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Sample records for intramolecular diffusive motion

  1. Intramolecular diffusion controls aggregation of the PAPf39 peptide.

    PubMed

    Srivastava, Kinshuk R; French, Kinsley C; Tzul, Franco O; Makhatadze, George I; Lapidus, Lisa J

    2016-09-01

    The 39-residue fragment of human prostatic acidic phosphatase (PAP) is found in high concentrations in semen and easily form fibrils. Previous work has shown that fibrillization is accelerated with a deletion of the first 8, mostly charged residues and it was hypothesized that fibrillization depended on the dynamics of these peptides. To test this hypothesis we have measured the intramolecular diffusion of the full length and 8-residue deletion peptides at two different pHs and found a correlation with fibrillization lag time. These results can be explained by a simple kinetic model of the early stages of aggregation in which oligomerization is controlled by the rate of peptide reconfiguration. PMID:27393931

  2. Molecular crowding inhibits intramolecular breathing motions in proteins.

    SciTech Connect

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

    2008-01-11

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

  3. 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.

  4. 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.

  5. Influence of end-to-end diffusion on intramolecular energy transfer as observed by frequency-domain fluorometry

    NASA Astrophysics Data System (ADS)

    Lakowicz, Joseph R.; Wiczk, Wieslaw M.; Gryczynski, Ignacy; Szmacinski, Henryk; Johnson, Michael L.

    1990-05-01

    We investigated the influence of end-to-end diffusion on intramolecular energy transfer between a naphthalene donor and dansyl acceptor linked by polymethylene chain. A range of viscosities of 0.6 - 200cP were obtained using propylene glycol at different temperatures (0-80°C) and methanol at 20°C. The intensity decays of naphthalene were measured in frequency-domain. Several theoretical models, including distance distributions were used to fit the data. The results indicate that end-to-end diffusion of flexible donor - acceptor pairs can be readily detected and quantified using frequency-domain fluorometry.

  6. 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.

  7. Relativistic diffusive motion in random electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Haba, Z.

    2011-08-01

    We show that the relativistic dynamics in a Gaussian random electromagnetic field can be approximated by the relativistic diffusion of Schay and Dudley. Lorentz invariant dynamics in the proper time leads to the diffusion in the proper time. The dynamics in the laboratory time gives the diffusive transport equation corresponding to the Jüttner equilibrium at the inverse temperature β-1 = mc2. The diffusion constant is expressed by the field strength correlation function (Kubo's formula).

  8. Relativistic diffusive motion in thermal electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Haba, Z.

    2013-04-01

    We discuss relativistic dynamics in a random electromagnetic field which can be considered as a high temperature limit of the quantum electromagnetic field in a heat bath (cavity) moving with a uniform velocity w. We derive a diffusion approximation for the particle’s dynamics generalizing the diffusion of Schay and Dudley. It is shown that the Jüttner distribution is the equilibrium state of the diffusion.

  9. 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.

  10. Anomalous diffusion in quantum Brownian motion with colored noise

    SciTech Connect

    Ford, G. W.; O'Connell, R. F.

    2006-03-15

    Anomalous diffusion is discussed in the context of quantum Brownian motion with colored noise. It is shown that earlier results follow simply and directly from the fluctuation-dissipation theorem. The limits on the long-time dependence of anomalous diffusion are shown to be a consequence of the second law of thermodynamics. The special case of an electron interacting with the radiation field is discussed in detail. We apply our results to wave-packet spreading.

  11. 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. PMID:27250281

  12. Analytical correlation functions for motion through diffusivity landscapes

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

  13. Motion Detection in Diffusion MRI via Online ODF Estimation

    PubMed Central

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

    2013-01-01

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

  14. Diffusion motions in hydrated sodium alginate by QENS

    SciTech Connect

    Tripadus, V.; Statescu, M.; Aranghel, D.; Gugiu, M.; Petre, M.; Precup, I.; Zanotti, J. M.; Mitra, S.

    2010-01-21

    QENS experiments are very suitable for the study of water-polysaccharides systems both for slow polymer chains dynamics as well as for faster solvent molecules dynamics. By a suitable choice of experimental conditions as well as a properly data processing we can get information about the motion modes of various molecular groups of polymer chains in aqueous solutions presumes. Virtually we can distinguish the polymer protons motions at nanosecond time scale by choosing a narrow energy resolution window. The present work presents the QENS measurements performed at LLB, MIBEMOL neutron spectrometer on sodium alginate hydrated samples. The experimental spectra were fitted using one lorentzian fit. At high polymer concentration the quasielastic part of the line is given by the translational-rotational diffusion performed by heavy water molecules in confined spaces created by the polymer coils. The experimental data are well described by Chudley Elliot and Hall-Ross models.

  15. 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.

  16. INTRAMOLECULAR MOTION AND REORIENTATIONAL BARRIERS IN 9-FLUORENONE, 4-METHYL-9-FLUORENONE AND 4,5-DIMETHYL-9-FLUORENONE

    EPA Science Inventory

    Carbon-13 nuclear magnetic resonance spin-lattice relaxation times and nuclear Overhauser enhancements were measured as functions of temperature for the hydrogen-bearing carbons in 9-fluorenone, 4-methyl-9-fluorenone, and 4,5-dimethyl-9-fluorenone. Reorientational diffusion const...

  17. 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.

  18. Unusual Aggregation-Induced Emission of a Coumarin Derivative as a Result of the Restriction of an Intramolecular Twisting Motion.

    PubMed

    Bu, Fan; Duan, Ruihong; Xie, Yujun; Yi, Yuanping; Peng, Qian; Hu, Rongrong; Qin, Anjun; Zhao, Zujin; Tang, Ben Zhong

    2015-11-23

    Aggregation-induced emission (AIE) is commonly observed for propeller-like luminogens with aromatic rotors and stators. Herein, we report that a coumarin derivative containing a seven-membered aliphatic ring (CD-7) but no rotors showed typical AIE characteristics, whereas its analogue with a five-membered aliphatic ring (CD-5) exhibited an opposite aggregation-caused quenching (ACQ) effect. Experimental and theoretical results revealed that a large aliphatic ring in CD-7 weakens structural rigidity and promotes out-of-plane twisting of the molecular backbone to drastically accelerate nonradiative excited-state decay, thus resulting in poor emission in solution. The restriction of twisting motion in aggregates blocks the nonradiative decay channels and enables CD-7 to fluoresce strongly. The results also show that AIE is a general phenomenon and not peculiar to propeller-like molecules. The AIE and ACQ effects can be switched readily by the modulation of molecular rigidity. PMID:26439884

  19. Quantitative assessment of motion correction for high angular resolution diffusion imaging.

    PubMed

    Sakaie, Ken E; Lowe, Mark J

    2010-02-01

    Several methods have been proposed for motion correction of high angular resolution diffusion imaging (HARDI) data. There have been few comparisons of these methods, partly due to a lack of quantitative metrics of performance. We compare two motion correction strategies using two figures of merit: displacement introduced by the motion correction and the 95% confidence interval of the cone of uncertainty of voxels with prolate tensors. What follows is a general approach for assessing motion correction of HARDI data that may have broad application for quality assurance and optimization of postprocessing protocols. Our analysis demonstrates two important issues related to motion correction of HARDI data: (1) although neither method we tested was dramatically superior in performance, both were dramatically better than performing no motion correction, and (2) iteration of motion correction can improve the final results. Based on the results demonstrated here, iterative motion correction is strongly recommended for HARDI acquisitions. PMID:19695824

  20. Tempered stable Lévy motion and transient super-diffusion

    NASA Astrophysics Data System (ADS)

    Baeumer, Boris; Meerschaert, Mark M.

    2010-03-01

    The space-fractional diffusion equation models anomalous super-diffusion. Its solutions are transition densities of a stable Lévy motion, representing the accumulation of power-law jumps. The tempered stable Lévy motion uses exponential tempering to cool these jumps. A tempered fractional diffusion equation governs the transition densities, which progress from super-diffusive early-time to diffusive late-time behavior. This article provides finite difference and particle tracking methods for solving the tempered fractional diffusion equation with drift. A temporal and spatial second-order Crank-Nicolson method is developed, based on a finite difference formula for tempered fractional derivatives. A new exponential rejection method for simulating tempered Lévy stables is presented to facilitate particle tracking codes.

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

    SciTech Connect

    Perry H. Leo

    2009-03-05

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Kreft, Jennifer; Chen, Yeng-Long

    2007-08-01

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

  4. Scan parameters and the diffusion emphasis effect in diffusion-weighted imaging using a motion-probing gradient preparation pulse.

    PubMed

    Takahashi, Daisuke; Tanji, Hajime; Yamaki, Tomoya; Obara, Makoto; Machida, Yoshio

    2014-07-01

    Diffusion-sensitized driven equilibrium preparation (DSDE) is a gradient echo (GRE) diffusion-weighted imaging (DWI) sequence that employs a motion-probing gradient (MPG) preparation pulse and phase cycling. In DSDE, several scan parameters of the MPG preparation pulse and the GRE sequence affect diffusion sensitivity. Our investigation of the relationship between these scan parameters and the diffusion emphasis effect revealed the importance of "prep.TE" in the MPG preparation pulse and "TFE shot interval" in the gradient echo sequence. Appropriate choice of these parameters allows DSDE to provide a similar DWI to that of conventional single-shot SEEPI DWI. We therefore concluded DSDE to be a useful DWI method. PMID:25055943

  5. Motion-induced phase error estimation and correction in 3D diffusion tensor imaging.

    PubMed

    Van, Anh T; Hernando, Diego; Sutton, Bradley P

    2011-11-01

    A multishot data acquisition strategy is one way to mitigate B0 distortion and T2∗ blurring for high-resolution diffusion-weighted magnetic resonance imaging experiments. However, different object motions that take place during different shots cause phase inconsistencies in the data, leading to significant image artifacts. This work proposes a maximum likelihood estimation and k-space correction of motion-induced phase errors in 3D multishot diffusion tensor imaging. The proposed error estimation is robust, unbiased, and approaches the Cramer-Rao lower bound. For rigid body motion, the proposed correction effectively removes motion-induced phase errors regardless of the k-space trajectory used and gives comparable performance to the more computationally expensive 3D iterative nonlinear phase error correction method. The method has been extended to handle multichannel data collected using phased-array coils. Simulation and in vivo data are shown to demonstrate the performance of the method. PMID:21652284

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

    SciTech Connect

    Deng Chuang; Schuh, Christopher A.

    2011-12-01

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

  7. 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.

  8. Fractional Diffusion Equation, Quantum Subdynamics and EINSTEIN'S Theory of Brownian Motion

    NASA Astrophysics Data System (ADS)

    Abe, Sumiyoshi

    The fractional diffusion equation for describing the anomalous diffusion phenomenon is derived in the spirit of Einstein's 1905 theory of Brownian motion. It is shown how naturally fractional calculus appears in the theory. Then, Einstein's theory is examined in view of quantum theory. An isolated quantum system composed of the objective system and the environment is considered, and then subdynamics of the objective system is formulated. The resulting quantum master equation is found to be of the Lindblad type.

  9. Brownian motion in a rotating fluid: Diffusivity is a function of the rotation rate

    NASA Astrophysics Data System (ADS)

    Ryskin, Gregory

    1988-09-01

    The phenomenological relations between thermodynamic fluxes and forces are normally assumed to be invariant with respect to arbitrary motion of the frame of reference. We describe a breakdown of this invariance strong enough to be observable. It is shown that the diffusivity in a rotating fluid is anisotropic and also smaller in magnitude than in a fluid at rest in an inertial frame, giving rise to a diffusion analog of the Hall effect. For large Brownian particles (e.g., biological macromolecules) the diffusivity may decrease by 50% at the rotation speeds achievable in ultracentrifuges.

  10. A Diffusion Approximation Based on Renewal Processes with Applications to Strongly Biased Run-Tumble Motion.

    PubMed

    Thygesen, Uffe Høgsbro

    2016-03-01

    We consider organisms which use a renewal strategy such as run-tumble when moving in space, for example to perform chemotaxis in chemical gradients. We derive a diffusion approximation for the motion, applying a central limit theorem due to Anscombe for renewal-reward processes; this theorem has not previously been applied in this context. Our results extend previous work, which has established the mean drift but not the diffusivity. For a classical model of tumble rates applied to chemotaxis, we find that the resulting chemotactic drift saturates to the swimming velocity of the organism when the chemical gradients grow increasingly steep. The dispersal becomes anisotropic in steep gradients, with larger dispersal across the gradient than along the gradient. In contrast to one-dimensional settings, strong bias increases dispersal. We next include Brownian rotation in the model and find that, in limit of high chemotactic sensitivity, the chemotactic drift is 64% of the swimming velocity, independent of the magnitude of the Brownian rotation. We finally derive characteristic timescales of the motion that can be used to assess whether the diffusion limit is justified in a given situation. The proposed technique for obtaining diffusion approximations is conceptually and computationally simple, and applicable also when statistics of the motion is obtained empirically or through Monte Carlo simulation of the motion. PMID:27012850

  11. Duality of diffusion dynamics in particle motion in soft-mode turbulence

    NASA Astrophysics Data System (ADS)

    Suzuki, Masaru; Sueto, Hiroshi; Hosokawa, Yusaku; Muramoto, Naoyuki; Narumi, Takayuki; Hidaka, Yoshiki; Kai, Shoichi

    2013-10-01

    Nonthermal Brownian motion is investigated experimentally by injecting a particle into soft-mode turbulence (SMT), in the electroconvection of a nematic liquid crystal. It is clarified that the particle motion can be classified into two phases: fast motion, where particles move with the local convective flow, and slow motion, where they are carried by global slow pattern dynamics. We propose a simplified model to clarify the mechanism of the short-time and asymptotic behavior of diffusion. In our model, the correlation time is estimated as a function of a control parameter ɛ. The scaling of the SMT pattern correlation time, τd˜ɛ-1, is estimated from the particle dynamics, which is consistent with a previous report observed from the Eulerian viewpoint. The origin of the non-Gaussian distribution of the displacement in the short-time regime is also discussed and an analytical curve is introduced that quantitatively agrees with the experimental data. Our results clearly illustrate the characteristics of diffusive motion in SMT, which are considerably different from the conventional Brownian motion.

  12. Far IR continua caused by large polarizabilities of intramolecular NLi+ ṡṡṡN ⇄ N ṡṡṡ Li+N bonds due to cation motion

    NASA Astrophysics Data System (ADS)

    Brzezinski, Bogumil; Zundel, Georg

    1984-08-01

    Aromatic N bases, compounds 1-4 and aliphatic N bases, compounds 5 and 6 were studied by IR spectroscopy pure and as 1:1 mixtures with LiClO4. In the pure LiClO4 solutions the Li+-ion motion band caused by vibrations of Li+ in a cage of acetonitrile molecules is found at about 400 cm-1. In the case of the solutions of the aromatic N bases 1-3 with LiClO4, continua are observed instead of the ion motion band, beginning at about 450 cm-1 and extending toward smaller wave numbers. They indicate the presence of intramolecular NLi+ṡṡṡN ⇄NṡṡṡLi+N bonds in which the Li+ ion may fluctuate. These Li+ bonds are homoconjugated, i.e., structurally symmetrical. The continua demonstrate that these bonds show large polarizability, so-called Li+ polarizability, due to the Li+ motion. Caused by their large polarizabilities they interact strongly with their environments. With the aliphatic N bases complexes with the Li+ ions are formed, but instead of the continua an ion motion band at 400 cm-1 occurs. This result shows that NṡṡṡLi+ṡṡṡN bonds with single minimum are present. The different behavior of the aromatic and the aliphatic compounds is explained since the affinity for the Li+ ions is much higher with the aromatic compared with the aliphatic N bases.

  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. PMID:21503294

  14. 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

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

    PubMed

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

    2016-01-01

    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

  16. QUANTUM DOT SINGLE MOLECULE TRACKING REVEALS A WIDE RANGE OF DIFFUSIVE MOTIONS OF MEMBRANE TRANSPORT PROTEINS.

    PubMed

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

    2009-03-01

    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. PMID:24386532

  17. 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.

  18. Brownian motion in a speckle light field: tunable anomalous diffusion and selective optical manipulation.

    PubMed

    Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain

    2014-02-01

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

  20. 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

  1. Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes.

