From caging to rouse dynamics in polymer melts with intramolecular barriers: a critical test of the mode coupling theory

By means of computer simulations and solution of the equations of the mode coupling theory (MCT),we investigate the role of the intramolecular barriers on several dynamic aspects of nonentangled polymers. The investigated dynamic range extends from the caging regime characteristic of glass-formers to the relaxation of the chain Rouse modes. We review our recent work on this question,provide new results, and critically discuss the limitations of the theory. Solutions of the MCT for the structural relaxation reproduce qualitative trends of simulations for weak and moderate barriers. However, a progressive discrepancy is revealed as the limit of stiff chains is approached. This dis-agreement does not seem related with dynamic heterogeneities, which indeed are not enhanced by increasing barrier strength. It is not connected either with the breakdown of the convolution approximation for three-point static correlations, which retains its validity for stiff chains. These findings suggest the need of an improvement of the MCT equations for polymer melts. Concerning the relaxation of the chain degrees of freedom, MCT provides a microscopic basis for time scales from chain reorientation down to the caging regime. It rationalizes, from first principles, the observed deviations from the Rouse model on increasing the barrier strength. These include anomalous scaling of relaxation times, long-time plateaux, and nonmonotonous wavelength dependence of the mode correlators.

The role of intramolecular barriers on the glass transition of polymers: computer simulations versus mode coupling theory

We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are analyzed within the framework of the mode coupling theory (MCT). Critical nonergodicity parameters, critical temperatures, and dynamic exponents are obtained from consistent fits of simulation data to MCT asymptotic laws. The so-obtained MCT λ-exponent increases from standard values for fully flexible chains to values close to the upper limit for stiff chains. In analogy with systems exhibiting higher-order MCT transitions, we suggest that the observed large λ-values arise form the interplay between two distinct mechanisms for dynamic arrest: general packing effects and polymer-specific intramolecular barriers. We compare simulation results with numerical solutions of the MCT equations for polymer systems, within the polymer reference interaction site model (PRISM) for static correlations. We verify that the approximations introduced by the PRISM are fulfilled by simulations, with the same quality for all the range of investigated barrier strength. The numerical solutions reproduce the qualitative trends of simulations for the dependence of the nonergodicity parameters and critical temperatures on the barrier strength. In particular, the increase in the barrier strength at fixed density increases the localization length and the critical temperature. However the qualitative agreement between theory and simulation breaks in the limit of stiff chains. We discuss the possible origin of this feature.

Dynamic arrest in polymer melts: competition between packing and intramolecular barriers

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within the framework of the mode coupling theory of the glass transition. Control parameters are tuned in order to induce a competition between general packing effects and polymer-specific intramolecular barriers as mechanisms for dynamic arrest. This competition yields unusually large values of the so-called mode coupling theory exponent parameter and rationalizes qualitatively different observations for simple bead-spring and realistic polymers. The systematic study of the effect of intramolecular barriers presented here also establishes a fundamental difference between the nature of the glass transition in polymers and in simple glass formers.

Dynamic ecosystems under anthropogenic stress : how does macrotidal sandy fauna respond to green tides?

Highly dynamic systems, often considered as resilient systems, are characterised by abiotic and biotic processes under continuous and strong changes in space and time. Because of this variability, the detection of overlapping anthropogenic stress is challenging. Coastal areas harbour dynamic ecosystems in the form of open sandy beaches, which cover the vast majority of the world’s ice-free coastline. These ecosystems are currently threatened by increasing human-induced pressure, among which mass-development of opportunistic macroalgae (mainly composed of Chlorophyta, so called green tides), resulting from the eutrophication of coastal waters. The ecological impact of opportunistic macroalgal blooms (green tides, and blooms formed by other opportunistic taxa), has long been evaluated within sheltered and non-tidal ecosystems. Little is known, however, on how more dynamic ecosystems, such as open macrotidal sandy beaches, respond to such stress. This thesis assesses the effects of anthropogenic stress on the structure and the functioning of highly dynamic ecosystems using sandy beaches impacted by green tides as a study case. The thesis is based on four field studies, which analyse natural sandy sediment benthic community dynamics over several temporal (from month to multi-year) and spatial (from local to regional) scales. In this thesis, I report long-lasting responses of sandy beach benthic invertebrate communities to green tides, across thousands of kilometres and over seven years; and highlight more pronounced responses of zoobenthos living in exposed sandy beaches compared to semi-exposed sands. Within exposed sandy sediments, and across a vertical scale (from inshore to nearshore sandy habitats), I also demonstrate that the effects of the presence of algal mats on intertidal benthic invertebrate communities is more pronounced than that on subtidal benthic invertebrate assemblages, but also than on flatfish communities. Focussing on small-scale variations in the most affected faunal group (i.e. benthic invertebrates living at low shore), this thesis reveals a decrease in overall beta-diversity along a eutrophication-gradient manifested in the form of green tides, as well as the increasing importance of biological variables in explaining ecological variability of sandy beach macrobenthic assemblages along the same gradient. To illustrate the processes associated with the structural shifts observed where green tides occurred, I investigated the effects of high biomasses of opportunistic macroalgae (Ulva spp.) on the trophic structure and functioning of sandy beaches. This work reveals a progressive simplification of sandy beach food web structure and a modification of energy pathways over time, through direct and indirect effects of Ulva mats on several trophic levels. Through this thesis I demonstrate that highly dynamic systems respond differently (e.g. shift in δ13C, not in δ15N) and more subtly (e.g. no mass-mortality in benthos was found) to anthropogenic stress compared to what has been previously shown within more sheltered and non-tidal systems. Obtaining these results would not have been possible without the approach used through this work; I thus present a framework coupling field investigations with analytical approaches to describe shifts in highly variable ecosystems under human-induced stress.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Variation in dynamic elastic shear modulus of sandstone upon fluid saturation and substitution

