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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. Influencing intramolecular motion with an alternating electric field

    PubMed

    Bermudez; Capron; Gase; Gatti; Kajzar; Leigh; Zerbetto; Zhang

    2000-08-10

    Analogues of mechanical devices that operate on the molecular level, such as shuttles, brakes, ratchets, turnstiles and unidirectional spinning motors, are current targets of both synthetic chemistry and nanotechnology. These structures are designed to restrict the degrees of freedom of submolecular components such that they can only move with respect to each other in a predetermined manner, ideally under the influence of some external stimuli. Alternating-current (a.c.) electric fields are commonly used to probe electronic structure, but can also change the orientation of molecules (a phenomenon exploited in liquid crystal displays), or interact with large-scale molecular motions, such as the backbone fluctuations of semi-rigid polymers. Here we show that modest a.c. fields can be used to monitor and influence the relative motion within certain rotaxanes, molecules comprising a ring that rotates around a linear 'thread' carrying bulky 'stoppers' at each end. We observe strong birefringence at frequencies that correspond to the rate at which the molecular ring pirouettes about the thread, with the frequency of maximum birefringence, and by inference also the rate of ring pirouetting giving rise to it, changing as the electric field strength is varied. Computer simulations and nuclear magnetic resonance spectroscopy show the ring rotation to be the only dynamic process occurring on a timescale corresponding to the frequency of maximum birefringence, thus confirming that mechanical motion within the rotaxanes can be addressed, and to some extent controlled, by oscillating electric fields.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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).

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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') .

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  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. 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.

  5. 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.

  6. 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

  7. [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.

  8. 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

  9. 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

  10. 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…

  11. 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…

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  20. 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. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Joint correction of Nyquist artifact and minuscule motion-induced aliasing artifact in interleaved diffusion weighted EPI data using a composite two-dimensional phase correction procedure.

    PubMed

    Chang, Hing-Chiu; Chen, Nan-Kuei

    2016-09-01

    Diffusion-weighted imaging (DWI) obtained with interleaved echo-planar imaging (EPI) pulse sequence has great potential of characterizing brain tissue properties at high spatial-resolution. However, interleaved EPI based DWI data may be corrupted by various types of aliasing artifacts. First, inconsistencies in k-space data obtained with opposite readout gradient polarities result in Nyquist artifact, which is usually reduced with 1D phase correction in post-processing. When there exist eddy current cross terms (e.g., in oblique-plane EPI), 2D phase correction is needed to effectively reduce Nyquist artifact. Second, minuscule motion induced phase inconsistencies in interleaved DWI scans result in image-domain aliasing artifact, which can be removed with reconstruction procedures that take shot-to-shot phase variations into consideration. In existing interleaved DWI reconstruction procedures, Nyquist artifact and minuscule motion-induced aliasing artifact are typically removed subsequently in two stages. Although the two-stage phase correction generally performs well for non-oblique plane EPI data obtained from well-calibrated system, the residual artifacts may still be pronounced in oblique-plane EPI data or when there exist eddy current cross terms. To address this challenge, here we report a new composite 2D phase correction procedure, which effective removes Nyquist artifact and minuscule motion induced aliasing artifact jointly in a single step. Our experimental results demonstrate that the new 2D phase correction method can much more effectively reduce artifacts in interleaved EPI based DWI data as compared with the existing two-stage artifact correction procedures. The new method robustly enables high-resolution DWI, and should prove highly valuable for clinical uses and research studies of DWI.

  10. 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

  11. 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.

  12. 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.

  13. 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).

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  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. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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…

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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].

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  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. 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.

  8. 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.

  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. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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)

  18. Motion Sickness

    MedlinePlus

    ... but it is more common in children, pregnant women, and people taking certain medicines. Motion sickness can start suddenly, with a queasy feeling and cold sweats. It can then lead to dizziness and nausea and vomiting. Your brain senses movement by getting signals from your inner ears, eyes, ...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. [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.

  6. 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

  7. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization.

    PubMed

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

    2016-10-18

    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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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).

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.}

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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…

  3. 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)

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  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 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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).

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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)

  5. Synthesis of chiral sultams via palladium-catalyzed intramolecular asymmetric reductive amination.

    PubMed

    Song, Bo; Yu, Chang-Bin; Ji, Yue; Chen, Mu-Wang; Zhou, Yong-Gui

    2017-02-04

    A novel palladium-catalyzed intramolecular reductive amination of ketones with weakly nucleophilic sulfonamides has been developed in the presence of a Brønsted acid, giving a wide range of chiral γ-, δ-, and ε-sultams in high yields and up to 99% of enantioselectivity.

  6. 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.

  7. 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.

  8. 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…

  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. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. THz Microscopy of Anisotropy and Correlated Motions in Protein Crystals

    NASA Astrophysics Data System (ADS)

    Niessen, Katherine; Acbas, Gheorghe; Snell, Edward; Markelz, Andrea

    2013-03-01

    We introduce a new technique, Crystal Anisotropy Terahertz Microscopy (CATM) which can directly measure correlated intra-molecular protein vibrations. The terahertz (THz) frequency range (5-100 cm-1) corresponds to global correlated protein motions, proposed to be essential to protein function [1, 2]. CATM accesses these motions by removal of the relaxational background of the solvent and residue side chain librational motions. We demonstrate narrowband features in the anisotropic absorbance for hen egg-white lysozyme (HEWL) single crystals as well as HEWL with triacetylglucosamine (HEWL-3NAG) inhibitor single crystals. The most prominent features for the HEWL crystals appear at 45 cm-1, 69 cm-1, and 78 cm-1 and the strength of the absorption varies with crystal orientation relative to the THz polarization. Calculations show similar anisotropic features, suggesting specific correlated mode identification is possible. 1. Hammes-Schiffer, S. and S.J. Benkovic, Relating Protein Motion to Catalysis. Annu. Rev. Biochem., 2006. 75: p. 519-41. 2. Henzler-Wildman, K.A., et al., Intrinsic motions along an enzymatic reaction trajectory. Nature, 2007. 450(7171): p. 838-U13. This work supported by NSF MRI2 grant DBI295998.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. 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…

  12. Diffusion imaging and tractography of congenital brain malformations.

    PubMed

    Wahl, Michael; Barkovich, A James; Mukherjee, Pratik

    2010-01-01

    Diffusion imaging is an MRI modality that measures the microscopic molecular motion of water in order to investigate white matter microstructure. The modality has been used extensively in recent years to investigate the neuroanatomical basis of congenital brain malformations. We review the basic principles of diffusion imaging and of specific techniques, including diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI). We show how DTI and HARDI, and their application to fiber tractography, has elucidated the aberrant connectivity underlying a number of congenital brain malformations. Finally, we discuss potential uses for diffusion imaging of developmental disorders in the clinical and research realms.

  13. Gas-phase intramolecular elimination reaction studies of steviol glycosides in positive electrospray and tandem mass spectrometry.

    PubMed

    Upreti, Mani; Clos, John F; Somayajula, Kasi V; Milanowski, Dennis J; Mocek, Ulla; Dubois, Grant E; Prakash, Indra

    2009-01-01

    This paper reports the first study of the gas-phase intramolecular elimination reaction of steviol glycosides in positive electrospray mass spectrometry. The observed glycosylated product ions are proposed to be formed via an intramolecular elimination of sugar units from the parent molecule ion. It was further proven by MS/MS studies and deuterium labeling experiments with one of the steviol glycosides, rebaudioside A. These mass spectrometric results confirmed that the new glycosylated product ions observed are most likely formed by the combination of glucose moieties (Glu) II-IV and Glu I via a gas-phase intramolecular elimination reaction.

  14. Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bond in the novel class of anionic H-chelates: 6-Nitro-2,3-dipyrrol-2-ylquinoxaline anion

    NASA Astrophysics Data System (ADS)

    Durlak, Piotr; Latajka, Zdzisław

    2009-10-01

    Theoretical studies of the structure and proton motion in the intramolecular N-H⋯N hydrogen bond in 6-nitro-2,3-dipyrrol-2-ylquinoxaline anion were carried out at the DFT, MP2 and molecular dynamics levels. Geometry optimization at the 6-311++G(2d,2p) level demonstrate existence of two tautomers on the potential energy surface. The difference in energy between both tautomers is equals 1.62 (1.42) kcal/mol. Dynamics of proton motion in the N-H⋯N hydrogen bond was investigated in vacuum at 233 K using Car-Parrinello and path integral molecular dynamics. Very large delocalization of bridging proton is noted especially in path integral simulation. DFT calculated the coupling constant across the hydrogen bond equals 16.5 Hz is in good agreement with experimental value.

  15. Gradient Driven Flow: Lattice Gas, Diffusion Equation and Measurement Scales

    DTIC Science & Technology

    2001-01-01

    03-200 1 Journal Article (refereed) 2001 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Gradient Driven Flow : Lattice Gas, Diffusion Equation and...time regime, the collective motion exhibits an onset of oscillation. 15. SUBJECT TERMS Diffusion; Fick’s Law; Gradient Driven Flow ; Lattice Gas 16...Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 20010907 062 Gradient driven flow : lattice gas, diffusion equation and measurement scales R.B

  16. Diffusion archeology for diffusion progression history reconstruction.

    PubMed

    Sefer, Emre; Kingsford, Carl

    2016-11-01

    Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.

  17. Diffusive dynamics on paper matrix

    NASA Astrophysics Data System (ADS)

    Chaudhury, Kaustav; Kar, Shantimoy; Chakraborty, Suman

    2016-11-01

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

  18. Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2012-07-01

    The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S1-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

  19. Nanoparticle Diffusion in Polymer Nanocomposites

    SciTech Connect

    Kalathi, Jagannathan; Yamamoto, Umi; Schweizer, Kenneth; Grest, Gary S.; Kumar, Sanat

    2014-01-01

    Large-scale molecular dynamics simulations show that nanoparticle (NP) diffusivity in weakly interacting mixtures of NPs and polymer melts has two very different classes of behavior depending on their size. NP relaxation times and their diffusivities are completely described by the local, Rouse dynamics of the polymer chains for NPs smaller than the polymer entanglement mesh size. The motion of larger NPs, which are comparable to the entanglement mesh size, is significantly slowed by chain entanglements, and is not describable by the Stokes-Einstein relationship. Our results are in essentially quantitative agreement with a force-level generalized Langevin equation theory for all the NP sizes and chain lengths explored, and imply that for these lightly entangled systems, activated NP hopping is not important.

  20. Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction

    SciTech Connect

    Pastorczak, Ewa; Prlj, Antonio; Corminboeuf, Clémence; Gonthier, Jérôme F.

    2015-12-14

    We introduce an intramolecular energy decomposition scheme for analyzing non-covalent interactions within molecules in the spirit of symmetry-adapted perturbation theory (SAPT). The proposed intra-SAPT approach is based upon the Chemical Hamiltonian of Mayer [Int. J. Quantum Chem. 23(2), 341–363 (1983)] and the recently introduced zeroth-order wavefunction [J. F. Gonthier and C. Corminboeuf, J. Chem. Phys. 140(15), 154107 (2014)]. The scheme decomposes the interaction energy between weakly bound fragments located within the same molecule into physically meaningful components, i.e., electrostatic-exchange, induction, and dispersion. Here, we discuss the key steps of the approach and demonstrate that a single-determinant wavefunction can already deliver a detailed and insightful description of a wide range of intramolecular non-covalent phenomena such as hydrogen bonds, dihydrogen contacts, and π − π stacking interactions. Intra-SAPT is also used to shed the light on competing intra- and intermolecular interactions.

  1. Enantioselective desymmetrization of cyclohexadienones via an intramolecular Rauhut–Currier reaction of allenoates

    PubMed Central

    Yao, Weijun; Dou, Xiaowei; Wen, Shan; Wu, Ji'en; Vittal, Jagadese J.; Lu, Yixin

    2016-01-01

    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. PMID:27698487

  2. Design Principles of Electronic Couplings for Intramolecular Singlet Fission in Covalently-Linked Systems.

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2016-08-11

    We theoretically investigate the singlet fission in three types of covalently-linked systems, that is, ortho-, meta- and para-linked pentacene dimers, where these are shown to have significantly different singlet fission rates. Each molecule is composed of two chromophores (pentacenes), which are active sites for singlet fission, and covalent bridges linking them. We clarify the origin of the difference in the electronic couplings in these systems, which are found to well support a recent experimental observation. It is also found that the next-nearest-neighbor interaction is indispensable for intramolecular singlet fission in these systems. On the basis of these results, we present design principles for efficient intramolecular singlet fission in covalently-linked systems and demonstrate the performance by using several novel conjugated linkers.

  3. Design of superbasic guanidines: the role of multiple intramolecular hydrogen bonds.

    PubMed

    Barić, Danijela; Dragičević, Ivan; Kovačević, Borislav

    2013-04-19

    New organic superbases have been designed using the concept of multiple intramolecular hydrogen bonds. Substituents capable of forming strong intramolecular H-bonds were selected on the basis of the energy of stabilization that occurs upon the formation of a complex between N,N',N"-trimethylguanidine and small model molecules. The proton affinities and the corresponding pK(a) values in acetonitrile of the new superbases are examined by Density Functional Theory (DFT). It is shown that N,N',N"-substitution of guanidine with appropriate substituents results in new organic superbases with gas phase proton affinities between 286 and 293 kcal mol(-1), thus being 15 to 20 kcal mol(-1) more basic than parental superbase N,N',N"-tris[(3-dimethylamino)propyl]-guanidine (tris-DMPG), whereas estimated pK(a) values in acetonitrile range between 29.5 and 33.2.

  4. Enantioselective Intramolecular Hydroarylation of Alkenes via Directed C-H Bond Activation

    SciTech Connect

    Harada, Hitoshi; Thalji, Reema; Bergman, Robert; Ellman, Jonathan

    2008-05-22

    Highly enantioselective catalytic intramolecular ortho-alkylation of aromatic imines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using [RhCl(coe){sub 2}]{sub 2} and chiral phosphoramidite ligands. Cyclization of substrates containing 1,1- and 1,2-disubstituted as well as trisubstituted alkenes were achieved with enantioselectivities >90% ee for each substrate class. Cyclization of substrates with Z-alkene isomers proceeded much more efficiently than substrates with E-alkene isomers. This further enabled the highly stereoselective intramolecular alkylation of certain substrates containing Z/E-alkene mixtures via a Rh-catalyzed alkene isomerization with preferential cyclization of the Z-isomer.

  5. Intramolecular Charge-Transfer Interaction of Donor-Acceptor-Donor Arrays Based on Anthracene Bisimide.

    PubMed

    Iwanaga, Tetsuo; Ogawa, Marina; Yamauchi, Tomokazu; Toyota, Shinji

    2016-05-20

    We designed anthracene bisimide (ABI) derivatives having two triphenylamine (TPA) groups as donor units at the 9,10-positions to form a novel π-conjugated donor-acceptor system. These compounds and their analogues with ethynylene linkers were synthesized by Suzuki-Miyaura and Sonogashira coupling reactions, respectively. In UV-vis spectra, the linker-free derivatives showed broad absorption bands arising from intramolecular charge-transfer interactions. Introducing ethynylene linkers resulted in a considerable red shift of the absorption bands. In fluorescence spectra, the ethynylene derivatives showed intense emission bands at 600-650 nm. Their photophysical and electrochemical properties were compared with those of the corresponding mono TPA derivatives on the basis of theoretical calculations and cyclic voltammetry to evaluate the intramolecular electronic interactions between the donor and acceptor units.

  6. Theoretical Investigation of Intramolecular Hydrogen Shift Reactions in 3-Methyltetrahydrofuran (3-MTHF) Oxidation.

    PubMed

    Parab, Prajakta R; Sakade, Naoki; Sakai, Yasuyuki; Fernandes, Ravi; Heufer, K Alexander

    2015-11-05

    3-Methyltetrahydrofuran (3-MTHF) is proposed to be a promising fuel component among the cyclic oxygenated species. To have detailed insight of its combustion kinetics, intramolecular hydrogen shift reactions for the ROO to QOOH reaction class are studied for eight ROO isomers of 3-MTHF. Rate constants of all possible reaction paths that involve formation of cyclic transition states are computed by employing the CBS-QB3 composite method. A Pitzer-Gwinn-like approximation has been applied for the internal rotations in reactants, products, and transition states for the accurate treatment of hindered rotors. Calculated relative barrier heights highlight that the most favorable reaction channel proceeds via a six membered transition state, which is consistent with the computed rate constants. Comparing total rate constants in ROO isomers of 3-MTHF with the corresponding isomers of methylcyclopentane depicts faster kinetics in 3-MTHF than methylcyclopentane reflecting the effect of ring oxygen on the intramolecular hydrogen shift reactions.

  7. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds.

    PubMed

    Hansen, Poul Erik

    2015-01-30

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between "static" and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N-. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.

  8. Motion through syntactic frames.

    PubMed

    Feist, Michele I

    2010-04-01

    The introduction of Talmy's (1985, 2000) typology sparked significant interest in linguistic relativity in the arena of motion language. Through careful analysis of the conflation patterns evident in the language of motion events, Talmy noted that one class of languages, V-languages, tends to encode path along with the fact of motion in motion verbs, while a second class, S-languages, tends to encode manner. In the experimental literature, it was reasoned that speakers may be expected to extend novel verbs in accordance with the lexicalization patterns of their native languages. However, the results regarding this prediction are mixed. In this paper, I examine the interplay between the meaning encoded in the motion verb itself and the meaning encoded in the motion description construction, offering a Gricean explanation for co-occurrence patterns and, by extension, for the mixed results. I then explore the implications of this argument for research on possible language effects on thought in this domain.

  9. Motion Tracking System

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Integrated Sensors, Inc. (ISI), under NASA contract, developed a sensor system for controlling robot vehicles. This technology would enable a robot supply vehicle to automatically dock with Earth-orbiting satellites or the International Space Station. During the docking phase the ISI-developed sensor must sense the satellite's relative motion, then spin so the robot vehicle can adjust its motion to align with the satellite and slowly close until docking is completed. ISI used the sensing/tracking technology as the basis of its OPAD system, which simultaneously tracks an object's movement in six degrees of freedom. Applications include human limb motion analysis, assembly line position analysis and auto crash dummy motion analysis. The NASA technology is also the basis for Motion Analysis Workstation software, a package to simplify the video motion analysis process.

  10. Protein diffusion in mammalian cell cytoplasm.

    PubMed

    Kühn, Thomas; Ihalainen, Teemu O; Hyväluoma, Jari; Dross, Nicolas; Willman, Sami F; Langowski, Jörg; Vihinen-Ranta, Maija; Timonen, Jussi

    2011-01-01

    We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.

  11. Nucleophilic Additions to Coordinated 1,10-Phenanthroline: Intramolecular, Intermolecular, Reversible, and Irreversible.

    PubMed

    Arévalo, Rebeca; Menéndez, M Isabel; López, Ramón; Merino, Isabel; Riera, Lucía; Pérez, Julio

    2016-12-12

    KN(SiMe3 )2 reacts with [Re(CO)3 (phen)(PMe3 )]OTf via reversible addition to the phen ligand and irreversible deprotonation of the PMe3 ligand followed by intramolecular attack to phen by the deprotonated phosphane, whereas MeLi irreversibly adds to phen. The addition of MeLi has been shown to be intermolecular, unlike previously known nucleophilic additions to pyridines.