    PubMed

    Berry, Hugues; Chaté, Hugues

    2014-02-01

    In vivo measurements of the passive movements of biomolecules or vesicles in cells consistently report "anomalous diffusion," where mean-squared displacements scale as a power law of time with exponent α<1 (subdiffusion). While the detailed mechanisms causing such behaviors are not always elucidated, movement hindrance by obstacles is often invoked. However, our understanding of how hindered diffusion leads to subdiffusion is based on diffusion amidst randomly located immobile obstacles. Here, we have used Monte Carlo simulations to investigate transient subdiffusion due to mobile obstacles with various modes of mobility. Our simulations confirm that the anomalous regimes rapidly disappear when the obstacles move by Brownian motion. By contrast, mobile obstacles with more confined displacements, e.g., Orstein-Ulhenbeck motion, are shown to preserve subdiffusive regimes. The mean-squared displacement of tracked protein displays convincing power laws with anomalous exponent α that varies with the density of Orstein-Ulhenbeck (OU) obstacles or the relaxation time scale of the OU process. In particular, some of the values we observed are significantly below the universal value predicted for immobile obstacles in two dimensions. Therefore, our results show that subdiffusion due to mobile obstacles with OU type of motion may account for the large variation range exhibited by experimental measurements in living cells and may explain that some experimental estimates are below the universal value predicted for immobile obstacles. PMID:25353510

  2. Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes

    NASA Astrophysics Data System (ADS)

    Berry, Hugues; Chaté, Hugues

    2014-02-01

    In vivo measurements of the passive movements of biomolecules or vesicles in cells consistently report "anomalous diffusion," where mean-squared displacements scale as a power law of time with exponent α <1 (subdiffusion). While the detailed mechanisms causing such behaviors are not always elucidated, movement hindrance by obstacles is often invoked. However, our understanding of how hindered diffusion leads to subdiffusion is based on diffusion amidst randomly located immobile obstacles. Here, we have used Monte Carlo simulations to investigate transient subdiffusion due to mobile obstacles with various modes of mobility. Our simulations confirm that the anomalous regimes rapidly disappear when the obstacles move by Brownian motion. By contrast, mobile obstacles with more confined displacements, e.g., Orstein-Ulhenbeck motion, are shown to preserve subdiffusive regimes. The mean-squared displacement of tracked protein displays convincing power laws with anomalous exponent α that varies with the density of Orstein-Ulhenbeck (OU) obstacles or the relaxation time scale of the OU process. In particular, some of the values we observed are significantly below the universal value predicted for immobile obstacles in two dimensions. Therefore, our results show that subdiffusion due to mobile obstacles with OU type of motion may account for the large variation range exhibited by experimental measurements in living cells and may explain that some experimental estimates are below the universal value predicted for immobile obstacles.

  3. Superdiffusion to normal diffusion: particle motion in three-dimensional force-free magnetic fields

    NASA Astrophysics Data System (ADS)

    Holguin, F.; Ram, A. K.; Krishnamurthy, V.; Dasgupta, B.

    2015-11-01

    Magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free as the Lorentz force vanishes. The Arnold-Beltrami-Childress (ABC) field is an example of a three-dimensional, force-free, helical magnetic field. The field lines form complex and varied structures in space that are a mix of regular and chaotic lines of force. Charged particles moving in the region of chaotic field lines exhibit anomalous superdiffusion. The sine field, or the Archontis field, is a special case of ABC field with the cosine terms left out. The lines of force of a sine field are completely chaotic in space. However, the diffusion of particles in the sine field is normal. The time evolution of an ensemble of particles can be divided into three domains. For short times, the motion is essentially ballistic. For intermediate times, the motion is characterized by a decay of the velocity autocorrelation function. For longer times, the particles undergo diffusion. We present results on the diffusion of field lines, and of particles, in the ABC and sine fields. In particular, the transition from superdiffusion to normal diffusion is discussed.

  4. Spatially-constrained probability distribution model of incoherent motion (SPIM) for abdominal diffusion-weighted MRI.

    PubMed

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

    2016-08-01

    Quantitative diffusion-weighted MR imaging (DW-MRI) of the body enables characterization of the tissue microenvironment by measuring variations in the mobility of water molecules. The diffusion signal decay model parameters are increasingly used to evaluate various diseases of abdominal organs such as the liver and spleen. However, previous signal decay models (i.e., mono-exponential, bi-exponential intra-voxel incoherent motion (IVIM) and stretched exponential models) only provide insight into the average of the distribution of the signal decay rather than explicitly describe the entire range of diffusion scales. In this work, we propose a probability distribution model of incoherent motion that uses a mixture of Gamma distributions to fully characterize the multi-scale nature of diffusion within a voxel. Further, we improve the robustness of the distribution parameter estimates by integrating spatial homogeneity prior into the probability distribution model of incoherent motion (SPIM) and by using the fusion bootstrap solver (FBM) to estimate the model parameters. We evaluated the improvement in quantitative DW-MRI analysis achieved with the SPIM model in terms of accuracy, precision and reproducibility of parameter estimation in both simulated data and in 68 abdominal in-vivo DW-MRIs. Our results show that the SPIM model not only substantially reduced parameter estimation errors by up to 26%; it also significantly improved the robustness of the parameter estimates (paired Student's t-test, p < 0.0001) by reducing the coefficient of variation (CV) of estimated parameters compared to those produced by previous models. In addition, the SPIM model improves the parameter estimates reproducibility for both intra- (up to 47%) and inter-session (up to 30%) estimates compared to those generated by previous models. Thus, the SPIM model has the potential to improve accuracy, precision and robustness of quantitative abdominal DW-MRI analysis for clinical applications. PMID

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  7. 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.

  8. 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

  9. Fractional diffusion by Levy stochastic motion of charged particles in the presence of a magnetic field

    NASA Astrophysics Data System (ADS)

    Moradi, Sara; Del-Castillo Negrete, Diego

    2015-11-01

    The motion of charged particles in the presence of alpha-stable Levy noise in a constant external magnetic field and linear friction is studied via Monte Carlo numerical simulations. The Levy noise is introduced to model the effect of non-local transport due to fractional diffusion in velocity space. The statistical properties of the velocity moments and energy for various values of the Levy index α are investigated. Of particular interest is the study of the resulting non-Maxwellian particle distribution functions and their dependence on alpha, the magnetic field amplitude, and the friction. We also explore the role of asymmetric Levy noise, the interplay of regular and fractional diffusion, and compute the statistical moments of displacements. Sara Moradi has benefited from a mobility grant funded by the Belgian Federal Science Policy Office and the MSCA of the European Commission (FP7-PEOPLE-COFUND-2008 no. 246540).

  10. An intramolecular hydrogen-bonded system with large proton polarizability — a model with regard to the proton pathway in bacteriorhodopsin and other systems with collective proton motion

    NASA Astrophysics Data System (ADS)

    Brzeziński, Bogumil; Radziejewski, Piotr; Olejnik, Jerzy; Zundel, Georg

    1994-07-01

    3-Diethylaminomethyl-2,2'-biphenol was synthesized and studied by FT-IR and 1H NMR spectroscopy. The compound forms a system with two hydrogen bonds which shows large proton polarizability due to collective proton motion. This result supports our earlier suggestion that the first part of the proton pathway in bacteriorhodopsin conducting protons is a hydrogen-bonded chain with large proton polarizability built up by arginine and tyrosine residues. Furthermore, we show that in the monotetrachloroaurate of 3,3'-bis(diethylaminomethyl)-2,2'-biphenol and in the tritetrachloroaurates of 3,3',5,5'-tetrakis(diethylaminomethyl)-2,2'-biphenol there is proton polarizability due to collective proton motion.

  11. Stochastic models for surface diffusion of molecules

    SciTech Connect

    Shea, Patrick Kreuzer, Hans Jürgen

    2014-07-28

    We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

  12. Due to intravascular multiple sequential scattering, Diffuse Correlation Spectroscopy of tissue primarily measures relative red blood cell motion within vessels.

    PubMed

    Carp, Stefan A; Roche-Labarbe, Nadàege; Franceschini, Maria-Angela; Srinivasan, Vivek J; Sakadžić, Sava; Boas, David A

    2011-07-01

    We suggest that Diffuse Correlation Spectroscopy (DCS) measurements of tissue blood flow primarily probe relative red blood cell (RBC) motion, due to the occurrence of multiple sequential scattering events within blood vessels. The magnitude of RBC shear-induced diffusion is known to correlate with flow velocity, explaining previous reports of linear scaling of the DCS "blood flow index" with tissue perfusion despite the observed diffusion-like auto-correlation decay. Further, by modeling RBC mean square displacement using a formulation that captures the transition from ballistic to diffusive motion, we improve the fit to experimental data and recover effective diffusion coefficients and velocity de-correlation time scales in the range expected from previous blood rheology studies. PMID:21750779

  13. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors.

    PubMed

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-22

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density. PMID:26939610

  14. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors

    NASA Astrophysics Data System (ADS)

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-01

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density.

  15. Intravoxel incoherent motion diffusion-weighted imaging in differentiating uterine fibroid from focal adenomyosis: initial results.

    PubMed

    Tian, Tao; Zhang, Guo-Fu; Zhang, He; Liu, Hui

    2016-01-01

    To evaluate the performance of intravoxel incoherent motion (IVIM)-diffusion-weighted imaging (DWI) in differentiating uterine fibroids from focal adenomyosises. Twenty-five uterine fibroids and 21 focal adenomyosises prospectively underwent IVIM-DWI examination prior to surgery. Four parameters including apparent diffusion coefficient total values (ADCtot), true diffusion coefficient (D), pseudodiffusion coefficient (D*) and perfusion fraction (f) derived from IVIM-DWI images were separately calculated and compared across four groups. There was a statistically significant difference in IVIM-derived f parameter between fibroid and focal adenomyosis (p = 0.01) and control group (p = 0.02). Uterine fibroids gave higher coefficient of variation (CV) of all IVIM-derived parameters than focal adenomyosises. IVIM-DWI could improve the sensitivity and specificity of detecting focal adenomyosis to 100 and 92.6 %, respectively. IVIM-f parameter could be potentially used to better distinguish uterine fibroid from focal adenomyosis. The higher CV of IVIM-derived parameters with acceptable range is often observed in the diseased group. PMID:26759748

  16. Evaluation of Hepatic Tumors Using Intravoxel Incoherent Motion Diffusion-Weighted MRI

    PubMed Central

    Wang, Mingjie; Li, Xudan; Zou, Jianxun; Chen, Xugao; Chen, Shuyan; Xiang, Wanqing

    2016-01-01

    Background This study aimed to evaluate the diagnostic value of the D value, D* value, and f magnitude for identifying benign and malignant hepatic tumors using intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI). Material/Methods Data of 89 cases (123 lesions) with hepatic tumor confirmed by surgical pathology and postoperative follow-up were retrospectively collected. Among these cases, 40 cases were benign hepatic tumors (57 lesions) and 49 cases were malignant hepatic tumors (66 lesions). All subjects underwent conventional MRI with T1WI, T2WI, multi-b-value DWI, and dynamic enhanced LAVA scan. Diffusion-weighted images with 11 b values (0, 10, 20, 30, 50, 80, 100, 200, 400, 800, and 1000 s/mm2) were obtained to calculate true molecular diffusion (D), perfusion-related diffusion coefficient (D*), and perfusion fraction (f). The diagnostic performance in differentiating between malignant and benign hepatic lesions was analyzed. Results Malignant lesions had a significantly lower D value ([1.04±0.34]×10−3 mm2/s) and D* value ([16.5±7.7]×10−3 mm2/s) compared to benign lesions (D value: [1.70±0.55]×10−3 mm2/s, P<0.01; D* value: [21.7±9.9]×10−3 mm2/s, P<0.01). There was no statistically significant difference in f values between malignant (23.3±9.5) and benign lesions (33.5±14.9, P=0.13). In addition, D exhibited a better diagnostic performance than D* in terms of the area under the curve, sensitivity, and specificity when identifying malignancies from benign lesions. Conclusions D and D* are significant parameters for diagnosing hepatic tumors. Moreover, the D value is a more reliable parameter in distinguishing benign and malignant hepatic tumors. PMID:26931063

  17. 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.

  18. 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. PMID:23609636

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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 C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-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 C60 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 C60 is an order of magnitude larger than the one for PCBM.

  1. 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.

  2. 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

  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. Carbon nanotube intramolecular junctions

    NASA Astrophysics Data System (ADS)

    Yao, Zhen; Postma, Henk W. Ch.; Balents, Leon; Dekker, Cees

    1999-11-01

    The ultimate device miniaturization would be to use individual molecules as functional devices. Single-wall carbon nanotubes (SWNTs) are promising candidates for achieving this: depending on their diameter and chirality, they are either one-dimensional metals or semiconductors. Single-electron transistors employing metallic nanotubes and field-effect transistors employing semiconducting nanotubes have been demonstrated. Intramolecular devices have also been proposed which should display a range of other device functions. For example, by introducing a pentagon and a heptagon into the hexagonal carbon lattice, two tube segments with different atomic and electronic structures can be seamlessly fused together to create intramolecular metal-metal, metal-semiconductor, or semiconductor-semiconductor junctions. Here we report electrical transport measurements on SWNTs with intramolecular junctions. We find that a metal-semiconductor junction behaves like a rectifying diode with nonlinear transport characteristics that are strongly asymmetric with respect to bias polarity. In the case of a metal-metal junction, the conductance appears to be strongly suppressed and it displays a power-law dependence on temperatures and applied voltage, consistent with tunnelling between the ends of two Luttinger liquids. Our results emphasize the need to consider screening and electron interactions when designing and modelling molecular devices. Realization of carbon-based molecular electronics will require future efforts in the controlled production of these intramolecular nanotube junctions.

  5. Intramolecular motion during stimulated surface processes

    SciTech Connect

    Burns, A.R.; Jennison, D.R.; Stechel, E.B. ); Li, Y.S. )

    1994-06-13

    Ammonia and deuterated ammonia exhibit an anomalously large isotope effect in their relative yields and rotational spinning energy for electron-stimulated desorption from Pt(111). Quantum-resolved desorption measurements and [ital ab] [ital initio], two-dimensional, potential energy calculations suggest that the desorbate undergoes a geometry change (molecular inversion) induced by the excited state. Inverted molecules deexcite to a repulsive hard wall potential and desorb. In general, [ital multidimensional] potential energy surfaces determine the dynamics of stimulated surface processes.

  6. 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.

  7. 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…

  8. 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…

  9. Motion of an atom in a weakly driven fiber-Bragg-grating cavity: Force, friction, and diffusion

    SciTech Connect

    Le Kien, Fam; Hakuta, K.

    2010-06-15

    We study the translational motion of an atom in the vicinity of a weakly driven nanofiber with two fiber-Bragg-grating mirrors. We calculate numerically and analytically the force, the friction coefficients, and the momentum diffusion. We find that the spatial dependences of the force, the friction coefficients, and the momentum diffusion are very complicated due to the evanescent-wave nature of the atom-field coupling as well as the effect of the van der Waals potential. We show that the time development of the mean number of photons in the cavity closely follows the translational motion of the atom through the nodes and antinodes of the fiber-guided cavity standing-wave field even though the cavity finesse is moderate, the cavity is long, and the probe field is weak.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation.

    PubMed

    Gill, Michelle L; Palmer, Arthur G

    2014-09-25

    The present work demonstrates that NMR spin relaxation rate constants for molecules interconverting between states with different diffusion tensors can be modeled theoretically by combining orientational correlation functions for exchanging spherical molecules with locally isotropic approximations for the diffusion anisotropic tensors. The resulting expressions are validated by comparison with correlation functions obtained by Monte Carlo simulations and are accurate for moderate degrees of diffusion anisotropy typically encountered in investigations of globular proteins. The results are complementary to an elegant, but more complex, formalism that is accurate for all degrees of diffusion anisotropy [Ryabov, Y.; Clore, G. M.; Schwieters, C. D. J. Chem. Phys. 2012, 136, 034108]. PMID:25167331

  15. 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.

  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. 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

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

    PubMed

    Iima, Mami; Le Bihan, Denis

    2016-01-01

    The concept of diffusion magnetic resonance (MR) imaging emerged in the mid-1980s, together with the first images of water diffusion in the human brain, as a way to probe tissue structure at a microscopic scale, although the images were acquired at a millimetric scale. Since then, diffusion MR imaging has become a pillar of modern clinical imaging. Diffusion MR imaging has mainly been used to investigate neurologic disorders. A dramatic application of diffusion MR imaging has been acute brain ischemia, providing patients with the opportunity to receive suitable treatment at a stage when brain tissue might still be salvageable, thus avoiding terrible handicaps. On the other hand, it was found that water diffusion is anisotropic in white matter, because axon membranes limit molecular movement perpendicularly to the nerve fibers. This feature can be exploited to produce stunning maps of the orientation in space of the white matter tracts and brain connections in just a few minutes. Diffusion MR imaging is now also rapidly expanding in oncology, for the detection of malignant lesions and metastases, as well as monitoring. Water diffusion is usually largely decreased in malignant tissues, and body diffusion MR imaging, which does not require any tracer injection, is rapidly becoming a modality of choice to detect, characterize, or even stage malignant lesions, especially for breast or prostate cancer. After a brief summary of the key methodological concepts beyond diffusion MR imaging, this article will give a review of the clinical literature, mainly focusing on current outstanding issues, followed by some innovative proposals for future improvements. PMID:26690990

  19. Ab initio of the intramolecular dynamics trifluoronitromethane

    SciTech Connect

    Roehrig, M.A.; McCarthy, W.J.; Kukolich, S.G.; Adamowicz, L.

