted in room temperature reactivity, consequently minimizing the competing hydroamination pathway. Collectively, this work highlights that controlled reactivity of aminoisocyanates is possible, and provides a broadly applicable alkene aminocarbonylation approach to heterocycles possessing the β-aminocarbonyl motif.

  4. Tracer diffusion in active suspensions

    NASA Astrophysics Data System (ADS)

    Burkholder, Eric W.; Brady, John F.

    2017-05-01

    We study the diffusion of a Brownian probe particle of size R in a dilute dispersion of active Brownian particles of size a , characteristic swim speed U0, reorientation time τR, and mechanical energy ksTs=ζaU02τR/6 , where ζa is the Stokes drag coefficient of a swimmer. The probe has a thermal diffusivity DP=kBT /ζP , where kBT is the thermal energy of the solvent and ζP is the Stokes drag coefficient for the probe. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. In competition with this steric hindrance is an enhancement driven by the activity of the swimmers. The strength of swimming relative to thermal diffusion is set by Pes=U0a /DP . The active contribution to the diffusivity scales as Pes2 for weak swimming and Pes for strong swimming, but the transition between these two regimes is nonmonotonic. When fluctuations in the probe motion decay on the time scale τR, the active diffusivity scales as ksTs/ζP : the probe moves as if it were immersed in a solvent with energy ksTs rather than kBT .

  5. Intramolecular Diels–Alder/1,3-Dipolar Cycloaddition Cascade of 1,3,4-Oxadiazoles

    PubMed Central

    Elliott, Gregory I.; Fuchs, James R.; Blagg, Brian S. J.; Ishikawa, Hayato; Tao, Houchao; Yuan, Z.-Q.; Boger, Dale L.

    2008-01-01

    Full details of a systematic exploration of the intramolecular [4+2]/[3+2] cycloaddition cascade of 1,3,4-oxadiazoles are disclosed in which the scope and utility of the reaction are defined. PMID:16895427

  6. Fluorescence turn-on response of a conjugated polyelectrolyte with intramolecular stack structure to biomacromolecules.

    PubMed

    Lee, Wang-Eun; Jin, Young-Jae; Kim, Shin-Il; Kwak, Giseop; Kim, Joon Heon; Sakaguchi, Toshikazu; Lee, Chang-Lyoul

    2013-10-28

    An anionic conjugated polyelectrolyte based on polydiphenylacetylene showed a significant fluorescence turn-on response to positively-charged proteins through a conformational relaxation of its intramolecular stack structure.

  7. Tree-ring cellulose exhibits several distinct intramolecular 13C signals

    NASA Astrophysics Data System (ADS)

    Wieloch, Thomas; Ehlers, Ina; Frank, David; Gessler, Arthur; Grabner, Michael; Yu, Jun; Schleucher, Jürgen

    2017-04-01

    Stable carbon isotopes are a key tool in biogeosciences. Present applications including compound-specific isotope analysis measure 13C/12C ratios (δ13C) of bulk material or of whole molecules. However, it is well known that primary metabolites also show large intramolecular 13C variation - also called isotopomer variation. This variation reflects 13C fractionation by enzyme reactions and therefore encodes metabolic information. Furthermore, δ13C must be considered an average of the intramolecular 13C distribution. Here we will present (1) methodology to analyse intramolecular 13C distributions of tree-ring cellulose by quantitative 13C NMR (Chaintreau et al., 2013, Anal Chim Acta, 788, 108-113); (2) intramolecular 13C distributions of an annually-resolved tree ring chronology (Pinus nigra, 1961-1995); (3) isotope parameters and terminology for analysis of intramolecular isotope time series; (4) a method for correcting for heterotrophic C redistribution. We will show that the intramolecular 13C distribution of tree-ring cellulose shows large variation, with differences between isotopomers exceeding 10‰Ṫhus, individual 13C isotopomers of cellulose constitute distinct 13C inputs into major global C pools such as wood and soil organic matter. When glucose units with the observed intramolecular 13C pattern are broken down along alternative catabolic pathways, it must be expected that respired CO2 with strongly differing δ13C will be released; indicating that intramolecular 13C variation affects isotope signals of atmosphere-biosphere C exchange fluxes. taking this variation into account will improve modelling of the global C cycle. Furthermore, cluster analysis shows that tree-ring glucose exhibits several independent intramolecular 13C signals, which constitute distinct ecophysiological information channels. Thus, whole-molecule 13C analysis likely misses a large part of the isotope information stored in tree rings. As we have shown for deuterium (Ehlers et al

  8. Total synthesis of virgatolide B via exploitation of intramolecular hydrogen bonding.

    PubMed

    Hume, Paul A; Furkert, Daniel P; Brimble, Margaret A

    2014-06-06

    A full account of the enantioselective total synthesis of virgatolide B is reported. Key features of the synthesis include an sp(3)-sp(2) Suzuki-Miyaura cross-coupling of a β-trifluoroboratoamide with an aryl bromide, regioselective intramolecular carboalkoxylation, and a 1,3-anti-selective Mukaiyama aldol reaction. Intramolecular hydrogen bonding governed the regioselectivity of the key spiroketalization step, affording the natural product as a single regioisomer.

  9. Stereoselective Intramolecular Cyclopropanation of α-Diazoacetates via Co(II)-Based Metalloradical Catalysis.

    PubMed

    Ruppel, Joshua V; Cui, Xin; Xu, Xue; Zhang, X Peter

    2014-07-01

    Co(II) complexes of D2-symmetric chiral porphyrins have been proven to be effective metalloradical catalysts for the asymmetric intramolecular cyclopropanation of allyl α-diazoacetates. 4-(Dimethylamino)pyridine (DMAP), through positive trans effect, plays an important role in the enhancement of the asymmetric induction for the intramolecular cyclopropanation process. This metalloradical catalytic system is suitable for cyclopropanation of allyl α-diazoacetates with varied functional groups and substitution patterns, producing bicyclic products with complete diastereocontrol and good enantiocontrol.

  10. Subpicosecond time-resolved intramolecular electronic energy transfer in flexible bichromophoric Coumarin molecules

    SciTech Connect

    Kaschke, M.; Ernsting, N.P. ); Valeur, B.; Bourson, J. )

    1990-07-26

    By excite-and-probe spectroscopy with subpicosecond time resolution, the authors have measured the intramolecular electronic energy transfer in bichromophoric coumarins linked by a flexible polymethylene chain. The transfer proceeds on a time scale between 1 and 20 ps depending on the polymethylene chain length. The results can be well described by a dipole-dipole interaction model that takes into account the statistical distribution of intramolecular distances between the two chromophores.

  11. Intramolecular excimer formation in hexakis(pyrenyloxy)cyclotriphosphazene: photophysical properties, crystal structure, and theoretical investigation.

    PubMed

    Yeşilot, Serkan; Coşut, Bünyemin; Alidaği, Hüsnüye Ardiç; Hacivelioğlu, Ferda; Özpinar, Gül Altinbaş; Kiliç, Adem

    2014-03-07

    A hexakis(pyrenyloxy)cyclotriphosphazene is synthesized by the reaction of N3P3Cl6 with 2-hydroxypyrene, and its excimer emission through intramolecular interactions in solution and in the solid state has been investigated by fluorescence spectroscopy and X-ray crystallography. Thermal and electrochemical properties were investigated. A DFT benchmark study has been performed to evaluate the intramolecular interactions and molecular orbital levels by comparing with the experimental results.

  12. Asymmetric Intramolecular Alkylation of Chiral Aromatic Imines via Catalytic C-H Bond Activation

    SciTech Connect

    Watzke, Anja; Wilson, Rebecca; O'Malley, Steven; Bergman, Robert; Ellman, Jonathan

    2007-04-16

    The asymmetric intramolecular alkylation of chiral aromatic aldimines, in which differentially substituted alkenes are tethered meta to the imine, was investigated. High enantioselectivities were obtained for imines prepared from aminoindane derivatives, which function as directing groups for the rhodium-catalyzed C-H bond activation. Initial demonstration of catalytic asymmetric intramolecular alkylation also was achieved by employing a sterically hindered achiral imine substrate and catalytic amounts of a chiral amine.

  13. The short-time intramolecular dynamics of solutes in liquids. II. Vibrational population relaxation

    NASA Astrophysics Data System (ADS)

    Goodyear, Grant; Stratt, Richard M.

    1997-08-01

    Events such as the vibrational relaxation of a solute are often well described by writing an effective equation of motion—a generalized Langevin equation—which expresses the surrounding medium's influence on the intramolecular dynamics in terms of a friction and a fluctuating force acting on the solute. These quantities, though, can be obtained from the instantaneous normal modes (INMs) of the system when the relaxation takes place in a fluid, suggesting that we should be able to analyze in some detail the solvent motions driving the relaxation, at least for short times. In this paper we show that this promise can indeed be realized for the specific case of a vibrating diatomic molecule dissolved in an atomic solvent. Despite the relatively long times typical of vibrational population relaxation, it turns out that understanding the behavior of the vibrational friction at the short times appropriate to INMs (a few hundred femtoseconds) often suffices to predict T1 times. We use this observation to probe the dependence of these relaxation rates on thermodynamic conditions and to look at the molecular mechanisms underlying the process. We find that raising the temperature at any given density or raising the density at any given temperature will invariably increase the rate of energy relaxation. However, since these two trends may be in conflict in a typical constant-pressure laboratory experiment, we also find that it is possible to make sense of the "anomalous" inverted temperature dependence recently seen experimentally. We find, as well, that the INM theory—which has no explicit collisions built into it—predicts exactly the same density dependence as the venerable independent-binary-collision (IBC) theory (an intriguing result in view of recent claims that experimental observations of this kind of dependence provide support for the IBC theory). The actual mechanisms behind vibrational population relaxation are revealed by looking in detail at the

  14. Diffusion barriers

    NASA Technical Reports Server (NTRS)

    Nicolet, M. A.

    1983-01-01

    The choice of the metallic film for the contact to a semiconductor device is discussed. One way to try to stabilize a contact is by interposing a thin film of a material that has low diffusivity for the atoms in question. This thin film application is known as a diffusion barrier. Three types of barriers can be distinguished. The stuffed barrier derives its low atomic diffusivity to impurities that concentrate along the extended defects of a polycrystalline layer. Sacrificial barriers exploit the fact that some (elemental) thin films react in a laterally uniform and reproducible fashion. Sacrificial barriers have the advantage that the point of their failure is predictable. Passive barriers are those most closely approximating an ideal barrier. The most-studied case is that of sputtered TiN films. Stuffed barriers may be viewed as passive barriers whose low diffusivity material extends along the defects of the polycrystalline host.

  15. Diffuse radiation

    NASA Technical Reports Server (NTRS)

    1981-01-01

    A diffuse celestial radiation which is isotropic at least on a course scale were measured from the soft X-ray region to about 150 MeV, at which energy the intensity falls below that of the galactic emission for most galactic latitudes. The spectral shape, the intensity, and the established degree of isotropy of this diffuse radiation already place severe constraints on the possible explanations for this radiation. Among the extragalactic theories, the more promising explanations of the isotropic diffuse emission appear to be radiation from exceptional galaxies from matter antimatter annihilation at the boundaries of superclusters of galaxies of matter and antimatter in baryon symmetric big bang models. Other possible sources for extragalactic diffuse gamma radiation are discussed and include normal galaxies, clusters of galaxies, primordial cosmic rays interacting with intergalactic matter, primordial black holes, and cosmic ray leakage from galaxies.

  16. Auditory Motion Elicits a Visual Motion Aftereffect

    PubMed Central

    Berger, Christopher C.; Ehrsson, H. Henrik

    2016-01-01

    The visual motion aftereffect is a visual illusion in which exposure to continuous motion in one direction leads to a subsequent illusion of visual motion in the opposite direction. Previous findings have been mixed with regard to whether this visual illusion can be induced cross-modally by auditory stimuli. Based on research on multisensory perception demonstrating the profound influence auditory perception can have on the interpretation and perceived motion of visual stimuli, we hypothesized that exposure to auditory stimuli with strong directional motion cues should induce a visual motion aftereffect. Here, we demonstrate that horizontally moving auditory stimuli induced a significant visual motion aftereffect—an effect that was driven primarily by a change in visual motion perception following exposure to leftward moving auditory stimuli. This finding is consistent with the notion that visual and auditory motion perception rely on at least partially overlapping neural substrates. PMID:27994538

  17. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging

    NASA Astrophysics Data System (ADS)

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-01

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch-Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients.

  18. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging.

    PubMed

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-07

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch-Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients.

  19. The Fluctuation-Dissipation Theorem of Colloidal Particle's energy on 2D Periodic Substrates: A Monte Carlo Study of thermal noise-like fluctuation and diffusion like Brownian motion

    NASA Astrophysics Data System (ADS)

    Najafi, Amin

    2014-05-01

    Using the Monte Carlo simulations, we have calculated mean-square fluctuations in statistical mechanics, such as those for colloids energy configuration are set on square 2D periodic substrates interacting via a long range screened Coulomb potential on any specific and fixed substrate. Random fluctuations with small deviations from the state of thermodynamic equilibrium arise from the granular structure of them and appear as thermal diffusion with Gaussian distribution structure as well. The variations are showing linear form of the Fluctuation-Dissipation Theorem on the energy of particles constitutive a canonical ensemble with continuous diffusion process of colloidal particle systems. The noise-like variation of the energy per particle and the order parameter versus the Brownian displacement of sum of large number of random steps of particles at low temperatures phase are presenting a markovian process on colloidal particles configuration, too.