  12. Influence of the intramolecular potential of adsorbed hydrogen on frequency shift calculations

    NASA Astrophysics Data System (ADS)

    Larin, Alexander V.

    1995-01-01

    The influence of the choice of the intramolecular potential on the resulting frequency shift of the fundamental vibrational transition in the dihydrogen molecule adsorbed on zeolite NaA is estimated. It is shown that an improved Morse potential and the potential calculated by Kołtsos and Wolniewicz lead to the same frequency shift value. Application of the Buckingham method for the frequency shift calculation to this case is discussed.

  13. Rhodium-catalyzed intramolecular hydroarylation of 1-halo-1-alkynes: regioselective synthesis of semihydrogenated aromatic heterocycles.

    PubMed

    Murase, Hirohiko; Senda, Kousuke; Senoo, Masato; Hata, Takeshi; Urabe, Hirokazu

    2014-01-03

    The regioselective intramolecular hydroarylation of (3-halo-2-propynyl)anilines, (3-halo-2-propynyl) aryl ethers, or (4-halo-3-butynyl) aryl ethers was efficiently catalyzed by Rh2(OCOCF3)4 to give semihydrogenated aromatic heterocycles, such as 4-halo-1,2-dihydroquinolines, 4-halo-3-chromenes, or 4-(halomethylene)chromans, in good to excellent yields. Some synthetic applications taking advantage of the halo-substituents of the products are also illustrated.

  14. A Chiral Thiourea as a Template for Enantioselective Intramolecular [2 + 2] Photocycloaddition Reactions

    PubMed Central

    2016-01-01

    A chiral (1R,2R)-diaminocyclohexane-derived bisthiourea was found to exhibit a significant asymmetric induction in the intramolecular [2 + 2] photocycloaddition of 2,3-dihydropyridone-5-carboxylates. Under optimized conditions, the reaction was performed with visible light employing 10 mol % of thioxanthone as triplet sensitizer. Due to the different electronic properties of its carbonyl oxygen atoms, a directed binding of the substrate to the template is possible, which in turn enables an efficient enantioface differentiation. PMID:27258626

  15. Iron(II)-catalyzed intramolecular aminohydroxylation of olefins with functionalized hydroxylamines.

    PubMed

    Liu, Guan-Sai; Zhang, Yong-Qiang; Yuan, Yong-An; Xu, Hao

    2013-03-06

    A diastereoselective aminohydroxylation of olefins with a functionalized hydroxylamine is catalyzed by new iron(II) complexes. This efficient intramolecular process readily affords synthetically useful amino alcohols with excellent selectivity (dr up to > 20:1). Asymmetric catalysis with chiral iron(II) complexes and preliminary mechanistic studies reveal an iron nitrenoid is a possible intermediate that can undergo either aminohydroxylation or aziridination, and the selectivity can be controlled by careful selection of counteranion/ligand combinations.

  16. A near infrared colorimetric and fluorometric probe for organophosphorus nerve agent mimics by intramolecular amidation.

    PubMed

    Hu, Xiao-Xiao; Su, Yue-Ting; Ma, Yun-Wei; Zhan, Xin-Qi; Zheng, Hong; Jiang, Yun-Bao

    2015-10-21

    A near infrared probe for sensitive colorimetric and fluorimetric detection of nerve agent mimics, DCP and DCNP, was reported based on the activation of a carboxylic acid group by the mimics to conduct an intramolecular amidation reaction in the heptamethine chromophore, where its absorption or excitation maximum wavelength could be greatly red-shifted by attenuating the electron-donating ability of the amine group in the bridgehead site of heptamethine cyanine.

  17. Intramolecular Diels–Alder Reactions of Cycloalkenones: Stereoselectivity, Lewis Acid Acceleration, and Halogen Substituent Effects

    PubMed Central

    2015-01-01

    The intramolecular Diels–Alder reactions of cycloalkenones and terminal dienes occur with high endo stereoselectivity, both thermally and under Lewis-acidic conditions. Through computations, we show that steric repulsion and tether conformation govern the selectivity of the reaction, and incorporation of either BF3 or α-halogenation increases the rate of cycloaddition. With a longer tether, isomerization from a terminal diene to the more stable internal diene results in a more facile cycloaddition. PMID:24410341

  18. Designed intramolecular blocking of the spin crossover of an Fe(ii) complex.

    PubMed

    Bartual-Murgui, C; Vela, S; Roubeau, O; Aromí, G

    2016-09-13

    A ligand derived from 1,3bpp (2-(pyrazol-1-yl)-6-(pyrazol-3-yl)-pyridine) has been prepared to prove that the spin crossover (SCO) of an Fe(ii) complex can be blocked by means of intramolecular interactions not related to the crystal field. Calculations show that the blocking is caused by the energy penalty incurred by the rotation of a phenyl ring, needed to avoid steric hindrance upon SCO.

  19. Influence of "remote" intramolecular hydrogen bonds on the stabilities of phenoxyl radicals and benzyl cations.

    PubMed

    Foti, Mario C; Amorati, Riccardo; Pedulli, Gian Franco; Daquino, Carmelo; Pratt, Derek A; Ingold, K U

    2010-07-02

    Remote intramolecular hydrogen bonds (HBs) in phenols and benzylammonium cations influence the dissociation enthalpies of their O-H and C-N bonds, respectively. The direction of these intramolecular HBs, para --> meta or meta --> para, determines the sign of the variation with respect to molecules lacking remote intramolecular HBs. For example, the O-H bond dissociation enthalpy of 3-methoxy-4-hydroxyphenol, 4, is about 2.5 kcal/mol lower than that of its isomer 3-hydroxy-4-methoxyphenol, 5, although group additivity rules would predict nearly identical values. In the case of 3-methoxy-4-hydroxybenzylammonium and 3-hydroxy-4-methoxybenzylammonium ions, the CBS-QB3 level calculated C-N eterolytic dissociation enthalpy is about 3.7 kcal/mol lower in the former ion. These effects are caused by the strong electron-withdrawing character of the -O(*) and -CH(2)(+) groups in the phenoxyl radical and benzyl cation, respectively, which modulates the strength of the HB. An O-H group in the para position of ArO(*) or ArCH(2)(+) becomes more acidic than in the parent molecules and hence forms stronger HBs with hydrogen bond acceptors (HBAs) in the meta position. Conversely, HBAs, such as OCH(3), in the para position become weaker HBAs in phenoxyl radicals and benzyl cations than in the parent molecules. These product thermochemistries are reflected in the transition states for, and hence in the kinetics of, hydrogen atom abstraction from phenols by free radicals (dpph(*) and ROO(*)). For example, the 298 K rate constant for the 4 + dpph(*) reaction is 22 times greater than that for the 5 + dpph(*) reaction. Fragmentation of ring-substituted benzylammonium ions, generated by ESI-MS, to form the benzyl cations reflects similar remote intramolecular HB effects.

  20. An intramolecular inverse electron demand Diels–Alder approach to annulated α-carbolines

    PubMed Central

    Ma, Zhiyuan; Ni, Feng; Woo, Grace H C; Lo, Sie-Mun; Roveto, Philip M; Schaus, Scott E

    2012-01-01

    Summary Intramolecular inverse electron demand cycloadditions of isatin-derived 1,2,4-triazines with acetylenic dienophiles tethered by amidations or transesterifications proceed in excellent yields to produce lactam- or lactone-fused α-carbolines. Beginning with various isatins and alkynyl dienophiles, a pilot-scale library of eighty-eight α-carbolines was prepared by using this robust methodology for biological evaluation. PMID:23015831

  1. Synthesis of derivatives of indole and quinoline by the intramolecular catalytic cyclization of allylanilines

    SciTech Connect

    Abdrakmanov, I.B.; Mustafin, A.G.; Tolstikov, G.A.; Fakhretdinov, R.N.; Dzhemilev, U.M.

    1986-09-01

    An effective method for the isolation of 3-methyl-2-ethylindole and 2,4-dimethyl-quinoline by the intramolecular cyclization of N-(1-methyl-2-butenyl)- and 2-(1-methyl-2-butenyl)anilines under the action of the catalyst PdCl/sub 2/ (DMSO)/sub n/ was developed. The influence of the nature of the solvent, the temperature, and the concentration of the catalyst on the yield and the ratio of the reaction products was investigated.

  2. Cobalt-catalyzed intramolecular C-H amination with arylsulfonyl azides.

    PubMed

    Ruppel, Joshua V; Kamble, Rajesh M; Zhang, X Peter

    2007-11-08

    Cobalt complexes of porphyrins are effective catalysts for intramolecular C-H amination with arylsulfonyl azides. The cobalt-catalyzed process can proceed efficiently under mild and neutral conditions in low catalyst loading without the need of other reagents or additives, generating nitrogen gas as the only byproduct. The catalytic system can be applied to primary, secondary, and tertiary C-H bonds and is suitable for a broad range of arylsulfonyl azides, leading to high-yielding syntheses of various benzosultams.

  3. Pseudo-cyclic face-to-face rigid structure caused by the intramolecular ion pair effect.

    PubMed

    Zhang, Sheng-Ling; Huang, Zhi-Shu; Gu, Lian-Quan

    2009-04-14

    Six 3-methylpyridine zwitterions and six quinoline zwitterions were synthesized through the reaction of 4-hydroxycoumarins, p-benzoquinone and the corresponding N-aromatics. The novel pseudo-cyclic face-to-face rigid structure of the zwitterion was elucidated by (1)H-NMR at different temperatures, and assumed to be caused by both the intramolecular ion pair attraction and the steric interaction.

  4. Intramolecular Dynamics: A Study of Molecules at High Levels of Vibrational Excitation.

    DTIC Science & Technology

    1988-05-27

    molecular modes , which occurs in molecules that are excited above the dissociation threshold,.- however, causes the course and rate of laser-induced...8217 mode -selective’ or ’bond-specific’ photochemistry, despite the high selectivity _ of infrared excitation. Whereas the equilibration of energy for...atoms. Most of these molecules have more than one Raman active mode and thus allow direct observation of the intramolecular U distribution of

  5. Enantioselective intramolecular propargylic amination using chiral copper-pybox complexes as catalysts.

    PubMed

    Shibata, Masashi; Nakajima, Kazunari; Nishibayashi, Yoshiaki

    2014-07-25

    Intramolecular propargylic amination of propargylic acetates bearing an amino group at the suitable position in the presence of chiral copper-pybox complexes proceeds enantioselectively to give optically active 1-ethynyl-isoindolines (up to 98% ee). The method described in this communication provides a useful synthetic approach to the enantioselective preparation of nitrogen containing heterocyclic compounds with an ethynyl group at the α-position.

  6. A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers

    DTIC Science & Technology

    2016-08-24

    A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers Eric G. Fuemmeler,†,‡ Samuel N. Sanders,‡,§ Andrew B. Pun...via a direct coupling mechanism that is independent of CT states. We show that a near-degeneracy in electronic state energies induced by vibronic...despite weak direct coupling. Singlet fission, the process by which one singlet exciton splitsinto two triplet excitons, is proving an important

  7. Localised Plate Motion on Venus

    NASA Astrophysics Data System (ADS)

    Ghail, R. C.

    1996-03-01

    The volcanic and tectonic features observed in Dali Vinculum, Parga Vinculum and Imdr Regio are concentrated at long, narrow, curvilinear zones, with relatively minor volcanism and tectonism between these zones. These zones, whilst more diffuse than terrestrial plate boundaries, nevertheless define the margins of tectonic plates. In contrast to Earth, however, it appears that venusian plates are neither created nor destroyed by lateral motion. Rather, plates are thinned and intruded at vincula plate boundaries, vertically accreted by small-scale intra-plate (planitia) volcanism and perhaps destroyed by delamination of thickened crust in tesserae and montane regions such as Thetis Regio and Ishtar Terra. The diversity in age both between and within these three areas together with the evidence for infrequent, small scale resurfacing in the planitiae are difficult to reconcile with a non-uniformitarian geological process.

  8. Iron(II) triflate as a catalyst for the synthesis of indoles by intramolecular C-H amination.

    PubMed

    Bonnamour, Julien; Bolm, Carsten

    2011-04-15

    A practical iron-catalyzed intramolecular C-H amination reaction and its application in the synthesis of indole derivatives are presented. As a catalyst, commercially available iron(II) triflate is used.

  9. Enantioselective cis-β-lactam synthesis by intramolecular C-H functionalization from enoldiazoacetamides and derivative donor-acceptor cyclopropenes

    PubMed Central

    Deng, Yongming; Yim, David N.; Zavalij, Peter Y.

    2015-01-01

    β-Lactam derivatives are produced through intermediate donor-acceptor cyclopropene intermediates in high yield, exclusive cis-diastereoselectivity, and high enantiocontrol in a chiral dirhodium carboxylate catalyzed intramolecular C-H functionalization reaction of enoldiazoacetamides. PMID:26029355

  10. A Diastereoselective Intramolecular Pauson-Khand Approach to the Construction of the BC Ring System in Tuberostemoninol

    PubMed Central

    Jia, Xiangna; Williams, Robert M

    2009-01-01

    Herein we describe an asymmetric approach to the synthesis of a BC-ring synthon in tuberostemoninol via an intramolecular Pauson-Khand reaction stereocontrolled by a commercially available chiral glycinate. PMID:19779590

  11. Molecular Orbital Study of the Formation of Intramolecular Hydrogen Bonding of a Ligand Molecule in a Protein Aromatic Hydrophobic Pocket.

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

    The natural product argadin is a cyclopentapeptide chitinase inhibitor that binds to chitinase B (ChiB) from the pathogenic bacteria Serratia marcescens. N(ω)-Acetyl-L-arginine and L-aminoadipic acid of argadin form intramolecular ionic hydrogen bonds in the aromatic hydrophobic pocket of ChiB. We performed ab initio molecular orbital and density functional theory calculations to elucidate the role of this intramolecular hydrogen bonding on intermolecular interactions between argadin and ChiB. We found that argadin accrues large stabilization energies from the van der Waals dispersion interactions, such as CH-π, π-π, and π-lone pair interactions, in the aromatic hydrophobic pocket of ChiB, although intramolecular hydrogen bonding within argadin might result in loss of entropy. The intramolecular ionic hydrogen bonding formation canceled local molecular charges and provided good van der Waals interactions with surrounding aromatic residues.

  12. New domino transposition/intramolecular Diels-Alder reaction in monocyclic allenols: a general strategy for tricyclic compounds.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Aragoncillo, Cristina; Redondo, María C

    2002-07-21

    A novel and direct synthetic strategy to prepare fused tricycles has been developed from monocyclic allenols, masked functionalized dienes, which underwent a domino allenol transposition/intramolecular Diels-Alder reaction.

  13. Asymmetric synthesis of planar chiral ferrocenes by enantioselective intramolecular C-H arylation of N-(2-haloaryl)ferrocenecarboxamides.

    PubMed

    Liu, Lantao; Zhang, An-An; Zhao, Rui-Juan; Li, Feng; Meng, Tuan-Jie; Ishida, Naoki; Murakami, Masahiro; Zhao, Wen-Xian

    2014-10-17

    The palladium-catalyzed intramolecular C-H arylation reaction of N-(2-bromoaryl)ferrocenecarboxamides furnishes planar chiral ferrocene derivatives. TADDOL-derived phosphoramide ligands induce enantioselectivities ranging from 91:9 to 98:2 er.

  14. Intramolecular disulfide bonds between conserved cysteines in wheat gliadins control their deposition into protein bodies.

    PubMed

    Shimoni, Y; Galili, G

    1996-08-02

    Following synthesis, wheat gliadin storage proteins are deposited into protein bodies inside the endomembrane system in a way that enables not only their efficient accumulation and dehydration during seed maturation, but also their rapid rehydration and degradation during germination. In the present report, we studied the mechanism of gliadin deposition and whether it was controlled by the conformation of these proteins. Although gliadins are generally known to be insoluble in aqueous solutions, sucrose gradient analysis showed that a considerable amount of these proteins appeared as relatively soluble monomers in developing grains. In vitro reduction of the intramolecular disulfide bonds that are present in natural monomeric gliadins caused their precipitation into insoluble aggregates. In addition, pulse-chase experiments in the absence or presence of reducing agents showed that formation of intramolecular disulfide bonds also played a major role in folding and deposition of the gliadins in vivo. Our results imply that following sequestration into the endoplasmic reticulum, the gliadins fold into relatively soluble monomers, which are incompetent for rapid aggregation and gradually assemble into protein bodies. This pattern of deposition apparently depends on the conformation of the gliadins, which is stabilized by intramolecular disulfide bonds formed between the conserved cysteines. The contribution of this study to the understanding of the evolution and function of gliadins is discussed.

  15. Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes.

    PubMed

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

    The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data.

  16. Regulation of interleukin-4 signaling by extracellular reduction of intramolecular disulfides

    SciTech Connect

    Curbo, Sophie; Gaudin, Raphael; Carlsten, Mattias; Malmberg, Karl-Johan; Troye-Blomberg, Marita; Ahlborg, Niklas; Karlsson, Anna; Johansson, Magnus; Lundberg, Mathias

    2009-12-25

    Interleukin-4 (IL-4) contains three structurally important intramolecular disulfides that are required for the bioactivity of the cytokine. We show that the cell surface of HeLa cells and endotoxin-activated monocytes can reduce IL-4 intramolecular disulfides in the extracellular space and inhibit binding of IL-4 to the IL-4R{alpha} receptor. IL-4 disulfides were in vitro reduced by thioredoxin 1 (Trx1) and protein disulfide isomerase (PDI). Reduction of IL-4 disulfides by the cell surface of HeLa cells was inhibited by auranofin, an inhibitor of thioredoxin reductase that is an electron donor to both Trx1 and PDI. Both Trx1 and PDI have been shown to be located at the cell surface and our data suggests that these enzymes are involved in catalyzing reduction of IL-4 disulfides. The pro-drug N-acetylcysteine (NAC) that promotes T-helper type 1 responses was also shown to mediate the reduction of IL-4 disulfides. Our data provides evidence for a novel redox dependent pathway for regulation of cytokine activity by extracellular reduction of intramolecular disulfides at the cell surface by members of the thioredoxin enzyme family.

  17. The interplay between inter- and intra-molecular dynamics in a series of alkylcitrates

    SciTech Connect

    Kipnusu, Wycliffe Kiprop; Kossack, Wilhelm; Iacob, Ciprian; Zeigermann, Philipp; Jasiurkowska, Malgorzata; Sangoro, Joshua R; Valiullin, Rustem; Kremer, Friedrich

    2013-01-01

    The inter- and intra-molecular dynamics in a series of glass-forming alkylcitrates is studied by a combination of Broadband Dielectric Spectroscopy (BDS), Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR), Fourier-Transform Infrared (FTIR) spectroscopy and Differential Scanning Calorimetry (DSC). Analyzing the temperature dependencies of specific IR absorption bands in terms of their spectral position and the corresponding oscillator strengths enables one to unravel the intramolecular dynamics of specific molecular moieties and to compare them with the (primarily dielectrically) determined intermolecular dynamics. With decreasing temperature, the IR band positions of carbonyls (part of the core units) and H-bonded moieties of citrates show a red shift with a kink at the calorimetric glass transition temperature (Tg) while other moieties, whose dynamics are decoupled from those of the core units, exhibit a blue shift with nominal changes at Tg. The oscillator strength of all units in citrates depicts stronger temperature dependencies above Tg and in some, the ester linkage and H-bonded units show a change of slope at a temperature where structural and faster secondary relaxations merge. By that, a wealth of novel information is obtained proving the fundamental importance of intramolecular mobility in the process of glass formation, beyond coarse-grained descriptions.