    1993-12-31

    Several experimental studies of trifluoronitromethane have indicated that this molecule undergoes a low energy motion corresponding to an internal rotation of the CF{sub 3} relative to the NO{sub 2} group. Values for the V{sub 6} barrier have been obtained by electron diffraction and microwave spectroscopy to be 3 kcal/mol and 74 cal/mol respectively. A theoretical study of this molecule investigating this and possible other low energy motions is currently underway. Results from this study should reveal new information on the low barrier dynamics and shed some light on this large discrepancy on the V{sub 6} barriers. Preliminary calculations seem to indicate that a simple V{sub 6} barrier does not adequately describe the intramolecular dynamics of this molecule.

  20. Intramolecular Aminoboration of Unfunctionalized Olefins.

    PubMed

    Yang, Chun-Hua; Zhang, Yu-Shi; Fan, Wen-Wen; Liu, Gong-Qing; Li, Yue-Ming

    2015-10-19

    A direct and catalyst-free method for the intramolecular aminoboration of unfunctionalized olefins is reported. In the presence of BCl3 (1 equiv) as the sole boron source, intramolecular aminoboration of sulfonamide derivatives of 4-penten-1-amines, 5-hexen-1-amines, and 2-allylanilines proceeded readily without the use of any catalyst. The boronic acids obtained after hydrolysis could be converted into the corresponding pinacol borates in a straightforward manner by treatment with pinacol under anhydrous conditions. PMID:26331979

  1. 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

  2. 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. PMID:26871103

  3. 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.

  4. 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

  5. Levy flights and super-diffusion in the motion of a semiclassical atom-field oscillator

    NASA Astrophysics Data System (ADS)

    Mintzopoulos, Dionyssios

    2004-03-01

    A massive atom strongly coupled to a resonant field mode, such as an RF or optical mode, exhibits strongly chaotic classical dynamics. This system is abstracted with a two-parameter Hamiltonian characterized by the dimensionless recoil frequency (ν ) and the dimensionless Rabi frequency, or atom-field coupling strength, (Λ ). We study large-scale dynamics and transport in the subspace of real-space trajectories x(t). For the magnitudes of interest of (Λ ) and (ν ) the large-scale dynamics is very strongly influenced by the presence of Levy flights. We have performed highly accurate simulations and have numerically reconstructed the probability density function (PDF), ψ(t), of Levy flights as a function of their duration; the PDF itself is, of course, also parametrized by Λ and ν. The Levy flights last for as long as a trajectory is trapped in a dynamical trap (quasi-trap); the probability density of the duration of Levy flights (density of exit times from the traps) has polynomial decay ψ(t) ˜ t^-γ. For the set of ν and Λ considered (Λ ≈ 1 and 1≤ ν ≤ 100), the exponents group into two families, γ_I= 2.65, γ_II=2.30. Transport is super-diffusive: < R^2 > ˜ t^μ where μ_I=1.3, μ_II =1.78. These results are in agreement with the theoretical prediction of the one-flight approximation, μ+γ=4. Fine-structure phenomena such as log-periodic oscillations are observed in both the decay law ψ(t) and in the anomalous diffusion law. Log-periodic oscillations are the signature of a discrete Renormalization transform. We present a powerful phenomenological theoretical framework, the Renormalization Group for Kinetics (RGK), whose main features are (1) a generalized Fokker-Planck equation with fractional exponents and (2) discrete-scale invariance. The RGK formalism explains both the fine structure as well as the general features of the dynamics.

  6. Levy flights and super-diffusion in the motion of a semiclassical atom-field oscillator

    NASA Astrophysics Data System (ADS)

    Mintzopoulos, Dionyssios

    A massive atom strongly coupled to a resonant field mode, such as an RF or optical mode, exhibits strongly chaotic classical dynamics. This system is abstracted with a two-parameter Hamiltonian characterized by the dimensionless recoil frequency v and the dimensionless Rabi frequency, or atom-field coupling strength, Λ. We study large-scale dynamics and transport in the subspace of real-space trajectories x( t). For the magnitudes of interest of Λ and v the large-scale dynamics is very strongly influenced by the presence of Levy flights. We have performed highly accurate simulations and have numerically reconstructed the probability density function (PDF), ψ(t), of Levy flights as a function of their duration; the PDF itself is, of course, also parametrized by Λ and v. The Levy flights last for as long as a trajectory is trapped in a dynamical trap (quasi-trap); the probability density of the duration of Levy flights (density of exit times from the traps) has polynomial decay psi(t) ˜ t-gamma. For the set of v and Λ considered (Λ ≈ 1 and 1 ≤ v ≤ 100), the exponents group into two families, gammaI = 2.64 +/- 0.02, gammaII = 2.44 +/- 0.06. Transport is super-diffusive: ˜ tmu where muI = 1.3342 +/- 0.0008 and muII = 1.779 +/- 0.002. These results are in reasonable agreement with the theoretical prediction of the one-flight approximation, mu + gamma = 4. Fine-structure phenomena such as log-periodic oscillations are observed in both the decay law ψ(t) and in the anomalous diffusion law. Log-periodic oscillations are the signature of a discrete Renormalization transform. We present a powerful phenomenological theoretical framework, the Renormalization Group for Kinetics (RGK), whose main features are (1) a generalized Fokker-Planck equation with fractional exponents and (2) discrete-scale invariance. The RGK formalism explains both the fine structure as well as the general features of the dynamics.

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

    NASA Astrophysics Data System (ADS)

    Bielenberg, James R.; Brenner, Howard

    2005-10-01

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

  8. Active Brownian motion of emulsion droplets: Coarsening dynamics at the interface and rotational diffusion.

    PubMed

    Schmitt, M; Stark, H

    2016-08-01

    A micron-sized droplet of bromine water immersed in a surfactant-laden oil phase can swim (S. Thutupalli, R. Seemann, S. Herminghaus, New J. Phys. 13 073021 (2011). The bromine reacts with the surfactant at the droplet interface and generates a surfactant mixture. It can spontaneously phase-separate due to solutocapillary Marangoni flow, which propels the droplet. We model the system by a diffusion-advection-reaction equation for the mixture order parameter at the interface including thermal noise and couple it to fluid flow. Going beyond previous work, we illustrate the coarsening dynamics of the surfactant mixture towards phase separation in the axisymmetric swimming state. Coarsening proceeds in two steps: an initially slow growth of domain size followed by a nearly ballistic regime. On larger time scales thermal fluctuations in the local surfactant composition initiates random changes in the swimming direction and the droplet performs a persistent random walk, as observed in experiments. Numerical solutions show that the rotational correlation time scales with the square of the inverse noise strength. We confirm this scaling by a perturbation theory for the fluctuations in the mixture order parameter and thereby identify the active emulsion droplet as an active Brownian particle. PMID:27562831

  9. Investigating the Disordered States of Two Proteins Using Intramolecular Contact Formation

    NASA Astrophysics Data System (ADS)

    Singh, Vijay; Kopka, Michaela; Chen, Yujie; Wedemeyer, William; Lapidus, Lisa

    2007-03-01

    Using the quenching of the triplet state of tryptophan by cysteine, we investigate the unfolded states of two structurally similar but sequentially non-homologous proteins, the IgG binding domain of proteins L and G, under a range of denaturing conditions. These proteins show remarkably similar dynamics of intramolecular diffusion marked by a decrease in contact formation at denaturant conditions that favor folding. A reaction limited rate and the diffusion limited rate are obtained by measuring the viscosity dependence of the intramolecular contact rate. To further investigate the polymer dynamics of the unfolded state under folding conditions, we modeled the proteins as a worm-like chain with excluded volume using Szabo, Schulten and Schulten (SSS) theory to estimate the effective persistence length and intramolecular diffusion constant at various concentrations of GdnHCl. The results reveal an unfolded state under folding conditions that is significantly more compact and less diffusive than the fully denatured state.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    SciTech Connect

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

    2015-04-28

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

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

    PubMed

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

    2015-04-28

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations. PMID:25933773

  13. 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.

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

    PubMed Central

    Magusin, P C; Hemminga, M A

    1993-01-01

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

  15. Modeling vibrational dephasing and energy relaxation of intramolecular anharmonic modes for multidimensional infrared spectroscopies.

    PubMed

    Ishizaki, Akihito; Tanimura, Yoshitaka

    2006-08-28

    Starting from a system-bath Hamiltonian in a molecular coordinate representation, we examine an applicability of a stochastic multilevel model for vibrational dephasing and energy relaxation in multidimensional infrared spectroscopy. We consider an intramolecular anharmonic mode nonlinearly coupled to a colored noise bath at finite temperature. The system-bath interaction is assumed linear plus square in the system coordinate, but linear in the bath coordinates. The square-linear system-bath interaction leads to dephasing due to the frequency fluctuation of system vibration, while the linear-linear interaction contributes to energy relaxation and a part of dephasing arises from anharmonicity. To clarify the role and origin of vibrational dephasing and energy relaxation in the stochastic model, the system part is then transformed into an energy eigenstate representation without using the rotating wave approximation. Two-dimensional (2D) infrared spectra are then calculated by solving a low-temperature corrected quantum Fokker-Planck (LTC-QFP) equation for a colored noise bath and by the stochastic theory. In motional narrowing regime, the spectra from the stochastic model are quite different from those from the LTC-QFP. In spectral diffusion regime, however, the 2D line shapes from the stochastic model resemble those from the LTC-QFP besides the blueshifts caused by the dissipation from the colored noise bath. The preconditions for validity of the stochastic theory for molecular vibrational motion are also discussed. PMID:16965023

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

    PubMed Central

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

    2016-01-01

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

  18. Intramolecular Fluorescence Correlation Spectroscopy in a Feedback Tracking Microscope

    NASA Astrophysics Data System (ADS)

    McHale, Kevin; Mabuchi, Hideo

    2010-07-01

    We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system, and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. We show that tracking provides enhanced sensitivity to translational diffusion, molecular size, heterogeneity and long time-scale decays in comparison to traditional fluorescence correlation spectroscopy. We demonstrate our approach by using a three-dimensional tracking microscope to study genomic $\\lambda$-phage DNA molecules with various fluorescence label configurations.

  19. Comparison of Apparent Diffusion Coefficient and Intravoxel Incoherent Motion for Differentiating among Glioblastoma, Metastasis, and Lymphoma Focusing on Diffusion-Related Parameter

    PubMed Central

    Shim, Woo Hyun; Kim, Ho Sung; Choi, Choong-Gon; Kim, Sang Joon

    2015-01-01

    Background and Purpose Brain tumor cellularity has been assessed by using apparent diffusion coefficient (ADC). However, the ADC value might be influenced by both perfusion and true molecular diffusion, and the perfusion effect on ADC can limit the reliability of ADC in the characterization of tumor cellularity, especially, in hypervascular brain tumors. In contrast, the IVIM technique estimates parameter values for diffusion and perfusion effects separately. The purpose of our study was to compare ADC and IVIM for differentiating among glioblastoma, metastatic tumor, and primary CNS lymphoma (PCNSL) focusing on diffusion-related parameter. Materials and Methods We retrospectively reviewed the data of 128 patients with pathologically confirmed glioblastoma (n = 55), metastasis (n = 31), and PCNSL (n = 42) prior to any treatment. Two neuroradiologists independently calculated the maximum IVIM-f (fmax) and minimum IVIM-D (Dmin) by using 16 different b-values with a bi-exponential fitting of diffusion signal decay, minimum ADC (ADCmin) by using 0 and 1000 b-values with a mono-exponential fitting and maximum normalized cerebral blood volume (nCBVmax). The differences in fmax, Dmin, nCBVmax, and ADCmin among the three tumor pathologies were determined by one-way ANOVA with multiple comparisons. The fmax and Dmin were correlated to the corresponding nCBV and ADC using partial correlation analysis, respectively. Results Using a mono-exponential fitting of diffusion signal decay, the mean ADCmin was significantly lower in PCNSL than in glioblastoma and metastasis. However, using a bi-exponential fitting, the mean Dmin did not significantly differ in the three groups. The mean fmax significantly increased in the glioblastomas (reader 1, 0.103; reader 2, 0.109) and the metastasis (reader 1, 0.105; reader 2, 0.107), compared to the primary CNS lymphomas (reader 1, 0.025; reader 2, 0.023) (P < .001 for each). The correlation between fmax and the corresponding nCBV was highest

  20. 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.

  1. 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. PMID:26249347

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

    DOE PAGESBeta

    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'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

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

    PubMed Central

    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.

    2015-01-01

    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. PMID:26249347

  4. Intravoxel Incoherent Motion MR Imaging: Comparison of Diffusion and Perfusion Characteristics for Differential Diagnosis of Soft Tissue Tumors

    PubMed Central

    Du, Jun; Li, Kun; Zhang, Weisheng; Wang, Shaowu; Song, Qingwei; Liu, Ailian; Miao, Yanwei; Lang, Zhijin; Zhang, Lina; Zheng, Minting

    2015-01-01

    Abstract We used intravoxel incoherent motion (IVIM) magnetic resonance imaging (MRI) to explore the possibility of preoperative diagnosis of soft tissue tumors (STTs). This prospective study enrolled 23 patients. Conventional MRI and IVIM examinations were performed on a 3.0T MR imager. Eight (35%) hemangiomas, 11 (47%) benign soft tissue tumors excluding hemangiomas (BSTTEHs) and 4 soft tissue sarcomas (STSs) were assessed. The mean tumor size was about 1652.36 ± 233.66 mm2. Ten b values (0–800 s/mm2) were used to evaluate diffusion and perfusion characteristics of IVIM. IVIM parameters (ADCstandard, ADCslow, ADCfast, and f) of STTs were measured and evaluated for differentiating hemangiomas, BSTTEHs, and STSs. ADCslow and ADCfast value were different for hemangiomas, BSTTEHs, and STSs separately (P < 0.001, P < 0.001, and P = 0.001). ADCslow, cut-off value smaller than 0.93 × 10–3 mm2/s, was the best parameter to differ STSs (0.689 ± 0.173 × 10−3 mm2/s) from hemangiomas (0.933 ± 0.237 × 10−3 mm2/s) and BSTTEHs (1.156 ± 0.120 × 10−3 mm2/s) (P = 0.001). ADCslow (0.93 × 10−3 mm2/s

  5. Intermediate State Dependence of Intramolecular Vibrations in Photoactive Yellow Protein

    NASA Astrophysics Data System (ADS)

    Deng, Yanting; Xu, Mengyang; Niessen, Katherine; Schmidt, Marius; Markelz, Andrea

    Photoactive proteins provide a testbed for the role of long-range collective motions in protein function. Long-range intramolecular vibrations of the protein scaffold may provide efficient energy relaxation, enhancement of chromophore vibrations that promote structural transitions and assistance in electron energy transfer. Photoactive yellow protein (PYP) is a cytoplasmic photocycling protein associated with the negative phototactic response to blue light in halohodospira halophile. We measure the intramolecular vibrations of PYP using crystal anisotropy terahertz microscopy (CATM) as a function of photoexcitation. Room temperature CATM measurements are performed in the dark and with continuous illumination at 488 nm, which is found to result in an approximately 20% steady photoexcited state (pB). We find a decrease in anisotropic absorption in frequency range 20-60 cm-1 with photoexcitation. This result may be due to an increase in sample disorder associated with the structural change in pB state. We compare the measured and calculated spectra using molecular dynamics and normal mode/quasiharmonic analysis to identify the nature of the motions giving rise to the resonant absorption bands.

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

    SciTech Connect

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

    2014-06-15

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

  7. Laser-Induced Dynamical Chirality and Intramolecular Energy Flow in the CH Chromophore

    SciTech Connect

    Thanopulos, Ioannis

    2007-11-29

    We review the quantum dynamics of intramolecular energy flow during and after coherent infrared multiphoton excitation of the CH organic chromophore. The understanding of the underlying dynamics is of central importance for a wide range of systems in molecular physics, chemistry and biology, due to the experimentally supported assumption that the chromophore dynamics is weakly-dependent on a specific environment, in particular on sub-picosecond time scale. The excitation process due to the interaction with the laser field is studied by computationally monitoring the wave packet motion in the configuration sub-space relevant to femtosecond dynamics, using global analytical potential energy and electric dipole functions previously developed. The features of the intramolecular vibrational energy redistribution and the related dynamical time scales are investigated. In particular, we discuss the generation of dynamical chirality in methane istopomers, the corresponding stereomutation and racemization phenomena on the femtosecond time scale, and their relation to intramolecular vibrational energy redistribution.