  20. Collective motion

    NASA Astrophysics Data System (ADS)

    Vicsek, Tamás; Zafeiris, Anna

    2012-08-01

    We review the observations and the basic laws describing the essential aspects of collective motion - being one of the most common and spectacular manifestation of coordinated behavior. Our aim is to provide a balanced discussion of the various facets of this highly multidisciplinary field, including experiments, mathematical methods and models for simulations, so that readers with a variety of background could get both the basics and a broader, more detailed picture of the field. The observations we report on include systems consisting of units ranging from macromolecules through metallic rods and robots to groups of animals and people. Some emphasis is put on models that are simple and realistic enough to reproduce the numerous related observations and are useful for developing concepts for a better understanding of the complexity of systems consisting of many simultaneously moving entities. As such, these models allow the establishing of a few fundamental principles of flocking. In particular, it is demonstrated, that in spite of considerable differences, a number of deep analogies exist between equilibrium statistical physics systems and those made of self-propelled (in most cases living) units. In both cases only a few well defined macroscopic/collective states occur and the transitions between these states follow a similar scenario, involving discontinuity and algebraic divergences.

  1. Fluid diffusion in porous silica

    NASA Astrophysics Data System (ADS)

    McCann, Lowell I.

    Fluid motion in porous media has received a great deal of theoretical and experimental attention due to its importance in systems as diverse as ground water aquifers, catalytic processes, and size separation schemes. Often, the motion of interest is the random thermal motion of molecules in a fluid undergoing no net flow. This diffusive motion is particularly important when the size of the pores is nearly the same as the size of the molecules. In this study, fluid diffusion is measured in several varieties of porous silica whose pore structure is determined by the process by which it is made. The samples in this study have porosities (φ, the ratio of the pore volume to the total sample volume) that vary from 0.3 to 0.75 and average pore radii that range from approximately 15 to 120 A. Determining the effect of the pore structure on the diffusion of a liquid in a porous material is complicated by the chemical interactions between the diffusing molecules and the pore surface. In this study, ions in a hydrophilic fluid are used to block the adsorption of the diffusing dye molecules to the hydroxyl groups covering the silica surface. This technique is unlike typical surface treatments of silica in that it does not permanently alter the pore geometry. In this work, fluid diffusion is measured with a transient holographic grating technique where interfering laser beams create a periodic refractive index modulation in the fluid. The diffraction of a third laser off this grating is monitored to determine how quickly the grating relaxes, thereby determining the diffusion coefficient of the molecules in the fluid. Varying the grating periodicity controls the length scale of the diffusion measurement from 1.2 to 100 μm which is much larger than the average pore sizes of the samples. Therefore, over these large scales, we measure 'normal' diffusion, where the mean squared displacement of a diffusing particle varies linearly with time. In one particular type of porous silica

  2. Fractional-calculus diffusion equation

    PubMed Central

    2010-01-01

    Background Sequel to the work on the quantization of nonconservative systems using fractional calculus and quantization of a system with Brownian motion, which aims to consider the dissipation effects in quantum-mechanical description of microscale systems. Results The canonical quantization of a system represented classically by one-dimensional Fick's law, and the diffusion equation is carried out according to the Dirac method. A suitable Lagrangian, and Hamiltonian, describing the diffusive system, are constructed and the Hamiltonian is transformed to Schrodinger's equation which is solved. An application regarding implementation of the developed mathematical method to the analysis of diffusion, osmosis, which is a biological application of the diffusion process, is carried out. Schrödinger's equation is solved. Conclusions The plot of the probability function represents clearly the dissipative and drift forces and hence the osmosis, which agrees totally with the macro-scale view, or the classical-version osmosis. PMID:20492677

  3. Intramolecular charge transfer with fluorazene and N-phenylpyrrole.

    PubMed

    Druzhinin, Sergey I; Kovalenko, Sergey A; Senyushkina, Tamara A; Demeter, Attila; Zachariasse, Klaas A

    2010-02-04

    The reaction from the initially prepared locally excited (LE) precursor to the intramolecular charge transfer (ICT) state of the planarized fluorazene (FPP) is investigated and compared with its flexible counterpart N-phenylpyrrole (PP). The fluorescence spectra of FPP and PP at 25 degrees C in solvents of different polarity reveal that the onset of a LE --> ICT reaction occurs at lower polarity (tetrahydrofuran, epsilon = 7.39) for FPP than for PP (1,2-dichloroethane, epsilon = 10.4). In accordance with this observation, the ICT reaction enthalpy -DeltaH is larger for FPP than for PP, 16.7 versus 6.7 kJ/mol in ethyl cyanide (EtCN). The larger ICT efficiency of FPP is related to the smaller energy gap between the two lowest excited singlet states DeltaE(S(1),S(2)): 3680 cm(-1) for FPP and 4070 cm(-1) for PP in n-hexane, as would be expected in the context of the PICT model. From picosecond fluorescence decays in EtCN at -45 degrees C it is found that the LE --> ICT reaction rate constant k(a) of FPP is with 9.8 x 10(10) s(-1) considerably larger than that of PP with 3.9 x 10(10) s(-1). From femtosecond transient absorption spectra in acetonitrile (MeCN) at 22 degrees C, an ICT reaction time of 1.6 ps is obtained for FPP, shorter than the 4.0 ps determined for PP. The results show that a perpendicular twist of the pyrrole and phenyl subgroups is not required for an efficient ICT reaction with PP, the planarization of FPP even making this reaction faster. The similarity of the ESA spectra of FPP with those of PP in MeCN, with ICT absorption maxima at 365 nm (FPP) and 370 nm (PP), leads to the conclusion that both ICT states have a planar structure.

  4. Visual motion aftereffect from understanding motion language.

    PubMed

    Dils, Alexia Toskos; Boroditsky, Lera

    2010-09-14

    Do people spontaneously form visual mental images when understanding language, and if so, how truly visual are these representations? We test whether processing linguistic descriptions of motion produces sufficiently vivid mental images to cause direction-selective motion adaptation in the visual system (i.e., cause a motion aftereffect illusion). We tested for motion aftereffects (MAEs) following explicit motion imagery, and after processing literal or metaphorical motion language (without instructions to imagine). Intentionally imagining motion produced reliable MAEs. The aftereffect from processing motion language gained strength as people heard more and more of a story (participants heard motion stories in four installments, with a test after each). For the last two story installments, motion language produced reliable MAEs across participants. Individuals differed in how early in the story this effect appeared, and this difference was predicted by the strength of an individual's MAE from imagining motion. Strong imagers (participants who showed the largest MAEs from imagining motion) were more likely to show an MAE in the course of understanding motion language than were weak imagers. The results demonstrate that processing language can spontaneously create sufficiently vivid mental images to produce direction-selective adaptation in the visual system. The timecourse of adaptation suggests that individuals may differ in how efficiently they recruit visual mechanisms in the service of language understanding. Further, the results reveal an intriguing link between the vividness of mental imagery and the nature of the processes and representations involved in language understanding.

  5. Anomalous diffusion of brain metabolites evidenced by diffusion-weighted magnetic resonance spectroscopy in vivo

    PubMed Central

    Marchadour, Charlotte; Brouillet, Emmanuel; Hantraye, Philippe; Lebon, Vincent; Valette, Julien

    2012-01-01

    Translational displacement of molecules within cells is a key process in cellular biology. Molecular motion potentially depends on many factors, including active transport, cytosol viscosity and molecular crowding, tortuosity resulting from cytoskeleton and organelles, and restriction barriers. However, the relative contribution of these factors to molecular motion in the cytoplasm remains poorly understood. In this work, we designed an original diffusion-weighted magnetic resonance spectroscopy strategy to probe molecular motion at subcellular scales in vivo. This led to the first observation of anomalous diffusion, that is, dependence of the apparent diffusion coefficient (ADC) on the diffusion time, for endogenous intracellular metabolites in the brain. The observed increase of the ADC at short diffusion time yields evidence that metabolite motion is characteristic of hindered random diffusion rather than active transport, for time scales up to the dozen milliseconds. Armed with this knowledge, data modeling based on geometrically constrained diffusion was performed. Results suggest that metabolite diffusion occurs in a low-viscosity cytosol hindered by ∼2-μm structures, which is consistent with known intracellular organization. PMID:22929443

  6. Optical observation of correlated motions in dihydrofolate reductase

    NASA Astrophysics Data System (ADS)

    Xu, Mengyang; Niessen, Katherine; Pace, James; Cody, Vivian; Markelz, Andrea

    2015-03-01

    Enzyme function relies on its structural flexibility to make conformational changes for substrate binding and product release. An example of a metabolic enzyme where such structural changes are vital is dihydrofolate reductase (DHFR). DHFR is essential in both prokaryotes and eukaryotes for the nucleotide biosynthesis by catalyzing the reduction of dihydrofolate to tetrahydrofolate. NMR dynamical measurements found large amplitude fast dynamics that could indicate rigid-body, twisting-hinge motion for ecDHFR that may mediate flux. The role of such long-range correlated motions in function was suggested by the observed sharp decrease in enzyme activity for the single point mutation G121V, which is remote from active sites. This decrease in activity may be caused by the mutation interfering with the long-range intramolecular vibrations necessary for rapid access to functional configurations. We use our new technique of crystal anisotropy terahertz microscopy (CATM), to observe correlated motions in ecDHFR crystals with the bonding of NADPH and methotrexate. We compare the measured intramolecular vibrational spectrum with calculations using normal mode analysis.

  7. Diffusion of Ellipsoids in Bacterial Suspensions

    NASA Astrophysics Data System (ADS)

    Peng, Yi; Lai, Lipeng; Tai, Yi-Shu; Zhang, Kechun; Xu, Xinliang; Cheng, Xiang

    2016-02-01

    Active fluids such as swarming bacteria and motile colloids exhibit exotic properties different from conventional equilibrium materials. As a peculiar example, a spherical tracer immersed inside active fluids shows an enhanced translational diffusion, orders of magnitude stronger than its intrinsic Brownian motion. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in a quasi-two-dimensional bacterial bath. Our study shows a nonlinear enhancement of both translational and rotational diffusions of ellipsoids. More importantly, we uncover an anomalous coupling between particles' translation and rotation that is strictly prohibited in Brownian diffusion. The coupling reveals a counterintuitive anisotropic particle diffusion, where an ellipsoid diffuses fastest along its minor axis in its body frame. Combining experiments with theoretical modeling, we show that such an anomalous diffusive behavior arises from the generic straining flow of swimming bacteria. Our work illustrates an unexpected feature of active fluids and deepens our understanding of transport processes in microbiological systems.

  8. Post-transition State Dynamics for Propene Ozonolysis: Intramolecular and Unimolecular Dynamics of Molozonide

    SciTech Connect

    Vayner, Grigoriy; Addepalli, Srirangam V.; Song, Kihyung; Hase, William L.

    2006-07-07

    intramolecular energy flow, which depend on molozonide’s symmetry (i.e., anti or syn). This symmetry related dynamics is not completely understood, but it is clearly related to the non-RRKM dynamics for anti↔syn isomerization and anti molozonide dissociation to CH₃CHO+H₂COO. Correlations are found between the stretching motions of molozonide, indicative of nonchaotic and non-RRKM dynamics. The non-RRKM dynamics of molozonide dissociation partitions vibration energy to H₂COO that is larger than statistical partitioning. Though the direct dynamics simulations are classical, better agreement is obtained using quantum instead of classical harmonic RRKM theory. This may result from the neglect of anharmonicity in the RRKM calculations, the non-RRKM dynamics of the classical trajectories, or a combination of these two effects. The trajectories suggest that the equilibrium syn/anti molozonide ratio is approximately 1.1–1.2 times larger than that predicted by the harmonic densities of state, indicating an anharmonic correction.

  9. Diffuser Test

    NASA Image and Video Library

    2007-09-13

    Tests begun at Stennis Space Center's E Complex Sept. 13 evaluated a liquid oxygen lead for engine start performance, part of the A-3 Test Facility Subscale Diffuser Risk Mitigation Project at SSC's E-3 Test Facility. Phase 1 of the subscale diffuser project, completed Sept. 24, was a series of 18 hot-fire tests using a 1,000-pound liquid oxygen and gaseous hydrogen thruster to verify maximum duration and repeatability for steam generation supporting the A-3 Test Stand project. The thruster is a stand-in for NASA's developing J-2X engine, to validate a 6 percent scale version of A-3's exhaust diffuser. Testing the J-2X at altitude conditions requires an enormous diffuser. Engineers will generate nearly 4,600 pounds per second of steam to reduce pressure inside A-3's test cell to simulate altitude conditions. A-3's exhaust diffuser has to be able to withstand regulated pressure, temperatures and the safe discharge of the steam produced during those tests. Before the real thing is built, engineers hope to work out any issues on the miniature version. Phase 2 testing is scheduled to begin this month.

  10. Self Motion Perception and Motion Sickness

    NASA Technical Reports Server (NTRS)

    Fox, Robert A. (Principal Investigator)

    1991-01-01

    The studies conducted in this research project examined several aspects of motion sickness in animal models. A principle objective of these studies was to investigate the neuroanatomy that is important in motion sickness with the objectives of examining both the utility of putative models and defining neural mechanisms that are important in motion sickness.

  11. Nuclear fission with diffusive dynamics

    NASA Astrophysics Data System (ADS)

    Cha, D.; Bertsch, G. F.

    1992-07-01

    We investigate the dynamics of nuclear fission, assuming purely diffusive motion up to the saddle point. The resulting Smoluchowski equation is solved for conditions appropriate to the 16O+142Nd-->158Er reaction at 207 MeV. The solution is characterized by an equilibration time τ0 for the system to reach steady state, and the fission decay rate in steady state, Λ. We find that the equilibration time τ0 plays a very small role in determining the number of prescission neutrons. The diffusion coefficient extracted from the experimental data is larger than the theoretical in the work of Bush, Bertsch, and Brown by a factor of 5-11.