  18. NIST Diffusion Data Center

    National Institute of Standards and Technology Data Gateway

    NIST Diffusion Data Center (Web, free access)   The NIST Diffusion Data Center is a collection of over 14,100 international papers, theses, and government reports on diffusion published before 1980.

  19. Parallel flow diffusion battery

    DOEpatents

    Yeh, Hsu-Chi; Cheng, Yung-Sung

    1984-08-07

    A parallel flow diffusion battery for determining the mass distribution of an aerosol has a plurality of diffusion cells mounted in parallel to an aerosol stream, each diffusion cell including a stack of mesh wire screens of different density.

  20. Parallel flow diffusion battery

    DOEpatents

    Yeh, H.C.; Cheng, Y.S.

    1984-01-01

    A parallel flow diffusion battery for determining the mass distribution of an aerosol has a plurality of diffusion cells mounted in parallel to an aerosol stream, each diffusion cell including a stack of mesh wire screens of different density.

  1. The Personal Motion Platform

    NASA Technical Reports Server (NTRS)

    Park, Brian Vandellyn

    1993-01-01

    The Neutral Body Posture experienced in microgravity creates a biomechanical equilibrium by enabling the internal forces within the body to find their own balance. A patented reclining chair based on this posture provides a minimal stress environment for interfacing with computer systems for extended periods. When the chair is mounted on a 3 or 6 axis motion platform, a generic motion simulator for simulated digital environments is created. The Personal Motion Platform provides motional feedback to the occupant in synchronization with their movements inside the digital world which enhances the simulation experience. Existing HMD based simulation systems can be integrated to the turnkey system. Future developments are discussed.

  2. Measurement of visual motion

    SciTech Connect

    Hildreth, E.C.

    1984-01-01

    This book examines the measurement of visual motion and the use of relative movement to locate the boundaries of physical objects in the environment. It investigates the nature of the computations that are necessary to perform this analysis by any vision system, biological or artificial. Contents: Introduction. Background. Computation of the Velocity Field. An Algorithm to Compute the Velocity Field. The Computation of Motion Discontinuities. Perceptual Studies of Motion Measurement. The Psychophysics of Discontinuity Detection. Neurophysiological Studies of Motion. Summary and Conclusions. References. Author and Subject Indexes.

  3. Silver(I)‐Catalyzed Intramolecular Cyclizations of Epoxide‐Propargylic Esters to 1,4‐Oxazine Derivatives

    PubMed Central

    Li, Peng‐Hua; Yang, Jin‐Ming; Wei, Yin

    2016-01-01

    Abstract An interesting silver(I)‐catalyzed, one‐pot intramolecular cyclization of epoxide‐propargylic esters is described. A variety of 1,4‐oxazine derivatives were obtained through a novel domino sequence, including three‐membered ring‐opening, 3,3‐sigmatropic rearrangement, 6‐exo‐cycloisomerization and subsequent intramolecular elimination in moderate yields under mild conditions. PMID:28168146

  4. Intramolecular direct dehydrohalide coupling promoted by KO(t)Bu: total synthesis of Amaryllidaceae alkaloids anhydrolycorinone and oxoassoanine.

    PubMed

    De, Subhadip; Ghosh, Santanu; Bhunia, Subhajit; Sheikh, Javeed Ahmad; Bisai, Alakesh

    2012-09-07

    A transition-metal-free intramolecular dehydrohalide coupling via intramolecular homolytic aromatic substitution (HAS) with aryl radicals has been developed in the presence of potassium tert-butoxide and an organic molecule as the catalyst. The methodology has been applied to a concise synthesis of Amaryllidaceae alkaloids viz. oxoassoanine (1b), anhydrolycorinone (1d), and other related structures. Interestingly, the method also works only in the presence of potassium tert-butoxide.

  5. FRACTIONAL PEARSON DIFFUSIONS.

    PubMed

    Leonenko, Nikolai N; Meerschaert, Mark M; Sikorskii, Alla

    2013-07-15

    Pearson diffusions are governed by diffusion equations with polynomial coefficients. Fractional Pearson diffusions are governed by the corresponding time-fractional diffusion equation. They are useful for modeling sub-diffusive phenomena, caused by particle sticking and trapping. This paper provides explicit strong solutions for fractional Pearson diffusions, using spectral methods. It also presents stochastic solutions, using a non-Markovian inverse stable time change.

  6. FRACTIONAL PEARSON DIFFUSIONS

    PubMed Central

    Leonenko, Nikolai N.; Meerschaert, Mark M.

    2013-01-01

    Pearson diffusions are governed by diffusion equations with polynomial coefficients. Fractional Pearson diffusions are governed by the corresponding time-fractional diffusion equation. They are useful for modeling sub-diffusive phenomena, caused by particle sticking and trapping. This paper provides explicit strong solutions for fractional Pearson diffusions, using spectral methods. It also presents stochastic solutions, using a non-Markovian inverse stable time change. PMID:23626377

  7. Creeping Motion of Self Interstitial Atom Clusters in Tungsten

    NASA Astrophysics Data System (ADS)

    Zhou, Wang Huai; Zhang, Chuan Guo; Li, Yong Gang; Zeng, Zhi

    2014-05-01

    The formation and motion features of self interstitial atom (SIA) clusters in tungsten are studied by molecular dynamics (MD) simulations. The static calculations show that the SIA clusters are stable with binding energy over 2 eV. The SIA clusters exhibit a fast one dimensional (1D) motion along <111>. Through analysis of the change of relative distance between SIAs, we find that SIAs jump in small displacements we call creeping motion, which is a new collective diffusion process different from that of iron. The potential energy surface of SIAs implicates that the creeping motion is due to the strong interaction between SIAs. These imply that several diffusion mechanism for SIA clusters can operate in BCC metals and could help us explore deep insight into the performance of materials under irradiation.

  8. A critical evaluation of the factors determining the effect of intramolecular hydrogen bonding on the O-H bond dissociation enthalpy of catechol and of flavonoid antioxidants.

    PubMed

    Lucarini, Marco; Pedulli, Gian Franco; Guerra, Maurizio

    2004-02-20

    New experimental results on the determination of the bond dissociation enthalpy (BDE) value of 3,5-di-tert-butylcatechol, a model compound for flavonoid antioxidants, by the EPR radical equilibration technique are reported. By measurement of the equilibrium constant for the reaction between 3,5-di-tert-butylcatechol and the 2,6-di-tert-butyl-4-methylphenoxyl radical, in UV irradiated isooctane solutions at different temperatures, it has been shown that the thermodynamic parameters for this reaction are DeltaH degrees = -2.8+/-0.1 kcal mol(-1) and DeltaS degrees = +1.3+/-0.2 cal mol(-1) K(-1). This demonstrates that the entropic variations in the hydrogen exchange reaction between phenols and the corresponding phenoxyl radicals are also negligible when one of the reacting species is a polyphenol and that the EPR radical equilibration technique also allows the determination of the Obond;H BDEs in intramolecularly hydrogen-bonded polyphenols. The BDE of 3,5-di-tert-butylcatechol (78.2 kcal mol(-1)) was determined to be identical to that of alpha-tocopherol. Through use of the group additivity rule, this piece of data was also used to calculate the strength of the intramolecular hydrogen bond between the hydroxyl proton and the oxygen radical centre in the corresponding semiquinone radical (5.6 kcal mol(-1)), which is responsible both for the excellent antioxidant properties of catechols and for the BDE of catechol (81.8 kcal mol(-1)). These values are in poor agreement with those predicted by DFT calculations reported in the literature (9.5 kcal mol(-1) and 77.6 kcal mol(-1), respectively). Extensive theoretical calculations indicate that the BDE of catechol is reproduced well (81.6 kcal mol(-1)) by use of diffuse functions on oxygen and the CCSD method.

  9. Constrained geometric simulation of diffusive motion in proteins

    NASA Astrophysics Data System (ADS)

    Wells, Stephen; Menor, Scott; Hespenheide, Brandon; Thorpe, M. F.

    2005-12-01

    We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.

  10. Phytoplankton's motion in turbulent ocean.

    PubMed

    Fouxon, Itzhak; Leshansky, Alexander

    2015-07-01

    We study the influence of turbulence on upward motion of phytoplankton. Interaction with the flow is described by the Pedley-Kessler model considering spherical microorganisms. We find a range of parameters when the upward drift is only weakly perturbed or when turbulence completely randomizes the drift direction. When the perturbation is small, the drift is either determined by the local vorticity or is Gaussian. We find a range of parameters where the phytoplankton interaction with the flow can be described consistently as diffusion of orientation in effective potential. By solving the corresponding Fokker-Planck equation we find exponential steady-state distribution of phytoplankton's propulsion orientation. We further identify the range of parameters where phytoplankton's drift velocity with respect to the flow is determined uniquely by its position. In this case, one can describe phytoplankton's motion by a smooth flow and phytoplankton concentrates on fractal. We find fractal dimensions and demonstrate that phytoplankton forms vertical stripes in space with a nonisotropic pair-correlation function of concentration increased in the vertical direction. The probability density function of the distance between two particles obeys power law with the negative exponent given by the ratio of integrals of the turbulent energy spectrum. We find the regime of strong clustering where the exponent is of order one so that turbulence increases the rate of collisions by a large factor. The predictions hold for Navier-Stokes turbulence and stand for testing.

  11. Intramolecular vibrational energy redistribution in bridged azulene-anthracene compounds: Ballistic energy transport through molecular chains

    NASA Astrophysics Data System (ADS)

    Schwarzer, D.; Kutne, P.; Schröder, C.; Troe, J.

    2004-07-01

    Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH2)m with m up to 6 as well as (CH2OCH2)n (n=1,2) and CH2SCH2. After light absorption into the azulene S1 band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S3 absorption band at 300 nm and/or the anthracene S1 absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants τIVR for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, τIVR is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially ballistic and, therefore

  12. Probing Intramolecular versus Intermolecular CO2 Adsorption on Amine-Grafted SBA-15.

    PubMed

    Yoo, Chun-Jae; Lee, Li-Chen; Jones, Christopher W

    2015-12-15

    A mesoporous silica SBA-15 is modified with an array of amine-containing organosilanes including (i) propylamine, SiCH2CH2CH2NH2 (MONO), (ii) propylethylenediamine, SiCH2CH2CH2NHCH2CH2NH2 (DI), (iii) propyldiethylenetriamine, SiCH2CH2CH2NHCH2CH2NHCH2CH2NH2 (TRI), and (iv) propyltriethylenetetramine, SiCH2CH2CH2NHCH2CH2N(CH2CH2NH2)2 (TREN) and the low loading silane adsorbents (∼0.45 mmol silane/g) are evaluated for their CO2 adsorption properties, with a focus on gaining insight into the propensity for intramolecular vs intermolecular CO2 adsorption. Adsorption isotherms at low CO2 coverages are measured while simultaneously recording the heat evolved via a Tian-Calvet calorimeter. The results are compared on a silane molecule efficiency basis (mol CO2 adsorbed/mol silane) to assess the potential for intramolecular CO2 adsorption, employing two amine groups in a single silane molecule. As the number of amines in the silane molecule increases (MONO < DI < TREN ∼ TRI), the silane molecule efficiency is enhanced owing to the ability to intramolecularly capture CO2. Analysis of the CO2 uptake for samples with the surface silanols removed by capping demonstrates that cooperative uptake due to amine-CO2-silanol interactions is also possible over these adsorbents and is the primary mode of sorption for the MONO material at the studied low silane loading. As the propensity for intramolecular CO2 capture increases due to the presence of multiple amines in a single silane molecule (MONO < DI < TREN ∼ TRI), the measured heat of adsorption also increases. This study of various amine-containing silanes at low coverage is the first to provide significant, direct evidence for intramolecular CO2 capture in a single silane molecule. Furthermore, it provides evidence for the relative heats of adsorption for physisorption on a silanol laden surface (ca. 37 kJ/mol), a silanol-capped surface (ca. 25 kJ/mol), via amine-CO2-silanol interactions (ca. 46 kJ/mol), and via amine-CO2

  13. Motion compensator for holographic motion picture camera

    NASA Technical Reports Server (NTRS)

    Kurtz, R. L.

    1973-01-01

    When reference beam strikes target it undergoes Doppler shift dependent upon target velocity. To compensate, object beam is first reflected from rotating cylinder that revolves in direction opposite to target but at same speed. When beam strikes target it is returned to original frequency and is in phase with reference beam. Alternatively this motion compensator may act on reference beam.

  14. Brownian motion of solitons in a Bose-Einstein condensate.

    PubMed

    Aycock, Lauren M; Hurst, Hilary M; Efimkin, Dmitry K; Genkina, Dina; Lu, Hsin-I; Galitski, Victor M; Spielman, I B

    2017-03-07

    We observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated [Formula: see text] Bose-Einstein condensates (BECs) and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one dimension (1D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton's diffusive behavior using a quasi-1D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment.

  15. Intramolecular stable isotope distributions detect plant metabolic responses on century time scales

    NASA Astrophysics Data System (ADS)

    Schleucher, Jürgen; Ehlers, Ina; Augusti, Angela; Betson, Tatiana

    2014-05-01

    Plants respond to environmental changes on a vast range of time scales, and plant gas exchanges constitute important feedback mechanisms in the global C cycle. Responses on time scales of decades to centuries are most important for climate models, for prediction of crop productivity, and for adaptation to climate change. Unfortunately, responses on these timescale are least understood. We argue that the knowledge gap on intermediate time scales is due to a lack of adequate methods that can bridge between short-term manipulative experiments (e.g. FACE) and paleo research. Manipulative experiments in plant ecophysiology give information on metabolism on time scales up to years. However, this information cannot be linked to results from retrospective studies in paleo research, because little metabolic information can be derived from paleo archives. Stable isotopes are prominent tools in plant ecophysiology, biogeochemistry and in paleo research, but in all applications to date, isotope ratios of whole molecules are measured. However, it is well established that stable isotope abundance varies among intramolecular groups of biochemical metabolites, that is each so-called "isotopomer" has a distinct abundance. This intramolecular variation carries information on metabolic regulation, which can even be traced to individual enzymes (Schleucher et al., Plant, Cell Environ 1999). Here, we apply intramolecular isotope distributions to study the metabolic response of plants to increasing atmospheric [CO2] during the past century. Greenhouse experiments show that the deuterium abundance among the two positions in the C6H2 group of photosynthetic glucose depends on [CO2] during growth. This is observed for all plants using C3 photosynthesis, and reflects the metabolic flux ratio between photorespiration and photosynthesis. Photorespiration is a major C flux that limits assimilation in C3 plants, which encompass the overwhelming fraction of terrestrial photosynthesis and the

  16. Objects in Motion

    ERIC Educational Resources Information Center

    Ashbrook, Peggy

    2008-01-01

    Objects in motion attract children. The following activity helps children explore the motion of bodies riding in a vehicle and safely demonstrates the answer to their questions, "Why do I need a seatbelt?" Children will enjoy moving the cup around, even if all they "see" is a cup rather than understanding it represents a car. They will understand…

  17. Teaching Projectile Motion

    ERIC Educational Resources Information Center

    Summers, M. K.

    1977-01-01

    Described is a novel approach to the teaching of projectile motion of sixth form level. Students are asked to use an analogue circuit to observe projectile motion and to graph the experimental results. Using knowledge of basic dynamics, students are asked to explain the shape of the curves theoretically. (Author/MA)

  18. Making Sense of Motion

    ERIC Educational Resources Information Center

    King, Kenneth

    2005-01-01

    When watching a small child with a toy car, it is seen that interest in motion comes early. Children often suggest speed through sounds such as "RRRrrrRRRooooommMMMmmmm" as the toy car is made to speed up, slow down, or accelerate through a turn. Older children start to consider force and motion studies in more detail, and experiences in school…

  19. Aristotle, Motion, and Rhetoric.

    ERIC Educational Resources Information Center

    Sutton, Jane

    Aristotle rejects a world vision of changing reality as neither useful nor beneficial to human life, and instead he reaffirms both change and eternal reality, fuses motion and rest, and ends up with "well-behaved" changes. This concept of motion is foundational to his world view, and from it emerges his theory of knowledge, philosophy of…

  20. Body Motion and Graphing.

    ERIC Educational Resources Information Center

    Nemirovsky, Ricardo; Tierney, Cornelia; Wright, Tracy

    1998-01-01

    Analyzed two children's use of a computer-based motion detector to make sense of symbolic expressions (Cartesian graphs). Found three themes: (1) tool perspectives, efforts to understand graphical responses to body motion; (2) fusion, emergent ways of talking and behaving that merge symbols and referents; and (3) graphical spaces, when changing…

  1. Naive Conceptions of Motion.

    ERIC Educational Resources Information Center

    McCloskey, Michael

    Two experiments were conducted to characterize the system of beliefs that make up the naive impetus theory of motion and to determine what effects physics instruction has on students' conceptions of motion. Thirteen college students were asked to solve several quantitative problems and were interviewed about their answers in the first experiment.…

  2. Measuring mandibular motions

    NASA Technical Reports Server (NTRS)

    Dimeff, J.; Rositano, S.; Taylor, R. C.

    1977-01-01

    Mandibular motion along three axes is measured by three motion transducers on floating yoke that rests against mandible. System includes electronics to provide variety of outputs for data display and processing. Head frame is strapped to test subject's skull to provide fixed point of reference for transducers.

  3. Object motion analysis study

    NASA Technical Reports Server (NTRS)

    1974-01-01

    The use of optical data processing (ODP) techniques for motion analysis in two-dimensional imagery was studied. The basic feasibility of this approach was demonstrated, but inconsistent performance of the photoplastic used for recording spatial filters prevented totally automatic operation. Promising solutions to the problems encountered are discussed, and it is concluded that ODP techniques could be quite useful for motion analysis.

  4. The Turbulent Diffusivity of Convective Overshoot

    NASA Astrophysics Data System (ADS)

    Lecoanet, Daniel; Schwab, Josiah; Quataert, Eliot; Bildsten, Lars; Timmes, Frank; Burns, Keaton; Vasil, Geoffrey; Oishi, Jeffrey; Brown, Benjamin

    2016-11-01

    There are many natural systems with convectively unstable fluid adjacent to stably stratified fluid; including the Earth's atmosphere, most stars, and perhaps even the Earth's liquid core. The convective motions penetrating into the stable region can enhance mixing, leading to changes in transport within the stable region. This work describes convective overshoot simulations. To study the extra mixing due to overshoot, we evolve a passive tracer field. The horizontal average of the passive tracer quickly approaches a self-similar state. The self-similar state is the solution to a diffusion equation with a spatially dependent turbulent diffusivity. We find the extra mixing due to convection can be accurately modeled as a turbulent diffusivity, and discuss implications of this turbulent diffusivity for the astrophysical problem of mixing in convectively bounded carbon flames.