  8. Intramolecular Hydrogen Bonding in Substituted Aminoalcohols.

    PubMed

    Lane, Joseph R; Schrøder, Sidsel D; Saunders, Graham C; Kjaergaard, Henrik G

    2016-08-18

    The qualifying features of a hydrogen bond can be contentious, particularly where the hydrogen bond is due to a constrained intramolecular interaction. Indeed there is disagreement within the literature whether it is even possible for an intramolecular hydrogen bond to form between functional groups on adjacent carbon atoms. This work considers the nature of the intramolecular interaction between the OH (donor) and NH2 (acceptor) groups of 2-aminoethanol, with varying substitution at the OH carbon. Gas-phase vibrational spectra of 1-amino-2-methyl-2-propanol (BMAE) and 1-amino-2,2-bis(trifluoromethyl)-2-ethanol (BFMAE) were recorded using Fourier transform infrared spectroscopy and compared to literature spectra of 2-aminoethanol (AE). Based on the experimental OH-stretching frequencies, the strength of the intramolecular hydrogen bond appears to increase from AE < BMAE ≪ BFMAE. Non-covalent interaction analysis shows evidence of an intramolecular hydrogen bond in all three molecules, with the order of the strength of interaction matching that of experiment. The experimental OH-stretching vibrational frequencies were found to correlate well with the calculated kinetic energy density, suggesting that this approach can be used to estimate the strength of an intramolecular hydrogen bond. PMID:27447952

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

    PubMed Central

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

    2015-01-01

    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. PMID:26811845

  10. 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

  11. Simulation of biomolecular diffusion and complex formation.

    PubMed Central

    Allison, S A; Northrup, S H; McCammon, J A

    1986-01-01

    Diffusion is a phenomenon of very widespread importance in molecular biophysics. Diffusion can determine the rates and character of the assembly of multisubunit structures, the binding of ligands to receptors, and the internal motions of molecules and assemblies that involve solvent surface displacements. Current computer simulation techniques provide much more detailed descriptions of diffusional processes than have been available in the past. Models can be constructed to include such realistic features as structural subunits at the submolecular level (domains, monomers, or atoms); detailed electrostatic charge distributions and corresponding solvent-screened inter- and intramolecular interactions; and hydrodynamic interactions. The trajectories can be analyzed either to provide direct information on biomolecular function (e.g., the bimolecular rate constant for formation of an electron-transfer complex between two proteins), or to provide or test models for the interpretation of experimental data (e.g., the time dependence of fluorescence depolarization for segments of DNA). Here, we first review the theory of diffusional simulations, with special emphasis on new techniques such as those for obtaining transport properties of flexible assemblies and rate constants of diffusion-controlled reactions. Then we survey a variety of recent applications, including studies of large-scale motion in DNA segments and substrate "steering" in enzyme-substrate binding. We conclude with a discussion of current work (e.g., formation of protein complexes) and possible areas for future work. PMID:3955168

  12. 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

  13. Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor

    PubMed Central

    Nishihara, Yasutaka; Kitao, Akio

    2015-01-01

    The proton permeation process of the stator complex MotA/B in the flagellar motor of Escherichia coli was investigated. The atomic model structure of the transmembrane part of MotA/B was constructed based on the previously published disulfide cross-linking and tryptophan scanning mutations. The dynamic permeation of hydronium/sodium ions and water molecule through the channel formed in MotA/B was observed using a steered molecular dynamics simulation. During the simulation, Leu46 of MotB acts as the gate for hydronium ion permeation, which induced the formation of water wire that may mediate the proton transfer to Asp32 on MotB. Free energy profiles for permeation were calculated by umbrella sampling. The free energy barrier for H3O+ permeation was consistent with the proton transfer rate deduced from the flagellar rotational speed and number of protons per rotation, which suggests that the gating is the rate-limiting step. Structure and dynamics of the MotA/B with nonprotonated and protonated Asp32, Val43Met, and Val43Leu mutants in MotB were investigated using molecular dynamics simulation. A narrowing of the channel was observed in the mutants, which is consistent with the size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintained a kink whereas the protonation induced a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, which may be correlated to the motion of the flagellar rotor. PMID:26056313

  14. Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor.

    PubMed

    Nishihara, Yasutaka; Kitao, Akio

    2015-06-23

    The proton permeation process of the stator complex MotA/B in the flagellar motor of Escherichia coli was investigated. The atomic model structure of the transmembrane part of MotA/B was constructed based on the previously published disulfide cross-linking and tryptophan scanning mutations. The dynamic permeation of hydronium/sodium ions and water molecule through the channel formed in MotA/B was observed using a steered molecular dynamics simulation. During the simulation, Leu46 of MotB acts as the gate for hydronium ion permeation, which induced the formation of water wire that may mediate the proton transfer to Asp32 on MotB. Free energy profiles for permeation were calculated by umbrella sampling. The free energy barrier for H3O(+) permeation was consistent with the proton transfer rate deduced from the flagellar rotational speed and number of protons per rotation, which suggests that the gating is the rate-limiting step. Structure and dynamics of the MotA/B with nonprotonated and protonated Asp32, Val43Met, and Val43Leu mutants in MotB were investigated using molecular dynamics simulation. A narrowing of the channel was observed in the mutants, which is consistent with the size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintained a kink whereas the protonation induced a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, which may be correlated to the motion of the flagellar rotor. PMID:26056313

  15. 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. PMID:27114342

  16. Assessing the Early Response of Advanced Cervical Cancer to Neoadjuvant Chemotherapy Using Intravoxel Incoherent Motion Diffusion-weighted Magnetic Resonance Imaging: A Pilot Study

    PubMed Central

    Wang, Yan-Chun; Hu, Dao-Yu; Hu, Xue-Mei; Shen, Ya-Qi; Meng, Xiao-Yan; Tang, Hao; Li, Zhen

    2016-01-01

    Background: Diffusion-weighted imaging (DWI) with the intravoxel incoherent motion (IVIM) model has shown promising results for providing both diffusion and perfusion information in cervical cancer; however, its use to predict and monitor the efficacy of neoadjuvant chemotherapy (NACT) in cervical cancer is relatively rare. The study aimed to evaluate the use of DWI with IVIM and monoexponential models to predict and monitor the efficacy of NACT in cervical cancer. Methods: Forty-two patients with primary cervical cancer underwent magnetic resonance exams at 3 time points (pre-NACT, 3 weeks after the first NACT cycle, and 3 weeks after the second NACT cycle). The response to treatment was determined according to the response evaluation criteria in solid tumors 3 weeks after the second NACT treatment, and the subjects were classified as two groups: responders and nonresponders groups. The apparent diffusion coefficient (ADC), true diffusion coefficient (D), perfusion-related pseudo-diffusion coefficient (D*), and perfusion fraction (f) values were determined. The differences in IVIM-derived variables and ADC between the different groups at the different time points were calculated using an independent samples t-test. Results: The D and ADC values were all significantly higher for the responders than for the nonresponders at all 3 time points, but no significant differences were observed in the D* and f values. An analysis of the receiver operating characteristic (ROC) curves indicated that a D value threshold <0.93 × 10−3 mm2/s and an ADC threshold <1.11 × 10−3 mm2/s could differentiate responders from nonresponders at pre-NACT time point, yielding area under the curve (AUC) of which were 0.771 and 0.806, respectively. The ROC indicated that the AUCs of D and ADC at the 3 weeks after the first NACT cycle and 3 weeks after the second NACT cycle were 0.823, 0.763, and 0.787, 0.794, respectively. The AUC values of D and ADC at these 3 time points were not

  17. Intravoxel Incoherent Motion Diffusion-Weighted MRI at 3.0 T Differentiates Malignant Breast Lesions From Benign Lesions and Breast Parenchyma

    PubMed Central

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

    2016-01-01

    Purpose To study the differentiation of malignant breast lesions from benign lesions and fibroglandular tissue (FGT) using apparent diffusion coefficient (ADC) and intravoxel incoherent motion (IVIM) parameters. Materials and Methods This retrospective study included 26 malignant and 14 benign breast lesions in 35 patients who underwent diffusion-weighted MRI at 3.0T and nine b-values (0–1000 s/mm2). ADC and IVIM parameters (perfusion fraction fp, pseudodiffusion coefficient Dp, and true diffusion coefficient Dd) were determined in lesions and FGT. For comparison, IVIM was also measured in 16 high-risk normal patients. A predictive model was constructed using linear discriminant analysis. Lesion discrimination based on ADC and IVIM parameters was assessed using receiver operating characteristic (ROC) and area under the ROC curve (AUC). Results In FGT of normal subjects, fp was 1.1 ± 1.1%. In malignant lesions, fp (6.4 ± 3.1%) was significantly higher than in benign lesions (3.1 ± 3.3%, P = 0.0025) or FGT (1.5 ± 1.2%, P < 0.001), and Dd ((1.29 ± 0.28) × 10−3 mm2/s) was lower than in benign lesions ((1.56 ± 0.28) × 10−3 mm2/s, P = 0.011) or FGT ((1.86 ± 0.34) × 10−3 mm2/s, P < 0.001). A combination of Dd and fp provided higher AUC for discrimination between malignant and benign lesions (0.84) or FGT (0.97) than ADC (0.72 and 0.86, respectively). Conclusion The IVIM parameters provide accurate identification of malignant lesions. PMID:24273096

  18. Organocatalyzed Intramolecular Carbonyl-Ene Reactions.

    PubMed

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

    2016-01-01

    An organocatalyzed intramolecular carbonyl-ene reaction was developed to produce carbocyclic and heterocyclic 5- and 6-membered rings from a citronellal-derived trifluoroketone and a variety of aldehydes. A phosphoramide derivative was found to promote the cyclization of the trifluoroketone, whereas a less acidic phosphoric acid proved to be a superior catalyst for the aldehyde substrates. PMID:27258238

  19. Intramolecular alpha–Glucosaminidation: Synthesis of Mycothiol

    PubMed Central

    Ajayi, Kehinde; Thakur, Vinay V.; Lapo, Robert C.; Knapp, Spencer

    2010-01-01

    A protected cyclitol aglycon was tethered to an (N-arylsulfonyl)glucosamine donor by a methylene linker; the exclusively alpha-selective intramolecular glycosyation reaction was then initiated by electrophilic activation of the thioglycoside donor portion. Further transformations of the glycosylation product to give the M. tuberculosis detoxifier mycothiol and its oxidized congener, the disulfide mycothione, are detailed. PMID:20443569

  20. RESIDENCE TIMES OF PARTICLES IN DIFFUSIVE PROTOPLANETARY DISK ENVIRONMENTS. II. RADIAL MOTIONS AND APPLICATIONS TO DUST ANNEALING

    SciTech Connect

    Ciesla, F. J.

    2011-10-10

    The origin of crystalline grains in comets and the outer regions of protoplanetary disks remains a mystery. It has been suggested that such grains form via annealing of amorphous precursors in the hot, inner region of a protoplanetary disk, where the temperatures needed for such transformations were found, and were then transported outward by some dynamical means. Here we develop a means of tracking the paths that dust grains would have taken through a diffusive protoplanetary disk and examine the types and ranges of environments that particles would have seen over a 10{sup 6} yr time period in the dynamic disk. We then combine this model with three annealing laws to examine how the dynamic evolution of amorphous grains would have led to their physical restructuring and their delivery to various regions of the disk. It is found that 'sibling particles' - those particles that reside at the same location at a given period of time-take a wide range of unique and independent paths through the disk to arrive there. While high temperatures can persist in the disk for very long time periods, we find that those grains that are delivered to the cold outer regions of the disk are largely annealed in the first few x10{sup 5} yr of disk history. This suggests that the crystallinity of grains in the outer disk would be determined early and remain unchanged for much of disk history, in agreement with recent astronomical observations.

  1. Characteristics of the motions, turbulence intensity, diffusivity, flux of momentum and sensible heat in the upper atmosphere

    NASA Technical Reports Server (NTRS)

    Kao, S. K.; Lordi, N. J.

    1977-01-01

    Analyses of the meteorological rocket data obtained from an experiment conducted at 3-hour intervals at 8 western meridional rocket stations are presented. Large variations in the meridional wind contribute substantially to overall turbulence in the tropical stratosphere. The solar semidiurnal component of wind oscillations in the tropics was observed to be much higher than predicted by theory, often exceeding the magnitude of the diurnal amplitude throughout the stratosphere. The observed value of the solar diurnal amplitude in the stratosphere was in line with theoretical prediction. The solar terdiurnal amplitudes for temperature, meridional and zonal winds were non-negligible and must be considered in any harmonic analysis. Phase angle variation with height was rapid for all harmonics; however, there was general agreement between predicted and observed phase angles. Because of large changes in the mean winds in the mesosphere with season, harmonic determinations are difficult. There appear to be large zonal wind changes even within the same season as mentioned previously. Turbulence diffusivity in the upper stratosphere is greater near the equator than in the mid-latitudes.

  2. 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.

  3. Multicomponent diffusive-convective fluid motions in porous layers: Ultimately boundedness, absence of subcritical instabilities, and global nonlinear stability for any number of salts

    NASA Astrophysics Data System (ADS)

    Rionero, Salvatore

    2013-05-01

    Either for its great geophysical relevance or the frequent occurrence of porous materials in real life, research on convective-diffusive fluid motions in porous horizontal layers has a notable relevance, which is increasing with the number of salts dissolved in the fluid. In the present paper, porous horizontal layers heated from below and salted by m salts partly from above and partly from below are studied forall min {N}. In the Darcy-Boussinesq scheme it is shown that: (i) the L2 solutions are bounded, uniquely determined, and asymptotically converging toward an absorbing set; (ii) for each Fourier component of the perturbations to the thermal conduction solution, there exists an own nonlinear admissible evolution system; (iii) subcritical instabilities do not exist and the conditions of linear stability also guarantee the global nonlinear stability; (iv) global nonlinear stability is guaranteed by the general condition (1.2) holding forall min {N}; (v) condition (1.2) is hidden in the Darcy-Boussinesq equations, it can be found by substituting the salt concentration fields via new suitable unknown fields and looking for symmetries and skew-symmetries in the new system of equations. The present paper - originating from Rionero ["Absence of subcritical instabilities and global nonlinear stability for porous ternary diffusive-convective fluid mixtures," Phys. Fluids 24, 104101 (2012)], 10.1063/1.4757858 - generalizes the properties (ii)-(iv) (obtained for m = 2) to any min {N} and furnishes the newly obtained properties (i) and (v). We stress the relevant physical meaning of (1.2). In fact (1.2) - in simple algebraic closed form - guarantees that the onset of convection cannot occur and appears to be useful not only for theoreticians but also for experimentalists in the research field of physics of fluids. Analogously, conditions guaranteeing the onset of convection - in simple algebraic closed form (cf. d6.18 d6.19">(6.18) and (6.19) reversed) - are furnished.

  4. Aptamer switch probe based on intramolecular displacement.

    PubMed

    Tang, Zhiwen; Mallikaratchy, Prabodhika; Yang, Ronghua; Kim, Youngmi; Zhu, Zhi; Wang, Hui; Tan, Weihong

    2008-08-27

    A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design utilizes both a fluorophore and a quencher which are respectively modified at the two termini of the ASP. In the absence of the target molecule, the short DNA will hybridize with the aptamer, keeping the fluorophore and quencher in close proximity, thus switching off the fluorescence. However, when the ASP meets its target, the binding between the aptamer and the target molecule will disturb the intramolecular DNA hybridization, move the quencher away from the fluorophore, and, in effect, switch on the fluorescence. Both ATP and human alpha-thrombin aptamers were engineered to demonstrate this design, and both showed that fluorescence enhancement could be quantitatively mediated by the addition of various amounts of target molecules. Both of these ASPs presented excellent selectivity and prompt response toward their targets. With intrinsic advantages resulting from its intramolecular signal transduction architecture, the ASP design holds promising potential for future applications, such as biochip and in situ imaging, which require reusability, excellent stability, prompt response, and high sensitivity. PMID:18680291

  5. Intramolecular energy transfer reactions in polymetallic

    SciTech Connect

    Petersen, J.

    1990-11-01

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

  6. 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

  7. Thiol dependent intramolecular locking of Orai1 channels.

    PubMed

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

    2016-01-01

    Store-operated Ca(2+) 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 Ca(2+) 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

  8. GPS Versus Seismological Observations in two Seismogenic Zones in the Adria-Alps- Pannon System; Block Motion vs. Diffuse Deformation, Increased Earthquake Potential vs. Aseismic Slip

    NASA Astrophysics Data System (ADS)

    Grenerczy, G.; Bus, Z.; Toth, L.; Monus, P.

    2008-12-01

    The tectonic activity, seismicity and the associated seismic hazard is highly variable in the Adria-Alps-Pannon region. The engine of the system is the Adria microplate that compresses a puzzle of crustal blocks towards the European Platform. Based on seismicity and data of continuous and campaign style GPS measurements between 1991 and 2007 we investigated the existence of different blocks and their present kinematics. At the resolution and signal level we have, deformation seems to be more diffuse and block motion is no longer recognizable over the Pannonian basin towards the Carpathains. Although towards the basin seismicity decreases to moderate, the vulnerability is still high, as three capital cities are located near to the two most active seismic zones in this subregion. Each cities and their suburbs produce about 30- 40 % of the GDP of the respective countries. In the second par of our analysis these two seismically active areas, the Mur-Murz and Central Pannonian zones, are investigated. Uniform strain rates and relative displacements were calculated for these regions. The GPS data confirm the mostly left lateral strike slip character of the Mur-Murz fault zone and suggest a contraction between the eastward moving Alpine-North Pannonian unit and the Carpathians. The computation of the seismic strain rate was based on the Kostrov summation. The averaged unit norm seismic moment tensor, which describes the characteristic style of deformation, has been obtained by using the available focal mechanism solutions, whereas the annual seismic moment release showing the rate of the deformation was estimated using the catalogs of historical and recent earthquakes. Our analysis reveals that in both zones the geodetic strain rate is significantly larger than the seismic deformation. Based on the weakness of the lithosphere, the stress magnitudes and the regional features of seismicity, we suggest that the low value of the seismic/geodetic strain rate ratio in the

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

    SciTech Connect

    Bellucci, Michael A.; Coker, David F.