  12. Phase diffusion in a chaotic pendulum

    SciTech Connect

    Blackburn, J.A.; Gro/nbech-Jensen, N.

    1996-04-01

    The rate of expansion of the phase coordinate for a harmonically driven pendulum is considered. The mean-squared displacement is found to grow as a linear function of time during chaotic motion, indicating deterministic diffusion. The diffusion coefficient can be significantly influenced by the proximity of a window containing a periodic solution. We find that diffusion associated with intermittent chaos can be described in terms of an interleaving of the diffusion properties of the separate modes taking part in the intermittency. {copyright} {ital 1996 The American Physical Society.}

  13. Mechanism for diffusion induced grain boundary migration

    SciTech Connect

    Balluffi, R.W.; Cahn, J.W.

    1980-08-01

    Grain boundaries are found to migrate under certain conditions when solute atoms are diffused along them. This phenomenon, termed diffusion induced grain boundary migration (DIGM), has now been found in six systems. The observed phenomenon and empirical data are used to discard certain concepts for the driving force and the mechanism. A mechanism is proposed in which differences in the diffusion coefficients of the diffusing species along the grain boundary cause a self-sustaining climb of grain boundary dislocations and motion of their associated grain boundary steps.

  14. Single file diffusion in microtubules

    NASA Astrophysics Data System (ADS)

    Rutenberg, Andrew; Farrell, Spencer; Brown, Aidan

    2015-03-01

    We investigate the single file diffusion (SFD) of large particles entering a confined tubular geometry, such as luminal diffusion of proteins inside microtubules or flagella. While single-file effects have no effect on particle density, we report significant single-file effects for individually-tracked tracer particle motion. Both exact and approximate ordering statistics of particles entering semi-infinite tubes agree well with our stochastic simulations. Considering initially empty semi-infinite tubes, with particles entering at one end starting from an initial time t = 0 , tracked particles display super-diffusive effective exponents just after they enter the system and trends towards diffusive exponents at later times. Equivalently, if diffusive exponents are assumed the effective diffusivity is reduced at early times and enhanced at later times through a logarithmic factor logN , where N is the number of particles in the tube. When we number each particle from the first (n = 1) to the most recent (n = N), we find good scaling collapse of the effective diffusivity for all n. Techniques that track individual particles, or local groups of particles, such as photo-activation or photobleaching, will exhibit single-file effects.

  15. Macromolecular Diffusion in Polymer Nanocomposites

    NASA Astrophysics Data System (ADS)

    Gam, Sangah; Meth, Jeff; Zane, Steve; Winey, Karen; Clarke, Nigel; Composto, Russell

    2011-03-01

    Macromolecular diffusion in crowded systems is important in biological and engineered systems. We have studied macromolecular diffusion through a model polymer nanocomposite (PNC) containing phenyl grafted silica nanoparticles (NPs), randomly distributed in a polystyrene matrix. Over a wide range of NP loading and tracer molecular weight (M), the scaling of the diffusion coefficient with M is in excellent agreement with the entropic barrier model (EBM) previously used to describe diffusion of DNA through confined media (e.g., gels and nanopores). To investigate the effect of NP size, diffusion was measured in PNC's with silica NPs having diameters of 28 and 12 nm. The normalized diffusion coefficients (D / D0) plotted against the interparticle separation relative to probe size (i.e., ID/ 2 Rg) collapse on a master curve. Diffusion in a poly(methyl methacrylate):silica NP system was also investigated to understand how attractive interactions (i.e., enthalpy) perturb motion relative to the polystyrene and phenyl-silica NP system which is athermal. Finally, a flux-based model is proposed and compared with experimental results.

  16. A Huygens principle for diffusion and anomalous diffusion in spatially extended systems

    PubMed Central

    Gottwald, Georg A.; Melbourne, Ian

    2013-01-01

    We present a universal view on diffusive behavior in chaotic spatially extended systems for anisotropic and isotropic media. For anisotropic systems, strong chaos leads to diffusive behavior (Brownian motion with drift) and weak chaos leads to superdiffusive behavior (Lévy processes with drift). For isotropic systems, the drift term vanishes and strong chaos again leads to Brownian motion. We establish the existence of a nonlinear Huygens principle for weakly chaotic systems in isotropic media whereby the dynamics behaves diffusively in even space dimension and exhibits superdiffusive behavior in odd space dimensions. PMID:23653481

  17. Self-Motion Perception and Motion Sickness

    NASA Technical Reports Server (NTRS)

    Fox, Robert A.

    1991-01-01

    Motion sickness typically is considered a bothersome artifact of exposure to passive motion in vehicles of conveyance. This condition seldom has significant impact on the health of individuals because it is of brief duration, it usually can be prevented by simply avoiding the eliciting condition and, when the conditions that produce it are unavoidable, sickness dissipates with continued exposure. The studies conducted examined several aspects of motion sickness in animal models. A principle objective of these studies was to investigate the neuroanatomy that is important in motion sickness with the objectives of examining both the utility of putative models and defining neural mechanisms that are important in motion sickness.

  18. Tracer diffusion inside fibrinogen layers

    NASA Astrophysics Data System (ADS)

    Cieśla, Michał; Gudowska-Nowak, Ewa; Sagués, Francesc; Sokolov, Igor M.

    2014-01-01

    We investigate the obstructed motion of tracer (test) particles in crowded environments by carrying simulations of two-dimensional Gaussian random walk in model fibrinogen monolayers of different orientational ordering. The fibrinogen molecules are significantly anisotropic and therefore they can form structures where orientational ordering, similar to the one observed in nematic liquid crystals, appears. The work focuses on the dependence between level of the orientational order (degree of environmental crowding) of fibrinogen molecules inside a layer and non-Fickian character of the diffusion process of spherical tracer particles moving within the domain. It is shown that in general particles motion is subdiffusive and strongly anisotropic, and its characteristic features significantly change with the orientational order parameter, concentration of fibrinogens, and radius of a diffusing probe.

  19. Molecular Motions During Physical Aging in Polystyrene

    NASA Astrophysics Data System (ADS)

    Thurau, Courtney T.; Ediger, M. D.

    2001-03-01

    A photobleaching method has been used to observe the segmental dynamics of a polystyrene melt during isothermal physical aging. Both rotational and translational diffusion measurements were performed by monitoring the motion of dilute tetracene probes dispersed in the polymer matrix. Following a temperature quench from T_g+2K into the glass, either probe rotational relaxation from an induced anisotropic state, or translational diffusion across a holographic grating, was periodically measured as a function of aging time. Rotation and translation times changed by nearly an order of magnitude during aging. The equilibration times ranged from 10^4-10^7s for the 3 temperatures investigted (T_g-1.4K-T_g-4.6K). Rotational and translational motion age differently. Immediately following a quench, the segmental motions sampled by probe rotation respond more rapidly to the perturbation than the motions sampled by translational motion. At 10^2s, rotational aging has relaxed 60translation shows only a 20T_g-4.5K, it appears that translational diffusion reaches equilibrium before rotation. These differences in aging behavior indicate a change in the distribution of relaxation times throughout the aging process, and may help elucidate the behavior of different observables aging at different rates.

  20. Counteranion-dependent mechanisms of intramolecular proton transfer in aprotic solution.

    PubMed

    Lesnichin, Stepan B; Tolstoy, Peter M; Limbach, Hans-Heinrich; Shenderovich, Ilja G

    2010-09-21

    Using the freon mixture CDF(3)/CDClF(2) as solvent we have been able to measure the (1)H and (15)N NMR spectra of the doubly (15)N labeled 2,2'-bipyridinium cation (BpyH(+)) at temperatures down to 115 K. The obtained NMR parameters strongly depend on the type of counteranions indicating the formation of ion pairs. In the case of the bulky poorly coordinating tetrakis[3,5-bis(trifluoromethyl)phenyl]-borate as the counteranion a strong intramolecular NHN hydrogen bond was observed in BpyH(+) exhibiting a degenerate intramolecular proton transfer which is of the order of 10(6) s(-1) even at 120 K. By contrast, the weak hydrogen bond acceptor tetrafluoroborate favors a weak intermolecular FHN interaction and quenches the intramolecular proton transfer. The intramolecular proton transfer requires in this case a dissociation of the ion pair which is hindered by the Coulomb interaction. A slow intramolecular proton transfer was observed in the case of dichloroacetate which forms a strong intermolecular OHN hydrogen bond to BpyH(+). The mechanism of this transfer presumably involves a preliminary intermolecular proton transfer from nitrogen towards oxygen followed by a hydrogen bond switch to the neighboring nitrogen to which the proton is then transferred.

  1. Conductance and activation energy for electron transport in series and parallel intramolecular circuits.

    PubMed

    Hsu, Liang-Yan; Wu, Ning; Rabitz, Herschel

    2016-11-30

    We investigate electron transport through series and parallel intramolecular circuits in the framework of the multi-level Redfield theory. Based on the assumption of weak monomer-bath couplings, the simulations depict the length and temperature dependence in six types of intramolecular circuits. In the tunneling regime, we find that the intramolecular circuit rule is only valid in the weak monomer coupling limit. In the thermally activated hopping regime, for circuits based on two different molecular units Ma and Mb with distinct activation energies Eact,a > Eact,b, the activation energies of Ma and Mb in series are nearly the same as Eact,a while those in parallel are nearly the same as Eact,b. This study gives a comprehensive description of electron transport through intramolecular circuits from tunneling to thermally activated hopping. We hope that this work can motivate additional studies to design intramolecular circuits based on different types of building blocks, and to explore the corresponding circuit laws and the length and temperature dependence of conductance.

  2. The structural basis of androgen receptor activation: intramolecular and intermolecular amino-carboxy interactions.

    PubMed

    Schaufele, Fred; Carbonell, Xavier; Guerbadot, Martin; Borngraeber, Sabine; Chapman, Mark S; Ma, Aye Aye K; Miner, Jeffrey N; Diamond, Marc I

    2005-07-12

    Nuclear receptors (NRs) are ligand-regulated transcription factors important in human physiology and disease. In certain NRs, including the androgen receptor (AR), ligand binding to the carboxy-terminal domain (LBD) regulates transcriptional activation functions in the LBD and amino-terminal domain (NTD). The basis for NTD-LBD communication is unknown but may involve NTD-LBD interactions either within a single receptor or between different members of an AR dimer. Here, measurement of FRET between fluorophores attached to the NTD and LBD of the AR established that agonist binding initiated an intramolecular NTD-LBD interaction in the nucleus and cytoplasm. This intramolecular folding was followed by AR self-association, which occurred preferentially in the nucleus. Rapid, ligand-induced intramolecular folding and delayed association also were observed for estrogen receptor-alpha but not for peroxisome proliferator activated receptor-gamma2. An antagonist ligand, hydroxyflutamide, blocked the NTD-LBD association within AR. NTD-LBD association also closely correlated with the transcriptional activation by heterologous ligands of AR mutants isolated from hormone-refractory prostate tumors. Intramolecular folding, but not AR-AR affinity, was disrupted by mutation of an alpha-helical ((23)FQNLF(27)) motif in the AR NTD previously described to interact with the AR LBD in vitro. This work establishes an intramolecular NTD-LBD conformational change as an initial component of ligand-regulated NR function.

  3. Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

    PubMed

    Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

    2012-11-28

    Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

  4. Defusing Diffusion

    ERIC Educational Resources Information Center

    Dou, Remy; Hogan, DaNel; Kossover, Mark; Spuck, Timothy; Young, Sarah

    2013-01-01

    Diffusion has often been taught in science courses as one of the primary ways by which molecules travel, particularly within organisms. For years, classroom teachers have used the same common demonstrations to illustrate this concept (e.g., placing drops of food coloring in a beaker of water). Most of the time, the main contributor to the motion…

  5. Demonstrating Diffusion

    ERIC Educational Resources Information Center

    Foy, Barry G.

    1977-01-01

    Two demonstrations are described. Materials and instructions for demonstrating movement of molecules into cytoplasm using agar blocks, phenolphthalein, and sodium hydroxide are given. A simple method for demonstrating that the rate of diffusion of a gas is inversely proportional to its molecular weight is also presented. (AJ)

  6. Defusing Diffusion

    ERIC Educational Resources Information Center

    Dou, Remy; Hogan, DaNel; Kossover, Mark; Spuck, Timothy; Young, Sarah

    2013-01-01

    Diffusion has often been taught in science courses as one of the primary ways by which molecules travel, particularly within organisms. For years, classroom teachers have used the same common demonstrations to illustrate this concept (e.g., placing drops of food coloring in a beaker of water). Most of the time, the main contributor to the motion…

  7. Demonstrating Diffusion

    ERIC Educational Resources Information Center

    Foy, Barry G.

    1977-01-01

    Two demonstrations are described. Materials and instructions for demonstrating movement of molecules into cytoplasm using agar blocks, phenolphthalein, and sodium hydroxide are given. A simple method for demonstrating that the rate of diffusion of a gas is inversely proportional to its molecular weight is also presented. (AJ)

  8. Enzymatically induced motion at nano- and micro-scales

    NASA Astrophysics Data System (ADS)

    Gáspár, Szilveszter

    2014-06-01

    In contrast to adenosine triphosphate (ATP)-dependent motor enzymes, other enzymes are little-known as ``motors'' or ``pumps'', that is, for their ability to induce motion. The enhanced diffusive movement of enzyme molecules, the self-propulsion of enzyme-based nanomotors, and liquid pumping with enzymatic micropumps were indeed only recently reported. Enzymatically induced motion can be achieved in mild conditions and without the use of external fields. It is thus better suited for use in living systems (from single-cell to whole-body) than most other ways to achieve motion at small scales. Enzymatically induced motion is thus not only new but also important. Therefore, the present work reviews the most significant discoveries in enzymatically induced motion. As we will learn, freely diffusing enzymes enhance their diffusive movement by nonreciprocal conformational changes which parallel their catalytic cycles. Meanwhile, enzyme-modified nano- and micro-objects turn chemical energy into kinetic energy through mechanisms such as bubble recoil propulsion, self-electrophoresis, and self-diffusiophoresis. Enzymatically induced motion of small objects ranges from enhanced diffusive movement to directed motion at speeds as high as 1 cm s-1. In spite of the progress made in understanding how the energy of enzyme reactions is turned into motion, most enzymatically powered devices remain inefficient and need improvements before we will witness their application in real world environments.