  5. Self diffusion of interacting membrane proteins.

    PubMed Central

    Abney, J R; Scalettar, B A; Owicki, J C

    1989-01-01

    A two-dimensional version of the generalized Smoluchowski equation is used to analyze the time (or distance) dependent self diffusion of interacting membrane proteins in concentrated membrane systems. This equation provides a well established starting point for descriptions of the diffusion of particles that interact through both direct and hydrodynamic forces; in this initial work only the effects of direct interactions are explicitly considered. Data describing diffusion in the presence of hard-core repulsions, soft repulsions, and soft repulsions with weak attractions are presented. The effect that interactions have on the self-diffusion coefficient of a real protein molecule from mouse liver gap junctions is also calculated. The results indicate that self diffusion is always inhibited by direct interactions; this observation is interpreted in terms of the caging that will exist at finite protein concentration. It is also noted that, over small distance scales, the diffusion coefficient is determined entirely by the very strong Brownian forces; therefore, as a function of displacement the self-diffusion coefficient decays (rapidly) from its value at infinite dilution to its steady-state interaction-averaged value. The steady-state self-diffusion coefficient describes motion over distance scales that range from approximately 10 nm to cellular dimensions and is the quantity measured in fluorescence recovery after photobleaching experiments. The short-ranged behavior of the diffusion coefficient is important on the interparticle-distance scale and may therefore influence the rate at which nearest-neighbor collisional processes take place. The hard-disk theoretical results presented here are in excellent agreement with lattice Monte-Carlo results obtained by other workers. The concentration dependence of experimentally measured diffusion coefficients of antibody-hapten complexes bound to the membrane surface is consistent with that predicted by the theory. The

  6. Stochastic ground motion simulation

    USGS Publications Warehouse

    Rezaeian, Sanaz; Xiaodan, Sun; Beer, Michael; Kougioumtzoglou, Ioannis A.; Patelli, Edoardo; Siu-Kui Au, Ivan

    2014-01-01

    Strong earthquake ground motion records are fundamental in engineering applications. Ground motion time series are used in response-history dynamic analysis of structural or geotechnical systems. In such analysis, the validity of predicted responses depends on the validity of the input excitations. Ground motion records are also used to develop ground motion prediction equations(GMPEs) for intensity measures such as spectral accelerations that are used in response-spectrum dynamic analysis. Despite the thousands of available strong ground motion records, there remains a shortage of records for large-magnitude earthquakes at short distances or in specific regions, as well as records that sample specific combinations of source, path, and site characteristics.

  7. Motion sickness in migraine sufferers.

    PubMed

    Marcus, Dawn A; Furman, Joseph M; Balaban, Carey D

    2005-12-01

    Motion sickness commonly occurs after exposure to actual motion, such as car or amusement park rides, or virtual motion, such as panoramic movies. Motion sickness symptoms may be disabling, significantly limiting business, travel and leisure activities. Motion sickness occurs in approximately 50% of migraine sufferers. Understanding motion sickness in migraine patients may improve understanding of the physiology of both conditions. Recent literature suggests important relationships between the trigeminal system and vestibular nuclei that may have implications for both motion sickness and migraine. Studies demonstrating an important relationship between serotonin receptors and motion sickness susceptibility in both rodents and humans suggest possible new motion sickness prevention therapies.

  8. Mapping intracellular diffusion distribution using single quantum dot tracking: compartmentalized diffusion defined by endoplasmic reticulum.

    PubMed

    Li, Hui; Dou, Shuo-Xing; Liu, Yu-Ru; Li, Wei; Xie, Ping; Wang, Wei-Chi; Wang, Peng-Ye

    2015-01-14

    The crowded intracellular environment influences the diffusion-mediated cellular processes, such as metabolism, signaling, and transport. The hindered diffusion of macromolecules in heterogeneous cytoplasm has been studied over years, but the detailed diffusion distribution and its origin still remain unclear. Here, we introduce a novel method to map rapidly the diffusion distribution in single cells based on single-particle tracking (SPT) of quantum dots (QDs). The diffusion map reveals the heterogeneous intracellular environment and, more importantly, an unreported compartmentalization of QD diffusions in cytoplasm. Simultaneous observations of QD motion and green fluorescent protein-tagged endoplasmic reticulum (ER) dynamics provide direct evidence that the compartmentalization results from micron-scale domains defined by ER tubules, and ER cisternae form perinuclear areas that restrict QDs to enter. The same phenomenon was observed using fluorescein isothiocyanate-dextrans, further confirming the compartmentalized diffusion. These results shed new light on the diffusive movements of macromolecules in the cell, and the mapping of intracellular diffusion distribution may be used to develop strategies for nanoparticle-based drug deliveries and therapeutics.

  9. Temporally Anticorrelated Motion of Nanoparticles at a Liquid Interface.

    PubMed

    Wang, Dapeng; Hu, Renfeng; Skaug, Michael J; Schwartz, Daniel K

    2015-01-02

    Quantum dots at the hexane-glycerol interface exhibited unexpected behavior including highly dynamic adsorption/desorption, where the lateral nanoparticle motion was anomalously fast immediately after adsorption and prior to desorption. At the interface, particles exhibited pseudo-Brownian lateral motion, in which the instantaneous diffusion coefficient was temporally anticorrelated, in agreement with our simulations involving fractional Brownian motion in the surface-normal direction. These phenomena suggest that, in contrast to the conventional picture for colloidal particles, nanoparticles explore a landscape of metastable interfacial positions, with different exposures to the two adjacent phases.

  10. Chaotic Motion of Relativistic Electrons Driven by Whistler Waves

    NASA Technical Reports Server (NTRS)

    Khazanov, G. V.; Telnikhin, A. A.; Kronberg, Tatiana K.

    2007-01-01

    Canonical equations governing an electron motion in electromagnetic field of the whistler mode waves propagating along the direction of an ambient magnetic field are derived. The physical processes on which the equations of motion are based .are identified. It is shown that relativistic electrons interacting with these fields demonstrate chaotic motion, which is accompanied by the particle stochastic heating and significant pitch angle diffusion. Evolution of distribution functions is described by the Fokker-Planck-Kolmogorov equations. It is shown that the whistler mode waves could provide a viable mechanism for stochastic energization of electrons with energies up to 50 MeV in the Jovian magnetosphere.

  11. Visualizing motion in video

    NASA Astrophysics Data System (ADS)

    Brown, Lisa M.; Crayne, Susan

    2000-05-01

    In this paper, we present a visualization system and method for measuring, inspecting and analyzing motion in video. Starting from a simple motion video, the system creates a still image representation which we call a digital strobe photograph. Similar to visualization techniques used in conventional film photography to capture high-speed motion using strobe lamps or very fast shutters, and to capture time-lapse motion where the shutter is left open, this methodology creates a single image showing the motion of one or a small number of objects over time. Based on digital background subtraction, we assume that the background is stationary or at most slowing changing and that the camera position is fixed. The method is capable of displaying the motion based on a parameter indicating the time step between successive movements. It can also overcome problems of visualizing movement that is obscured by previous movements. The method is used in an educational software tool for children to measure and analyze various motions. Examples are given using simple physical objects such as balls and pendulums, astronomical events such as the path of the stars around the north pole at night, or the different types of locomotion used by snakes.

  12. Binary Mixtures of Particles with Different Diffusivities Demix.

    PubMed

    Weber, Simon N; Weber, Christoph A; Frey, Erwin

    2016-02-05

    The influence of size differences, shape, mass, and persistent motion on phase separation in binary mixtures has been intensively studied. Here we focus on the exclusive role of diffusivity differences in binary mixtures of equal-sized particles. We find an effective attraction between the less diffusive particles, which are essentially caged in the surrounding species with the higher diffusion constant. This effect leads to phase separation for systems above a critical size: A single close-packed cluster made up of the less diffusive species emerges. Experiments for testing our predictions are outlined.

  13. Motion Recognition and Modifying Motion Generation for Imitation Robot Based on Motion Knowledge Formation

    NASA Astrophysics Data System (ADS)

    Okuzawa, Yuki; Kato, Shohei; Kanoh, Masayoshi; Itoh, Hidenori

    A knowledge-based approach to imitation learning of motion generation for humanoid robots and an imitative motion generation system based on motion knowledge learning and modification are described. The system has three parts: recognizing, learning, and modifying parts. The first part recognizes an instructed motion distinguishing it from the motion knowledge database by the continuous hidden markov model. When the motion is recognized as being unfamiliar, the second part learns it using locally weighted regression and acquires a knowledge of the motion. When a robot recognizes the instructed motion as familiar or judges that its acquired knowledge is applicable to the motion generation, the third part imitates the instructed motion by modifying a learned motion. This paper reports some performance results: the motion imitation of several radio gymnastics motions.

  14. Inflation and cyclotron motion

    NASA Astrophysics Data System (ADS)

    Greensite, Jeff

    2017-01-01

    We consider, in the context of a braneworld cosmology, the motion of the Universe coupled to a four-form gauge field, with constant field strength, defined in higher dimensions. It is found, under rather general initial conditions, that in this situation there is a period of exponential inflation combined with cyclotron motion in the inflaton field space. The main effect of the cyclotron motion is that slow roll conditions on the inflaton potential, which are typically necessary for exponential inflation, can be evaded. There are Landau levels associated with the four-form gauge field, and these correspond to quantum excitations of the inflaton field satisfying unconventional dispersion relations.

  15. Generalized compliant motion primitive

    NASA Astrophysics Data System (ADS)

    Backes, Paul G.

    1994-08-01

    This invention relates to a general primitive for controlling a telerobot with a set of input parameters. The primitive includes a trajectory generator; a teleoperation sensor; a joint limit generator; a force setpoint generator; a dither function generator, which produces telerobot motion inputs in a common coordinate frame for simultaneous combination in sensor summers. Virtual return spring motion input is provided by a restoration spring subsystem. The novel features of this invention include use of a single general motion primitive at a remote site to permit the shared and supervisory control of the robot manipulator to perform tasks via a remotely transferred input parameter set.

  16. The origin of ultrafast proton transfer: Multidimensional wave packet motion vs. tunneling

    NASA Astrophysics Data System (ADS)

    Schriever, Christian; Lochbrunner, Stefan; Ofial, Armin R.; Riedle, Eberhard

    2011-02-01

    We investigate the reaction kinetics of ultrafast excited state intramolecular proton transfer (ESIPT) and discuss the possible origins of the process: tunneling of the reactive proton, vibrationally enhanced tunneling, and multidimensional wave packet dynamics of the entire system. Comparison of the measured kinetics for the protonated and the deuterated form of 2-(2‧-hydroxyphenyl)benzothiazole (HBT) to numerical simulations allows us to ascribe the characteristic 50 fs time found for the ESIPT solely to a ballistic wave packet motion along skeletal coordinates that mainly affect the donor acceptor distance. Tunneling is not found to be decisive.

  17. Diffusion of active chiral particles

    NASA Astrophysics Data System (ADS)

    Sevilla, Francisco J.

    2016-12-01

    The diffusion of chiral active Brownian particles in three-dimensional space is studied analytically, by consideration of the corresponding Fokker-Planck equation for the probability density of finding a particle at position x and moving along the direction v ̂ at time t , and numerically, by the use of Langevin dynamics simulations. The analysis is focused on the marginal probability density of finding a particle at a given location and at a given time (independently of its direction of motion), which is found from an infinite hierarchy of differential-recurrence relations for the coefficients that appear in the multipole expansion of the probability distribution, which contains the whole kinematic information. This approach allows the explicit calculation of the time dependence of the mean-squared displacement and the time dependence of the kurtosis of the marginal probability distribution, quantities from which the effective diffusion coefficient and the "shape" of the positions distribution are examined. Oscillations between two characteristic values were found in the time evolution of the kurtosis, namely, between the value that corresponds to a Gaussian and the one that corresponds to a distribution of spherical shell shape. In the case of an ensemble of particles, each one rotating around a uniformly distributed random axis, evidence is found of the so-called effect "anomalous, yet Brownian, diffusion," for which particles follow a non-Gaussian distribution for the positions yet the mean-squared displacement is a linear function of time.

  18. Self-Referenced Coherent Diffraction X-Ray Movie of Ångstrom- and Femtosecond-Scale Atomic Motion

    NASA Astrophysics Data System (ADS)

    Glownia, J. M.; Natan, A.; Cryan, J. P.; Hartsock, R.; Kozina, M.; Minitti, M. P.; Nelson, S.; Robinson, J.; Sato, T.; van Driel, T.; Welch, G.; Weninger, C.; Zhu, D.; Bucksbaum, P. H.

    2016-10-01

    Time-resolved femtosecond x-ray diffraction patterns from laser-excited molecular iodine are used to create a movie of intramolecular motion with a temporal and spatial resolution of 30 fs and 0.3 Å. This high fidelity is due to interference between the nonstationary excitation and the stationary initial charge distribution. The initial state is used as the local oscillator for heterodyne amplification of the excited charge distribution to retrieve real-space movies of atomic motion on ångstrom and femtosecond scales. This x-ray interference has not been employed to image internal motion in molecules before. Coherent vibrational motion and dispersion, dissociation, and rotational dephasing are all clearly visible in the data, thereby demonstrating the stunning sensitivity of heterodyne methods.

  19. Self-referenced coherent diffraction x-ray movie of Ångstrom- and femtosecond-scale atomic motion

    SciTech Connect

    Glownia, J. M.; Natan, A.; Cryan, J. P.; Hartsock, R.; Kozina, M.; Minitti, M. P.; Nelson, S.; Robinson, J.; Sato, T.; van Driel, T.; Welch, G.; Weninger, C.; Zhu, D.; Bucksbaum, P. H.

    2016-10-03

    Time-resolved femtosecond x-ray diffraction patterns from laser-excited molecular iodine are used to create a movie of intramolecular motion with a temporal and spatial resolution of 30 fs and 0.3 Å. This high fidelity is due to interference between the nonstationary excitation and the stationary initial charge distribution. The initial state is used as the local oscillator for heterodyne amplification of the excited charge distribution to retrieve real-space movies of atomic motion on ångstrom and femtosecond scales. This x-ray interference has not been employed to image internal motion in molecules before. In conclusion, coherent vibrational motion and dispersion, dissociation, and rotational dephasing are all clearly visible in the data, thereby demonstrating the stunning sensitivity of heterodyne methods.

  20. Self-referenced coherent diffraction x-ray movie of Ångstrom- and femtosecond-scale atomic motion

    DOE PAGES

    Glownia, J. M.; Natan, A.; Cryan, J. P.; ...

    2016-10-03

    Time-resolved femtosecond x-ray diffraction patterns from laser-excited molecular iodine are used to create a movie of intramolecular motion with a temporal and spatial resolution of 30 fs and 0.3 Å. This high fidelity is due to interference between the nonstationary excitation and the stationary initial charge distribution. The initial state is used as the local oscillator for heterodyne amplification of the excited charge distribution to retrieve real-space movies of atomic motion on ångstrom and femtosecond scales. This x-ray interference has not been employed to image internal motion in molecules before. In conclusion, coherent vibrational motion and dispersion, dissociation, and rotationalmore » dephasing are all clearly visible in the data, thereby demonstrating the stunning sensitivity of heterodyne methods.« less

  1. Inhibition of intramolecular electron transfer in ascorbate oxidase by Ag+: redox state dependent binding.

    PubMed

    Santagostini, Laura; Gullotti, Michele; Hazzard, James T; Maritano, Silvana; Tollin, Gordon; Marchesini, Augusto

    2005-02-01

    Intramolecular electron transfer within zucchini squash ascorbate oxidase is inhibited in a novel manner in the presence of an equimolar concentration of Ag(+). At pH 5.5 in acetate buffer reduction of the enzyme by laser flash photolytically generated 5-deazariboflavin semiquinone occurs at the Type I Cu with a rate constant of 5 x 10(8) M(-1)s(-1). Subsequent to this initial reduction step, equilibration of the reducing equivalent between the Type I Cu and the trinuclear Type II, III copper cluster (TNC) occurs with rate constant of 430 s(-1). The 41% of the reduced Type I Cu is oxidized by this intramolecular electron transfer reaction. When these reactions are performed in the presence of Ag(+) equimolar to dimeric AO, the bimolecular reduction of the enzyme by the 5-deazariboflavin semiquinone is not affected. As in the case of the native enzyme, intramolecular electron transfer between the Type I Cu and the TNC occurs, which continues until 25% of the reducing equivalent has been transferred. At that point, the reducing equivalent is observed to more slowly return to the Type I Cu, resulting a second reduction phase whose rate constant (100 s(-1)) is protein and Ag(+) concentration independent. The data suggest that partial reduction of the TNC results in Ag(+) binding to the enzyme which causes the apparent midpoint potential of the TNC as a whole to decrease thereby reversing the direction of electron flow. These results are consistent with the inhibitory effect of Ag(+) on the steady-state activity of ascorbate oxidase [S. Maritano, E. Malusa, A. Marchesini, presented at The Meeting on Metalloproteins, SERC Daresbury Laboratory, Warrington, England, 1992; A. Marchesini, XIX Convegno Nazionale SICA, Italian Society of Agricultural Chemistry, Reggio Calabria, Italy, September 2001.].

  2. Intramolecular quadruplex conformation of human telomeric DNA assessed with 125I-radioprobing

    PubMed Central

    He, Yujian; Neumann, Ronald D.; Panyutin, Igor G.

    2004-01-01

    A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG)3, antiparallel and parallel, have been solved by NMR and X-ray crystallography. In both structures, the telomeric sequence adopts an intramolecular quadruplex structure that is stabilized by G-4 quartets, but the ways in which the sequence folds into the quadruplex are different. The folds of the human telomeric DNA were described as an anti-parallel basket-type and a parallel propeller-type. We applied 125I-radioprobing to determine the conformation of the telomeric quadruplex in solution, in the presence of either Na+ or K+ ions. The probability of DNA breaks caused by decay of 125I is inversely related to the distance between the radionuclide and the sugar unit of the DNA backbone; hence, the conformation of the DNA backbone can be deduced from the distribution of breaks. The probability of breaks measured in the presence of Na+ and K+ were compared with the distances in basket-type and propeller-type quadruplexes obtained from the NMR and crystal structures. Our radioprobing data demonstrate that the antiparallel conformation was present in solution in the presence of both K+ and Na+. The preferable conformation in the Na+-containing solution was the basket-type antiparallel quadruplex whereas the presence of K+ favored the chair-type antiparallel quadruplex. Thus, we believe that the two antiparallel and the parallel conformations may coexist in solution, and that their relative proportion is determined by the type and concentration of ions. PMID:15475390

  3. Vapor-liquid equilibria for copolymer+solvent systems: Effect of intramolecular repulsion

    SciTech Connect

    Gupta, R.B.; Prausnitz, J.M.

    1995-03-01

    Role of intramolecular interactions in blend miscibility is well documented for polymer+copolymer mixtures. Some copolymer+polymer mixtures are miscible although their corresponding homopolymers are not miscible; for example, over a range of acrylonitrile content, styrene/acrylonitrile copolymers are miscible with poly(methyl methacrylate) but neither polystyrene nor polyacrylonitrile is miscible with poly(methyl methacrylate). Similarly, over a composition range, butadiene/acrylonitrile copolymers are miscible with poly(vinyl chloride) while none of the binary combinations of the homopolymers [polybutadiene, polyacrylonitrile, and poly(vinyl chloride)] are miscible. This behavior has been attributed to ``intramolecular repulsion`` between unlike copolymer segments. We have observed similar behavior in vapor-liquid equilibria (VLE) of copolymer+solvent systems. We find that acrylonitrile/butadiene copolymers have higher affinity for acetonitrile solvent than do polyacrylonitrile or polybutadiene. We attribute this non-intuitive behavior to ``intramolecular repulsion`` between unlike segments of the copolymer. This repulsive interaction is weakened when acetonitrile molecules are in the vicinity of unlike copolymer segments, favoring copolymer+solvent miscibility. We find similar behavior when acetonitrile is replaced by methyl ethyl ketone. To best knowledge, this effect has not been reported previously for VLE. We have obtained VLE data for mixtures containing a solvent and a copolymer as a function of copolymer composition. It appears that, at a given solvent partial pressure, there may be copolymer composition that yields maximum absorption of the solvent. This highly non-ideal VLE phase behavior may be useful for optimum design of a membrane for a separation process.