    2012-05-21

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

  10. Quantitative Intramolecular Singlet Fission in Bipentacenes.

    PubMed

    Sanders, Samuel N; Kumarasamy, Elango; Pun, Andrew B; Trinh, M Tuan; Choi, Bonnie; Xia, Jianlong; Taffet, Elliot J; Low, Jonathan Z; Miller, John R; Roy, Xavier; Zhu, X-Y; Steigerwald, Michael L; Sfeir, Matthew Y; Campos, Luis M

    2015-07-22

    Singlet fission (SF) has the potential to significantly enhance the photocurrent in single-junction solar cells and thus raise the power conversion efficiency from the Shockley-Queisser limit of 33% to 44%. Until now, quantitative SF yield at room temperature has been observed only in crystalline solids or aggregates of oligoacenes. Here, we employ transient absorption spectroscopy, ultrafast photoluminescence spectroscopy, and triplet photosensitization to demonstrate intramolecular singlet fission (iSF) with triplet yields approaching 200% per absorbed photon in a series of bipentacenes. Crucially, in dilute solution of these systems, SF does not depend on intermolecular interactions. Instead, SF is an intrinsic property of the molecules, with both the fission rate and resulting triplet lifetime determined by the degree of electronic coupling between covalently linked pentacene molecules. We found that the triplet pair lifetime can be as short as 0.5 ns but can be extended up to 270 ns. PMID:26102432

  11. Simple intramolecular model potentials for water

    SciTech Connect

    Dang, L.X.; Pettitt, B.M.

    1987-06-04

    An effective intramolecular potential is presented for use in conjunction with existing three-site models of water. Two commonly used internal geometries were fit to the same form yielding slightly different parametrizations. By including a Urey-Bradley-like term in an otherwise standard molecular mechanics form it was found that the experimental transition frequencies of water monomer can be reproduced accurately. Good qualitative agreements for spectral shifts were subsequently found for the models in condensed-phase applications. Harmonic analysis of clusters indicates good qualitative agreement with experimental environmental shifts in frequencies at low temperatures for these models. This model should be useful for a wide variety of applications including simulations of biopolymers and ionic solutions.

  12. Are intramolecular frustrated Lewis pairs also intramolecular catalysts? A theoretical study on H2 activation.

    PubMed

    Zeonjuk, Lei Liu; St Petkov, Petko; Heine, Thomas; Röschenthaler, Gerd-Volker; Eicher, Johannes; Vankova, Nina

    2015-04-28

    We investigate computationally a series of intramolecular frustrated Lewis pairs (FLPs), with the general formula Mes2PCHRCH2B(C6F5)2, that are known from the literature to either activate molecular hydrogen (FLPs with R = H (1) or Me (4)), or remain inert (FLPs with R = Ph (2) or SiMe3 (3)). The prototypical system Mes2PCH2CH2B(C6F5)2 (1) has been described in the literature (Grimme et al., Angew. Chem., Int. Ed., 2010; Rokob et al., J. Am. Chem. Soc., 2013) as an intramolecular reactant that triggers the reaction with H2 in a bimolecular concerted fashion. In the current study, we show that the concept of intramolecular H2 activation by linked FLPs is not able to explain the inertness of the derivative compounds 2 and 3 towards H2. To cope with this, we propose an alternative intermolecular mechanism for the investigated reaction, assuming stacking of two open-chain FLP conformers, and formation of a dimeric reactant with two Lewis acid–base domains, that can split up to two hydrogen molecules. Using quantum-chemical methods, we compute the reaction profiles describing these alternative mechanisms, and compare the derived predictions with earlier reported experimental results. We show that only the concept of intermolecular H2 activation could explain both the activity of the FLPs having small substituents in the bridging molecular region, and the inertness of the FLPs with a bulkier substitution, in a consistent way. Importantly, the intermolecular H2 activation driven by intramolecular FLPs indicates the key role of steric factors and noncovalent interactions for the design of metal-free systems that can efficiently split H2, and possibly serve as metal-free hydrogenation catalysts. PMID:25812167

  13. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water.

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

    Full classical molecular dynamics (MD) simulations of two-dimensional (2D) infrared-Raman and 2D Raman spectroscopies of liquid water were carried out to elucidate a mode-mode coupling mechanism using a polarizable water model for intermolecular and intramolecular vibrational spectroscopy (POLI2VS). This model is capable of describing both infrared and Raman spectra. Second-order response functions, which consist of one molecular polarizability and two molecular dipole moments for 2D IR-Raman and three molecular polarizabilities for 2D Raman spectroscopies, were calculated using an equilibrium-non-equilibrium hybrid MD approach. The obtained signals were analyzed using a multi-mode Brownian oscillator (BO) model with nonlinear system-bath interactions representing the intramolecular OH stretching, intramolecular HOH bending, hydrogen bonded (HB)-intermolecular librational motion and HB-intermolecular vibrational (translational) motion of liquid water. This model was applied through use of hierarchal Fokker-Planck equations. The qualitative features of the peak profiles in the 2D spectra obtained from the MD simulations are accurately reproduced with the BO model. This indicates that this model captures the essential features of the intermolecular and intramolecular motion. We elucidate the mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling, the nonlinearities of the polarizability and dipole moment, and the vibrational dephasing processes of liquid water even in the case that the 2D spectral peaks obtained from the MD simulation overlap or are unclear. The mode coupling peaks caused by electrical anharmonic coupling (EAHC) and mechanical anharmonic coupling (MAHC) are observed in all of the 2D spectra. We find that the strength of the MAHC between the OH-stretching and HB-intermolecular vibrational modes is comparable to that between the OH-stretching and HOH bending modes. Moreover, we find that this OH-stretching and HB

  14. Protein Motions and Folding Investigated by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2002-03-01

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

  15. Spatio - temporal features of protein specific motions. The influence of hydration.

    PubMed

    Krupyanskii, Yu F; Esin, S V; Eshenko, G V; Mikhailyuk, M G

    2002-06-01

    The angular dependencies of inelastic intensities of Rayleigh scatteringof Moessbauer radiation were measured for lysozyme and myoglobin (fordifferent degrees of hydration: from h = 0.05 till h = 0.7). The treating ofthe data at h > 0.05 approves the existence of segmental motions(α-helices for myoglobin, α-helices and β-sheets forlysozyme) as well as of individual motions. Further hydration increase themean-square displacements for both types of intraglobular motions for theseproteins, while the motions of the globule as a whole remain nearlythe same as for h = 0.05. Results of the study of the radial distributionfunction deduced by Fourier - transform from the diffuse x-raymeasurements together with RSMR data allow to conclude that the waterduring hydration of proteins competes with the intramolecular hydrogenbonds, loosens the protein and increases the internal dynamics. At the sametime water arranges the ordering of macromolecule from `glassy' state ath ≈ 0.02 to the native state at h = 0.4-0.7. Differentarchitecture of proteins leads to the different structural dynamics as in thecase of lysozyme and myoglobin. PMID:23345763

  16. Brownian motion goes ballistic

    NASA Astrophysics Data System (ADS)

    Florin, Ernst-Ludwig

    2012-02-01

    It is the randomness that is considered the hallmark of Brownian motion, but already in Einstein's seminal 1905 paper on Brownian motion it is implied that this randomness must break down at short time scales when the inertia of the particle kicks in. As a result, the particle's trajectories should lose its randomness and become smooth. The characteristic time scale for this transition is given by the ratio of the particle's mass to its viscous drag coefficient. For a 1 μm glass particle in water and at room temperature, this timescale is on the order of 100 ns. Early calculations, however, neglected the inertia of the liquid surrounding the particle which induces a transition from random diffusive to non-diffusive Brownian motion already at much larger timescales. In this first non-diffusive regime, particles of the same size but with different densities still move at almost the same rate as a result of hydrodynamic correlations. To observe Brownian motion that is dominated by the inertia of the particle, i.e. ballistic motion, one has to observe the particle at significantly shorter time scales on the order of nanoseconds. Due to the lack of sufficiently fast and precise detectors, such experiments were so far not possible on individual particles. I will describe how we were able to observe the transition from hydrodynamically dominated Brownian motion to ballistic Brownian motion in a liquid. I will compare our data with current theories for Brownian motion on fast timescales that take into account the inertia of both the liquid and the particle. The newly gained ability to measure the fast Brownian motion of an individual particle paves the way for detailed studies of confined Brownian motion and Brownian motion in heterogeneous media. [4pt] [1] Einstein, A. "Uber die von der molekularkinetischen Theorie der W"arme geforderte Bewegung von in ruhenden Fl"ussigkeiten suspendierten Teilchen. Ann. Phys. 322, 549--560 (1905). [0pt] [2] Lukic, B., S. Jeney, C

  17. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    NASA Astrophysics Data System (ADS)

    Belkov, M. V.; Harbachova, A. N.; Ksendzova, G. A.; Polozov, G. I.; Skornyakov, I. V.; Sorokin, V. L.; Tolstorozhev, G. B.; Shadyro, O. I.

    2010-07-01

    IR Fourier spectroscopy methods have been adopted to study intramolecular interactions that occur in CCl4 solutions of antiviral derivatives of aminophenol. Analysis of the IR spectra showed that intramolecular bonds O-H···N, O-H···O=C, N-H···O=S=O, and O-H···O=S=O can occur in these compounds depending on the substituent on the amino group. Not only the presence of intramolecular O-H···N, O-H···O=S=O, and N- H···O=S=O hydrogen bonds in 2-amino-4,6-di-tert-butylphenol derivatives containing a sulfonamide fragment but also conformational equilibrium among these types of intramolecular interactions are essential for the manifestation of high efficiency in suppressing HIV-infection in cell culture.

  18. Synchronous intramolecular cycloadditions of the polyene macrolactam polyketide heronamide C.

    PubMed

    Booth, Thomas J; Alt, Silke; Capon, Robert J; Wilkinson, Barrie

    2016-05-11

    A growing number of natural products appear to arise from biosynthetic pathways that involve pericyclic reactions. We show here that for the heronamides this can occur via two spontaneous pathways involving alternative thermal or photochemical intramolecular cycloadditions. PMID:27091090

  19. Exciton Correlations in Intramolecular Singlet Fission.

    PubMed

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

    2016-06-15

    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. PMID:27183040

  20. 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

  1. 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…

  2. 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.

  3. Intramolecular energy transfer in fullerene pyrazine dyads

    SciTech Connect

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

    1998-11-26

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

  4. Characteristics of Intramolecular Charge Transfer by J-Aggregates in Merocyanine Dye LB Films.

    PubMed

    Yang, Chang Heon; Kwon, Young-Soo; Shin, Hoon-Kyu

    2016-06-01

    In this study, for the development of future molecular electronic devices, we have investigated the characteristics of the aggregates of Langmuir-Blodgett films. The characteristics of intramolecular charge transfer by J-aggregates in merocyanine dye LB films have been studied experimentally by using UV irradiation and heat treatment. In addition to intramolecular charge transfer, we also studied the conjugation and energy changes of the molecules. In case a dye is thinned by LB method, the alkyl chain is often displaced in order to form a mono-molecular film with ease. Since the molecular association form is often made by self-organization of molecules themselves, in case the dye and the alkyl chain are strongly bonded by the covalent bond, it may be said that the properties of the LB film to be built up are almost determined at the time of synthesis of film-forming molecules. Meanwhile, since, in case LB film is fabricated by the diffusion absorption method, the cohesive force between the water-soluble dye and the surface-active mono-molecular film is electrostatic, the dye molecule can move relatively freely on the air/water interface, which may be regarded as a two-dimensional crystal growth process. PMID:27427711

  5. Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

    PubMed

    Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

    2015-06-01

    Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design. PMID:25894091

  6. Shape of the proton potential in an intramolecular hydrogen-bonded system

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2001-09-01

    5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide was studied by IR and NMR spectroscopy in chloroform and acetonitrile solutions. Two intramolecular hydrogen bonds are present in these molecules. The NO⋯H +⋯O - bond formed between the OH and the N-oxide groups is very strong. The proton potential is flat and broad and has probably no barrier. This hydrogen bond shows only slight proton polarizability. The other hydrogen bond formed between two hydroxyl groups OH⋯O -⇌ -O⋯HO is weaker and show large proton polarizability. The proton motions in both hydrogen bonds are not coupled and therefore these hydrogen bonds are not cooperative.

  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

    2016-05-01

    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. PMID:27027800

  8. Silver-catalysed intramolecular hydroamination of alkynes with trichloroacetimidates.

    PubMed

    Wong, Valerie H L; Hor, T S Andy; Hii, King Kuok Mimi

    2013-10-18

    Silver(I) complexes catalyse the intramolecular addition of trichloroacetimidates to alkynes. In the absence of a ligand, the selectivity of the reaction is dependent upon the nature of the counter-anion and solvent. The introduction of non-chelating nitrogeneous ligands suppresses competitive Brønsted acid catalysis, improving the yield and selectivity of the reaction. PMID:23999555

  9. Fractional Levy motion through path integrals

    SciTech Connect

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

    2009-01-01

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

  10. 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.

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

    PubMed Central

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

    2014-01-01

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

  12. Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

    PubMed Central

    Papaleo, Elena; Renzetti, Giulia; Tiberti, Matteo

    2012-01-01

    Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface. PMID:22558199

  13. Intramolecular vibrational dephasing obeys a power law at intermediate times

    PubMed Central

    Gruebele, M.

    1998-01-01

    Experimental intramolecular vibrational dephasing transients for several large organic molecules are reanalyzed. Fits to the experimental data, as well as full numerical quantum calculations with a factorized potential surface for all active degrees of freedom of fluorene indicate that power law decays, not exponentials, occur at intermediate times. The results support a proposal that power law decays describe vibrational dephasing dynamics in large molecules at intermediate times because of the local nature of energy flow. PMID:9600900

  14. Stereodivergent Synthesis of Chromanones and Flavanones via Intramolecular Benzoin Reaction.

    PubMed

    Wen, Genfa; Su, Yingpeng; Zhang, Guoxiang; Lin, Qiqiao; Zhu, Yujin; Zhang, Qianqian; Fang, Xinqiang

    2016-08-19

    The strategy of stereodivergent reactions on racemic mixtures (stereodivergent RRM) was employed for the first time in intramolecular benzoin reactions and led to the rapid access of chromanones/flavanones with two consecutive stereocenters. The easily separable stereoisomers of the products were obtained with moderate to excellent enantioselectivities in a single step. Catechol type additives proved crucial in achieving the desired diastereo- and enantioselectivities. PMID:27490010

  15. Intramolecular interaction and dynamics of the cationic argon trimer

    SciTech Connect

    Ragnetti, F.; Zuhrt, C.; Zuelicke, L.

    1996-12-31

    For the simplest cationic argon cluster, Ar{sub 3}{sup +}, the topographical characteristics of the ground-state potential energy surface (PES), the mode coupling and the claswsical intramolecular dynamics are studied; PES data have been obtained by the diatomics-in-molecules approach of Kuntz et al. The results show that Ar{sub 3}{sup +} s a rather floppy system with rapid vibrational energy redistribution and early onset of classical chaos.

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

    PubMed Central

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

    2008-01-01

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

  17. 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

  18. Mechanism of intramolecular transformations of nickel phosphanido hydride complexes.

    PubMed

    Latypov, Shamil K; Polyancev, Fedor M; Ganushevich, Yulia S; Miluykov, Vasily A; Sinyashin, Oleg G

    2016-02-01

    In solution, nickel phosphanido hydride complexes ([NiH{P(Ar)(H)}(dtbpe)], Ar = Dmp, Mes*) undergo a degenerate intramolecular exchange, with the Ni-H and P-H hydrogens and both halves of the dtbpe moiety interchanging. This intramolecular rearrangement was shown to occur in three steps: first, the hydride proton migrates to phosphorus, then the P-Aryl moiety rotates around the P-Ni bond, and finally the back migration of one proton to Ni completes the process. Both migration and rotation were determined to be characterized by high barriers (on the NMR time scale) and to depend on the type of aryl group at the terminal phosphorus. Compared to that observed for the Ni complexes, the same isomeric preference, but with a slower rate of intramolecular rearrangement, is predicted for the corresponding Pt complexes. An opposite isomeric preference, however, is expected for the corresponding Pd complexes. Thus, it is likely that some of the catalytic reactions of Pd and Pt complexes are driven by the relative thermodynamic stabilities of their main forms. PMID:26407302

  19. Competing intramolecular vs. intermolecular hydrogen bonds in solution.

    PubMed

    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. Dipyrenylphosphatidylcholines as membrane fluidity probes. Pressure and temperature dependence of the intramolecular excimer formation rate.