  9. Collective organization in aerotactic motion

    NASA Astrophysics Data System (ADS)

    Mazza, Marco G.

    Some bacteria exhibit interesting behavior in the presence of an oxygen concentration. They perform an aerotactic motion along the gradient until they reach their optimal oxygen concentration. But they often organize collectively by forming dense regions, called 'bands', that travel towards the oxygen source. We have developed a model of swimmers with stochastic interaction rules moving in proximity of an air bubble. We perform molecular dynamics simulations and also solve advection-diffusion equations that reproduce the aerotactic behavior of mono-flagellated, facultative anaerobic bacteria. If the oxygen concentration in the system sinks locally below a threshold value, the formation of a migrating aerotactic band toward the bubble can be observed.

  10. Ultrafast Intramolecular Electron and Proton Transfer in Bis(imino)isoindole Derivatives.

    PubMed

    Driscoll, Eric; Sorenson, Shayne; Dawlaty, Jahan M

    2015-06-04

    Concerted motion of electrons and protons in the excited state is pertinent to a wide range of chemical phenomena, including those relevant for solar-to-fuel light harvesting. The excited state dynamics of small proton-bearing molecules are expected to serve as models for better understanding such phenomena. In particular, for designing the next generation of multielectron and multiproton redox catalysts, understanding the dynamics of more than one proton in the excited state is important. Toward this goal, we have measured the ultrafast dynamics of intramolecular excited state proton transfer in a recently synthesized dye with two equivalent transferable protons. We have used a visible ultrafast pump to initiate the proton transfer in the excited state, and have probed the transient absorption of the molecule over a wide bandwidth in the visible range. The measurement shows that the signal which is characteristic of proton transfer emerges within ∼710 fs. To identify whether both protons were transferred in the excited state, we have measured the ultrafast dynamics of a related derivative, where only a single proton was available for transfer. The measured proton transfer time in that molecule was ∼427 fs. The observed dynamics in both cases were reasonably fit with single exponentials. Supported by the ultrafast observations, steady-state fluorescence, and preliminary computations of the relaxed excited states, we argue that the doubly protonated derivative most likely transfers only one of its two protons in the excited state. We have performed calculations of the frontier molecular orbitals in the Franck-Condon region. The calculations show that in both derivatives, the excitation is primarily from the HOMO to LUMO causing a large rearrangement of the electronic charge density immediately after photoexcitation. In particular, charge density is shifted away from the phenolic protons and toward the proton acceptor nitrogens. The proton transfer is

  11. de Gennes Narrowing Describes the Relative Motion of Protein Domains

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smolin, Nikolai; Smith, Jeremy C.

    2014-04-01

    The relative motion of structural domains is essential for the biological function of many proteins. Here, by analyzing neutron scattering data and performing molecular dynamics simulations, we find that interdomain motion in several proteins obeys the principle of de Gennes narrowing, in which the wave vector dependence of the interdomain diffusion coefficient is inversely proportional to the interdomain structure factor. Thus, the rate of interdomain motion is inversely proportional to the probability distribution of the spatial configurations of domains.

  12. The influence of intramolecular hydrogen bonds on the adsorption properties of aromatic alcohols and thiols

    NASA Astrophysics Data System (ADS)

    Varfolomeeva, V. V.; Terent'ev, A. V.; Buryak, A. K.

    2008-06-01

    The thermodynamic characteristics of adsorption equilibria of primary aromatic alcohols and thiols on graphitized carbon black at 300 K were determined by the molecular-statistical method. The influence of intramolecular effects under the action of the force field of the sorbent on the conformation of the molecules studied was considered in comparison with n-alkylbenzenes having similar structures. An increase in the chain length by one-CH2 group was shown to influence the formation of intramolecular H-bonds in alcohol and thiol molecules. In adsorption, a considerable fraction of molecules assumed configurations close to planar. An exception was the nonplanar conformation of the 2-phenylethanol molecule stabilized by the intramolecular H-bond.

  13. Intramolecular aggregation and optical limiting properties of triazine-linked mono-, bis- and tris-phthalocyanines.

    PubMed

    Chen, Jun; Zhang, Tao; Wang, Shuangqing; Hu, Rui; Li, Shayu; Ma, Jin Shi; Yang, Guoqiang

    2015-10-05

    A series of triazine-linked mono-, bis- and tris-phthalocyanines are synthesized, intramolecular aggregation is found in bis- and tris-phthalocyanines via π-π stacking interaction. Theoretical and experimental studies reveal the formation of the intramolecular aggregation. The spectrographic, photophysical and nonlinear optical properties of these compounds are adjusted for the formation of the intramolecular aggregation. The bis-phthalocyanine dimer presents smaller fluorescence quantum yield, lower triplet formation yield and the triplet-minus-ground state extinction coefficient, which causes poorer optical limiting performance. It is interesting that the tris-phthalocyanine is composed of a mono-phthalocyanine part and a bis-phthalocyanine part, the optical limiting property of the tris-phthalocyanine is similar to that of mono-phthalocyanine.

  14. The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding: phosphorylated azoles.

    PubMed

    Chernyshev, Kirill A; Larina, Ludmila I; Chirkina, Elena A; Krivdin, Leonid B

    2012-02-01

    The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding have been investigated in the series of tetracoordinated, pentacoordinated and hexacoordinated N-vinylpyrazoles and intermolecular complexes of N-vinylimidazole and 1-allyl-3,5-dimethylpyrazole with phosphorous pentachloride both experimentally and theoretically. It was shown that either intramolecular or intermolecular coordination involving phosphorous results in a dramatic (31)P nuclear shielding amounting to approximately 150 ppm on changing the phosphorous coordination number by one. A major importance of solvent effects on (31)P nuclear shielding of intramolecular and intermolecular complexes involving N → P coordination bond has been demonstrated. It was found that the zeroth-order regular approximation-gauge-including atomic orbital-B1PW91/DZP method was sufficiently accurate for the calculation of (31)P NMR chemical shifts, provided relativistic corrections are taken into account, the latter being of crucial importance in the description of (31)P nuclear shielding.

  15. Mean-Field Theory of Intra-Molecular Charge Ordering in (TTM--TTP)I3

    NASA Astrophysics Data System (ADS)

    Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu

    2011-02-01

    We examine an intra-molecular charge-ordered (ICO) state in the multi-orbital molecular compound (TTM--TTP)I3 on the basis of an effective two-orbital model derived from ab initio calculations. Representing the model in terms of the fragment molecular-orbital (MO) picture, the ICO state is described as the charge disproportionation on the left and right fragment MOs. By applying the mean-field theory, the phase diagram of the ground state is obtained as a function of the inter-molecular Coulomb repulsion and the intra-molecular transfer integral. The ICO state is stabilized by large inter-fragment Coulomb interactions, and the small intra-molecular transfer energy between two fragment MOs. Furthermore, we examine the finite-temperature phase diagram. The relevance to the experimental observations in the molecular compound of (TTM--TTP)I3 is also discussed.

  16. Synthesis of the carbon framework of scholarisine A by intramolecular oxidative coupling.

    PubMed

    Watanabe, Tsugunori; Kato, Nobuki; Umezawa, Naoki; Higuchi, Tsunehiko

    2013-03-25

    Scholarisine A, isolated from the leaves of Alstonia scholaris, is a monoterpene indole alkaloid with an unprecedented cage-like structure. In this paper, preparation of the distinctive cage-like core skeleton of scholarisine A is described. The key feature of this synthetic strategy is an intramolecular oxidative coupling reaction at the late stage to construct a 10-oxa-tricyclo[5.3.1.0(3, 8)]undecan-9-one structure fused with indolenine. Intramolecular oxidative coupling by using N-iodosuccinimide gave the carbon framework of scholarisine A in moderate yield, which is the first example of intramolecular oxidative-coupling reaction between non-activated enolate and indole. This study lays the foundation for continued investigations towards the total synthesis of scholarisine A. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Intramolecular Benzoin Reaction Catalyzed by Benzaldehyde Lyase from Pseudomonas Fluorescens Biovar I.

    PubMed

    Hernández, Karel; Parella, Teodor; Petrillo, Giovanna; Usón, Isabel; Wandtke, Claudia M; Joglar, Jesús; Bujons, Jordi; Clapés, Pere

    2017-05-02

    Intramolecular benzoin reactions catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I (BAL) are reported. The structure of the substrates envisaged for this reaction consists of two benzaldehyde derivatives linked by an alkyl chain. The structural requirements needed to achieve the intramolecular carbon-carbon bond reaction catalyzed by BAL were established. Thus, a linker consisting of a linear alkyl chain of three carbon atoms connected through ether-type bonds to the 2 and 2' positions of two benzaldehyde moieties, which could be substituted with either Cl, Br, or OCH3 at either the 3 and 3' or 5 and 5' positions, were suitable substrates for BAL. Reactions with 61-84 % yields of the intramolecular product and ee values between 64 and 98 %, were achieved. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Fluorescent amino acid undergoing excited state intramolecular proton transfer for site-specific probing and imaging of peptide interactions.

    PubMed

    Sholokh, Marianna; Zamotaiev, Oleksandr M; Das, Ranjan; Postupalenko, Viktoriia Y; Richert, Ludovic; Dujardin, Denis; Zaporozhets, Olga A; Pivovarenko, Vasyl G; Klymchenko, Andrey S; Mély, Yves

    2015-02-12

    Fluorescent amino acids bearing environment-sensitive fluorophores are highly valuable tools for site-selective probing of peptide/ligand interactions. Herein, we synthesized a fluorescent l-amino acid bearing the 4'-methoxy-3-hydroxyflavone fluorophore (M3HFaa) that shows dual emission, as a result of an excited state intramolecular proton transfer (ESIPT). The dual emission of M3HFaa was found to be substantially more sensitive to hydration as compared to previous analogues. By replacing the Ala30 and Trp37 residues of a HIV-1 nucleocapsid peptide, M3HFaa was observed to preserve the peptide structure and functions. Interaction of the labeled peptides with nucleic acids and lipid vesicles produced a strong switch in their dual emission, favoring the emission of the ESIPT product. This switch was associated with the appearance of long-lived fluorescence lifetimes for the ESIPT product, as a consequence of the rigid environment in the complexes that restricted the relative motions of the M3HFaa aromatic moieties. The strongest restriction and thus the longest fluorescence lifetimes were observed at position 37 in complexes with nucleic acids, where the probe likely stacks with the nucleobases. Based on the dependence of the lifetime values on the nature of the ligand and the labeled position, two-photon fluorescence lifetime imaging was used to identify the binding partners of the labeled peptides microinjected into living cells. Thus, M3HFaa appears as a sensitive tool for monitoring site selectively peptide interactions in solution and living cells.

  19. Spectroscopic probing of location and dynamics of an environment-sensitive intramolecular charge transfer probe within liposome membranes.

    PubMed

    Paul, Bijan Kumar; Guchhait, Nikhil

    2011-11-15

    The present work demonstrates the interaction of an intramolecular charge transfer (ICT) probe 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid methyl ester (DPDAME) with liposome membranes of dimyristoyl-L-α-phosphatidylcholine (DMPC) and dimyristoyl-L-α-phosphatidylglycerol (DMPG) studied by steady-state absorption, emission and time-resolved emission techniques. A huge hypsochromic shift together with remarkable enhancement of fluorescence quantum yield of the polarity sensitive ICT emission of DPDAME upon interaction with the lipids has been rationalized in terms of incorporation of the probe into hydrophobic interior of the lipids. Compelling evidences for penetration of the probe into the hydrocarbon interior of the lipids have been deduced from intertwining different experimental results e.g., micropolarity in the immediate vicinity of the probe in lipid environments, steady-state anisotropy, red-edge excitation shift (REES), fluorescence quenching experiments and time-resolved measurements. The rotational relaxation dynamics study of the membrane-bound probe unveils the impartation of high degree of motional rigidity. Wavelength-selective emission behaviour paves way for monitoring of solvent-relaxation in the membranes. Overall, the ICT probe DPDAME displays its commendable sensitivity in deciphering the microheterogeneous environments of liposomal membranes of DMPC and DMPG and promises a new membrane-polarity sensitizing probe.

  20. The influence of interchain coupling on intramolecular oscillation mobility in coupled macromolecular chains: The case of coplanar parallel chains

    NASA Astrophysics Data System (ADS)

    Čevizović, D.; Petković, S.; Galović, S.; Chizhov, A.; Reshetnyak, A.

    2015-10-01

    We enlarge our results from the study of the hopping mechanism of the oscillation excitation transport in 1D model of one biologica-likel macromolecular chain to the case of a system composed from two 1D parallel macromolecular chains with consideration of the properties of intramolecular oscillation excitations. We suppose, that due to the exciton interaction with thermal oscillation (generated by mechanical phonon subsystem) of structural elements (consisting of the peptide group) of the chains, the exciton becomes by self trapped and forms the polaron state. We suggest a model which generalizes the modified Holstein polaron model to the case of two macromolecular chains and find that because of the interchain coupling, the exciton energy band is splitted into two subbands. The hopping process of exciton migration along the macromolecular chains is studied in dependence of system parameters and temperature. We pay an special attention to the temperature range (near T = 300 K) in which living cells operate. It is found that for the certain values of the system parameters there exists the abrupt change of the exciton migration nature from practically free (light) exciton motion to an immobile (heavy, dressed by phonon cloud) quasiparticle We discuss an application of the obtained results to the exciton transport both within deoxyribonucleic acid molecule and in the 2D polymer films organized from such macromolecular chains.