  4. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    SciTech Connect

    Niu, B.

    1992-09-01

    High resolution He I[alpha] photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a soft'' mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  5. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    SciTech Connect

    Niu, B.

    1992-09-01

    High resolution He I{alpha} photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a ``soft`` mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  6. Projectile Motion with Mathematica.

    ERIC Educational Resources Information Center

    de Alwis, Tilak

    2000-01-01

    Describes how to use the computer algebra system (CAS) Mathematica to analyze projectile motion with and without air resistance. These experiments result in several conjectures leading to theorems. (Contains 17 references.) (Author/ASK)

  7. Projectile Motion Details.

    ERIC Educational Resources Information Center

    Schnick, Jeffrey W.

    1994-01-01

    Presents an exercise that attempts to correct for the common discrepancies between theoretical and experimental predictions concerning projectile motion using a spring-loaded projectile ball launcher. Includes common correction factors for student use. (MVL)

  8. Toying with Motion.

    ERIC Educational Resources Information Center

    Galus, Pamela J.

    2002-01-01

    Presents a variety of activities that support the development of an understanding of Newton's laws of motion. Activities use toy cars, mobile roads, and a seat-of-nails. Includes a scoring rubric. (DDR)

  9. Vision and Motion Pictures.

    ERIC Educational Resources Information Center

    Grambo, Gregory

    1998-01-01

    Presents activities on persistence of vision that involve students in a hands-on approach to the study of early methods of creating motion pictures. Students construct flip books, a Zoetrope, and an early movie machine. (DDR)

  10. Motion Sickness: First Aid

    MedlinePlus

    ... soon as the motion stops. The more you travel, the more easily you'll adjust to being ... at least 30 to 60 minutes before you travel. Expect drowsiness as a side effect. Consider scopolamine ( ...

  11. A Projectile Motion Bullseye.

    ERIC Educational Resources Information Center

    Lamb, William G.

    1985-01-01

    Explains a projectile motion experiment involving a bow and arrow. Procedures to measure "muzzle" velocity, bow elastic potential energy, range, flight time, wind resistance, and masses are considered. (DH)

  12. Motion Alters Color Appearance

    PubMed Central

    Hong, Sang-Wook; Kang, Min-Suk

    2016-01-01

    Chromatic induction compellingly demonstrates that chromatic context as well as spectral lights reflected from an object determines its color appearance. Here, we show that when one colored object moves around an identical stationary object, the perceived saturation of the stationary object decreases dramatically whereas the saturation of the moving object increases. These color appearance shifts in the opposite directions suggest that normalization induced by the object’s motion may mediate the shift in color appearance. We ruled out other plausible alternatives such as local adaptation, attention, and transient neural responses that could explain the color shift without assuming interaction between color and motion processing. These results demonstrate that the motion of an object affects both its own color appearance and the color appearance of a nearby object, suggesting a tight coupling between color and motion processing. PMID:27824098

  13. Explanations of Superluminal Motion

    NASA Astrophysics Data System (ADS)

    Scheuer, P. A. G.

    Recent developments in models of core-jet sources with apparent superluminal motions are reviewed. Emphasis is given to new versions of the so-called "Christmas tree" model and the relativistic beaming model.

  14. Intrinsic and extrinsic measurement for Brownian motion

    NASA Astrophysics Data System (ADS)

    Castro-Villarreal, Pavel

    2014-05-01

    Based upon the Smoluchowski equation on curved manifolds, three physical observables are considered for Brownian displacement, namely geodesic displacement s, Euclidean displacement δR, and projected displacement δR⊥. The Weingarten-Gauss equations are used to calculate the mean-square Euclidean displacements in the short-time regime. Our findings show that from an extrinsic point of view the geometry of the space affects the Brownian motion in such a way that the particle’s diffusion is decelerated, contrasting with the intrinsic point of view where dynamics is controlled by the sign of the Gaussian curvature (Castro-Villarreal, 2010 J. Stat. Mech. P08006). Furthermore, it is possible to give exact formulas for <δR> and <δR2> on spheres and minimal surfaces, which are valid for all values of time. In the latter case, surprisingly, Brownian motion corresponds to the usual diffusion in flat geometries, albeit minimal surfaces have non-zero Gaussian curvature. Finally, the two-dimensional case is emphasized due to its close relation to surface self-diffusion in fluid membranes.

  15. Synthesis of anionic phosphorus-containing heterocycles by intramolecular cyclizations involving N-functionalized phosphinecarboxamides.

    PubMed

    Robinson, Thomas P; Goicoechea, Jose M

    2015-04-07

    We report that the 2-phosphaethynolate anion (PCO(-)) reacts with propargylamines in the presence of a proton source to afford novel N-derivatized phosphinecarboxamides bearing alkyne functionalities. Deprotonation of these species gives rise to novel five- and six-membered anionic heterocycles resulting from intramolecular nucleophilic attack of the resulting phosphide at the alkyne functionality (via 5-exo-dig or 6-endo-dig cyclizations, respectively). The nature of the substituents on the phosphinecarboxamide can be used to influence the outcome of these reactions. This strategy represents a unique approach to phosphorus-containing heterocylic systems that are closely related to known organic molecules with interesting bio-active properties.

  16. Intramolecular interactions in ortho-methoxyalkylphenylboronic acids and their catechol esters

    NASA Astrophysics Data System (ADS)

    Adamczyk-Woźniak, Agnieszka; Borys, Krzysztof M.; Czerwińska, Karolina; Gierczyk, Błażej; Jakubczyk, Michał; Madura, Izabela D.; Sporzyński, Andrzej; Tomecka, Ewelina

    2013-12-01

    Catechol esters of ortho-methoxyalkylphenylboronic acids have been synthesized and characterized by 17O NMR spectroscopy. The results were compared with the data for the parent acids. The influence of intramolecular and intermolecular hydrogen bonds on the properties of the boronic acids has been discussed. The 17O NMR data for the boronic esters proved that there are no O → B interactions in the investigated compounds. This fact is connected with weak Lewis acidity of the parent acids and their low sugars' receptors activity. Crystal structure of ortho-methoxyphenylboronic acid catechol ester was determined.

  17. Diastereoselective syntheses of substituted cis-hydrindanones featuring sequential inter- and intramolecular Michael reactions.

    PubMed

    Liu, Junjia; Marsini, Maurice A; Bedell, T Aaron; Reider, Paul J; Sorensen, Erik J

    2016-06-30

    The hydrindane (bicyclo[4.3.0]nonane) structural motif (1) and related cis-1-hydrindanone skeleton (2) are common substructures in many natural products. Herein, we describe efficient access to substituted cis-1-hydrindanones enabled by a sequence of Michael reactions. A copper-catalyzed intermolecular Michael addition of a cyclic silyl ketene acetal to a β-substituted-α-alkoxycarbonyl-cyclopentenone enables construction of a quaternary center and is followed, after incorporation of an additional Michael acceptor, by a second, intramolecular addition of a nucleophilic β-ketoester. This strategy affords stereoselective access to substituted bicyclic cis-hydrindanone ring systems containing up to three contiguous stereocenters.

  18. GTP binding to the ROC domain of DAP-kinase regulates its function through intramolecular signalling.

    PubMed

    Carlessi, Rodrigo; Levin-Salomon, Vered; Ciprut, Sara; Bialik, Shani; Berissi, Hanna; Albeck, Shira; Peleg, Yoav; Kimchi, Adi

    2011-09-01

    Death-associated protein kinase (DAPk) was recently suggested by sequence homology to be a member of the ROCO family of proteins. Here, we show that DAPk has a functional ROC (Ras of complex proteins) domain that mediates homo-oligomerization and GTP binding through a defined P-loop motif. Upon binding to GTP, the ROC domain negatively regulates the catalytic activity of DAPk and its cellular effects. Mechanistically, GTP binding enhances an inhibitory autophosphorylation at a distal site that suppresses kinase activity. This study presents a new mechanism of intramolecular signal transduction, by which GTP binding operates in cis to affect the catalytic activity of a distal domain in the protein.

  19. Molecular orbital assistance in the design of intramolecular and photoinduced electron transfer systems

    NASA Astrophysics Data System (ADS)

    Petsalakis, Ioannis D.; Theodorakopoulos, Giannoula

    2012-02-01

    A theoretical approach is described for the design of donor-acceptor intramolecular charge transfer (ICT) systems and for photoinduced electron transfer (PET) hybrids of fullerene, based on orbital level diagrams of the separate donor and acceptor moieties. Minimization of the HOMO-LUMO (highest occupied-lowest unoccupied orbital) gap in ICT systems, translates to a requirement for near degeneracy of the HOMO of the donor and LUMO of the acceptor, determined separately for the two moieties by density functional theory calculations. Similarly, near degeneracy of the LUMO of the donor and LUMO of the acceptor moieties would indicate the possibility of PET in the combined hybrid.

  20. Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform.

    PubMed

    Nagymihály, Zoltán; Caturello, Naidel A M S; Takátsy, Anikó; Aragay, Gemma; Kollár, László; Albuquerque, Rodrigo Q; Csók, Zsolt

    2017-01-06

    Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by (1)H or (13)C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

  1. Path-integral calculation of the second virial coefficient including intramolecular flexibility effects

    NASA Astrophysics Data System (ADS)

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H.

    2014-07-01

    We present a path-integral Monte Carlo procedure for the fully quantum calculation of the second molecular virial coefficient accounting for intramolecular flexibility. This method is applied to molecular hydrogen (H2) and deuterium (D2) in the temperature range 15-2000 K, showing that the effect of molecular flexibility is not negligible. Our results are in good agreement with experimental data, as well as with virials given by recent empirical equations of state, although some discrepancies are observed for H2 between 100 and 200 K.

  2. Path-integral calculation of the second virial coefficient including intramolecular flexibility effects.

    PubMed

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H

    2014-07-28

    We present a path-integral Monte Carlo procedure for the fully quantum calculation of the second molecular virial coefficient accounting for intramolecular flexibility. This method is applied to molecular hydrogen (H2) and deuterium (D2) in the temperature range 15-2000 K, showing that the effect of molecular flexibility is not negligible. Our results are in good agreement with experimental data, as well as with virials given by recent empirical equations of state, although some discrepancies are observed for H2 between 100 and 200 K.

  3. Stereocontrolled synthesis of rosuvastatin calcium via iodine chloride-induced intramolecular cyclization.

    PubMed

    Xiong, Fangjun; Wang, Haifeng; Yan, Lingjie; Han, Sheng; Tao, Yuan; Wu, Yan; Chen, Fener

    2016-01-28

    A novel, stereoselective approach towards rosuvastatin calcium from the known (S)-homoallylic alcohol has been developed. The synthesis is highlighted by a regio- and stereocontrolled ICl-induced intramolecular cyclization of chiral homoallylic carbonate to deliver the C6-formyl statin side chain with a syn-1,3-diol moiety. An improved synthesis of the rosuvastatin pyrimidine core moiety is also included. Moreover, this methodology is useful in the asymmetric synthesis of structural variants of statins such as pitavastatin calcium and atorvastatin calcium and their related analogs.

  4. Construction of a Chiral Silicon Center by Rhodium-Catalyzed Enantioselective Intramolecular Hydrosilylation.

    PubMed

    Naganawa, Yuki; Namba, Tomoya; Kawagishi, Mayu; Nishiyama, Hisao

    2015-06-22

    Rhodium-catalyzed enantioselective desymmetrizing intramolecular hydrosilylation of symmetrically disubstituted hydrosilanes is described. The original axially chiral phenanthroline ligand (S)-BinThro (Binol-derived phenanthroline) was found to work as an effective chiral catalyst for this transformation. A chiral silicon stereogenic center is one of the chiral motifs gaining much attention in asymmetric syntheses and the present protocol provides cyclic five-membered organosilanes incorporating chiral silicon centers with high enantioselectivities (up to 91 % ee). The putative active Rh(I) catalyst takes the form of an N,N,O-tridentate coordination complex, as determined by several complementary experiments.

  5. Solvent-tuned intramolecular charge-recombination rates in a conjugated donor-acceptor molecule

    NASA Technical Reports Server (NTRS)

    Khundkar, Lutfur R.; Stiegman, A. E.; Perry, Joseph W.

    1990-01-01

    The nonradiative charge-recombination rates from the charge-transfer state of a new conjugated donor-acceptor molecule (p-cyano-p-prime-methylthiodiphenylacetylene) can be tuned over almost an order of magnitude by varying the polarity of the solvent. These measurements of intramolecular recombination show a turnover of rates as a function of emission energy, consistent with the 'normal' and 'inverted' behavior of Marcus theory. Steady-state spectra and time-resolved measurements make it possible to quantitatively compare thermal and optical electron-transfer rates as a function of driving force and demonstrate their correspondence.

  6. Stereoselection in Intramolecular Diels-Alder Reactions of 2-Cyano-1-azadienes: Indolizidine and Quinolizidine Synthesis.

    PubMed

    Tay, Gidget C; Sizemore, Nicholas; Rychnovsky, Scott D

    2016-07-01

    Progress toward understanding the scope and diastereoselectivity of intramolecular Diels-Alder reactions using 2-cyano-1-azadienes is described herein. The resulting cyanoenamine products are underutilized intermediates in organic synthesis. Assembly of the Diels-Alder precursors was achieved using an improved imine condensation/oxidative cyanation protocol. By this method, several highly substituted indolizidine and quinolizidine architectures were constructed. Quantum mechanical DFT calculations at the B3LYP/6-31+G(d) level of theory were performed for these cyclizations and provide insights into the origins of the observed diastereoselectivities.

  7. Path-integral calculation of the second virial coefficient including intramolecular flexibility effects

    SciTech Connect

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H.

    2014-07-28

    We present a path-integral Monte Carlo procedure for the fully quantum calculation of the second molecular virial coefficient accounting for intramolecular flexibility. This method is applied to molecular hydrogen (H{sub 2}) and deuterium (D{sub 2}) in the temperature range 15–2000 K, showing that the effect of molecular flexibility is not negligible. Our results are in good agreement with experimental data, as well as with virials given by recent empirical equations of state, although some discrepancies are observed for H{sub 2} between 100 and 200 K.

  8. Enantioselective Organocatalytic Construction of Spiroindane Derivatives by Intramolecular Friedel-Crafts-Type 1,4-Addition.

    PubMed

    Yoshida, Keisuke; Itatsu, Yukihiro; Fujino, Yuta; Inoue, Hiroki; Takao, Ken-Ichi

    2016-06-01

    The highly enantioselective organocatalytic construction of spiroindanes containing an all-carbon quaternary stereocenter by intramolecular Friedel-Crafts-type 1,4-addition is described. The reaction was catalyzed by a cinchonidine-based primary amine and accelerated by water and p-bromophenol. A variety of spiro compounds containing quaternary stereocenters were obtained with excellent enantioselectivity (up to 95 % ee). The reaction was applied to the asymmetric formal synthesis of the spirocyclic natural products (-)-cannabispirenones A and B.

  9. Photoinduced intramolecular charge transfer process of betaine pyridinium: A theoretical spectroscopic study

    NASA Astrophysics Data System (ADS)

    Perrier, Aurélie; Aloïse, Stéphane; Pawlowska, Zuzanna; Sliwa, Michel; Maurel, François; Abe, Jiro

    2011-10-01

    Using Time-Dependent Density Functional Theory and taking into account bulk solvent effects, we investigate the absorption and emission spectra of a betaine pyridinium molecule, the 2-(1-pyridinio) benzimidazolate (SBPa). This molecule exhibits strong photoinduced intramolecular charge transfer (ICT). We have identified two different electronic states involved, respectively, in the strong bathochromic ICT absorption band (S 2) and in the moderate emission band (S 1). The ICT process is analyzed in terms of charge distribution and dipole moment evolutions upon photoexcitation. These results are compared with steady-state spectroscopic measurements.

  10. Gold(I)-catalyzed intramolecular amination of allylic alcohols with alkylamines.

    PubMed

    Mukherjee, Paramita; Widenhoefer, Ross A

    2011-03-18

    A 1:1 mixture of (1)AuCl [1 = P(t-Bu)(2)o-biphenyl] and AgSbF(6) catalyzes the intramolecular amination of allylic alcohols with alkylamines to form substituted pyrrolidine and piperidine derivatives. Gold(I)-catalyzed cyclization of (R,Z)-8-(N-benzylamino)-3-octen-2-ol (96% ee, 95% de) led to isolation of (R,E)-1-benzyl-2-(1-propenyl)piperidine in 99% yield with 96% ee, consistent with the net syn addition of the amine relative to the departing hydroxyl group.

  11. Time-dependent Hartree approaches for the study of intramolecular dynamics in dimer systems

    NASA Astrophysics Data System (ADS)

    Roy, Pierre-Nicholas; Light, John C.

    2000-06-01

    We apply and the time-dependent Hartree (TDH) method to the study of intramolecular dynamics in dimer systems. The HCl dimer is chosen as test case. Model calculations are performed on reduced dimensional representation of this system namely two-, three-, and four-dimensional ones. We assess the validity of different implementations of the TDH method including the account of direct correlations between coordinate pairs, and mixed quantum-classical and quantum-Gaussian wave packets treatments. The latter yields very good results compared to the fully quantal treatment.

  12. Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors.

    PubMed

    Nguyen, Thanh Ha; Hibbs, David E; Howard, Siân T

    2005-09-01

    The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.

  13. Assessment of Nanosecond Time Scale Motions in Native and Non-Native States of Ubiquitin.

    PubMed

    Morozova, Olga B; Yurkovskaya, Alexandra V

    2015-10-01

    The paramagnetic relaxation times of the aromatic and β protons of Tyr59 and His68 residues of the native ubiquitin and of Tyr59 residue of the non-native ubiquitin were determined from an analysis of chemically induced dynamic nuclear polarization (CIDNP) kinetics obtained during the photoreaction of the protein and 2,2'-dipyridyl excited in the triplet state. Using the paramagnetic relaxation times determined earlier for the radicals of free amino acids as an internal standard and assuming that the hyperfine interaction (HFI) anisotropy is very similar for the radicals of free amino acids and the corresponding radicals of amino acid residues in the proteins, we determined parameters that characterize the intramolecular mobility of different protons in native and two non-native states of ubiquitin. The latter are denatured at pH 2 and 57 °C, and the A-state at pH 2 in a 60%/40% methanol/water mixture. The determination of the two parameters of intramolecular mobility (i.e., the correlation time of internal motion, τ(e), and the order parameter, S(2)) was only possible by analyzing paramagnetic relaxation data obtained at two magnetic fields (4.7 and 9.4 T) using nuclear magnetic resonance (NMR) spectrometry. Intramolecular correlation times fall into the submicrosecond-microsecond time scale. Longer correlation times and higher order parameters were found for the less accessible Tyr59 residue than for the His68 residue, as well as for the more buried β protons than for the aromatic protons for both of the protein residues in the native state. For Tyr59, intramolecular mobility increases following the loss of the tertiary structure of ubiquitin. These findings strongly support the reliability of the obtained data.