    PubMed Central

    Sassaroli, M; Vauhkonen, M; Somerharju, P; Scarlata, S

    1993-01-01

    We have measured the pressure dependence of the intramolecular excimer formation rate, K(p), for di-(1'-pyrenedecanoyl)-phosphatidylcholine (dipy10PC) probes in single-component lipid multilamellar vesicles (MLV) as a function of temperature. Apparent volumes of activation (V(a)) for intramolecular excimer formation are obtained from the slopes of plots of log K(p) versus P. For liquid-crystalline saturated lipid MLV (DMPC and DPPC), these plots are linear and yield a unique V(a) at each temperature, whereas for unsaturated lipids (POPC and DOPC) they are curvilinear and V(a) appears to decrease with pressure. The isothermal pressure induced phase transition is marked by an abrupt drop in the values of K(p). The pressure to temperature equivalence values, dPm/dT, estimated from the midpoint of the transitions, are 47.0, 43.5, and 52.5 bar degree C-1 for DMPC, DPPC, and POPC, respectively. In liquid-crystalline DMPC, V(a) decreases linearly as a function of temperature, with a coefficient -dVa/dT = 0.65 +/- 0.11 ml degree C-1 mol-1. Using a modified free volume model of diffusion, we show that this value corresponds to the thermal expansivity of DMPC. Both the apparent energy and entropy of activation, Ea and delta Sa, increase with pressure in DMPC, whereas both decrease in POPC and DOPC. This difference is attributed to the sensitivity of the dynamics and/or packing of the dipy10PC probes to the location of the cis-double bonds in the chains of the unsaturated host phospholipids. Finally, the atmospheric pressure values of Ea and delta Sa for the four host MLV examined are shown to be linearly related. The relevance of this finding with respect to the structure of the excimers formed by the dipy10PC probes is briefly discussed. PMID:8431538

  1. Ultraslow scaled Brownian motion

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  2. 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. PMID:21867316

  3. Teaching Diffusion with a Coin

    ERIC Educational Resources Information Center

    Haddad, Hamilton; Baldo, Marcus Vinicius Chrysostomo

    2010-01-01

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

  4. Anomalous diffusion in time-fluctuating non-stationary diffusivity landscapes.

    PubMed

    Cherstvy, Andrey G; Metzler, Ralf

    2016-08-24

    We investigate the ensemble and time averaged mean squared displacements for particle diffusion in a simple model for disordered media by assuming that the local diffusivity is both fluctuating in time and has a deterministic average growth or decay in time. In this study we compare computer simulations of the stochastic Langevin equation for this random diffusion process with analytical results. We explore the regimes of normal Brownian motion as well as anomalous diffusion in the sub- and superdiffusive regimes. We also consider effects of the inertial term on the particle motion. The investigation of the resulting diffusion is performed for unconfined and confined motion. PMID:27523709

  5. Circular motion

    NASA Astrophysics Data System (ADS)

    Newton, Isaac; Henry, Richard Conn

    2000-07-01

    An extraordinarily simple and transparent derivation of the formula for the acceleration that occurs in uniform circular motion is presented, and is advocated for use in high school and college freshman physics textbooks.

  6. Polar motion

    NASA Technical Reports Server (NTRS)

    Kolenkiewicz, R.

    1973-01-01

    Tracking of the Beacon Explorer-C satellite by a precision laser system was used to measure the polar motion and solid earth tide. The tidal perturbation of satellite latitude is plotted as variation in maximum latitude in seconds of arc on earth's surface as a function of the date, and polar motion is shown by plotting the variation in latitude of the laser in seconds of arc along the earth's surface as a function of date

  7. 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

  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. Catalytic Intramolecular Ketone Alkylation with Olefins by Dual Activation.

    PubMed

    Lim, Hee Nam; Dong, Guangbin

    2015-12-01

    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. PMID:26486569

  10. 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

  11. 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

  12. 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.

  13. Effects of Intramolecular Distance between Amyloidogenic Domains on Amyloid Aggregation

    PubMed Central

    Ko, Ahra; Kim, Jin Ryoun

    2012-01-01

    Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation. PMID:23202890

  14. 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.

  15. Slow Intramolecular Vibrational Relaxation Leads to Long-Lived Excited-State Wavepackets.

    PubMed

    Rafiq, Shahnawaz; Scholes, Gregory D

    2016-09-01

    Broadband optical pump and compressed white light continuum probe were used to measure the transient excited-state absorption, ground-state bleach, and stimulated emission signals of cresyl violet solution in methanol. Amplitude oscillations caused by wavepacket motion in the ground and excited electronic states were analyzed. It was found that vibrational coherences in the excited state persist for more than the experimental waiting time window of 6 ps, and the strongest mode had a dephasing time constant of 2.4 ps. We hypothesize the dephasing of the wavepacket in the excited state is predominantly caused by intramolecular vibrational relaxation (IVR). Slow IVR indicates weak mode-mode coupling and therefore weak anharmonicity of the potential of this vibration. Thus, the initially prepared vibrational wavepacket in the excited state is not significantly perturbed by nonadiabatic coupling to other electronic states, and hence the diabatic and adiabatic representations of the system are essentially identical within the Born-Oppenheimer approximation. The wavepacket therefore evolves with time in an almost harmonic potential, slowly dephased by IVR and the pure vibrational decoherence. The consistency in the position of node (phase change in the wavepacket) in the excited-state absorption and stimulated emission signals without undergoing any frequency shift until the wavepacket is completely dephased conforms to the absence of any reactive internal conversion. PMID:27510098

  16. Asteroid Motions

    NASA Astrophysics Data System (ADS)

    Sykes, Mary V.; Moynihan, P. Daniel

    1996-12-01

    Equations are derived which describe the apparent motion of an asteroid traveling on an elliptical orbit in geocentric ecliptic coordinates. At opposition, the equations are identical to those derived by Bowellet al. (Bowell, E., B. Skiff, and L. Wasserman 1990. InAsteroids, Comets, Meteors III(C.-I. Lagerkvist, M. Rickman, B. A. Lindblad, and M. Lindgren, Eds.), pp. 19-24. Uppsala Universitet, Uppsala, Sweden). These equations can be an important component in the optimization of search strategies for specific asteroid populations based on their apparent motions relative to other populations when observed away from opposition.

  17. Multinomial Diffusion Equation

    SciTech Connect

    Balter, Ariel I.; Tartakovsky, Alexandre M.

    2011-06-01

    We have developed a novel stochastic, space/time discrete representation of particle diffusion (e.g. Brownian motion) based on discrete probability distributions. We show that in the limit of both very small time step and large concentration, our description is equivalent to the space/time continuous stochastic diffusion equation. Being discrete in both time and space, our model can be used as an extremely accurate, efficient, and stable stochastic finite-difference diffusion algorithm when concentrations are so small that computationally expensive particle-based methods are usually needed. Through numerical simulations, we show that our method can generate realizations that capture the statistical properties of particle simulations. While our method converges converges to both the correct ensemble mean and ensemble variance very quickly with decreasing time step, but for small concentration, the stochastic diffusion PDE does not, even for very small time steps.

  18. Synthesis and intramolecular cyclization of methylenediphosphorus bisalkylamides containing one or two 4-coordinate phosphorus atoms

    SciTech Connect

    Novikova, Z.S.; Monin, E.A.; Kabachnik, M.M.; Lutsenko, I.F.

    1987-10-10

    We have previously reported on the synthesis of methylenediphosphorus bisalkylamides containing two 3-coordinate phosphorus atoms and their intramolecular cyclization into 1,2,4-azadiphosphetidines. In this work we have synthesized methylenediphosphorus bisalkylamides containing one or two 4-coordinate phosphorus atoms and have studied their intramolecular cyclization. The bisalkylamides were characterized in ether solution by their /sup 31/ NMR spectra.

  19. Deterministic Brownian Motion

    NASA Astrophysics Data System (ADS)

    Trefan, Gyorgy

    1993-01-01

    The goal of this thesis is to contribute to the ambitious program of the foundation of developing statistical physics using chaos. We build a deterministic model of Brownian motion and provide a microscopic derivation of the Fokker-Planck equation. Since the Brownian motion of a particle is the result of the competing processes of diffusion and dissipation, we create a model where both diffusion and dissipation originate from the same deterministic mechanism--the deterministic interaction of that particle with its environment. We show that standard diffusion which is the basis of the Fokker-Planck equation rests on the Central Limit Theorem, and, consequently, on the possibility of deriving it from a deterministic process with a quickly decaying correlation function. The sensitive dependence on initial conditions, one of the defining properties of chaos insures this rapid decay. We carefully address the problem of deriving dissipation from the interaction of a particle with a fully deterministic nonlinear bath, that we term the booster. We show that the solution of this problem essentially rests on the linear response of a booster to an external perturbation. This raises a long-standing problem concerned with Kubo's Linear Response Theory and the strong criticism against it by van Kampen. Kubo's theory is based on a perturbation treatment of the Liouville equation, which, in turn, is expected to be totally equivalent to a first-order perturbation treatment of single trajectories. Since the boosters are chaotic, and chaos is essential to generate diffusion, the single trajectories are highly unstable and do not respond linearly to weak external perturbation. We adopt chaotic maps as boosters of a Brownian particle, and therefore address the problem of the response of a chaotic booster to an external perturbation. We notice that a fully chaotic map is characterized by an invariant measure which is a continuous function of the control parameters of the map

  20. Direct Observation of Cascade of Photoinduced Ultrafast Intramolecular Charge Transfer Dynamics in Diphenyl Acetylene Derivatives: Via Solvation and Intramolecular Relaxation.

    PubMed

    Karunakaran, Venugopal; Das, Suresh

    2016-07-21

    Interaction of light with electron donor-acceptor π-conjugated systems leading to intramolecular charge transfer (ICT) plays an essential role in transformation of light energy. Here the cascade of photoinduced ICT processes is directly observed by investigating the excited state relaxation dynamics of cyano and mono/di methoxy substituted diphenyl acetylene derivatives using femtosecond pump-probe spectroscopy and nanosecond laser flash photolysis. The femtosecond transient absorption spectra of the chromophores upon ultrafast excitation reveal the dynamics of intermediates involved in transition from initially populated Frank-Condon state to local excited state (LE). It also provides the dynamic details of the transition from the LE to the charge transfer state yielding the formation of the radical ions. Finally, the charge transfer state decays to the triplet state by geminate charge recombination. The latter dynamics are observed in the nanosecond transient absorption spectra. It is found that excited state relaxation pathways are controlled by different stages of solvation and intramolecular relaxation depending on the solvent polarity. The twisted ICT state is more stabilized (978 ps) in acetonitrile than cyclohexane where major components of transient absorption originate from the S1 state. PMID:27347705

  1. Towards in vivo imaging of intramolecular fluorescence resonance energy transfer parameters.

    PubMed

    Gaind, Vaibhav; Webb, Kevin J; Kularatne, Sumith; Bouman, Charles A

    2009-08-01

    Fluorescence resonance energy transfer (FRET) is a nonradiative energy transfer process based on dipole-dipole interaction between donor and acceptor fluorophores that are spatially separated by a distance of a few nanometers. FRET has proved to be of immense value in the study of cellular function and the underlying cause of disease due to, for example, protein misfolding (of consequence in Alzheimer's disease). The standard parameterization in intramolecular FRET is the lifetime and yield, which can be related to the donor-acceptor (DA) distance. FRET imaging has thus far been limited to in vitro or near-surface microscopy because of the deleterious effects of substantial scatter. We show that it is possible to extract the microscopic FRET parameters in a highly scattering environment by incorporating the FRET kinetics of an ensemble of DA molecules connected by a flexible or rigid linker into an optical diffusion tomography (ODT) framework. We demonstrate the efficacy of our approach for extracting the microscopic DA distance through simulations and an experiment using a phantom with scattering properties similar to tissue. Our method will allow the in vivo imaging of FRET parameters in deep tissue, and hence provide a new vehicle for the fundamental study of disease. PMID:19649115

  2. Very strong intramolecular hydrogen bonding of 1,2-dithenoylcyclopentadiene; DFT and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Nekoei, A.-R.; Tayyari, S. F.; Vakili, M.

    2014-10-01

    Structure and intramolecular hydrogen bond (IHB) of 1,2-dithenoylcyclopentadiene (DTCP) have been investigated with quantum mechanical calculations using density functional theory at B3LYP level using some Pople-style basis sets augmented with polarized and diffuse functions. The full isomeric and conformational analyses have been done, and the relative stabilities for different chelated and non-chelated enol and different keto forms have been reported. The estimated IHB energy and the barrier height for proton transfer (19.34 and 0.31 kcal/mol, respectively), together with the value of 0.082 Å for the Q Gilli’s symmetry coordinate and the σ-skeleton of the molecule (O⋯O distance of 1.463 Å), confirm a very strong, nearly symmetric, linear and short distance resonance assisted IHB (RAHB) in DTCP. The values of 18.29 ppm for the enolated proton chemical shift and 1128 cm-1 for out-of-plain bending of the OH bond, besides investigations on other IR and Raman bands associated with the IHB strength and electron delocalization in different segments of the molecule, confirm the results of the theoretical studies and a very strong RAHB in DTCP.

  3. What's Motion Sickness?

    MedlinePlus

    ... Homework? Here's Help White House Lunch Recipes What's Motion Sickness? KidsHealth > For Kids > What's Motion Sickness? Print ... motion sickness might get even worse. continue Avoiding Motion Sickness To avoid motion sickness: Put your best ...

  4. 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)

  5. 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

  6. 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.

  7. Intramolecular strain coordinates kinesin stepping behavior along microtubules

    PubMed Central

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

    2008-01-01

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

  8. Intramolecular dynamics of structure of alkaline phosphatase from Escherichia coli

    NASA Astrophysics Data System (ADS)

    Mazhul, Vladimir M.; Mjakinnik, Igor V.; Volkova, Alena N.

    1995-01-01

    The luminescent analysis with nano- and millisecond time resolution of intramolecular dynamics of Escherichia coli alkaline phosphatase was carried out. The effect of pH within the range 7.2 - 9.0, thermal inactivation, limited proteolysis by trypsin, binding of pyrophosphate, interconversion of enzyme and apoenzyme, the replacement of Zn2+ and Mg2+ in the active site by Cd2+ and Ni2+ on the spectral and kinetic parameters of luminescence was investigated. The essential changes of the level of nano- and millisecond dynamics of protein structure were found to correlate with the shift of enzymatic activity. The importance of small- and large-scale flexibility of protein structure for the act of enzymatic catalysis realization was shown.

  9. Sequence and intramolecular distance scoring analyses of microbial rhodopsins

    PubMed Central

    Asano, Miki; Ide, Shunta; Kamata, Atsushi; Takahasi, Kiyohiro; Okada, Tetsuji

    2016-01-01

    Recent accumulation of sequence and structural data, in conjunction with systematical classification into a set of families, has significantly advanced our understanding of diverse and specific protein functions. Analysis and interpretation of protein family data requires comprehensive sequence and structural alignments. Here, we present a simple scheme for analyzing a set of experimental structures of a given protein or family of proteins, using microbial rhodopsins as an example. For a data set comprised of around a dozen highly similar structures to each other (overall pairwise root-mean-squared deviation < 2.3 Å), intramolecular distance scoring analysis yielded valuable information with respect to structural properties, such as differences in the relative variability of transmembrane helices. Furthermore, a comparison with recent results for G protein-coupled receptors demonstrates how the results of the present analysis can be interpreted and effectively utilized for structural characterization of diverse protein families in general. PMID:26998236

  10. Gold‐Catalyzed Intramolecular Cyclizations of Cyclopropenes with Propargylic Esters

    PubMed Central

    Zhu, Peng‐Long

    2015-01-01

    Abstract Homogeneous gold catalysts are interesting as they can act as potent carbophilic Lewis acids to activate the π bonds of alkynes, allenes, and alkenes. Many impressive applications for the formation of C−C or C−heteroatom bonds have been found due to the excellent functional group compatibility of these catalysts and the air and moisture tolerance of their reactions. Here, we have developed gold‐catalyzed novel intramolecular cycloisomerizations of nitrogen or oxygen‐tethered cyclopropenes with propargylic esters. The reaction proceeded through different pathways according to different substituent styles, affording 5‐azaspiro[2.5]oct‐7‐enes and bicyclo[4.1.0]heptanes. PMID:27308208

  11. Universal prediction of intramolecular hydrogen bonds in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2010-04-01

    A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB. PMID:20305358

  12. Structural studies of photoinduced intramolecular electron transfer in cyclopentadienylnickelnitrosyl

    SciTech Connect

    Chen, L.X.; Bowman, M.K.; Wang, Zhiyu; Norris, J.R. |; Montano, P.A. |

    1994-03-01

    A structural study based on EXAFS, FTIR, and optical absorption spectroscopies has been conducted on a photogenerated, metastable state of cyclopentadienylnickelnitrosyl (CpNiNO) produced by a reversible photochemical reaction. The photogenerated, metastable state with distinctively different EXAFS, IR, and optical absorption spectra from those of the ground state molecules was created by irradiating the sample with the 365 nm line of a mercury lamp at 20K . At the same temperature, the reverse reaction was induced by irradiation with the 313 nm line from the mercury lamp. Based on the analysis of the EXAFS data, the photogenerated, metastable state of CpNiNO has undergone considerable nuclear rearrangements compared to its ground state. The nuclear movement is characterized by a 0.12{angstrom} elongation of Ni-N bond and by a bending of Ni-N-O. A shift of the N-O stretching frequency from 1824 to 1387 cm{sup {minus}1} was observed in the photoinduced reaction with 365 nm light, implying that a NO{sup {minus}} like species results from intramolecular electron transfer from Ni to NO. The changes in the absorption spectra for the same reaction showed reduced absorption of the 385 nm band and a newly generated broad band near IR region. Temperature dependence of the Debye-Waller factor of CpNiNO was in good agreement with the diatomic harmonic oscillator for the Ni-N bond, but deviated for the Ni-O and the Ni-C bonds. Based on the structures obtained from EXAFS, ZINDO calculations for both the ground state and the photogenerated, metastable state of CpNiNO reproduced the general features of the observed absorption spectra and qualitatively explained the wavelength dependence of the reaction. The calculated partial charges on each atom in the ground state and the photogenerated, metastable state of CpNiNO are consistent with intramolecular electron transfer upon photoexcitation by 365 nm light.