  1. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  2. Rare-earth metal diisopropylamide-catalyzed intramolecular hydroamination.

    PubMed

    Spallek, Tatiana; Anwander, Reiner

    2016-10-18

    Rare-earth metal diisopropylamide complexes LiLn(NiPr2)4(THF) (Ln = Sc, Y, La), [LiY(NiPr2)4]n, NaLn(NiPr2)4(THF) (Ln = Sc, Y), Sc(NiPr2)3(THF) and Ce(NiPr2)4 were screened as catalysts for the intramolecular hydroamination/cyclization (IHC) of 1-amino-2,2-dimethyl-4-pentene, 1-amino-2,2-diphenyl-4-pentene, and 1-amino-2,2-diphenyl-5-hexene at ambient and moderately increased temperature of 60 °C in C6D6. The lithium ate complexes displayed the most efficient precatalysts with high conversion rates at 60 °C for the phenyl-substituted substrates and Ln = Y and La, affording turnover frequencies Nt as high as 164 h(-1). The catalytic activity could be increased by employing THF-free complex [LiY(NiPr2)4]n (Nt = 45.8 h(-1) at 26 °C; 34.1 h(-1) for LiY(NiPr2)4(THF)). In situ generation of putative LiY(NiPr2)4(THF) from YCl3(THF)3.3 and four equivalents of LiNiPr2 (LDA) in C6D6 generated a catalyst revealing Nt comparable to pre-isolated crystallized LiY(NiPr2)4(THF) but yielding even higher substrate conversion. The IHC reactions were also examined for rare-earth metal bis(trimethylsilyl)amide catalysts Ln[N(SiMe3)2]3 (Ln = Sc, Y, La) as well as for LDA using the same reaction conditions, revealing overall superior activity of the silylamide derivatives but poor performance of LDA compared to the rare-earth metal diisopropylamide complexes LiLn(NiPr2)4(THF). Cyclization of 1-amino-2,2-diphenyl-5-hexene to the 6-membered heterocycle 2-methyl-4,4-diphenylpiperidine by lanthanum derivative LiLa(NiPr2)4(THF) was accompanied by a competitive isomerization reaction affording max. 20% of 1-amino-2,2-diphenyl-4-hexene after 2 h at 60 °C. Crystalline tetravalent Ce(NiPr2)4 showed a better IHC performance than crystalline trivalent Sc(NiPr2)3(THF) as preliminary examined for 1-amino-2,2-diphenyl-4-pentene at 26 °C (Nt = 5.6 and 0.9 h(-1), respectively), but cyclization came to a halt after 2 h, probably due to decomposition of the catalyst.

  3. Ratiometric fluorescent/colorimetric cyanide-selective sensor based on excited-state intramolecular charge transfer-excited-state intramolecular proton transfer switching.

    PubMed

    Lin, Wei-Chi; Fang, Sin-Kai; Hu, Jiun-Wei; Tsai, Hsing-Yang; Chen, Kew-Yu

    2014-05-20

    A novel salicylideneaniline-based fluorescent sensor, SB1, with a unique excited-state intramolecular charge transfer-excited-state intramolecular proton transfer (ESICT-ESIPT) coupled system was synthesized and demonstrated to fluorescently sense CN(-) with specific selectivity and high sensitivity in aqueous media based on ESICT-ESIPT switching. A large blue shift (96 nm) was also observed in the absorption spectra in response to CN(-). The bleaching of the color could be clearly observed by the naked eye. Moreover, SB1-based test strips were easily fabricated and low-cost, and could be used in practical and efficient CN(-) test kits. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations further support the cyanide-induced ESICT-ESIPT switching mechanism. The results provide the proof of concept that the colorimetric and ratiometric fluorescent cyanide-selective chemodosimeter can be created based on an ESICT-ESIPT coupled system.

  4. A novel non-fluorescent excited state intramolecular proton transfer phenomenon induced by intramolecular hydrogen bonds: an experimental and theoretical investigation

    NASA Astrophysics Data System (ADS)

    Yin, Hang; Li, Hui; Xia, Guomin; Ruan, Chengyan; Shi, Ying; Wang, Hongming; Jin, Mingxing; Ding, Dajun

    2016-01-01

    Two molecules, 1-hydroxypyrene-2-carbaldehyde (HP) and 1-methoxypyrene-2-carbaldehyde (MP) were explored. We investigated their photophysical properties, using experimental transient absorption and theoretical density functional theory/time-dependent density functional theory (DFT/TDDFT). HP and MP have similar geometric conformations but exhibit entirely different photophysical properties upon excitation into the S1 state. In contrast to traditional excited state intramolecular proton transfer (ESIPT) in molecules that exhibit either single or dual fluorescence, HP has an unusual non-fluorescent property. Specifically, the ultrafast ESIPT process occurs in 158 fs and is followed by an intersystem crossing (ISC) component of 11.38 ps. In contrast to HP, MP undergoes only an 8 ps timescale process, which was attributed to interactions between solute and solvent. We concluded that this difference arises from intramolecular hydrogen bonds (IMHBs), which induce drastic structural alterntion upon excitation.

  5. 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.

  6. Diffusion in porous crystalline materials.

    PubMed

    Krishna, Rajamani

    2012-04-21

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

  7. Diffusion MRI in the heart

    PubMed Central

    Mekkaoui, Choukri; Reese, Timothy G.; Jackowski, Marcel P.; Bhat, Himanshu

    2015-01-01

    Diffusion MRI provides unique information on the structure, organization, and integrity of the myocardium without the need for exogenous contrast agents. Diffusion MRI in the heart, however, has proven technically challenging because of the intrinsic non‐rigid deformation during the cardiac cycle, displacement of the myocardium due to respiratory motion, signal inhomogeneity within the thorax, and short transverse relaxation times. Recently developed accelerated diffusion‐weighted MR acquisition sequences combined with advanced post‐processing techniques have improved the accuracy and efficiency of diffusion MRI in the myocardium. In this review, we describe the solutions and approaches that have been developed to enable diffusion MRI of the heart in vivo, including a dual‐gated stimulated echo approach, a velocity‐ (M 1) or an acceleration‐ (M 2) compensated pulsed gradient spin echo approach, and the use of principal component analysis filtering. The structure of the myocardium and the application of these techniques in ischemic heart disease are also briefly reviewed. The advent of clinical MR systems with stronger gradients will likely facilitate the translation of cardiac diffusion MRI into clinical use. The addition of diffusion MRI to the well‐established set of cardiovascular imaging techniques should lead to new and complementary approaches for the diagnosis and evaluation of patients with heart disease. © 2015 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd. PMID:26484848

  8. Stereoselective Intramolecular Cyclopropanation of α-Diazoacetates via Co(II)-Based Metalloradical Catalysis

    PubMed Central

    Ruppel, Joshua V.; Cui, Xin; Xu, Xue

    2014-01-01

    Co(II) complexes of D2-symmetric chiral porphyrins have been proven to be effective metalloradical catalysts for the asymmetric intramolecular cyclopropanation of allyl α-diazoacetates. 4-(Dimethylamino)pyridine (DMAP), through positive trans effect, plays an important role in the enhancement of the asymmetric induction for the intramolecular cyclopropanation process. This metalloradical catalytic system is suitable for cyclopropanation of allyl α-diazoacetates with varied functional groups and substitution patterns, producing bicyclic products with complete diastereocontrol and good enantiocontrol. PMID:24910778

  9. Examination of the Mechanism of Rh2(II)-Catalyzed Carbazole Formation Using Intramolecular Competition Experiments

    PubMed Central

    Stokes, Benjamin J.; Richert, Kathleen J.; Driver, Tom G.

    2009-01-01

    The use of a rhodium(II) carboxylate catalyst enables the mild and stereoselective formation of carbazoles from biaryl azides. Intramolecular competition experiments of triaryl azides suggested the source of the selectivity. A primary intramolecular kinetic isotope effect was not observed and correlation of the product ratios with Hammett σ+-values produced a plot with two intersecting lines with opposite ρ-values. These data suggest that electronic donation by the biaryl π-system accelerates the formation of rhodium nitrenoid and that C–N bond formation occurs through a 4π-electron-5-atom electrocyclization. PMID:19663433

  10. Intramolecular, reductive cyclization of beta-ketoisothiocyanates promoted by using samarium diiodide.

    PubMed

    Cho, Min Seok; Lee, In Sang; Kang, Sung Ho; Kim, Yong Hae

    2005-02-18

    A novel samarium diiodide (SmI2) promoted intramolecular cyclization of beta-ketoisothiocyanate, derived from alpha,beta-unsaturated esters and ammonium thiocyanate led to alpha-hydroxythiolactams and/or thiolactams in high yields. Treatment of beta-ketoisothiocyanate with two equivalents of SmI2 gave a mixture of alpha-hydroxythiolactam and thiolactam. Four equivalents of SmI2 afforded only thiolactam in high yields. The intramolecular cyclization took place with high to complete stereoselectivity. A mechanism to explain this transformation is proposed.

  11. Enantioselective desymmetrization of cyclohexadienones via an intramolecular Rauhut-Currier reaction of allenoates

    NASA Astrophysics Data System (ADS)

    Yao, Weijun; Dou, Xiaowei; Wen, Shan; Wu, Ji'en; Vittal, Jagadese J.; Lu, Yixin

    2016-10-01

    The Rauhut-Currier (RC) reaction represents an efficient method for the construction of carbon-carbon bond in organic synthesis. However, the RC reactions involving allenoate substrates are very rare, and in particular, asymmetric intramolecular RC reaction of allenoates is yet to be discovered. Here, we show that the intramolecular RC reaction proceeds smoothly in the presence of 1 mol% β-ICD, and bicyclic lactones are obtained in high yields and with excellent enantiomeric excesses. With the employment of γ-substituted allenoates as racemic precursors, a novel dynamic kinetic resolution of allenes via RC reaction is observed, which allows for facile synthesis of highly enantiomerically enriched allenes.

  12. Molecular Coplanarity and Self-Assembly Promoted by Intramolecular Hydrogen Bonds.

    PubMed

    Zhu, Congzhi; Mu, Anthony U; Lin, Yen-Hao; Guo, Zi-Hao; Yuan, Tianyu; Wheeler, Steven E; Fang, Lei

    2016-12-16

    Active conformational control is realized in a conjugated system using intramolecular hydrogen bonds to achieve tailored molecular, supramolecular, and solid-state properties. The hydrogen bonding functionalities are fused to the backbone and precisely preorganized to enforce a fully coplanar conformation of the π-system, leading to short π-π stacking distances, controllable molecular self-assembly, and solid-state growth of one-dimensional nano-/microfibers. This investigation demonstrates the efficiency and significance of an intramolecular noncovalent approach in promoting conformational control and self-assembly of organic molecules.

  13. Intramolecular features of individual C 60 molecules on Si(100) observed by STM

    NASA Astrophysics Data System (ADS)

    Yao, Xiaowei; Ruskell, Todd G.; Workman, Richard K.; Sarid, Dror; Chen, Dong

    1996-12-01

    Intramolecular features (IMF) of a variety of individual C 60 molecules adsorbed on an Si(100)-(2 × 1) surface have been imaged by scanning tunneling microscopy under ultrahigh vacuum conditions. Features of individual C 60 molecules clearly show the local density of states superimposed on their cage structure. Both physisorbed (pre-annealed) and chemisorbed (post-annealed) species have been imaged on the same surface, exhibiting characteristics that depend on their bonding nature. Intramolecular features of a physisorbed C 60 molecule and of two chemisorbed molecules are presented.

  14. Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis†

    PubMed Central

    Reber, Keith P.; Tilley, S. David

    2011-01-01

    The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon–carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give β-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products. PMID:19847338

  15. Photoinduced Intramolecular Cyclopentanation vs Photoprotolytic Oxametathesis in Polycyclic Alkenes Outfitted with Conformationally Constrained Aroylmethyl Chromophores‡

    PubMed Central

    Valiulin, Roman A.; Arisco, Teresa M.; Kutateladze, Andrei G.

    2012-01-01

    Intramolecular photoinduced cyclizations are investigated in photoprecursors assembled in a modular fashion via a Diels-Alder reaction of acetylenic dienophiles with subsequent Michael additions of aromatic ketones to install a chromophore capable of initiating Paternò-Büchi cycloadditions or radical cyclization cascades. The protolytic oxametathesis in these systems allows for rapid access to novel polycyclic scaffolds decorated by formyl groups and carboxylates suitable for subsequent modifications. In conformationally constrained photoprecursors a radical rearrangement takes place resulting in intramolecular 1,3-diradical cyclopentanation of the double bond. PMID:23106813

  16. Spectral and photophysical properties of intramolecular charge transfer fluorescence probe: 4'-Dimethylamino-2,5-dihydroxychalcone

    NASA Astrophysics Data System (ADS)

    Xu, Zhicheng; Bai, Guan; Dong, Chuan

    2005-12-01

    The spectral and photophysical properties of a new intramolecular charge transfer (ICT) probe, namely 4'-dimethylamino-2,5-dihydroxychalcone (DMADHC) were studied in different solvents by using steady-state absorption and emission spectroscopy. Whereas the absorption spectrum undergoes minor change with increasing polarity of the solvents, the fluorescence spectrum experiences a distinct bathochromic shift in the band position and the fluorescence quantum yield increases reaching a maximum before decrease with increasing the solvent polarity. The magnitude of change in the dipole moment was calculated based on the Lippert-Mataga equation. These results give the evidence about the intramolecular charge transfer character in the emitting singlet state of this compound.