  14. Diffusion of water in nano-porous polyamide membranes: Quasielastic neutron scattering study

    NASA Astrophysics Data System (ADS)

    Sharma, V. K.; Mitra, S.; Singh, P.; Jurányi, F.; Mukhopadhyay, R.

    2010-10-01

    Dynamics of water sorbed in a reverse osmosis polyamide membrane (ROPM) as studied by quasielastic neutron scattering (QENS) is reported here. The trimesoylchloride-m-phenylene diamine based ROPM is synthesized by interfacial polymerization technique. QENS data indicates that translational motion of water confined in ROPM gets modified compared to bulk water whereas rotational motion remains unaltered. Translational motion of water in ROPM is found to follow random jump diffusion with lower diffusivity compared to bulk water. Translational diffusivity does not show the Arrhenius behaviour.

  15. Microfabricated diffusion source

    DOEpatents

    Oborny, Michael C.; Frye-Mason, Gregory C.; Manginell, Ronald P.

    2008-07-15

    A microfabricated diffusion source to provide for a controlled diffusion rate of a vapor comprises a porous reservoir formed in a substrate that can be filled with a liquid, a headspace cavity for evaporation of the vapor therein, a diffusion channel to provide a controlled diffusion of the vapor, and an outlet to release the vapor into a gas stream. The microfabricated diffusion source can provide a calibration standard for a microanalytical system. The microanalytical system with an integral diffusion source can be fabricated with microelectromechanical systems technologies.

  16. PROMOTIONS: PROper MOTION Software

    NASA Astrophysics Data System (ADS)

    Caleb Wherry, John; Sahai, R.

    2009-05-01

    We report on the development of a software tool (PROMOTIONS) to streamline the process of measuring proper motions of material in expanding nebulae. Our tool makes use of IDL's widget programming capabilities to design a unique GUI that is used to compare images of the objects from two epochs. The software allows us to first orient and register the images to a common frame of reference and pixel scale, using field stars in each of the images. We then cross-correlate specific morphological features in order to determine their proper motions, which consist of the proper motion of the nebula as a whole (PM-neb), and expansion motions of the features relative to the center. If the central star is not visible (quite common in bipolar nebulae with dense dusty waists), point-symmetric expansion is assumed and we use the average motion of high-quality symmetric pairs of features on opposite sides of the nebular center to compute PM-neb. This is then subtracted out to determine the individual movements of these and additional features relative to the nebular center. PROMOTIONS should find wide applicability in measuring proper motions in astrophysical objects such as the expanding outflows/jets commonly seen around young and dying stars. We present first results from using PROMOTIONS to successfully measure proper motions in several pre-planetary nebulae (transition objects between the red giant and planetary nebula phases), using images taken 7-10 years apart with the WFPC2 and ACS instruments on board HST. The authors are grateful to NASA's Undergradute Scholars Research Program (USRP) for supporting this research.

  17. A multiscale guide to Brownian motion

    NASA Astrophysics Data System (ADS)

    Grebenkov, Denis S.; Belyaev, Dmitry; Jones, Peter W.

    2016-01-01

    We revise the Lévy construction of Brownian motion as a simple though rigorous approach to operate with various Gaussian processes. A Brownian path is explicitly constructed as a linear combination of wavelet-based ‘geometrical features’ at multiple length scales with random weights. Such a wavelet representation gives a closed formula mapping of the unit interval onto the functional space of Brownian paths. This formula elucidates many classical results about Brownian motion (e.g., non-differentiability of its path), providing an intuitive feeling for non-mathematicians. The illustrative character of the wavelet representation, along with the simple structure of the underlying probability space, is different from the usual presentation of most classical textbooks. Similar concepts are discussed for the Brownian bridge, fractional Brownian motion, the Ornstein-Uhlenbeck process, Gaussian free fields, and fractional Gaussian fields. Wavelet representations and dyadic decompositions form the basis of many highly efficient numerical methods to simulate Gaussian processes and fields, including Brownian motion and other diffusive processes in confining domains.

  18. Broadband boundary effects on Brownian motion

    NASA Astrophysics Data System (ADS)

    Mo, Jianyong; Simha, Akarsh; Raizen, Mark G.

    2015-12-01

    Brownian motion of particles in confined fluids is important for many applications, yet the effects of the boundary over a wide range of time scales are still not well understood. We report high-bandwidth, comprehensive measurements of Brownian motion of an optically trapped micrometer-sized silica sphere in water near an approximately flat wall. At short distances we observe anisotropic Brownian motion with respect to the wall. We find that surface confinement not only occurs in the long time scale diffusive regime but also in the short time scale ballistic regime, and the velocity autocorrelation function of the Brownian particle decays faster than that of a particle in bulk fluid. Furthermore, at low frequencies the thermal force loses its color due to the reflected flow from the no-slip boundary. The power spectrum of the thermal force on the particle near a no-slip boundary becomes flat at low frequencies. This detailed understanding of boundary effects on Brownian motion opens a door to developing a 3D microscope using particles as remote sensors.

  19. Synthesis of triazafluoranthenones via silver(I)-mediated nonoxidative and oxidative intramolecular palladium-catalyzed cyclizations.

    PubMed

    Koutentis, Panayiotis A; Loizou, Georgia; Lo Re, Daniele

    2011-07-15

    Silver(I) fluoride (AgF)-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 1,3-diphenyl- and 8-iodo-1,3-diphenylbenzo[e][1,2,4]triazin-7(1H)-ones 6a (R = H) and 7a (R = I) afford a new 'alkaloid like' ring system 2-phenyl-6H-[1,2,4]triazino[5,6,1-jk]carbazol-6-one 8a (triazafluoranthenone) in 86 and 100% yields, respectively. Furthermore, these cyclization protocols were used to prepare triazafluoranthenone analogues 8b-e bearing dialkylamino, methoxy, and phenylsulfanyl substituents at C-5, which were also independently synthesized from triazafluoranthenone 8a by regioselective nucleophilic addition. Similar AgF-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 8,10-dihydro-1-iodo-10-phenylphenazin-2(7H)-ones 13 gave the new 'alkaloid like' ring system 8H-indolo[1,2,3-mn]phenazin-8-one 14 in 80 and 18% yields, respectively.

  20. Demonstration of intramolecular energy transfer in asymmetric bimetallic ruthenium(ii) complexes.

    PubMed

    Bar, Manoranjan; Maity, Dinesh; Das, Shyamal; Baitalik, Sujoy

    2016-11-01

    A new family of bimetallic Ru(ii) complexes derived from an asymmetric bridging ligand (tpy-Hbzim-dipy) consisting of both bipyridine and terpyridine chelating sites covalently connected via phenyl-imidazole spacer were designed in this work to demonstrate intramolecular energy transfer from one component to the other in asymmetric dyads. To fine tune the photo-redox properties, both bidentate and tridentate terminal ligands in the complexes were varied systematically. Both steady state and time-resolved luminescence spectral results indicated photo-induced intramolecular energy transfer from the excited MLCT state of the [(bpy/phen)2Ru(II)(dipy-Hbzim-tpy)] component to the MLCT state of the tpy-containing unit [(dipy-Hbzim-tpy)Ru(II)(tpy-PhCH3/H2pbbzim)] in dyads with rate constant values on the order of 10(6)-10(7) s(-1). Temperature-dependent luminescence studies indicated an enhancement in the luminescence intensity and excited state lifetimes upon decreasing the temperature.

  1. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

    PubMed Central

    Seddiqzai, Meriam; Dahmen, Tobias; Sure, Rebecca

    2013-01-01

    Summary The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol−1 and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG ‡ and ΔG R) are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically. PMID:24062821

  2. Probing intramolecular interactions in arylselenides using a property descriptor based approach.

    PubMed

    Roy, Dipankar; Patel, Chandan; Liebman, Joel F; Sunoj, Raghavan B

    2008-09-18

    Although a large volume of experimental evidence is available on the existence of intramolecular nonbonding interactions between chalcogen atoms in main group organometallic compounds, the primary focus has been on the contact distances involving the chalcogen atoms. The important class of intramolecular Se...X (where X is O, S, N) nonbonding interaction in a series of organoselenium compounds is quantified using a new scheme based on a molecular property descriptor. In the present study, we have employed the nucleus-independent chemical shift [NICS(0)] values, as a property descriptor to evaluate the strength of exocyclic nonbonding interactions in a series of aryl selenides. The ab initio MP2 as well as density functional theory methods have been used in conjunction with Dunning's cc-pVDZ basis set. The quantified values of Se...X nonbonding interactions are compared with other schemes based on thermochemical equations such as homodesmic and ortho-para methods. The changes in NICS(0) values at the aryl ring center are found to be sensitive to the strength of exocyclic Se...X interaction.

  3. ALG-2 activates the MVB sorting function of ALIX through relieving its intramolecular interaction.

    PubMed

    Sun, Sheng; Zhou, Xi; Corvera, Joe; Gallick, Gary E; Lin, Sue-Hwa; Kuang, Jian

    2015-01-01

    The modular adaptor protein ALIX is critically involved in endosomal sorting complexes required for transport (ESCRT)-mediated multivesicular body (MVB) sorting of activated epidermal growth factor receptor (EGFR); however, ALIX contains a default intramolecular interaction that renders ALIX unable to perform this ESCRT function. The ALIX partner protein ALG-2 is a calcium-binding protein that belongs to the calmodulin superfamily. Prompted by a defined biological function of calmodulin, we determined the role of ALG-2 in regulating ALIX involvement in MVB sorting of activated EGFR. Our results show that calcium-dependent ALG-2 interaction with ALIX completely relieves the intramolecular interaction of ALIX and promotes CHMP4-dependent ALIX association with the membrane. EGFR activation induces increased ALG-2 interaction with ALIX, and this increased interaction is responsible for increased ALIX association with the membrane. Functionally, inhibition of ALIX activation by ALG-2 inhibits MVB sorting of activated EGFR as effectively as inhibition of ALIX interaction with CHMP4 does; however, inhibition of ALIX activation by ALG-2 does not affect cytokinetic abscission or equine infectious anemia virus (EIAV) budding. These findings indicate that calcium-dependent ALG-2 interaction with ALIX is specifically responsible for generating functional ALIX that supports MVB sorting of ubiquitinated membrane receptors.

  4. Rate of intramolecular reduction of oxyferryl iron in horse heart myoglobin

    SciTech Connect

    Fenwick, C.; Marmor, S.; Govindaraju, K.; English, A.M. ); Wishart, J.F.; Sun, J. )

    1994-04-06

    Like heme peroxidases and other heme enzymes, myoglobin forms oxyferryl (Fe[sup IV][triple bond]O) on reaction with peroxides. We have recently observed slow intramolecular electron transfer (ET) to the oxyferryl heme of cytochrome c peroxidase (CCP) from a[sub 5]Ru[sup II] (a[sub 5]Ru = pentaammineruthenium) bound at His60 and proposed a large reorganizational energy ([lambda]) for oxyferryl heme. An obvious test of this large postulated [lambda] is to directly compare intramolecular ET rates between oxyferryl and a[sub 5]Ru centers in myoglobin with the corresponding rates in zinc-substituted sperm whale (SWMb) and recombinant human myoglobins (RHMb). Since the oxyferryl heme of horse heart myoglobin (HHMb) is significantly more stable than that of SWMb, the former protein was chosen for this study. A a[sub 5]Ru group was attached to the surface His48 of HHMb, and rates of ET over the 12.7-angstrom distance between the a[sub 5]Ru center and the ferric and oxyferryl hemes were measured by pulse radiolysis at Brookhaven National Laboratory. HHMb (0.5-10 [mu]M) solutions were prepared in N[sub 2]O-saturated sodium phosphate buffer at pH 7.0 (40 mM) containing 12 mM HCOONa to generate CO[sub 2][sup .[minus

  5. Growth factor control of epidermal growth factor receptor kinase activity via an intramolecular mechanism.

    PubMed

    Koland, J G; Cerione, R A

    1988-02-15

    The mechanism by which the protein kinase activity of the epidermal growth factor (EGF) receptor is activated by binding of growth factor was investigated. Detergent-solubilized receptor in monomeric form was isolated by sucrose density gradient centrifugation and both its kinase and autophosphorylation activities monitored. In a low ionic strength medium and with MnCl2 as an activator, the activity of the monomeric receptor was EGF-independent. However, with 0.25 M ammonium sulfate present, the MnCl2-stimulated kinase activity was strikingly EGF-dependent. In contrast, the kinase activity expressed in the presence of MgCl2 showed growth factor control in the absence of added salt. Under the conditions of these experiments there was apparently little tendency for growth factor to induce aggregation of the receptor, indicating that the allosteric activation of the receptor kinase by EGF occurred via an intramolecular mechanism. Whereas detergent-solubilized receptor was the subject of these studies, the kinase activity of cell surface receptors might also be controlled by an intramolecular mechanism. These results indicate that an individual receptor molecule has the potential to function as a transmembrane signal transducer.

  6. Structural and biochemical characterizations of an intramolecular tandem coiled coil protein.

    PubMed

    Shin, Donghyuk; Kim, Gwanho; Kim, Gyuhee; Zheng, Xu; Kim, Yang-Gyun; Lee, Sangho

    2014-12-12

    Coiled coil has served as an excellent model system for studying protein folding and developing protein-based biomaterials. Most designed coiled coils function as oligomers, namely intermolecular coiled coils. However, less is known about structural and biochemical behavior of intramolecular coiled coils where coiled coil domains are covalently linked in one polypeptide. Here we prepare a protein which harbors three coiled coil domains with two short linkers, termed intramolecular tandem coiled coil (ITCC) and characterize its structural and biochemical behavior in solution. ITCC consists of three coiled coil domains whose sequences are derived from Coil-Ser and its domain swapped dimer. Modifications include positioning E (Glu) residue at "e" and K (Lys) at "g" positions throughout heptad repeats to enhance ionic interaction among its constituent coiled coil domains. Molecular modeling of ITCC suggests a compact triple helical bundle structure with the second and the third coiled coil domains forming a canonical coiled coil. ITCC exists as a mixture of monomeric and dimeric species in solution. Small-angle X-ray scattering reveals ellipsoidal molecular envelopes for both dimeric and monomeric ITCC in solution. The theoretically modeled structures of ITCC dock well into the envelopes of both species. Higher ionic strength shifts the equilibrium into monomer with apparently more compact structure while secondary structure remains unchanged. Taken together, our results suggest that our designed ITCC is predominantly monomeric structure through the enhanced ionic interactions, and its conformation is affected by the concentration of ionic species in the buffer.

  7. A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers

    PubMed Central

    2016-01-01

    Interest in materials that undergo singlet fission (SF) has been catalyzed by the potential to exceed the Shockley–Queisser limit of solar power conversion efficiency. In conventional materials, the mechanism of SF is an intermolecular process (xSF), which is mediated by charge transfer (CT) states and depends sensitively on crystal packing or molecular collisions. In contrast, recently reported covalently coupled pentacenes yield ∼2 triplets per photon absorbed in individual molecules: the hallmark of intramolecular singlet fission (iSF). However, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur via a direct coupling mechanism that is independent of CT states. We show that a near-degeneracy in electronic state energies induced by vibronic coupling to intramolecular modes of the covalent dimer allows for strong mixing between the correlated triplet pair state and the local excitonic state, despite weak direct coupling. PMID:27280166

  8. Intramolecular hydrogen bond in 3-imino-propenylamine isomers: AIM and NBO studies

    NASA Astrophysics Data System (ADS)

    Raissi, H.; Jalbout, Abraham F.; Abbasi, B.; Fazli, F.; Farzad, F.; Nadim, E.; Leon, Aned De

    The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3-imino-propenyl-amine were investigated at MP2 and B3LYP levels of theory using the standard 6-311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (rho), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3-imino-propenyl-amin in water solution were also carried out at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine-amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA-1 as global minimum. This stability is mainly due to the formation of a strong N bond H···N intramolecular hydrogen bond, which is assisted by pi-electrons resonance, and this pi-electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3-imino-propenyl-amine were obtained from the related rotamers methods.

  9. Intermolecular disintegration and intramolecular strand transfer activities of wild-type and mutant HIV-1 integrase.

    PubMed Central

    Mazumder, A; Engelman, A; Craigie, R; Fesen, M; Pommier, Y

    1994-01-01

    We report the activities of HIV integrase protein on a novel DNA substrate, consisting of a pair of gapped duplex molecules. Integrase catalyzed an intermolecular disintegration reaction that requires positioning of a pair of the gapped duplexes in a configuration that resembles the intgration intermediate. However, the major reaction resulted from an intramolecular reaction involving a single gapped duplex, giving rise to a hairpin. Surprisingly, a deletion mutant of integrase that lacks both the amino and carboxyl terminal regions still catalyzed the intermolecular disintegration reaction, but supported only a very low level of the intramolecular reaction. The central core region of integrase is therefore sufficient to both bind the gapped duplex DNA and juxtapose a pair of such molecules through protein-protein interactions. We suggest that the branched DNA structures of the previously reported disintegration substrate, and the intermolecular disintegration substrate described here, assist in stabilizing protein-protein interactions that otherwise require the amino and carboxy terminal regions of integrase. Images PMID:8152908

  10. An excited-state intramolecular photon transfer fluorescence probe for localizable live cell imaging of cysteine

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Chen, Wen; Liu, Si-Jia; Jiang, Jian-Hui

    2017-03-01

    Small molecule probes suitable for selective and specific fluorescence imaging of some important but low-concentration intracellular reactive sulfur species such as cysteine (Cys) pose a challenge in chemical biology. We present a readily available, fast-response fluorescence probe CHCQ-Ac, with 2-(5‧-chloro-2-hydroxyl-phenyl)-6-chloro-4(3 H)-quinazolinone (CHCQ) as the fluorophore and acrylate group as the functional moiety, that enables high-selectivity and high-sensitivity for detecting Cys in both solution and biological system. After specifically reacted with Cys, the probe undergoes a seven-membered intramolecular cyclization and released the fluorophore CHCQ with excited-state intramolecular photon transfer effect. A highly fluorescent, insoluble aggregate was then formed to facilitate high-sensitivity and high-resolution imaging. The results showed that probe CHCQ-Ac affords a remarkably large Stokes shift and can detect Cys under physiological pH condition with no interference from other analytes. Moreover, this probe was proved to have excellent chemical stability, low cytotoxicity and good cell permeability. Our design of this probe provides a novel potential tool to visualize and localize cysteine in bioimaging of live cells that would greatly help to explore various Cys-related physiological and pathological cellular processes in cell biology and diagnostics.

  11. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    NASA Astrophysics Data System (ADS)

    van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with `self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

  12. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    PubMed Central

    van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with ‘self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer–dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard. PMID:26751640

  13. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization.