  13. Intramolecular Long-Distance Electron Transfer in Organic Molecules

    NASA Astrophysics Data System (ADS)

    Closs, Gerhard L.; Miller, John R.

    1988-04-01

    Intramolecular long-distance electron transfer (ET) has been actively studied in recent years in order to test existing theories in a quantitative way and to provide the necessary constants for predicting ET rates from simple structural parameters. Theoretical predictions of an ``inverted region,'' where increasing the driving force of the reaction will decrease its rate, have begun to be experimentally confirmed. A predicted nonlinear dependence of ET rates on the polarity of the solvent has also been confirmed. This work has implications for the design of efficient photochemical charge-separation devices. Other studies have been directed toward determining the distance dependence of ET reactions. Model studies on different series of compounds give similar distance dependences. When different stereochemical structures are compared, it becomes apparent that geometrical factors must be taken into account. Finally, the mechanism of coupling between donor and acceptor in weakly interacting systems has become of major importance. The theoretical and experimental evidence favors a model in which coupling is provided by the interaction with the orbitals of the intervening molecular fragments, although more experimental evidence is needed. Studies on intramolecular ET in organic model compounds have established that current theories give an adequate description of the process. The separation of electronic from nuclear coordinates is only a convenient approximation applied to many models, but in long-distance ET it works remarkably well. It is particularly gratifying to see Marcus' ideas finally confirmed after three decades of skepticism. By obtaining the numbers for quantitative correlations between rates and distances, these experiments have shown that saturated hydrocarbon fragments can ``conduct'' electrons over tens of angstroms. A dramatic demonstration of this fact has recently been obtained by tunneling electron microscopy on Langmuir-Blodgett films, showing in a

  14. 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.

  15. The Riesz-Bessel Fractional Diffusion Equation

    SciTech Connect

    Anh, V.V. McVinish, R.

    2004-05-15

    This paper examines the properties of a fractional diffusion equation defined by the composition of the inverses of the Riesz potential and the Bessel potential. The first part determines the conditions under which the Green function of this equation is the transition probability density function of a Levy motion. This Levy motion is obtained by the subordination of Brownian motion, and the Levy representation of the subordinator is determined. The second part studies the semigroup formed by the Green function of the fractional diffusion equation. Applications of these results to certain evolution equations is considered. Some results on the numerical solution of the fractional diffusion equation are also provided.

  16. Diffusive mixing and Tsallis entropy

    DOE PAGESBeta

    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.

  17. Holographic diffusers

    NASA Astrophysics Data System (ADS)

    Wadle, Stephen; Wuest, Daniel; Cantalupo, John; Lakes, Roderic S.

    1994-01-01

    Holographic diffusers are prepared using silver halide (Agfa 8E75 and Kodak 649F) and photopolymer (Polaroid DMP 128 and DuPont 600, 705, and 150 series) media. It is possible to control the diffusion angle in three ways: by selection of the properties of the source diffuser, by control of its subtended angle, and by selection of the holographic medium. Several conventional diffusers based on refraction or scattering of light are examined for comparison.

  18. Vibrational spectroscopy and intramolecular energy transfer in isocyanic acid (HNCO)

    SciTech Connect

    Coffey, M.J.; Berghout, H.L.; Woods, E. III; Crim, F.F.

    1999-06-01

    Room temperature photoacoustic spectra in the region of the first through the fourth overtones (2{nu}{sub 1} to 5{nu}{sub 1}) and free-jet action spectra of the second through the fourth overtones (3{nu}{sub 1} to 5{nu}{sub 1}) of the N{endash}H stretching vibration permit analysis of the vibrational and rotational structure of HNCO. The analysis identifies the strong intramolecular couplings that control the early stages of intramolecular vibrational energy redistribution (IVR) and gives the interaction matrix elements between the zero-order N{endash}H stretching states and the other zero-order states with which they interact. The experimentally determined couplings and zero-order state separations are consistent with {ital ab initio} calculations of East, Johnson, and Allen [J. Chem. Phys. {bold 98}, 1299 (1993)], and comparison with the calculation identifies the coupled states and likely interactions. The states most strongly coupled to the pure N{endash}H stretching zero-order states are ones with a quantum of N{endash}H stretching excitation ({nu}{sub 1}) replaced by different combinations of N{endash}C{endash}O asymmetric or symmetric stretching excitation ({nu}{sub 2} or {nu}{sub 3}) and {ital trans}-bending excitation ({nu}{sub 4}). The two strongest couplings of the n{nu}{sub 1} state are to the states (n{minus}1){nu}{sub 1}+{nu}{sub 2}+{nu}{sub 4} and (n{minus}1){nu}{sub 1}+{nu}{sub 3}+2{nu}{sub 4}, and sequential couplings through a series of low order resonances potentially play a role. The analysis shows that if the pure N{endash}H stretch zero-order state were excited, energy would initially flow out of that mode into the strongly coupled mode in 100 fs to 700 fs, depending on the level of initial excitation. {copyright} {ital 1999 American Institute of Physics.}

  19. 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.

  20. 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.

  1. Intramolecular Hydrogen-Bonding Effects on the Fluorescence of PRODAN Derivatives.

    PubMed

    Alty, Isaac G; Cheek, Douglas W; Chen, Tao; Smith, David B; Walhout, Emma Q; Abelt, Christopher J

    2016-05-26

    The effects of intramolecular hydrogen-bonding on the fluorescence behavior of three derivatives of 6-propionyl-2-dimethylaminonaphthalene are reported. The H-bonding effects are revealed through comparisons with corresponding reference compounds in which the H-bond-donating hydroxyl groups are replaced with methoxy groups. In toluene, intramolecular H bonding gives rise to a dramatic increase in the fluorescence intensity but only a slight red shift in the position. This behavior is attributed to decreased efficiency in intersystem crossing due to an increase in the energy of the n → π* triplet state. The intramolecular H bond does not induce quenching in acetonitrile; however, in the presence of a very small concentration of methanol, a dual intramolecular, intermolecular H-bonding arrangement does lead to partial quenching as revealed by preferential solvation studies. PMID:27127907

  2. Synthesis of 2-Cyclopentenone Derivatives via Palladium-Catalyzed Intramolecular Carbonyl α-Alkenylation.

    PubMed

    Chen, Panpan; Meng, Yinggao; Wang, Han; Han, Feipeng; Wang, Yulong; Song, Chuanjun; Chang, Junbiao

    2016-08-01

    2-Cyclopentenone derivatives have been efficiently synthesized from 5-bromo-5-hexen-2-ones via palladium-catalyzed intramolecular carbonyl α-alkenylation followed by double-bond migration under mild reaction conditions. PMID:27463262

  3. Light induced catalytic intramolecular hydrofunctionalization of allylphenols mediated by porphyrin rhodium(iii) complexes.

    PubMed

    Liu, Xu; Wang, Zikuan; Fu, Xuefeng

    2016-09-14

    Catalytic intramolecular hydrofunctionalization of allylphenols to heterocyclic compounds mediated by rhodium(iii) porphyrin complexes was described. The Wacker-type intermediate β-heterocyclic alkyl rhodium complex was independently synthesized and crystallized. PMID:27482840

  4. Intramolecular Interactions That Induce Helical Rearrangement upon Rhodopsin Activation

    PubMed Central

    Yamazaki, Yoichi; Nagata, Tomoko; Terakita, Akihisa; Kandori, Hideki; Shichida, Yoshinori; Imamoto, Yasushi

    2014-01-01

    Rhodopsin undergoes rearrangements of its transmembrane helices after photon absorption to transfer a light signal to the G-protein transducin. To investigate the mechanism by which rhodopsin adopts the transducin-activating conformation, the local environmental changes in the transmembrane region were probed using the cysteine S-H group, whose stretching frequency is well isolated from the other protein vibrational modes. The S-H stretching modes of cysteine residues introduced into Helix III, which contains several key residues for the helical movements, and of native cysteine residues were measured by Fourier transform infrared spectroscopy. This method was applied to metarhodopsin IIa, a precursor of the transducin-activating state in which the intramolecular interactions are likely to produce a state ready for helical movements. No environmental change was observed near the ionic lock between Arg-135 in Helix III and Glu-247 in Helix VI that maintains the inactive conformation. Rather, the cysteine residues that showed environmental changes were located around the chromophore, Ala-164, His-211, and Phe-261. These findings imply that the hydrogen bond between Helix III and Helix V involving Glu-122 and His-211 and the hydrophobic packing between Helix III and Helix VI involving Gly-121, Leu-125, Phe-261, and Trp-265 are altered before the helical rearrangement leading toward the active conformation. PMID:24692562

  5. Catalytic, Enantioselective, Intramolecular Carbosulfenylation of Olefins. Preparative and Stereochemical Aspects

    PubMed Central

    Denmark, Scott E.; Jaunet, Alex

    2014-01-01

    The first catalytic, enantioselective, intramolecular carbosulfenylation of isolated alkenes with aromatic nucleophiles is described. The combination of N-phenylsulfenylphthalimide, a chiral selenophosphoramide derived from BINAM, and ethanesulfonic acid as a co-catalytic Brønsted acid induced an efficient and selective cyclofunctionalization of various alkenes (aliphatic and aromatic) tethered to a 3,4-methylenedioxyphenyl ring. Under these conditions, 6-phenylthio-5,6,7,8-tetrahydronaphthalenes are formed diastereospecifically in good yields (50–92%) and high enantioselectivities (71:29 – 97:3 er). E-Alkenes reacted much more rapidly and with much higher selectivity than Z-alkenes, whereas electron rich alkenes reacted more rapidly but with comparable selectivity to electron-neutral alkenes and electron deficient alkenes. The Brønsted acid played a critical role in effecting reproducible enantioselectivity. A model for the origin of enantioselectivity and the dependence of rate and selectivity on alkene structure is proposed along with a rationale for the site selectivity in reactions with mono-activated arene nucleophiles. PMID:24328051

  6. 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

  7. Chirally selective, intramolecular interaction observed in an aminoacyl adenylate anhydride

    NASA Astrophysics Data System (ADS)

    Lacey, James C.; Hall, Leo M.; Mullins, Dail W.; Watkins, Charles L.

    1985-06-01

    All earthly creatures use only L-amino acids in template directed protein synthesis. The reason for this exclusive use of the L-isomer is not yet apparent, although recent experiments by Usher and his colleagues have shown some stereoselctivity in the aminoacylation of di- and polynucleotides [1 3]. We have separately reported on intramolecular interactions between hydrophobic amino acid side chains and the adenine ring in aminoacyl adenylates [4]. There was a preferential association of Phe > Leu = Ile > Val with the adenine in these studies, but we made no attempts to address the question of D, L selectivity. Recently, in1H NMR studies of N-acetylphenylalanyl adenylate anhydride, we noticed evidence that both D- and L-isomers of the amino acid were present and, furthermore, that one isomer seemed to be associating with the adenine ring more strongly than the other. Using HPLC, we have separated the two diastereoisomers and have enzymatically determined that the isomer which associates more strongly is the biologically important one, the L-isomer. We present those studies here and discuss the evolutionary significance of this finding.

  8. Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

    PubMed

    Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

    2016-02-18

    The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. PMID:26797690

  9. Intramolecular phenotypic capacitance in a modular RNA molecule

    PubMed Central

    Hayden, Eric J.; Bendixsen, Devin P.; Wagner, Andreas

    2015-01-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA’s ancient role in life suggests that phenotypic capacitance may have influenced evolution since life’s origins. PMID:26401020

  10. 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.

  11. Intramolecular electronic energy transfer in bichromophoric molecular macrocyclic systems

    NASA Astrophysics Data System (ADS)

    Speiser, Shammai

    1993-01-01

    The structures and spectral properties of several bichromophoric molecules, suitable for optical data processing, are presented. The bichromophoric molecules are composed of an aromatic ring connected by two methylene chains to an (alpha) -diketone moiety. Both the absorption and emission spectra of these compounds can be attributed to a superposition of the individual spectra of the separate chromophores. The critical transfer radia for electronic energy transfer from the aromatic (donor) chromophore to the (alpha) -diketone (acceptor) chromophore was calculated from the spectral overlap between the fluorescence spectrum of the aromatic ring with the absorption spectrum of the (alpha) -diketone chromophore. The results show that this series of molecules is well suited for a mechanistic study of short-range intramolecular electronic energy transfer (intra-EET). The temperature and the molecular structure dependence of the intra-EET efficiency in this series was measured and analyzed for both singlet-singlet and triplet-triplet routes. The results show that the transfer efficiency is strongly temperature and structure dependent, indicating that exchange interaction is responsible for intra-EET between close chromophores in a bichromophoric molecule. The relative contributions of interchromophoric distance and that of the relative orientation of the two chromophores to exchange interaction are discussed.

  12. Intramolecular phenotypic capacitance in a modular RNA molecule.

    PubMed

    Hayden, Eric J; Bendixsen, Devin P; Wagner, Andreas

    2015-10-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA's ancient role in life suggests that phenotypic capacitance may have influenced evolution since life's origins. PMID:26401020

  13. 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. PMID:27112602

  14. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

    We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation. PMID:26864943

  15. 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

    2016-01-01

    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

  16. 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.

  17. Fast diffusion of water nanodroplets on graphene

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  18. Fast diffusion of water nanodroplets on graphene.

    PubMed

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

    2016-01-01

    Diffusion across surfaces generally involves motion on a vibrating but otherwise stationary substrate. Here, using molecular dynamics, we show that a layered material such as graphene opens up a new mechanism for surface diffusion whereby adsorbates are carried by propagating ripples in a motion similar to surfing. For water nanodroplets, we demonstrate that the mechanism leads to exceedingly fast diffusion that is 2-3 orders of magnitude faster than the self-diffusion of water molecules in liquid water. We also reveal the underlying principles that regulate this new mechanism for diffusion and show how it also applies to adsorbates other than water, thus opening up the prospect of achieving fast and controllable motion of adsorbates across material surfaces more generally. PMID:26480227

  19. 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.

  20. Diffusion of Particles in Polymer Solutions

    NASA Astrophysics Data System (ADS)

    Cai, Liheng; Rubinstein, Michael

    2010-03-01

    We use scaling theory to derive the time dependence of the mean-square-displacement <δr^2> of a probe particle of size d in an entangled semidilute polymer solution. Particles with size smaller than solution correlation length ξ undergo ordinary diffusion (<δr^2 (t)>˜t) with diffusion coefficient determined by the solvent viscosity. The motion of particles with intermediate sizes (ξ˜t^1/2) at short time scales since their motion is affected by sub-sections of polymer chains. At long time scales the motion of these particles is diffusive and their diffusion coefficient is determined by effective viscosity of a polymer solution with chains of size comparable to particle diameter d. The motion of particles larger than tube diameter (d>a) at time scales shorter than the relaxation time of an entanglement strand τe is similar to the motion of particles with intermediate sizes. At longer time scales (t>τe) large particles (d>a) are trapped by entanglement mesh and cannot move until the surrounding chains relax at the reptation time scale τrep. At longer times t>τrep, the motion of large particles becomes diffusive with diffusion coefficient determined by the bulk viscosity of the entangled polymer solution.

  1. In vivo distribution and elimination of hemoglobin modified by intramolecular cross-linking with 2-nor-2-formylpyridoxal 5'-phosphate

    SciTech Connect

    Bleeker, W.K.; van der Plas, J.; Feitsma, R.I.; Agterberg, J.; Rigter, G.; de Vries-van Rossen, A.; Pauwels, E.K.; Bakker, J.C.