  17. Large molecules on surfaces: deposition and intramolecular STM manipulation by directional forces

    NASA Astrophysics Data System (ADS)

    Grill, Leonhard

    2010-03-01

    Intramolecular manipulation of single molecules on a surface with a scanning tunnelling microscope enables the controlled modification of their structure and, consequently, their physical and chemical properties. This review presents examples of intramolecular manipulation experiments with rather large molecules, driven by directional, i.e. chemical or electrostatic, forces between tip and molecule. It is shown how various regimes of forces can be explored and characterized with one and the same manipulation of a single molecule by changing the tip-surface distance. Furthermore, different deposition techniques under ultrahigh vacuum conditions are discussed because the increasing functionality of such molecules can lead to fragmentation during the heating step, making their clean deposition difficult.

  18. Response of an environment-sensitive intramolecular charge transfer probe towards solubilization of liposome membranes by a non-ionic detergent: association and dissociation kinetics.

    PubMed

    Paul, Bijan Kumar; Guchhait, Nikhil

    2012-10-01

    The present report describes an endeavor to follow the solubilization of DMPC and DMPG liposome membranes by a non-ionic detergent Triton X-100 on the lexicon of environment-sensitive intramolecular charge transfer (ICT) photophysics of an extrinsic molecular probe 5-(4-dimethylamino-phenyl)-penta-2, 4-dienoic acid methyl ester (DPDAME). The prospective applicability of the probe to function as a reporter for detergent-sequestered solubilization of liposome membranes is argued on the basis of comparison of the spectral properties of the probe in various environments. Fluorescence anisotropy study delineates the degree of motional restriction imposed on the probe in different microheterogeneous assemblies. The kinetics of association of the probe with the liposome membranes and the dissociation kinetics of TX-100-sequestered solubilization process of the liposomes have been monitored by the stopped-flow fluorescence technique and the results are rationalized in relevance to fluorescence anisotropy study.

  19. Response of an environment-sensitive intramolecular charge transfer probe towards solubilization of liposome membranes by a non-ionic detergent: Association and dissociation kinetics

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2012-10-01

    The present report describes an endeavor to follow the solubilization of DMPC and DMPG liposome membranes by a non-ionic detergent Triton X-100 on the lexicon of environment-sensitive intramolecular charge transfer (ICT) photophysics of an extrinsic molecular probe 5-(4-dimethylamino-phenyl)-penta-2, 4-dienoic acid methyl ester (DPDAME). The prospective applicability of the probe to function as a reporter for detergent-sequestered solubilization of liposome membranes is argued on the basis of comparison of the spectral properties of the probe in various environments. Fluorescence anisotropy study delineates the degree of motional restriction imposed on the probe in different microheterogeneous assemblies. The kinetics of association of the probe with the liposome membranes and the dissociation kinetics of TX-100-sequestered solubilization process of the liposomes have been monitored by the stopped-flow fluorescence technique and the results are rationalized in relevance to fluorescence anisotropy study.

  20. Efficient Estimators for Quantum Instanton Evaluation of theKinetic Isotope Effects: Application to the Intramolecular HydrogenTransfer in Pentadiene

    SciTech Connect

    Vanicek, Jiri; Miller, William H.

    2007-06-13

    The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient 'virial' estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum-mechanically and uses an empirical valence bond potential based on a modified general AMBER force field.

  1. Fractional reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Seki, Kazuhiko; Wojcik, Mariusz; Tachiya, M.

    2003-07-01

    A fractional reaction-diffusion equation is derived from a continuous time random walk model when the transport is dispersive. The exit from the encounter distance, which is described by the algebraic waiting time distribution of jump motion, interferes with the reaction at the encounter distance. Therefore, the reaction term has a memory effect. The derived equation is applied to the geminate recombination problem. The recombination is shown to depend on the intrinsic reaction rate, in contrast with the results of Sung et al. [J. Chem. Phys. 116, 2338 (2002)], which were obtained from the fractional reaction-diffusion equation where the diffusion term has a memory effect but the reaction term does not. The reactivity dependence of the recombination probability is confirmed by numerical simulations.

  2. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    DOE PAGES

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; ...

    2015-03-02

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

  3. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    SciTech Connect

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin -ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

    2015-03-02

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.

  4. Intra-molecular cohesion of coils mediated by phenylalanine-glycine motifs in the natively unfolded domain of a nucleoporin

    SciTech Connect

    Krishnan, V V; Lau, E Y; Yamada, J; Denning, D P; Patel, S S; Colvin, M E; Rexach, M F

    2007-04-19

    The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and cytoplasm of cells. Its conduit contains a size-selective gate and is populated by a family of NPC proteins that feature long natively-unfolded domains with phenylalanine-glycine repeats. These FG nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results show that its FG motifs function as intra-molecular cohesion elements that impart order to the FG domain. The cohesion of coils mediated by FG motifs in the natively unfolded domain of Nup116 supports a type of tertiary structure, a native pre-molten globule, that could become quaternary at the NPC through recruitment of neighboring FG nucleoporins, forming one cohesive meshwork of intertwined filaments capable of gating protein diffusion across the NPC by size exclusion.

  5. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    PubMed Central

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

    2015-01-01

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

  6. Langevin formulation for single-file diffusion

    NASA Astrophysics Data System (ADS)

    Taloni, Alessandro; Lomholt, Michael A.

    2008-11-01

    We introduce a stochastic equation for the microscopic motion of a tagged particle in the single-file model. This equation provides a compact representation of several of the system’s properties such as fluctuation-dissipation and linear-response relations, achieved by means of a diffusion noise approach. Most importantly, the proposed Langevin equation reproduces quantitatively the three temporal regimes and the corresponding time scales: ballistic, diffusive, and subdiffusive.

  7. Collective motion of microswimmers in viscoelastic fluids

    NASA Astrophysics Data System (ADS)

    Li, Gaojin; Ardekani, Arezoo

    2015-11-01

    The dynamics of suspension of self-propelled microorganisms show fascinating hydrodynamic phenomena, such as, large scale swarming motion, locally correlated motion, enhanced particle diffusion, and enhanced fluid mixing. Even though many studies have been conducted in a Newtonian fluid, the collective motion of microorganisms in non-Newtonian fluids is less understood. The non-Newtonian fluid rheological properties, such as viscoelasticity and shear-dependent viscosity in saliva, mucus and biofilm, significantly affect the swimming properties and hydrodynamic interaction of microorganisms. In this work, we use direct numerical simulation to investigate the collective motion of rod-like swimmers in viscoelastic fluids. Two swimming types, pusher and puller, are investigated. The background viscoelastic fluid is modeled using an Oldroyd-B constitutive equation. This work is supported by NSF CBET-1445955 and Indiana CTSI TR001108.

  8. Chemistry in motion: tiny synthetic motors.

    PubMed

    Colberg, Peter H; Reigh, Shang Yik; Robertson, Bryan; Kapral, Raymond

    2014-12-16

    CONSPECTUS: Diffusion is the principal transport mechanism that controls the motion of solute molecules and other species in solution; however, the random walk process that underlies diffusion is slow and often nonspecific. Although diffusion is an essential mechanism for transport in the biological realm, biological systems have devised more efficient transport mechanisms using molecular motors. Most biological motors utilize some form of chemical energy derived from their surroundings to induce conformational changes in order to carry out specific functions. These small molecular motors operate in the presence of strong thermal fluctuations and in the regime of low Reynolds numbers, where viscous forces dominate inertial forces. Thus, their dynamical behavior is fundamentally different from that of macroscopic motors, and different mechanisms are responsible for the production of useful mechanical motion. There is no reason why our interest should be confined to the small motors that occur naturally in biological systems. Recently, micron and nanoscale motors that use chemical energy to produce directed motion by a number of different mechanisms have been made in the laboratory. These small synthetic motors also experience strong thermal fluctuations and operate in regimes where viscous forces dominate. Potentially, these motors could be directed to perform different transport tasks, analogous to those of biological motors, for both in vivo and in vitro applications. Although some synthetic motors execute conformational changes to effect motion, the majority do not, and, instead, they use other mechanisms to convert chemical energy into directed motion. In this Account, we describe how synthetic motors that operate by self-diffusiophoresis make use of a self-generated concentration gradient to drive motor motion. A description of propulsion by self-diffusiophoresis is presented for Janus particle motors comprising catalytic and noncatalytic faces. The properties

  9. On the effect of nuclear motion on chemical binding

    NASA Astrophysics Data System (ADS)

    Dohnert, A.

    1985-05-01

    The surfaces defined by Berlin (1951) to characterize the role of intramolecular forces in chemical binding are obtained analytically for the case in which the atomic nuclei are in motion. The generalized equation for the force function is derived from the hypervirial theorem rather than by the method of coordinate scaling as reported by Garcia-Sucre et al. (1984). Numerical results for the lowest vibrational level of the ground state of the H2 molecule are presented in a graph, and the inclusion of nuclear motion is shown to reduce the volume of the spatial 'binding region' and hence to localize the bond and reduce the degree of binding (relative to the fixed-nucleus model).

  10. Photochromic Dithienylethene-Containing Boron(III) Ketoiminates: Modulation of Photo-Responsive Behavior through Variation of Intramolecular Motion.

    PubMed

    Wong, Cheok-Lam; Poon, Chun-Ting; Yam, Vivian Wing-Wah

    2016-08-26

    A series of dithienylethene-containing boron(III) ketoiminates, as well as their corresponding β-ketoimine ligands, have been synthesized and characterized. The photophysical, electrochemical, and photochromic properties of the compounds have been studied. Photocyclization has been found to be suppressed upon introduction of a phenyl substituent on the nitrogen atom of the β-ketoiminate core, whereas photochromism could be observed by replacement of the phenyl substituent with a bulky mesityl group. It is believed that the steric effect of the mesityl unit restricts molecular rotation, resulting in such a prominent difference in the photochromic properties.

  11. Photoinduced intramolecular charge transfer in push-pull polyenes: effects of solvation, electron-donor group, and polyenic chain length.

    PubMed

    Akemann, Walther; Laage, Damien; Plaza, Pascal; Martin, Monique M; Blanchard-Desce, Mireille

    2008-01-17

    Subpicosecond absorption spectroscopy is used to characterize the primary photoinduced processes in a class of push-pull polyenes bearing a julolidine end group as the electron donor and a diethylthiobarbituric acid end group as the electron acceptor. The excited-state decay time and relaxation pathway have been studied for four polyenes of increasing chain length (n = 2-5 double bonds) in aprotic solvents of different solvation time, polarity, and viscosity. Intramolecular charge transfer (ICT) leading to a transient state of cyanine-like structure (fully conjugated with no bond length alternation) is observed in all polar solvents at a solvent dependent rate, but the reaction is not observed in cyclohexane, a nonpolar solvent. In polar solvents, the reaction time increases with the average solvation time but remains slightly larger, except in the viscous solvent triacetin. These facts are interpreted as an indication that both solvent reorganization and internal restructuring are involved in the ICT-state formation. The observed photodynamics resemble those we previously found for another class of polyenes bearing a dibutylaniline group as the donor, including a similar charge-transfer rate in spite of the larger electron donor character of the julolidine group. This observation brings further support to the proposal that an intramolecular coordinate is involved in the charge-transfer reaction, possibly a torsional motion of the donor end group. On the other hand, relaxation of the ICT state leads to cis-trans isomerization or crossing to the triplet state, depending on the length of the polyenic chain. In dioxane, tetrahydrofuran, and triacetin, the ICT state of the shorter chains (n = 2, 3) relaxes to the isomer with a viscosity-dependent rate, while that of the longer ones (n = 4, 5) leads to the triplet state with a viscosity-independent rate, as expected. In acetonitrile, the ICT-state lifetime is generally much shorter. A change from photoisomerization to

  12. Electron-triggered motions in technomimetic molecules.

    PubMed

    Carella, Alexandre; Coudret, Christophe; Guirado, Gonzalo; Rapenne, Gwénaël; Vives, Guillaume; Launay, Jean-Pierre

    2007-01-14

    Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with motions triggered by electrons. The first part is devoted to our work in the field of molecular switches: after having demonstrated the possibility of controlling an intramolecular electron transfer by photoisomerisation, we are now trying to control the isomerisation, either by electrochemistry, or by embedding the photochromic compound in a self-assembled monolayer and testing the electrical conduction with a STM tip. In a second part, we present our strategy on controlling the rotation in a molecular rotary motor and the family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active groups, so that addressing the molecule with nano-electrodes would trigger rotation. The electrical control of the charge state of a molecule by a STM tip is developed in a final part.

  13. Motion regularization for matting motion blurred objects.

    PubMed

    Lin, Hai Ting; Tai, Yu-Wing; Brown, Michael S

    2011-11-01

    This paper addresses the problem of matting motion blurred objects from a single image. Existing single image matting methods are designed to extract static objects that have fractional pixel occupancy. This arises because the physical scene object has a finer resolution than the discrete image pixel and therefore only occupies a fraction of the pixel. For a motion blurred object, however, fractional pixel occupancy is attributed to the object’s motion over the exposure period. While conventional matting techniques can be used to matte motion blurred objects, they are not formulated in a manner that considers the object’s motion and tend to work only when the object is on a homogeneous background. We show how to obtain better alpha mattes by introducing a regularization term in the matting formulation to account for the object’s motion. In addition, we outline a method for estimating local object motion based on local gradient statistics from the original image. For the sake of completeness, we also discuss how user markup can be used to denote the local direction in lieu of motion estimation. Improvements to alpha mattes computed with our regularization are demonstrated on a variety of examples.

  14. DIFFUSION PUMP

    DOEpatents

    Levenson, L.