    PubMed

    van der Velde, Jasper H M; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-11

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

  14. Intra-molecular Triplet Energy Transfer is a General Approach to Improve Organic Fluorophore Photostability

    PubMed Central

    Zheng, Qinsi; Jockusch, Steffen; Rodríguez-Calero, Gabriel G.; Zhou, Zhou; Zhao, Hong; Altman, Roger B.; Abruña, Héctor D.; Blanchard, Scott C.

    2015-01-01

    Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability. PMID:26700693

  15. Intramolecular electron transport in quinoprotein alcohol dehydrogenase of Acetobacter methanolicus: a redox-titration study

    PubMed

    Frébortova; Matsushita; Arata; Adachi

    1998-01-27

    Quinohemoprotein-cytochrome c complex alcohol dehydrogenase (ADH) of acetic acid bacteria consists of three subunits, of which subunit I contains pyrroloquinoline quinone (PQQ) and heme c, and subunit II contains three heme c components. The PQQ and heme c components are believed to be involved in the intramolecular electron transfer from ethanol to ubiquinone. To study the intramolecular electron transfer in ADH of Acetobacter methanolicus, the redox potentials of heme c components were determined with ADH complex and the isolated subunits I and II of A. methanolicus, as well as hybrid ADH consisting of the subunit I/III complex of Gluconobacter suboxydans ADH and subunit II of A. methanolicus ADH. The redox potentials of hemes c in ADH complex were -130, 49, 188, and 188 mV at pH 7.0 and 24, 187, 190, and 255 mV at pH 4.5. In hybrid ADH, one of these heme c components was largely changed in the redox potential. Reduced ADH was fully oxidized with potassium ferricyanide, while ubiquinone oxidized the enzyme partially. The results indicate that electrons extracted from ethanol at PQQ site are transferred to ubiquinone via heme c in subunit I and two of the three hemes c in subunit II. Copyright 1998 Elsevier Science B.V.

  16. Direct Observation and Control of Ultrafast Photoinduced Twisted Intramolecular Charge Transfer (TICT) in Triphenyl-Methane Dyes

    PubMed Central

    Li, Guifeng; Magana, Donny; Dyer, R. Brian

    2012-01-01

    Femtosecond time-resolved infrared spectroscopy was employed to study intramolecular charge transfer in triphenylmethane dyes, including malachite green (MG), malachite green carbinol base (MGCB), and leucomalachite green (LMG). A local excited state (LE) and a twisted intramolecular charge-transfer (TICT) state have been observed directly in MG. Furthermore, solvent-controlled TICT measurements in a series of linear alcohols indicate that the transition time (4–11 ps) from LE to TICT is strongly dependent on alcohol viscosity, which is due to rotational hindrance of dimethylaniline in high-viscosity solvents. For LMG, no TICT is observed due to steric hindrance caused by the sp3-hybridized central carbon atom. However, for MGCB, TICT is rescued by the addition of the electron-donating hydroxyl group to the bridge. These results for MG and its analogues provide new insight regarding the dynamics and mechanism of twisted intramolecular charge transfer (TICT) in triphenylmethane dyes. PMID:23009668

  17. Thermophoretic motion of water nanodroplets confined inside carbon nanotubes.

    PubMed

    Zambrano, Harvey A; Walther, Jens H; Koumoutsakos, Petros; Sbalzarini, Ivo F

    2009-01-01

    We study the thermophoretic motion of water nanodroplets confined inside carbon nanotubes using molecular dynamics simulations. We find that the nanodroplets move in the direction opposite the imposed thermal gradient with a terminal velocity that is linearly proportional to the gradient. The translational motion is associated with a solid body rotation of the water nanodroplet coinciding with the helical symmetry of the carbon nanotube. The thermal diffusion displays a weak dependence on the wetting of the water-carbon nanotube interface. We introduce the use of the moment scaling spectrum (MSS) in order to determine the characteristics of the motion of the nanoparticles inside the carbon nanotube. The MSS indicates that affinity of the nanodroplet with the walls of the carbon nanotubes is important for the isothermal diffusion and hence for the Soret coefficient of the system.

  18. Intramolecular cyclopropanation and C-H insertion reactions with metal carbenoids generated from cyclopropenes.

    PubMed

    Archambeau, Alexis; Miege, Frédéric; Meyer, Christophe; Cossy, Janine

    2015-04-21

    Activation of unsaturated carbon-carbon bonds by means of transition metal catalysts is an exceptionally active research field in organic synthesis. In this context, due to their high ring strain, cyclopropenes constitute an interesting class of substrates that displays a versatile reactivity in the presence of transition metal catalysts. Metal complexes of vinyl carbenes are involved as key intermediates in a wide variety of transition metal-catalyzed ring-opening reactions of cyclopropenes. Most of the reported transformations rely on intermolecular or intramolecular addition of nucleophiles to these latter reactive species. This Account focuses specifically on the reactivity of carbenoids resulting from the ring-opening of cyclopropenes in cyclopropanation and C-H insertion reactions, which are arguably two of the most representative transformations of metal complexes of carbenes. Compared with the more conventional α-diazo carbonyl compounds, the use of cyclopropenes as precursors of metal carbenoids in intramolecular cyclopropanation or C-H insertion reactions has been largely underexploited. One of the challenges is to devise appropriately substituted and readily available cyclopropenes that would not only undergo regioselective ring-opening under mild conditions but also trigger the subsequent desired transformations with a high level of chemoselectivity and stereoselectivity. These goals were met by considering several substrates derived from the readily available 3,3-dimethylcyclopropenylcarbinols or 3,3-dimethylcyclopropenylcarbinyl amines. In the case of 1,6-cyclopropene-enes, highly efficient and diastereoselective gold(I)-catalyzed ring-opening/intramolecular cyclopropanations were developed as a route to diversely substituted heterocycles and carbocycles possessing a bicyclo[4.1.0]heptane framework. The use of rhodium(II) catalysts enabled us to widen the scope of this transformation for the synthesis of medium-sized heterocyclic scaffolds

  19. Diffusion-weighted and diffusion-tensor imaging of normal and diseased uterus

    PubMed Central

    Kara Bozkurt, Duygu; Bozkurt, Murat; Nazli, Mehmet Ali; Mutlu, Ilhan Nahit; Kilickesmez, Ozgur

    2015-01-01

    Owing to technical advances and improvement of the software, diffusion weighted imaging and diffusion tensor imaging (DWI and DTI) greatly improved the diagnostic value of magnetic resonance imaging (MRI) of the pelvic region. These imaging sequences can exhibit important tissue contrast on the basis of random diffusion (Brownian motion) of water molecules in tissues. Quantitative measurements can be done with DWI and DTI by apparent diffusion coefficient (ADC) and fractional anisotropy (FA) values respectively. ADC and FA values may be changed by various physiological and pathological conditions providing additional information to conventional MRI. The quantitative DWI assists significantly in the differentiation of benign and malignant lesions. It can demonstrate the microstructural architecture and celluler density of the normal and diseased uterine zones. On the other hand, DWI and DTI are useful for monitoring the treatment outcome of the uterine lesions. In this review, we discussed advantages of DWI and DTI of the normal and diseased uterus. PMID:26217454

  20. Reconstruction of a geometrically correct diffusion tensor image of a moving human fetal brain

    NASA Astrophysics Data System (ADS)

    Kim, Kio; Habas, Piotr A.; Rousseau, Francois; Glenn, Orit A.; Barkovich, A. J.; Koob, Meriam; Dietemann, Jean-Louis; Robinson, Ashley J.; Poskitt, Kenneth J.; Miller, Steven P.; Studholme, Colin

    2010-03-01

    Recent studies reported the development of methods for rigid registration of 2D fetal brain imaging data to correct for unconstrained fetal and maternal motion, and allow the formation of a true 3D image of conventional fetal brain anatomy from conventional MRI. Diffusion tensor imaging provides additional valuable insight into the developing brain anatomy, however the correction of motion artifacts in clinical fetal diffusion imaging is still a challenging problem. This is due to the challenging problem of matching lower signal-to-noise ratio diffusion weighted EPI slice data to recover between-slice motion, compounded by the presence of possible geometric distortions in the EPI data. In addition, the problem of estimating a diffusion model (such as a tensor) on a regular grid that takes into account the inconsistent spatial and orientation sampling of the diffusion measurements needs to be solved in a robust way. Previous methods have used slice to volume registration within the diffusion dataset. In this work, we describe an alternative approach that makes use of an alignment of diffusion weighted EPI slices to a conventional structural MRI scan which provides a geometrically correct reference image. After spatial realignment of each diffusion slice, a tensor field representing the diffusion profile is estimated by weighted least squared fitting. By qualitative and quantitative evaluation of the results, we confirm the proposed algorithm successfully corrects the motion and reconstructs the diffusion tensor field.

  1. Yugoslav strong motion network

    NASA Astrophysics Data System (ADS)

    Mihailov, Vladimir

    1985-04-01

    Data concerning ground motion and the response of structures during strong earthquakes are necessary for seismic hazard evaluation and the definition of design criteria for structures to be constructed in seismically active zones. The only way to obtain such data is the installation of a strong-motion instrument network. The Yugoslav strong-motion programme was created in 1972 to recover strong-motion response data used by the structural engineering community in developing earthquake resistant design. Instruments, accelerographs SMA-1 and seismoscopes WM-1, were installed in free-field stations and on structures (high-rise buildings, dams, bridges, etc.). A total number of 176 accelerographs and 137 seismoscopes have been installed and are operating in Yugoslavia. The strong-motion programme in Yugoslavia consists of five subactivities: network design, network operation, data processing, network management and research as well as application. All these activities are under the responsibility of IZIIS in cooperation with the Yugoslav Association of Seismology. By 1975 in the realisation of this project participated the CALTECH as cooperative institution in the joint American-Yugoslav cooperative project. The results obtained which are presented in this paper, and their application in the aseismic design justify the necessity for the existence of such a network in Yugoslavia.

  2. Space motion sickness

    NASA Technical Reports Server (NTRS)

    Homick, J. L.

    1979-01-01

    Research on the etiology, prediction, treatment and prevention of space motion sickness, designed to minimize the impact of this syndrome which was experienced frequently and with severity by individuals on the Skylab missions, on Space Shuttle crews is reviewed. Theories of the cause of space motion sickness currently under investigation by NASA include sensory conflict, which argues that motion sickness symptoms result from a mismatch between the total pattern of information from the spatial senses and that stored from previous experiences, and fluid shift, based upon the redistribution of bodily fluids that occurs upon continued exposure to weightlessness. Attempts are underway to correlate space motion sickness susceptibility to different provocative environments, vestibular and nonvestibular responses, and the rate of acquisition and length of retention of sensory adaptation. Space motion sickness countermeasures under investigation include various drug combinations, of which the equal combination of promethazine and ephedrine has been found to be as effective as the scopolomine and dexedrine combination, and vestibular adaptation and biofeedback training and autogenic therapy.

  3. Diffusion bonding aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, G. A.; Broughton, T.

    1988-10-01

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

  4. Order and disorder in fluid motion.

    PubMed Central

    Gollub, J P

    1995-01-01

    The development of complex states of fluid motion is illustrated by reviewing a series of experiments, emphasizing film flows, surface waves, and thermal convection. In one dimension, cellular patterns bifurcate to states of spatiotemporal chaos. In two dimensions, even ordered patterns can be surprisingly intricate when quasiperiodic patterns are included. Spatiotemporal chaos is best characterized statistically, and methods for doing so are evolving. Transport and mixing phenomena can also lead to spatial complexity, but the degree depends on the significance of molecular or thermal diffusion. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 PMID:11607563

  5. Motion of clusters on complex surfaces

    NASA Astrophysics Data System (ADS)

    Alkis, Sabri; Krause, Jeffrey; Cheng, Hai-Ping

    2007-03-01

    Polymer and organic molecule assemblies have been investigated intensely in the past decade, due to their vast range of applications in nano-molecular electronics and as bio-sensors. In particular, self-assembled monolyers (SAMs) of alkanethiol on the Au(111) surface are used widely in surface studies because they are simple structurally, stable thermodynamically and have well-defined order. In this project, inspired by recent experiments, we use classical molecular dynamics simulations to study motions of Agn clusters with various sizes on the alkanthiol SAMs. We report detailed results on dynamics, diffusion, and sintering processes of these nano-clusters.

  6. Effective diffusivity in active Brownian suspensions

    NASA Astrophysics Data System (ADS)

    Burkholder, Eric; Brady, John

    2016-11-01

    We study the single-particle diffusion of a Brownian probe of size R in a suspension comprised of a Newtonian solvent and a dilute dispersion of active Brownian particles (ABPs) with size a, characteristic swim velocity U0, and a reorientation time τR. These ABPs, or "swimmers," have a run length l =U0τR , and a mechanical activity ksTs =ζaU02τR / 6 , where ζa is the Stokes drag coefficient of a swimmer. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. When the activity of the swimmers is greater than the Boltzmann energy, ksTs >kB T , rather than being sterically hindered, the probe diffusivity is actually greater than its Stokes-Einstein-Sutherland diffusivity due to the mechanical energy imparted to the probe upon collisions with the swimmers. The active contribution to the effective diffusivity is a non-monotonic function of the swimmers' run length compared to the contact length between the probe and a swimmer: l / (R + a) . Comparisons are made to previous theoretical and experimental investigations of the hydrodynamic diffusion of a colloidal particle in a dilute suspension of swimming bacteria. NSF Grant No. CBET 1437570.

  7. Diffusion with varying drag; the runaway problem

    SciTech Connect

    Rollins, D.K.

    1986-01-01

    The motion of electrons in an ionized plasma of electrons and ions in an external electric field is studied. A probability distribution function describes the electron motion and is a solution of a Fokker-Planck equation. In zero field, the solution approaches an equilibrium Maxwellian. For arbitrarily small field, electrons overcome the diffusive effects and are freely accelerated by the field. This is the electron-runaway phenomenon. The electric field is treated as a small perturbation. Various diffusion coefficients are considered for the one dimensional problem, and the runaway current is determined as a function of the field strength. Diffusion coefficients, non-zero on a finite interval are examined. Some non-trivial cases of these can be solved exactly in terms of known special functions. The more realistic case where the diffusion coeffient decays with velocity are then considered. To determine the runaway current, the equivalent Schroedinger eigenvalue problem is analyzed. The smallest eigenvalue is shown to be equal to the runaway current. Using asymptotic matching, a solution can be constructed which is then used to evaluate the runaway current. The runaway current is exponentially small as a function of field strength. This method is used to extract results from the three dimensional problem.

  8. The Particle--Motion Problem.

    ERIC Educational Resources Information Center

    Demana, Franklin; Waits, Bert K.

    1993-01-01

    Discusses solutions to real-world linear particle-motion problems using graphing calculators to simulate the motion and traditional analytic methods of calculus. Applications include (1) changing circular or curvilinear motion into linear motion and (2) linear particle accelerators in physics. (MDH)

  9. Ring-diffusion mediated homogeneous melting in the superheating regime

    NASA Astrophysics Data System (ADS)

    Bai, Xian-Ming; Li, Mo

    2008-04-01

    Homogeneous melting in the superheating regime is investigated by using molecular dynamics simulation of a Lennard-Jones model system. We show that the commonly observed catastrophic melting at the superheating limit is caused by fast heating rate. By keeping the system isothermally at temperatures below the superheating limit, we observe intense self-diffusion motions as the precursor of melting. The highly correlated atomic motions are related to the self-diffusion loops or rings. Two types of loops are observed, closed loop and open loop, where the latter is directly related to the homogeneous nucleation of the liquid phase. Homogeneous melting occurs when the number density of diffusion loops reaches a critical value. Our results suggest that homogeneous melting in the superheating regime is a first-order thermodynamic phase transition triggered by the self-diffusion loops when the kinetic constraint imposed by heating rate is lessened.

  10. Anomalous Diffusion of Single Particles in Cytoplasm

    PubMed Central

    Regner, Benjamin M.; Vučinić, Dejan; Domnisoru, Cristina; Bartol, Thomas M.; Hetzer, Martin W.; Tartakovsky, Daniel M.; Sejnowski, Terrence J.

    2013-01-01

    The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM. PMID:23601312

  11. Diffusion of tungsten hexafluoride

    NASA Astrophysics Data System (ADS)

    Winkelmann, J.

    This document is part of Subvolume A `Gases in Gases, Liquids and their Mixtures' of Volume 15 `Diffusion in Gases, Liquids and Electrolytes' of Landolt-Börnstein Group IV `Physical Chemistry'. It is part of the chapter of the chapter `Diffusion in Pure Gases' and contains data on diffusion of tungsten hexafluoride

  12. Reduce Confusion about Diffusion.

    ERIC Educational Resources Information Center

    Hebrank, Mary R.

    1997-01-01

    Presents activities that allow students to explore the fundamental but poorly understood concept of diffusion by appealing to their kinesthetic senses first, then challenging their analytical skills as they try to deduce the mathematical principle involved. Presents a computer simulation of diffusion and discusses diffusion's limitations and…

  13. Diffusion Strategy Guide.

    ERIC Educational Resources Information Center

    McCutcheon, James R.; Sanders, John R.

    A methodology is presented for planning and managing the spread of educational innovations. The first portion of the guide develops a theoretical framework for diffusion which summarizes and capitalizes on the latest marketing and on the latest marketing and diffusion research findings. Major stages in the diffusion paradigm discussed include…

  14. A Student Diffusion Activity

    NASA Astrophysics Data System (ADS)

    Kutzner, Mickey; Pearson, Bryan

    2017-02-01

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

  15. Handbook on atmospheric diffusion

    SciTech Connect

    Hanna, S.R.; Briggs, G.A.; Hosker, R.P. Jr.

    1982-01-01

    Basic meteorological concepts are covered as well as plume rise, source effects, and diffusion models. Chapters are included on cooling tower plumes and urban diffusion. Suggestions are given for calculating diffusion in special situations, such as for instantaneous releases over complex terrain, over long distances, and during times when chemical reactions or dry or wet deposition are important. (PSB)

  16. Ruthenium-catalyzed intramolecular [2+2+2] cycloaddition and tandem cross-metathesis of triynes and enediynes.

    PubMed

    Yuan, Wei; Wei, Yin; Shi, Min

    2013-04-01

    [2+2+2] Cycloadditions can be applied to specifically build up derivatives of benzene and cyclohexadiene and, therefore, have attracted much attention. Herein, we present an intramolecular [2+2+2] cycloaddition of triynes catalyzed by the first-generation Grubbs ruthenium complex (Ru gen-1), which can efficiently afford benzene derivatives in good yields under mild conditions. Moreover, we also report on a novel tandem cross-metathesis transformation of intramolecular enediynes also catalyzed by Ru gen-1, which has not been observed previously in related reports. On the basis of deuterium labeling experiments, a possible reaction mechanism is presented.

  17. Intramolecular catalytic asymmetric carbon-hydrogen insertion reactions. Synthetic advantages in total synthesis in comparison with alternative approaches.

    PubMed

    Doyle, Michael P; Ratnikov, Maxim; Liu, Yu

    2011-06-07

    The synthetic potential of highly directional formal insertion of a carbene between carbon and hydrogen of a carbon-hydrogen bond has recently been developed for intramolecular reactions that lead to compounds of biological and medicinal interest. Stereoselective and regiocontrolled intramolecular processes from diazoacetate reactants, catalyzed by dirhodium(II) compounds with chiral carboxamidate ligands, provide efficient and selective access to compounds as diverse as enterolactone, baclofen, imperanene, xylolactone, and rolipram. A comparison of the C-H insertion methodology with alternative approaches is presented.