    1989-02-01

    Modified hemoglobin solutions have potential application as plasma expanders with oxygen-transporting capacity. In a previous study it was found that modification of hemoglobin by intramolecular cross-linking with 2-nor-2-formylpyridoxal 5'-phosphate (NFPLP) improves the vascular retention time by a factor of three, and it also improves the oxygen-transporting properties. In the present study we investigated in rats how, after exchange transfusion of a clinically relevant dose, the modified hemoglobin (HbNFPLP) was distributed in the body compared with how the unmodified hemoglobin was distributed. By using a new technetium 99m labeling technique, we found in a scintigraphic study that accumulation of hemoglobin in the kidneys was greatly diminished by the intramolecular cross-linking with NFPLP. These findings were confirmed by light-microscopic observations after diaminobenzidine staining. It was concluded that the impairment of kidney function caused by blockade of the tubuli is not to be expected from HbNFPLP. In the liver and spleen, where the free HbNFPLP is possibly eliminated, some accumulation of 99mTc label was observed, but the major part of the extravascular label was diffusely spread throughout the body. This led to the conclusion that important accumulation of undegraded HbNFPLP does not occur in the liver and spleen. Rapid appearance of both hemoglobin and HbNFPLP in the lymph showed that cross-linking with NFPLP does not prevent the distribution of hemoglobin over the interstitial space in the first hours after administration. However, pharmacokinetic analysis demonstrated that transcapillary transfer contributes only to a limited extent to the disappearance from the circulation. During 24-hour infusions of HbNFPLP, a steady state with a constant plasma concentration was easily reached.

  2. Intramolecular hydrogen bond in biologically active o-carbonyl hydroquinones.

    PubMed

    Martínez-Cifuentes, Maximiliano; Weiss-López, Boris E; Santos, Leonardo S; Araya-Maturana, Ramiro

    2014-01-01

    Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LP-->σ* interactions for IHBs, O1…O2-H2 and the delocalization LP-->π* for O2-C2=Cα(β). For the O1…O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2-->π* C2=Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted. PMID:24995921

  3. Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate

    PubMed Central

    2015-01-01

    Carboxyphosphate, a suspected intermediate in ATP-dependent carboxylases, has not been isolated nor observed directly by experiment. Consequently, little is known concerning its structure, stability, and ionization state. Recently, carboxyphosphate as either a monoanion or dianion has been shown computationally to adopt a novel pseudochair conformation featuring an intramolecular charge-assisted hydrogen bond (CAHB). In this work, additive and subtractive correction schemes to the commonly employed open–closed method are used to estimate the strength of the CAHB. Truhlar’s Minnesota M06-2X functional with Dunning’s aug-cc-pVTZ basis set has been used for geometry optimization, energy evaluation, and frequency analysis. The CHARMM force field has been used to approximate the Pauli repulsive terms in the closed and open forms of carboxyphosphate. From our additive correction scheme, differential Pauli repulsion contributions between the pseudochair (closed) and open conformations of carboxyphosphate are found to be significant in determining the CAHB strength. The additive correction modifies the CAHB prediction (ΔEclosed–open) of −14 kcal/mol for the monoanion and −12 kcal/mol for the dianion to −22.9 and −18.4 kcal/mol, respectively. Results from the subtractive technique reinforce those from our additive procedure, where the predicted CAHB strength ranges from −17.8 to −25.4 kcal/mol for the monoanion and from −15.7 to −20.9 kcal/mol for the dianion. Ultimately, we find that the CAHB in carboxyphosphate meets the criteria for short-strong hydrogen bonds. However, carboxyphosphate has a unique energy profile that does not result in the symmetric double-well behavior of low-barrier hydrogen bonds. These findings provide deeper insight into the pseudochair conformation of carboxyphosphate, and lead to an improved mechanistic understanding of this intermediate in ATP-dependent carboxylases. PMID:25405523

  4. Probabilistic methods for robot motion determination

    NASA Technical Reports Server (NTRS)

    Balaram, J.

    1989-01-01

    The outline of a research effort in probabilistic approaches to robot motion determination is presented. A heuristic path planner that has met with considerable success in the JPL telerobot testbed is presented together with an interpretation of its performance. The relevance of techniques from stochastic geometry and stochastic diffusion is addressed, as is the possibility of using sensor data directly in the motion determination process.

  5. 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.

  6. Neoclassical diffusion in a turbulent plasma

    SciTech Connect

    Yushmanov, P. |

    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.

  7. 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.

  8. Auditory motion affects visual biological motion processing.

    PubMed

    Brooks, A; van der Zwan, R; Billard, A; Petreska, B; Clarke, S; Blanke, O

    2007-02-01

    The processing of biological motion is a critical, everyday task performed with remarkable efficiency by human sensory systems. Interest in this ability has focused to a large extent on biological motion processing in the visual modality (see, for example, Cutting, J. E., Moore, C., & Morrison, R. (1988). Masking the motions of human gait. Perception and Psychophysics, 44(4), 339-347). In naturalistic settings, however, it is often the case that biological motion is defined by input to more than one sensory modality. For this reason, here in a series of experiments we investigate behavioural correlates of multisensory, in particular audiovisual, integration in the processing of biological motion cues. More specifically, using a new psychophysical paradigm we investigate the effect of suprathreshold auditory motion on perceptions of visually defined biological motion. Unlike data from previous studies investigating audiovisual integration in linear motion processing [Meyer, G. F. & Wuerger, S. M. (2001). Cross-modal integration of auditory and visual motion signals. Neuroreport, 12(11), 2557-2560; Wuerger, S. M., Hofbauer, M., & Meyer, G. F. (2003). The integration of auditory and motion signals at threshold. Perception and Psychophysics, 65(8), 1188-1196; Alais, D. & Burr, D. (2004). No direction-specific bimodal facilitation for audiovisual motion detection. Cognitive Brain Research, 19, 185-194], we report the existence of direction-selective effects: relative to control (stationary) auditory conditions, auditory motion in the same direction as the visually defined biological motion target increased its detectability, whereas auditory motion in the opposite direction had the inverse effect. Our data suggest these effects do not arise through general shifts in visuo-spatial attention, but instead are a consequence of motion-sensitive, direction-tuned integration mechanisms that are, if not unique to biological visual motion, at least not common to all types of

  9. Limited range of motion

    MedlinePlus

    Limited range of motion is a term meaning that a joint or body part cannot move through its normal range of motion. ... Motion may be limited because of a problem within the joint, swelling of tissue around the joint, ...

  10. Self Motion Perception and Motion Sickness

    NASA Technical Reports Server (NTRS)

    Fox, Robert A. (Principal Investigator)

    1991-01-01

    The studies conducted in this research project examined several aspects of motion sickness in animal models. A principle objective of these studies was to investigate the neuroanatomy that is important in motion sickness with the objectives of examining both the utility of putative models and defining neural mechanisms that are important in motion sickness.

  11. 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.

  12. An Introduction to Fractional Diffusion

    NASA Astrophysics Data System (ADS)

    Henry, B. I.; Langlands, T. A. M.; Straka, P.

    The mathematical description of diffusion has a long history with many different formulations including phenomenological models based on conservation of mass and constitutive laws; probabilistic models based on random walks and central limit theorems; microscopic stochastic models based on Brownian motion and Langevin equations; and mesoscopic stochastic models based on master equations and Fokker-Planck equations. A fundamental result common to the different approaches is that the mean square displacement of a diffusing particle scales linearly with time. However there have been numerous experimental measurements in which the mean square displacement of diffusing particles scales as a fractional order power law in time. In recent years a great deal of progress has been made in extending the different models for diffusion to incorporate this fractional diffusion. The tools of fractional calculus have proven very useful in these developments, linking together fractional constitutive laws, continuous time random walks, fractional Langevin equations and fractional Brownian motions. These notes provide a tutorial style overview of standard and fractional diffusion processes.

  13. Nanoscale topography influences polymer surface diffusion.

    PubMed

    Wang, Dapeng; He, Chunlin; Stoykovich, Mark P; Schwartz, Daniel K

    2015-02-24

    Using high-throughput single-molecule tracking, we studied the diffusion of poly(ethylene glycol) chains at the interface between water and a hydrophobic surface patterned with an array of hexagonally arranged nanopillars. Polymer molecules displayed anomalous diffusion; in particular, they exhibited intermittent motion (i.e., immobilization and "hopping") suggestive of continuous-time random walk (CTRW) behavior associated with desorption-mediated surface diffusion. The statistics of the molecular trajectories changed systematically on surfaces with pillars of increasing height, exhibiting motion that was increasingly subdiffusive and with longer waiting times between diffusive steps. The trajectories were well-described by kinetic Monte Carlo simulations of CTRW motion in the presence of randomly distributed permeable obstacles, where the permeability (the main undetermined parameter) was conceptually related to the obstacle height. These findings provide new insights into the mechanisms of interfacial transport in the presence of obstacles and on nanotopographically patterned surfaces. PMID:25621372

  14. Ionic motion in crystalline cryolite.

    PubMed

    Foy, Lindsay; Madden, Paul A

    2006-08-10

    The character of the ion dynamics in crystalline cryolite, Na(3)AlF(6), a model double perovskite-structured mineral, has been examined in computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. NMR studies, and conductivity measurements, have indicated a high degree of mobility, in both Na(+) ion diffusion and reorientation of the AlF(6) octahedral units. The simulations reproduce the low-temperature (tilted) crystal structure and the existence of a transition to a cubic structure at elevated temperatures, in agreement with diffraction measurements, though the calculated transition temperature is too low. The reorientational dynamics of the AlF(6) octahedra is shown to consist of a hopping motion between the various tilted positions of the low-temperature form, even above the transition temperature. The rate of reorientation estimated by extrapolation to the temperature régime of the NMR measurements is consistent with the experimental data. In addition, we report a novel cooperative "tilt-swapping" motion of the differently tilted sublattices, just below the transition temperature. The perfect crystals show no Na(+) diffusion, in apparent disagreement with observation. We argue, following previous analyses of the cryolite phase diagram, that the diffusion observed in the experimental studies is a consequence of defects that are intrinsic to the thermodynamically stable form of cryolite. By introducing defects into the simulation cell, we obtain diffusion rates that are consistent with the NMR and conductivity measurements. Finally, we demonstrate a link between diffusion of the Na(+) ions and the reorientation of AlF(6) units, though the correlation between the two is not very strong. PMID:16884249

  15. Vaneless diffusers

    NASA Astrophysics Data System (ADS)

    Senoo, Y.

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

  16. 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.

  17. A Spin Echo Sequence with a Single-Sided Bipolar Diffusion Gradient Pulse to Obtain Snapshot Diffusion Weighted Images in Moving Media

    PubMed Central

    Freidlin, R. Z.; Kakareka, J. W.; Pohida, T. J.; Komlosh, M. E.; Basser, P. J.

    2013-01-01

    In vivo MRI data can be corrupted by motion. Motion artifacts are particularly troublesome in Diffusion Weighted MRI (DWI), since the MR signal attenuation due to Brownian motion can be much less than the signal loss due to dephasing from other types of complex tissue motion, which can significantly degrade the estimation of self-diffusion coefficients, diffusion tensors, etc. This paper describes a snapshot DWI sequence, which utilizes a novel single-sided bipolar diffusion sensitizing gradient pulse within a spin echo sequence. The proposed method shortens the diffusion time by applying a single refocused bipolar diffusion gradient on one side of a refocusing RF pulse, instead of a set of diffusion sensitizing gradients, separated by a refocusing RF pulse, while reducing the impact of magnetic field inhomogeneity by using a spin echo sequence. A novel MRI phantom that can exhibit a range of complex motions was designed to demonstrate the robustness of the proposed DWI sequence. PMID:22743539

  18. 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.

  19. 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

    2016-08-01

    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. PMID:27385441

  20. Intramolecular circuits connected to N electrodes using a scattering matrix approach

    NASA Astrophysics Data System (ADS)

    Ami, S.; Joachim, C.

    2002-04-01

    The scattering matrix technique is extended to describe the electronic transport characteristics of intramolecular circuits driven in a ballistic or a tunnel transport regime. The circuit is assumed to be connected by N electrodes. As a working example, the electronic properties of a T-node circuit are presented leading to the design of an OR logic gate working in a ballistic regime. In the tunnel regime, only the ``node'' Kirchhoff law of circuit remains valid at the nodes of an intramolecular tunnel circuit and the electronic characteristics of the branches composing the circuit are mutually independent. It results in a difficult design of a logic OR intramolecular gate of high performance and stability, pointing out the urge for new architectures to implement complex logic functions inside a single molecule.

  1. 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.

  2. 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.

  3. 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.

  4. Modulation of Symmetry-Breaking Intramolecular Charge-Transfer Dynamics Assisted by Pendant Side Chains in π-Linkers in Quadrupolar Diketopyrrolopyrrole Derivatives.

    PubMed

    Kim, Woojae; Sung, Jooyoung; Grzybowski, Marek; Gryko, Daniel T; Kim, Dongho

    2016-08-01

    The effect of the length of pendant side chains in centrosymmetric quadrupolar molecules on dynamics of their most perplexing photophysical phenomenon, i.e., symmetry-breaking intramolecular charge transfer, has been discovered. Unexpectedly, considerable influence of length of these pendant side chains in π-linkers arose as a structural factor enabling the control of the degree of fluorescence solvatochromism. The symmetry-breaking intramolecular charge-transfer dynamics has been described on quadrupolar diketopyrrolopyrrole derivatives possessing fluorene moieties as π-linkers and diarylamino groups as electron donors. On the basis of the evolution of transient fluorescence spectra obtained by a femtosecond broadband fluorescence up-conversion spectroscopy, it was found that the relative contribution of diffusive solvation and torsional relaxation in overall spectral relaxation can be modulated by the length of pendant side chain in π-linkers. Consequently, we demonstrated that this modulation plays a significant role in determining the photophysical properties of diketopyrrolopyrroles in a polar medium. PMID:27455383

  5. 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.

  6. Photophysics of 2-(4'-amino-2'-hydroxyphenyl)-1H-imidazo-[4,5-c]pyridine and its analogues: intramolecular proton transfer versus intramolecular charge transfer.

    PubMed

    Behera, Santosh Kumar; Karak, Ananda; Krishnamoorthy, G

    2015-02-12

    Photophysical characteristics of 2-(4'-amino-2'-hydroxyphenyl)-1H-imidazo-[4,5-c]pyridine (AHPIP-c) have been studied in various aprotic and protic solvents using UV-visible, steady state fluorescence and time-resolved fluorescence spectroscopic techniques. To comprehend the competition between the intramolecular charge transfer (ICT) and the excited state intramolecular proton transfer (ESIPT) processes, the photophysical properties of 2-(4'-amino-2'-methoxyphenyl)-1H-imidazo-[4,5-c]pyridine (AMPIP-c) and 2-(4'-aminophenyl)-1H-imidazo-[4,5-c]pyridine (APIP-c) were also investigated. Though APIP-c displays twisted ICT (TICT) emission in protic solvents, AHPIP-c exhibits normal and tautomer emissions in aprotic as well as in protic solvents due to ESIPT. However, the methoxy derivative, AMPIP-c, emits weak TICT fluorescence in methanol. PMID:25337987

  7. A novel non-fluorescent excited state intramolecular proton transfer phenomenon induced by intramolecular hydrogen bonds: an experimental and theoretical investigation

    PubMed Central

    Yin, Hang; Li, Hui; Xia, Guomin; Ruan, Chengyan; Shi, Ying; Wang, Hongming; Jin, Mingxing; Ding, Dajun

    2016-01-01

    Two molecules, 1-hydroxypyrene-2-carbaldehyde (HP) and 1-methoxypyrene-2-carbaldehyde (MP) were explored. We investigated their photophysical properties, using experimental transient absorption and theoretical density functional theory/time-dependent density functional theory (DFT/TDDFT). HP and MP have similar geometric conformations but exhibit entirely different photophysical properties upon excitation into the S1 state. In contrast to traditional excited state intramolecular proton transfer (ESIPT) in molecules that exhibit either single or dual fluorescence, HP has an unusual non-fluorescent property. Specifically, the ultrafast ESIPT process occurs in 158 fs and is followed by an intersystem crossing (ISC) component of 11.38 ps. In contrast to HP, MP undergoes only an 8 ps timescale process, which was attributed to interactions between solute and solvent. We concluded that this difference arises from intramolecular hydrogen bonds (IMHBs), which induce drastic structural alterntion upon excitation. PMID:26790961

  8. Fractional-calculus diffusion equation

    PubMed Central

    2010-01-01

    Background Sequel to the work on the quantization of nonconservative systems using fractional calculus and quantization of a system with Brownian motion, which aims to consider the dissipation effects in quantum-mechanical description of microscale systems. Results The canonical quantization of a system represented classically by one-dimensional Fick's law, and the diffusion equation is carried out according to the Dirac method. A suitable Lagrangian, and Hamiltonian, describing the diffusive system, are constructed and the Hamiltonian is transformed to Schrodinger's equation which is solved. An application regarding implementation of the developed mathematical method to the analysis of diffusion, osmosis, which is a biological application of the diffusion process, is carried out. Schrödinger's equation is solved. Conclusions The plot of the probability function represents clearly the dissipative and drift forces and hence the osmosis, which agrees totally with the macro-scale view, or the classical-version osmosis. PMID:20492677

  9. 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

  10. Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis†

    PubMed Central

    Reber, Keith P.; Tilley, S. David

    2011-01-01

    The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon–carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give β-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products. PMID:19847338