    1963-09-01

    A high-vacuum diffusion pump is described, featuring a novel housing geometry for enhancing pumping speed. An upright, cylindrical lower housing portion is surmounted by a concentric, upright, cylindrical upper housing portion of substantially larger diameter; an uppermost nozzle, disposed concentrically within the upper portion, is adapted to eject downwardly a conical sheet of liquid outwardly to impinge upon the uppermost extremity of the interior wall of the lower portion. Preferably this nozzle is mounted upon a pedestal rising coaxially from within the lower portion and projecting up into said upper portion. (AEC)

  15. Usnic Acid and the Intramolecular Hydrogen Bond: A Computational Experiment for the Organic Laboratory

    ERIC Educational Resources Information Center

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

    A computational experiment is described for the organic chemistry laboratory that allows students to estimate the relative strengths of the intramolecular hydrogen bonds of usnic and isousnic acids, two related lichen secondary metabolites. Students first extract and purify usnic acid from common lichens and obtain [superscript 1]H NMR and IR…

  16. Distance dependence in photoinduced intramolecular electron transfer. Additional remarks and calculations

    NASA Astrophysics Data System (ADS)

    Larsson, Sven; Volosov, Andrey

    1987-12-01

    Rate constants for photoinduced intramolecular electron transfer are calculated for four of the molecules studied by Hush et al. The electronic factor is obtained in quantum chemical calculations using the CNDO/S method. The results agree reasonably well with experiments for the forward reaction. Possible reasons for the disagreement for the charge recombination process are offered.

  17. Functionalized azabicycloalkane amino acids by nitrone 1,3-dipolar intramolecular cycloaddition.

    PubMed

    Manzoni, Leonardo; Arosio, Daniela; Belvisi, Laura; Bracci, Antonio; Colombo, Matteo; Invernizzi, Donatella; Scolastico, Carlo

    2005-05-13

    [reaction: see text] An efficient and operationally simple method for the synthesis of functionalized azaoxobicyclo[X.3.0]alkane amino acids has been devised. The key step is an intramolecular nitrone cycloaddition on 5-allyl- or 5-homoallylproline that was found to be completely regio- and stereoselective.

  18. A novel chiral yttrium complex with a tridentate linked amido-indenyl ligand for intramolecular hydroamination.

    PubMed

    Chai, Zhuo; Hua, Dezhi; Li, Kui; Chu, Jiang; Yang, Gaosheng

    2014-01-07

    A new chiral silicon-linked tridentate amido-indenyl ligand was developed from indene and enantiopure 1,2-cyclohexanediamine. Its yttrium complex was synthesized, characterized and applied to efficiently catalyze the intramolecular hydroamination of non-activated olefins with up to 97% ee.

  19. Chiral N,N'-dioxide-FeCl3 complex-catalyzed asymmetric intramolecular Cannizzaro reaction.

    PubMed

    Wu, Wangbin; Liu, Xiaohua; Zhang, Yuheng; Ji, Jie; Huang, Tianyu; Lin, Lili; Feng, Xiaoming

    2015-07-25

    An environmentally benign catalyst, the N,N'-dioxide-FeCl3 complex, has been developed for the asymmetric intramolecular Cannizzaro reaction. Aryl and alkyl glyoxal monohydrates were applied to obtain α-hydroxy acid esters with excellent results. Deuterium-label and control experiments shed light on the reaction mechanism.

  20. Pressure dependence of intramolecular mode frequencies in solid N2, O2, and CO2

    NASA Technical Reports Server (NTRS)

    Etters, R. D.; Helmy, A.

    1983-01-01

    A microscopic description of the pressure dependence of intramolecular vibrational modes in simple molecular crystals has been formulated using a classical perturbation theory. Quantitative agreement with experiment is demonstrated and it is shown that frequency changes at phase transitions are large enough to be observed optically.

  1. Chemoselective intramolecular Wittig reactions for the synthesis of oxazoles and benzofurans.

    PubMed

    Fan, Yu-Shiou; Das, Utpal; Hsiao, Ming-Yu; Liu, Meng-Hsien; Lin, Wenwei

    2014-12-05

    A chemoselective approach was developed for the synthesis of highly functionalized oxazoles and benzofurans using an intramolecular Wittig reaction as the key step. By choosing proper trapping reagent or method of addition of reagents, chemoselectivity can be controlled toward either oxazole or benzofuran derivatives.

  2. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.

    PubMed

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.

  3. Intramolecular Imidoylative Heck Reaction: Synthesis of Cyclic Ketoimines from Functionalized Isocyanide.

    PubMed

    Wang, Jian; Tang, Shi; Zhu, Qiang

    2016-07-01

    Efficient access to five- to seven-membered cyclic ketoimines, through palladium-catalyzed intramolecular imidoylative Heck reaction of alkene-containing isocyanides, has been developed. Consecutive isocyanide and alkene insertion into aryl or alkyl Pd(II) intermediates takes place in this process. No byproduct derived from monoinsertion or reversed sequence is detected.

  4. Enantioselective organocatalytic intramolecular ring-closing Friedel-Crafts-type alkylation of indoles.

    PubMed

    Li, Chang-Feng; Liu, Hiu; Liao, Jie; Cao, Yi-Ju; Liu, Xiao-Peng; Xiao, Wen-Jing

    2007-05-10

    An enantioselective organocatalytic intramolecular ring-closing Friedel-Crafts-type alkylation of indolyl alpha,beta-unsaturated aldehydes has been developed. This powerful new strategy allows enantioselective access to THPIs and THBCs in a straightforward and atom-economical manner.

  5. The first porphyrin-subphthalocyaninatoboron(iii)-fused hybrid with unique conformation and intramolecular charge transfer behavior.

    PubMed

    Zhang, Yuehong; Oh, Juwon; Wang, Kang; Shin, Dongju; Zhan, Xiaopeng; Zheng, Yingting; Kim, Dongho; Jiang, Jianzhuang

    2016-08-18

    Porphyrin and subphthalocyaninatoboron(iii) chromophores have been fused through a quinoxaline moiety, resulting in the first porphyrin-subphthalocyaninatoboron(iii)-fused hybrid with intramolecular charge transfer from tetrapyrrole/tripyrrole chromophores to the quinoxaline moiety. The unique plane-bowl molecular structure of this hybrid was revealed based on single crystal X-ray diffraction analysis for the first time.

  6. Using Open-Ended Questions to Diagnose Students' Understanding of Inter- and Intramolecular Forces

    ERIC Educational Resources Information Center

    Rompayom, Patcharee; Tambunchong, Chinda; Wongyounoi, Somson; Dechsri, Precharn

    2011-01-01

    The purpose of this study was to investigate Grade 10 Thai students about their understanding on inter- and intramolecular forces. Sixty four students were elicited by administered open-ended questions after finishing normal instruction on chemical bonding topics. The instrument was in a set of open-ended questions which contained a number of…

  7. Usnic Acid and the Intramolecular Hydrogen Bond: A Computational Experiment for the Organic Laboratory

    ERIC Educational Resources Information Center

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

    A computational experiment is described for the organic chemistry laboratory that allows students to estimate the relative strengths of the intramolecular hydrogen bonds of usnic and isousnic acids, two related lichen secondary metabolites. Students first extract and purify usnic acid from common lichens and obtain [superscript 1]H NMR and IR…

  8. Capped guanidino-α-cyclodextrin first synthesis based on intramolecular Staudinger-Aza-Wittig (SAW) reaction.

    PubMed

    Couturier, C; Dumarcay-Charbonnier, F; Lambert, A; Barth, D; Marsura, A

    2014-11-01

    An intramolecularly promoted SAW reaction between a phosphinimide and an isocyanate intermediate led to an original bridged trisubstituted ((A,C),E)-α-cyclodextrin. The latter was in a second step converted into a new capped (ACE)-(guanidino)-α-cyclodextrin.

  9. A novel synthesis of 4H-chromen-4-ones via intramolecular wittig reaction

    PubMed

    Kumar; Bodas

    2000-11-30

    The acylphosphoranes formed in a sequential manner from the reaction of the silyl ester of O-acyl(aroyl)salicylic acids and (trimethylsilyl)methylenetriphenylphosphorane undergo intramolecular Wittig cyclization on the ester carbonyl to afford the 4H-chromen-4-ones in good to excellent yields.

  10. Intramolecular hydrogen bonding as a synthetic tool to induce chemical selectivity in acid catalyzed porphyrin synthesis.

    PubMed

    Megiatto, Jackson D; Patterson, Dustin; Sherman, Benjamin D; Moore, Thomas A; Gust, Devens; Moore, Ana L

    2012-05-14

    A straightforward procedure based on the formation of intramolecular hydrogen bonds to impart selectivity in the preparation of multi-functionalized porphyrins has been developed. To illustrate the concept, the synthesis of a biomimetic artificial photosynthetic model able to undergo electron and proton transfer reactions upon irradiation is reported. This journal is © The Royal Society of Chemistry 2012

  11. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  12. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-02-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  13. Enantioselective synthesis of planar-chiral benzosiloloferrocenes by Rh-catalyzed intramolecular C-H silylation.

    PubMed

    Shibata, Takanori; Shizuno, Tsubasa; Sasaki, Tomoya

    2015-05-07

    The first synthesis of planar-chiral benzosiloloferrocenes was achieved by the intramolecular reaction of 2-(dimethylhydrosilyl)arylferrocenes. The enantioselective cross dehydrogenative coupling of an sp(2) C-H bond of ferrocene with a Si-H bond proceeded efficiently with the use of a Rh-chiral diene catalyst.

  14. Gold(I)-Catalyzed Inter- and Intramolecular Additions of Carbonyl Compounds to Allenenes

    PubMed Central

    2016-01-01

    The gold(I)-catalyzed intramolecular reaction of allenes with oxoalkenes leads to bicyclo[6.3.0]undecane ring systems, although in the case of terminally disubstituted allenes, seven-membered rings are formed. The related intermolecular addition of aldehydes to allenenes also gives seven-membered rings. PMID:26918852

  15. Intramolecular C-H···O hydrogen bonding in 1,4-dihydropyridine derivatives.

    PubMed

    Petrova, Marina; Muhamadejev, Ruslan; Vigante, Brigita; Cekavicus, Brigita; Plotniece, Aiva; Duburs, Gunars; Liepinsh, Edvards

    2011-09-19

    The diastereotopy of the methylene protons at positions 2 and 6 in 1,4-dihydropiridine derivatives with various substituents has been investigated. NMR spectroscopy and quantum chemistry calculations show that the CH···O intramolecular hydrogen bond is one of the factors amplifying the chemical shift differences in the 1H-NMR spectra.

  16. The effect of posture on diffusion into lumbar intervertebral discs.

    PubMed Central

    Adams, M A; Hutton, W C

    1986-01-01

    The diffusion of small solutes into the intervertebral discs of cadaveric lumbar motion segments was measured using a radioactive tracer technique. The motion segments were wedged and loaded to simulate erect posture and flexed sitting postures. The results show that erect posture favours diffusion into the anterior half of the disc compared to the posterior half. Flexed posture, by deforming the annulus fibrosus, reverses this imbalance. PMID:3693067

  17. Self-diffusion of Colloidal Spheres and Ellipsoids in Nematic Phases of fd-virus

    NASA Astrophysics Data System (ADS)

    Zhang, J.

    2005-03-01

    We report on the self-diffusion of micron sized colloidal spheres and ellipsoids in nematic phases of fd-virus. The mean square displacements (MSDs) of the spheres are diffusive along the nematic director, with the diffusion coefficients displaying an inverse dependence on sphere radius. Displacements perpendicular to the nematic director, however, are markedly slower and are sub-diffusive. The colloidal ellipsoids align with their long axis along the nematic director and also exhibit diffusive motion along the nematic director and a sub-diffusive motion perpendicular to the nematic director. The rotational motions of the ellipsoids are sub-diffusive at short time, and exhibit caged behavior at long times. We examine these motions as a function of nematic order parameter, and compare our results to theories of hindered tracer dynamics. This work has been partially supported by the NSF through MRSEC Grants DMR 00-79909 and DMR-0203378, and by NASA Grant NAG8-2172.

  18. Disentangling Random Motion and Flow in a Complex Medium.

    PubMed

    Koslover, Elena F; Chan, Caleb K; Theriot, Julie A

    2016-02-02

    We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Disentangling Random Motion and Flow in a Complex Medium

    PubMed Central

    Koslover, Elena F.; Chan, Caleb K.; Theriot, Julie A.

    2016-01-01

    We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined. PMID:26840734

  20. Cooperative jump motions of jammed particles in a one-dimensional periodic potential.

    PubMed

    Sakaguchi, Hidetsugu

    2009-12-01

    Cooperative jump motions are studied for mutually interacting particles in a one-dimensional periodic potential. The diffusion constant for the cooperative motion in systems including a small number of particles is numerically calculated and it is compared with theoretical estimates. We find that the size distribution of the cooperative jump motions obeys an exponential law in a large system.

  1. Starvation driven diffusion as a survival strategy of biological organisms.

    PubMed

    Cho, Eunjoo; Kim, Yong-Jung

    2013-05-01

    The purpose of this article is to introduce a diffusion model for biological organisms that increase their motility when food or other resource is insufficient. It is shown in this paper that Fick's diffusion law does not explain such a starvation driven diffusion correctly. The diffusion model for nonuniform Brownian motion in Kim (Einstein's random walk and thermal diffusion, preprint http://amath.kaist.ac.kr/papers/Kim/31.pdf , 2013) is employed in this paper and a Fokker-Planck type diffusion law is obtained. Lotka-Volterra type competition systems with spatial heterogeneity are tested, where one species follows the starvation driven diffusion and the other follows the linear diffusion. In heterogeneous environments, the starvation driven diffusion turns out to be a better survival strategy than the linear one. Various issues such as the global asymptotic stability, convergence to an ideal free distribution, the extinction and coexistence of competing species are discussed.