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

    NASA Astrophysics Data System (ADS)

    Jakse, N.; Pasturel, A.

    2014-09-01

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

  19. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water.

    PubMed

    Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu

    2014-08-28

    In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps(-1), which is about 2.5 times faster than that in vacuum, 0.27 ps(-1). This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.

  20. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

    SciTech Connect

    Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu

    2014-08-28

    In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.

  1. Brownian motion of graphene.

    PubMed

    Maragó, Onofrio M; Bonaccorso, Francesco; Saija, Rosalba; Privitera, Giulia; Gucciardi, Pietro G; Iatì, Maria Antonia; Calogero, Giuseppe; Jones, Philip H; Borghese, Ferdinando; Denti, Paolo; Nicolosi, Valeria; Ferrari, Andrea C

    2010-12-28

    Brownian motion is a manifestation of the fluctuation-dissipation theorem of statistical mechanics. It regulates systems in physics, biology, chemistry, and finance. We use graphene as prototype material to unravel the consequences of the fluctuation-dissipation theorem in two dimensions, by studying the Brownian motion of optically trapped graphene flakes. These orient orthogonal to the light polarization, due to the optical constants anisotropy. We explain the flake dynamics in the optical trap and measure force and torque constants from the correlation functions of the tracking signals, as well as comparing experiments with a full electromagnetic theory of optical trapping. The understanding of optical trapping of two-dimensional nanostructures gained through our Brownian motion analysis paves the way to light-controlled manipulation and all-optical sorting of biological membranes and anisotropic macromolecules.

  2. Intrinsic Feature Motion Tracking

    SciTech Connect

    Goddard, Jr., James S.

    2013-03-19

    Subject motion during 3D medical scanning can cause blurring and artifacts in the 3D images resulting in either rescans or poor diagnosis. Anesthesia or physical restraints may be used to eliminate motion but are undesirable and can affect results. This software measures the six degree of freedom 3D motion of the subject during the scan under a rigidity assumption using only the intrinsic features present on the subject area being monitored. This movement over time can then be used to correct the scan data removing the blur and artifacts. The software acquires images from external cameras or images stored on disk for processing. The images are from two or three calibrated cameras in a stereo arrangement. Algorithms extract and track the features over time and calculate position and orientation changes relative to an initial position. Output is the 3D position and orientation change measured at each image.

  3. Motion detector and analyzer

    DOEpatents

    Unruh, W.P.

    1987-03-23

    Method and apparatus are provided for deriving positive and negative Doppler spectrum to enable analysis of objects in motion, and particularly, objects having rotary motion. First and second returned radar signals are mixed with internal signals to obtain an in-phase process signal and a quadrature process signal. A broad-band phase shifter shifts the quadrature signal through 90/degree/ relative to the in-phase signal over a predetermined frequency range. A pair of signals is output from the broad-band phase shifter which are then combined to provide a first side band signal which is functionally related to a negative Doppler shift spectrum. The distinct positive and negative Doppler spectra may then be analyzed for the motion characteristics of the object being examined.

  4. Muscle Motion Solenoid Actuator

    NASA Astrophysics Data System (ADS)

    Obata, Shuji

    It is one of our dreams to mechanically recover the lost body for damaged humans. Realistic humanoid robots composed of such machines require muscle motion actuators controlled by all pulling actions. Particularly, antagonistic pairs of bi-articular muscles are very important in animal's motions. A system of actuators is proposed using the electromagnetic force of the solenoids with the abilities of the stroke length over 10 cm and the strength about 20 N, which are needed to move the real human arm. The devised actuators are based on developments of recent modern electro-magnetic materials, where old time materials can not give such possibility. Composite actuators are controlled by a high ability computer and software making genuine motions.

  5. Field theory of propagating reaction-diffusion fronts

    SciTech Connect

    Escudero, C.

    2004-10-01

    The problem of velocity selection of reaction-diffusion fronts has been widely investigated. While the mean-field limit results are well known theoretically, there is a lack of analytic progress in those cases in which fluctuations are to be taken into account. Here, we construct an analytic theory connecting the first principles of the reaction-diffusion process to an effective equation of motion via field-theoretic arguments, and we arrive at results already confirmed by numerical simulations.

  6. Direct observations of atomic diffusion by scanning transmission electron microscopy

    PubMed Central

    Isaacson, M.; Kopf, D.; Utlaut, M.; Parker, N. W.; Crewe, A. V.

    1977-01-01

    The feasibility of using a high-resolution scanning transmission electron microscope to study the diffusion of heavy atoms on thin film substrates of low atomic number has been investigated. We have shown that it is possible to visualize the diffusion of individual uranium atoms adsorbed to thin carbon film substrates and that the observed motion of the atoms does not appear to be induced by the incident electron beam. Images PMID:16592396

  7. Dislocation motion and instability

    NASA Astrophysics Data System (ADS)

    Zhu, Yichao; Chapman, Stephen Jonathan; Acharya, Amit

    2013-08-01

    The Peach-Koehler expression for the stress generated by a single (non-planar) curvilinear dislocation is evaluated to calculate the dislocation self stress. This is combined with a law of motion to give the self-induced motion of a general dislocation curve. A stability analysis of a rectilinear, uniformly translating dislocation is then performed. The dislocation is found to be susceptible to a helical instability, with the maximum growth rate occurring when the dislocation is almost, but not exactly, pure screw. The non-linear evolution of the instability is determined numerically, and implications for slip band formation and non-Schmid behavior in yielding are discussed.

  8. Motion in microfluidic ratchets.

    PubMed

    Caballero, D; Katuri, J; Samitier, J; Sánchez, S

    2016-11-15

    The ubiquitous random motion of mesoscopic active particles, such as cells, can be "rectified" or directed by embedding the particles in systems containing local and periodic asymmetric cues. Incorporated on lab-on-a-chip devices, these microratchet-like structures can be used to self-propel fluids, transport particles, and direct cell motion in the absence of external power sources. In this Focus article we discuss recent advances in the use of ratchet-like geometries in microfluidics which could open new avenues in biomedicine for applications in diagnosis, cancer biology, and bioengineering.

  9. Analysis of swimming motions.

    NASA Technical Reports Server (NTRS)

    Gallenstein, J.; Huston, R. L.

    1973-01-01

    This paper presents an analysis of swimming motion with specific attention given to the flutter kick, the breast-stroke kick, and the breast stroke. The analysis is completely theoretical. It employs a mathematical model of the human body consisting of frustrums of elliptical cones. Dynamical equations are written for this model including both viscous and inertia forces. These equations are then applied with approximated swimming strokes and solved numerically using a digital computer. The procedure is to specify the input of the swimming motion. The computer solution then provides the output displacement, velocity, and rotation or body roll of the swimmer.

  10. Effect of varying the 1-4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model.

    PubMed

    Ye, Xianggui; Cui, Shengting; de Almeida, Valmor F; Khomami, Bamin

    2013-03-01

    A comprehensive molecular dynamics simulation study of n-alkanes using the optimized potential for liquid simulation with all-atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better understand the effects of reducing the scaling factor, its influence on the torsion potential profile, and the corresponding gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane were investigated. This relatively simple procedure enables more accurate predictions of the thermo-physical properties of longer n-alkanes.

  11. Effect of Varying the 1-4 Intramolecular Scaling Factor in Atomistic Simulations of Long-Chain N-alkanes with the OPLS-AA Model

    SciTech Connect

    de Almeida, Valmor F; Ye, Xianggui; Cui, Shengting; Khomami, Bamin

    2013-01-01

    A comprehensive molecular dynamics simulation study of n-alkanes using the Optimized Potential for Liquid Simulation-All Atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better un-derstand the effects of reducing the scaling factor, we analyzed the variation of the torsion potential pro-file with the scaling factor, and the corresponding impact on the gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane. This relatively simple procedure thus allows for more accurate predictions of the thermo-physical properties of longer n-alkanes.

  12. Theoretical model of blood flow measurement by diffuse correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Sakadžić, Sava; Boas, David A.; Carp, Stefan

    2017-02-01

    Diffuse correlation spectroscopy (DCS) is a noninvasive method to quantify tissue perfusion from measurements of the intensity temporal autocorrelation function of diffusely scattered light. However, DCS autocorrelation function measurements in tissue better match theoretical predictions based on the diffusive motion of the scatterers than those based on a model where the advective nature of blood flow dominates the stochastic properties of the scattered light. We have recently shown using Monte Carlo (MC) simulations and assuming a simplistic vascular geometry and laminar flow profile that the diffusive nature of the DCS autocorrelation function decay is likely a result of the shear-induced diffusion of the red blood cells. Here, we provide theoretical derivations supporting and generalizing the previous MC results. Based on the theory of diffusing-wave spectroscopy, we derive an expression for the autocorrelation function along the photon path through a vessel that takes into account both diffusive and advective scatterer motion, and we provide the solution for the DCS autocorrelation function in a semi-infinite geometry. We also derive the correlation diffusion and correlation transfer equation, which can be applied for an arbitrary sample geometry. Further, we propose a method to take into account realistic vascular morphology and flow profile.

  13. The Diffusion of Charged Particles in Collisional Plasmas: Free and Ambipolar Diffusion at Low and Moderate Pressures

    PubMed Central

    Phelps, A. V.

    1990-01-01

    The interpretation of measurements of the properties of weakly ionized plasmas in terms of diffusion of electrons and ions is reviewed both critically and tutorially. A particular effort is made to tie together various aspects of charged particle diffusion phenomena in quiescent, partially ionized plasmas. The concepts of diffusion length and effective diffusion coefficient and the treatment of partially reflecting boundaries are developed in the limit of the space-charge-free motion of the electrons or ions. A simplified derivation of the screening length for space charge electric fields is followed by a review of the conventional derivation of diffusion in the ambipolar limit. A discussion of the scaling parameters of the ratio of the diffusion length to the screening length and the ratio of the diffusion length to the ion mean-free-path leads to a map used to correlate published models covering the complete range of these parameters. The models of measurements of the diffusion of electrons, several types of positive ions, and negative ions are reviewed. The role of diffusion in the decay of charged particle densities and wall currents during the afterglow of a discharge is then considered. The effects of collapse of the space charge field and of diffusion cooling are reviewed. Finally, the application of the diffusion models to a number of different discharges is discussed. PMID:28179784

  14. Induced motion at texture-defined motion boundaries.

    PubMed Central

    Johnston, A; Benton, C P; McOwan, P W

    1999-01-01

    When a static textured background is covered and uncovered by a moving bar of the same mean luminance we can clearly see the motion of the bar. Texture-defined motion provides an example of a naturally occurring second-order motion. Second-order motion sequences defeat standard spatio-temporal energy models of motion perception. It has been proposed that second-order stimuli are analysed by separate systems, operating in parallel with luminance-defined motion processing, which incorporate identifiable pre-processing stages that make second-order patterns visible to standard techniques. However, the proposal of multiple paths to motion analysis remains controversial. Here we describe the behaviour of a model that recovers both luminance-defined and an important class of texture-defined motion. The model also accounts for the induced motion that is seen in some texture-defined motion sequences. We measured the perceived direction and speed of both the contrast envelope and induced motion in the case of a contrast modulation of static noise textures. Significantly, the model predicts the perceived speed of the induced motion seen at second-order texture boundaries. The induced motion investigated here appears distinct from classical induced effects resulting from motion contrast or the movement of a reference frame. PMID:10643088

  15. Subdiffusive molecular motion in nanochannels observed by fluorescence correlation spectroscopy.

    PubMed

    De Santo, Ilaria; Causa, Filippo; Netti, Paolo A

    2010-02-01

    The influence of confinement on biomolecule motion in glass channels of nanometric height has been investigated with fluorescence correlation spectroscopy (FCS). We measured intrachannel molecule diffusion time and concentration based on a single-component diffusion model as a function of molecule size to channel height (r(g)/h). Poly(ethylene glycol) (PEG) of 20 kDa and dextran of 40 kDa showed a reduction of their diffusion coefficients of almost 1 order of magnitude when nanochannel height approached probe diameter, whereas rhodamine 6G (Rh6G) was shown to be almost unaffected from confinement. Subdiffusive motion has been proven for flexible molecules in nanochannels, and deviations toward a square root dependence of mobility with time for confinement up to molecule size r(g)/h approximately 0.5 were registered. Diffusion coefficient time dependence has been evaluated and described with a model that accounts for diffusion time increase due to molecule rearrangements related to molecule flexibility and surface interactions dynamics. The evaluation of the subdiffusive mode and the key parameters extracted at the single-molecule level of partitioning, intrachannel diffusion time, desorption time, and binding probability at surfaces can be exploited for the engineering of bioanalytic nanodevices.

  16. Intramolecular ferro- and antiferromagnetic interactions in oxo-carboxylate bridged digadolinium(III) complexes.

    PubMed

    Cañadillas-Delgado, Laura; Fabelo, Oscar; Pasán, Jorge; Delgado, Fernando S; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

    2010-08-21

    Two new digadolinium(III) complexes with monocarboxylate ligands, [Gd2(pac)6(H2O)4] (1) and [Gd2(tpac)6(H2O)4] (2) (Hpac = pentanoic acid and Htpac = 3-thiopheneacetic acid), have been prepared and their structures determined by X-ray diffraction on single crystals. Their structures consist of neutral and isolated digadolinium(III) units, containing six monocarboxylate ligands and four coordinated water molecules, the bridging skeleton being built by a muO(1):kappa2O(1)O(2) framework. This structural pattern has already been observed in the parent acetate-containing compound [Gd2(ac)6(H2O)4] x 4 H2O (3) whose structure and magnetic properties were reported elsewhere (L. Cañadillas-Delgado, O. Fabelo, J. Cano, J. Pasán, F. S. Delgado, M. Julve, F. Lloret and C. Ruiz-Pérez, CrystEngComm, 2009, 11, 2131). Each gadolinium(III) ion in 1 and 2 is nine-coordinated with seven carboxylate-oxygen atoms from four pac (1)/tpac (2) ligands and two water molecules (1 and 2) building a distorted monocapped square antiprism. The values of the intramolecular gadolinium-gadolinium separation are 4.1215(5) (1), 4.1255(6) (2) and 4.1589(3) A (3) and those of the angle at the oxo-carboxylate bridge (theta) are 113.16(13) (1), 112.5(2) (2) and 115.47(7) degrees (3). Magnetic susceptibility measurements in the temperature range 1.9-300 K reveal the occurrence of a weak intramolecular antiferromagnetic interaction [J = -0.032(1) (1) and -0.012(1) cm(-1) (2), the Hamiltonian being defined as H = -JS(A) x S(B)] in contrast with the intramolecular ferromagnetic coupling which occurs in 3 (J = +0.031(1) cm(-1)). The magneto-structural data of 1-3 show the relevance of the geometrical parameters at the muO(1):kappa2O(1)O(2) bridge on the nature of the magnetic coupling between two gadolinium(III) ions.

  17. Nonergodic diffusion of single atoms in a periodic potential

    NASA Astrophysics Data System (ADS)

    Kindermann, Farina; Dechant, Andreas; Hohmann, Michael; Lausch, Tobias; Mayer, Daniel; Schmidt, Felix; Lutz, Eric; Widera, Artur

    2016-10-01

    Diffusion can be used to infer the microscopic features of a system from the observation of its macroscopic dynamics. Brownian motion accurately describes many diffusive systems, but non-Brownian and nonergodic features are often observed on short timescales. Here, we trap a single ultracold caesium atom in a periodic potential and measure its diffusion. We engineer the particle-environment interaction to fully control motion over a broad range of diffusion constants and timescales. We use a powerful stroboscopic imaging method to detect single-particle trajectories and analyse both non-equilibrium diffusion properties and the approach to ergodicity. Whereas the variance and two-time correlation function exhibit apparent Brownian motion at all times, higher-order correlations reveal strong non-Brownian behaviour. We additionally observe the slow convergence of the exponential displacement distribution to a Gaussian and--unexpectedly--a much slower approach to ergodicity, in perfect agreement with an analytical continuous-time random-walk model. Our experimental system offers an ideal testbed for the detailed investigation of complex diffusion processes.

  18. Nuclear magnetic resonance diffusion pore imaging: Experimental phase detection by double diffusion encoding

    NASA Astrophysics Data System (ADS)

    Demberg, Kerstin; Laun, Frederik Bernd; Windschuh, Johannes; Umathum, Reiner; Bachert, Peter; Kuder, Tristan Anselm

    2017-02-01

    Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging. It has been previously experimentally demonstrated that pore imaging using a combination of a long and a narrow magnetic field gradient pulse is feasible. In this work, an experimental verification is presented showing that pores can be imaged using short gradient pulses only. Experiments were carried out using hyperpolarized xenon gas in well-defined pores. The phase required for pore image reconstruction was retrieved from double diffusion encoded (DDE) measurements, while the magnitude could either be obtained from DDE signals or classical diffusion measurements with single encoding. The occurring image artifacts caused by restrictions of the gradient system, insufficient diffusion time, and by the phase reconstruction approach were investigated. Employing short gradient pulses only is advantageous compared to the initial long-narrow approach due to a more flexible sequence design when omitting the long gradient and due to faster convergence to the diffusion long-time limit, which may enable application to larger pores.

  19. A world in motion

    SciTech Connect

    Boynton, J.A.

    1994-12-31

    A World in Motion is a physical science curriculum supplement for grades four, five, and six which responds to the need to promote and teach sound science and mathematics concepts. Using the A World in Motion kits, teachers work in partnership with practicing engineer or scientists volunteers to provide students with fun, exciting, and relevant hands-on science and math experiences. During the A World in Motion experience, students work together in {open_quotes}Engineering Design Teams{close_quotes} exploring physics concepts through a series of activities. Each student is assigned a role as either a facilities engineer, development engineer, test engineer, or project engineer and is given responsibilities paralleling those of engineers in industry. The program culminates in a {open_quotes}Design Review{close_quotes} where students can communicate their results, demonstrate their designs, and receive recognition for their efforts. They are given a chance to take on responsibility and build self-esteem. Since January 1991, over 12,000 volunteers engineers have been involved with the program, with a distribution of 20,000 A World in Motion kit throughout the U.S. and Canada.

  20. Superluminal motion (review)

    NASA Astrophysics Data System (ADS)

    Malykin, G. B.; Romanets, E. A.

    2012-06-01

    Prior to the development of Special Relativity, no restrictions were imposed on the velocity of the motion of particles and material bodies, as well as on energy transfer and signal propagation. At the end of the 19th century and the beginning of the 20th century, it was shown that a charge that moves at a velocity faster than the speed of light in an optical medium, in particular, in vacuum, gives rise to impact radiation, which later was termed the Vavilov-Cherenkov radiation. Shortly after the development of Special Relativity, some researchers considered the possibility of superluminal motion. In 1923, the Soviet physicist L.Ya. Strum suggested the existence of tachyons, which, however, have not been discovered yet. Superluminal motions can occur only for images, e.g., for so-called "light spots," which were considered in 1972 by V.L. Ginzburg and B.M. Bolotovskii. These spots can move with a superluminal phase velocity but are incapable of transferring energy and information. Nevertheless, these light spots may induce quite real generation of microwave radiation in closed waveguides and create the Vavilov-Cherenkov radiation in vacuum. In this work, we consider various paradoxes, illusions, and artifacts associated with superluminal motion.