  2. Diffusion Background Model for Moving Objects Detection

    NASA Astrophysics Data System (ADS)

    Vishnyakov, B. V.; Sidyakin, S. V.; Vizilter, Y. V.

    2015-05-01

    In this paper, we propose a new approach for moving objects detection in video surveillance systems. It is based on construction of the regression diffusion maps for the image sequence. This approach is completely different from the state of the art approaches. We show that the motion analysis method, based on diffusion maps, allows objects that move with different speed or even stop for a short while to be uniformly detected. We show that proposed model is comparable to the most popular modern background models. We also show several ways of speeding up diffusion maps algorithm itself.

  3. Three-dimensional diffusion with helical persistence

    NASA Astrophysics Data System (ADS)

    Larralde, Hernán; Leyvraz, François

    2015-07-01

    We formulate the the problem of persistent diffusion in three dimensions from the perspective of the Frenet-Serret equations. In contrast to one and two-dimensional systems, in three-dimensions persistent diffusion is, in general, a third order process. In this paper we derive a Fokker-Planck equation for the process and we calculate its effective diffusion constant. We also provide expressions for the asymptotic average displacement of the walk, as well as explicit expressions for the Fourier-Laplace transform of the correlations between the tangent, normal and binormal vectors of the motion.

  4. Diffusion of spherical particles in microcavities.

    PubMed

    Imperio, A; Padding, J T; Briels, W J

    2011-04-21

    The diffusive motion of a colloidal particle trapped inside a small cavity filled with fluid is reduced by hydrodynamic interactions with the confining walls. In this work, we study these wall effects on a spherical particle entrapped in a closed cylinder. We calculate the diffusion coefficient along the radial, azimuthal, and axial direction for different particle positions. At all locations the diffusion is smaller than in a bulk fluid and it becomes anisotropic near the container's walls. We present a simple model which reasonably well describes the simulation results for the given dimensions of the cylinder, which are taken from the recent experimental work.

  5. Computing intramolecular charge and energy transfer rates using optimal modes

    SciTech Connect

    Yang, Xunmo; Bittner, Eric R.

    2015-06-28

    In our recent work [X. Yang and E. R. Bittner, J. Phys. Chem. A 118, 5196 (2014)], we showed how to construct a reduced set of nuclear motions that capture the coupling between electronic and nuclear degrees of freedom over the course of an electronic transition. We construct these modes, referred to as “Lanczos modes,” by applying a search algorithm to find linear combinations of vibrational normal modes that optimize the electronic/nuclear coupling operator. Here, we analyze the irreducible representations of the dominant contributions of these modes and find that for the cases considered here, these belong to totally symmetric irreducible representations of the donor and acceptor moieties. Upon investigating the molecular geometry changes following the transition, we propose that the electronic transition process can be broken into two steps, in the agreement of Born-Oppenheimer approximation: a fast excitation transfer occurs, facilitated by the “primary Lanczos mode,” followed by slow nuclear relaxation on the final electronic diabatic surface.

  6. Aromatic ring strain in arylselenenyl bromides: role in facile synthesis of selenenate esters via intramolecular cyclization.

    PubMed

    Selvakumar, K; Singh, Harkesh B; Butcher, Ray J

    2010-09-10

    The synthesis and reactivity of 2,6-disubstituted arylselenium compounds derived from 2-bromo-5-tert-butylisophthalic acid (43) are described. The syntheses of bis(5-tert-butylisophthalic acid dimethyl ester)diselenide (46) and bis(5-tert-butylisophthalic acid diisopropyl ester)diselenide (47) have been achieved by the reaction of the corresponding ester precursors with disodium diselenide. Reduction of diselenide 46 with lithium aluminum hydride affords 2,2'-bis(5-tert-butylbenzene-1,3-dimethanol)diselenide (53). Diselenides 46 and 47 exhibit intramolecular Se...O interaction. Compound 53 does not show any intramolecular Se...O interaction. The anomalous Se...O nonbonded coordination observed in the single-crystal X-ray structures of compounds 46, 47 and 53 is compared and contrasted. The corresponding selenenyl bromides 54 and 55, derived from the reaction of diselenides 46 and 47 with bromine, are quite stable in the solid state. However, they undergo hydrolysis and subsequent intramolecular cyclization upon heating or after having been kept in solution over a period of time to give the corresponding selenenate esters 56 and 57. The X-ray crystallographic study and density functional theory calculations on 54 at the B3LYP/6-31G(d) level of theory indicate a significant distortion in planarity of the aromatic ring. Glutathione peroxidase-like activities of diselenides 46 and 47 and their selenenate esters 56 and 57 have been studied both by thiophenol and bioassay methods. The very low glutathione peroxidase-like activity of the diselenides (46 and 47) and their selenenate esters (56 and 57) in the thiophenol assay is attributed to the presence of the relatively strong Se...O intramolecular interaction in the selenenyl sulfide intermediates. The interaction retards the catalytic activity through both thiol exchange and an intramolecular cyclization reaction.

  7. Elucidating hydrogenase surfaces and tracing the intramolecular tunnels for hydrogenase inhibition in microalgal species

    PubMed Central

    Dixit, Kritika; Rahman, Md.Akhlaqur; Nath, Adi; Sundaram, Shanthy

    2016-01-01

    Intramolecular tunnels are majorly attracting attention as possible pathways for entry of inhibitors like oxygen and carbon monoxide to the active sites of the enzymes, hydrogenases. The results of homology modeling of the HydSL protein, a NiFe-hydrogenase from Chlamydomonas reinhardtii and Chlorella vulgaris are presented in this work. Here we identify and describe molecular tunnels observed in HydSL hydrogenase enzyme systems. The possible determinant of the oxygen stability of already studied hydrogenases could be the lack of several intramolecular tunnels. The possible tunnels were traced out using MOLE 2 software, which showed several intramolecular pathways that may be connecting the active sites of the enzyme. The RMSD value showed a great deal of significance in the enzyme homology. This is the first report of its kind in which mapping of the intramolecular tunnels in the four-hydrogenase enzymes disclosed potential variations between designed models and acknowledged structures. We are seeking out the explanations for oxygen sensitivity of studied hydrogenases within the structure of intramolecular tunnels. Local and Global RMSD (Root mean square deviation) was calculated for models and templates, which showed value of 1.284 indicating a successful homology model. The tunnel tracing study by Mole 2 indicated two tunnels joined into one in C. reinhardtii model whereas C. vulgaris model showed one tunnel almost like two tunnels. Templates of both the A. vinosum and D. vulgaris hydrogenase consisted of six tunnels. For HydSL from Chlamydomonas and Chlorella Species the maximal potential was set to 250 kcal/mol (1,046 kJ/mol) and the positive potential areas were marked. Electrostatic studies define electrostatic potential (ESP) that help shuttle protons to the active site. PMID:28149051

  8. Managing Motion Sickness

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_166982.html Managing Motion Sickness You may never love some pursuits, like ... there anything you can do to quell your motion sickness so you can join in the fun? ...

  9. Essay on Gyroscopic Motions.

    ERIC Educational Resources Information Center

    Tea, Peter L., Jr.

    1988-01-01

    Explains gyroscopic motions to college freshman or high school seniors who have learned about centripetal acceleration and the transformations of a couple. Contains several figures showing the direction of forces and motion. (YP)

  10. Conceptualizing Mathematics "Motion Problems"

    ERIC Educational Resources Information Center

    McKeough, William J.

    1970-01-01

    Describes an instructional method in secondary school mathematics applicable to physics instruction, to develop conceptual understanding of motion word problems. Distance, rate, and time are defined, used as variables and considered with relative motion as a unifying concept. (JM)

  11. Limited range of motion

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/003173.htm Limited range of motion To use the sharing features on this page, please enable JavaScript. Limited range of motion is a term meaning that a joint or ...

  12. Quantitative measurement of tissue perfusion and diffusion in vivo.

    PubMed

    Chenevert, T L; Pipe, J G; Williams, D M; Brunberg, J A

    1991-01-01

    Magnetic resonance imaging techniques designed for sensitivity to microscopic motions of water diffusion and blood flow in the capillary network are also exceptionally sensitive to bulk motion properties of the tissue, which may lead to contrast artifact and large quantitative errors. The magnitude of bulk motion error that exists in human brain perfusion/diffusion imaging and the inability of cardiac gating to adequately control this motion are demonstrated by direct measurement of phase stability of voxels localized in the brain. Two methods are introduced to reduce bulk motion phase error. The first, a postprocessing phase correction algorithm, reduces coarse phase error but is inadequate by itself for quantitative perfusion/diffusion MRI. The second method employs orthogonal slice selection gradients to define a column of tissue in the object, from which echoes may be combined in a phase-insensitive manner to measure more reliably the targeted signal attenuation. Applying this acquisition technique and a simplistic model of perfusion and diffusion signal attenuations yields an estimated perfusion fraction of 3.4 +/- 1.1% and diffusion coefficient of 1.1 +/- 0.2 x 10(-5) cm2/s in the white matter of one normal volunteer. Successful separation of perfusion and diffusion effects by this technique is supported in a dynamic study of calf muscle. Periods of normal blood flow, low flow, and reactive hyperemia are clearly distinguished in the quantitative perfusion results, whereas measured diffusion remained nearly constant.

  13. Objects in Motion

    ERIC Educational Resources Information Center

    Damonte, Kathleen

    2004-01-01

    One thing scientists study is how objects move. A famous scientist named Sir Isaac Newton (1642-1727) spent a lot of time observing objects in motion and came up with three laws that describe how things move. This explanation only deals with the first of his three laws of motion. Newton's First Law of Motion says that moving objects will continue…

  14. Objects in Motion

    ERIC Educational Resources Information Center

    Damonte, Kathleen

    2004-01-01

    One thing scientists study is how objects move. A famous scientist named Sir Isaac Newton (1642-1727) spent a lot of time observing objects in motion and came up with three laws that describe how things move. This explanation only deals with the first of his three laws of motion. Newton's First Law of Motion says that moving objects will continue…

  15. Analyse de la diffusion diffuse donnée par les cristaux de protéines

    NASA Astrophysics Data System (ADS)

    Doucet, J.; Benoit, J.-P.; Faure, P.; Durant, D.

    1992-06-01

    This paper is devoted to the contribution offered by the X-ray diffuse scattering analysis to the problem of plasticity of crystallized protein molecules. We first review the main published results, then we try to perform a synthesis of these results and of new observations that we have obtained on various proteins. Two types of displacements emerge from this review : intramolecular displacements correlated at very short range and long-range correlated intermolecular displacements. The possibility of detecting diffuse scattering resulting from intramolecular displacements correlated within entire parts of proteins is discussed. Cet article est consacré à l'apport de l'analyse de la diffusion diffuse de rayons X au problème de la déformabilité des protéines cristallisées. Nous passons d'abord en revue les principales études publiées, puis nous tentons d'effectuer une synthèse de ces résultats en y incluant des observations nouvelles que nous avons obtenues sur d'autres protéines. Il apparaît que deux types principaux de déplacements affectent les molécules: des déplacements intramoléculaires corrélés seulement à très courte distance et des déplacements intermoléculaires corrélés sur plusieurs mailles. La possibilité de détection de diffusion diffuse provenant de déplacements intramoléculaires corrélés à l'échelle de portions entières de molécules est discutée.

  16. Time-averaged MSD of Brownian motion

    NASA Astrophysics Data System (ADS)

    Andreanov, Alexei; Grebenkov, Denis S.

    2012-07-01

    We study the statistical properties of the time-averaged mean-square displacements (TAMSD). This is a standard non-local quadratic functional for inferring the diffusion coefficient from an individual random trajectory of a diffusing tracer in single-particle tracking experiments. For Brownian motion, we derive an exact formula for the Laplace transform of the probability density of the TAMSD by mapping the original problem onto chains of coupled harmonic oscillators. From this formula, we deduce the first four cumulant moments of the TAMSD, the asymptotic behavior of the probability density and its accurate approximation by a generalized Gamma distribution.

  17. Dual motion valve with single motion input

    NASA Technical Reports Server (NTRS)

    Belew, Robert (Inventor)

    1987-01-01

    A dual motion valve includes two dual motion valve assemblies with a rotary input which allows the benefits of applying both rotary and axial motion to a rotary sealing element with a plurality of ports. The motion of the rotary sealing element during actuation provides axial engagement of the rotary sealing element with a stationary valve plate which also has ports. Fluid passages are created through the valve when the ports of the rotary sealing element are aligned with the ports of the stationary valve plate. Alignment is achieved through rotation of the rotary sealing element with respect to the stationary valve plate. The fluid passages provide direct paths which minimize fluid turbulence created in the fluid as it passes through the valve.

  18. Active Teaching of Diffusion through History of Science, Computer Animation and Role Playing

    ERIC Educational Resources Information Center

    Krajsek, Simona Strgulc; Vilhar, Barbara

    2010-01-01

    We developed and tested a lesson plan for active teaching of diffusion in secondary schools (grades 10-13), which stimulates understanding of the thermal (Brownian) motion of particles as the principle underlying diffusion. During the lesson, students actively explore the Brownian motion through microscope observations of irregularly moving small…

  19. Active Teaching of Diffusion through History of Science, Computer Animation and Role Playing

    ERIC Educational Resources Information Center

    Krajsek, Simona Strgulc; Vilhar, Barbara

    2010-01-01

    We developed and tested a lesson plan for active teaching of diffusion in secondary schools (grades 10-13), which stimulates understanding of the thermal (Brownian) motion of particles as the principle underlying diffusion. During the lesson, students actively explore the Brownian motion through microscope observations of irregularly moving small…

  20. O'Connell's process as a vicious Brownian motion

    SciTech Connect

    Katori, Makoto

    2011-12-15

    Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of the quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.