Experimental acoustic measurements on sandstone rocks at both sonic and ultrasonic frequencies show that fluid saturation can cause a noticeable change in both the dynamic bulk and shear elastic moduli of sandstones. We observed that the change in dynamic shear modulus upon fluid saturation is highly dependent on the type of saturant, its viscosity, rock microstructure, and applied pressures. Frequency dispersion has some influence on dynamic elastic moduli too, but its effect is limited to the ultrasonic frequency ranges and above. We propose that viscous coupling, reduction in free surface energy, and, to a limited extent, frequency dispersion due to both local and global flow are the main mechanisms responsible for the change in dynamic shear elastic modulus upon fluid saturation and substitution, and we quantify influences.

Synthesis and properties of polyaromatic dendrimers possessing a repetitive amide-ester coupling sequence

A series of novel polyaromatic dendrimers that feature tris-(2-ethylamino)amine as the central core unit has been synthesized up to the third generation by employing a convergent growth strategy. The building blocks 1,3-diamino-2-hydroxypropane and 4-carboxybenzaldehyde were used for dendron construction, a process that involved the cyclic repetition of esterification, oxidation and selective amidation steps. Molecular modelling of this class of dendrimers has been used to predict potential solution state conformations employing molecular mechanics and molecular dynamic simulations. In addition, the results of preliminary metal binding studies using the first generation dendritic system are also outlined. (C) 2003 Elsevier Science Ltd. All rights reserved.

Design of a minimum variance multiple input-multiple output neuro self-tuning proportional-integral-derivative controller for non-linear dynamic systems

In this study a minimum variance neuro self-tuning proportional-integral-derivative (PID) controller is designed for complex multiple input-multiple output (MIMO) dynamic systems. An approximation model is constructed, which consists of two functional blocks. The first block uses a linear submodel to approximate dominant system dynamics around a selected number of operating points. The second block is used as an error agent, implemented by a neural network, to accommodate the inaccuracy possibly introduced by the linear submodel approximation, various complexities/uncertainties, and complicated coupling effects frequently exhibited in non-linear MIMO dynamic systems. With the proposed model structure, controller design of an MIMO plant with n inputs and n outputs could be, for example, decomposed into n independent single input-single output (SISO) subsystem designs. The effectiveness of the controller design procedure is initially verified through simulations of industrial examples.

Dynamic auroral structure in the vicinity of the polar cusp - multipoint observations during southward and northward IMF

The low- and high-latitude boundary layers of the earth's magnetosphere [low-latitude boundary layer (LLBL) and mantle] play important roles in transferring momentum and energy from the solar wind to the magnetosphere-ionosphere system. Particle precipitation, field-aligned current, auroral emission, ionospheric ion drift and ground magnetic perturbations are among the low-altitude parameters that show signatures of various plasma processes in the LLBL and the magnetopause current layer. Magnetic merging events, Kelvin-Helmholtz waves, and pressure pulses excited by the variable solar wind/magnetosheath plasma are examples of boundary phenomena that may be coupled to the ionosphere via field-aligned currents. Optical auroral observation, by photometry and all-sky TV cameras, is a unique technique for investigating the spatial and temporal structure of the electron precipitation associated with such phenomena. However, the distinction between the different boundary layer plasma populations cannot in general be unambiguously determined by optics alone. Additional information, such as satellite observations of particle boundaries and field-aligned currents, is needed in order to identify the plasma source(s) and the magnetosphere-ionosphere coupling mode(s). Two categories of auroral activity/structure in the vicinity of the polar cusp are discussed in this paper, based on combined ground and satellite data. In one case, the quasi-periodic sequence of auroral events at the polar cap boundary involves accelerated electrons (< 1 keV) moving poleward (< 1 km s-1) and azimuthally along the persistent cusp/cleft arc poleward boundary with velocities (< 4 km s-1), comparable to the local ionospheric ion drift during periods of southward IMF. A critical question is whether or not the optical events signify a corresponding plasma flow across the open/closed field line boundary in such cases. Near-simultaneous observations of magnetopause flux transfer events (FTEs) and such optical/ion drift events are reported. The reverse pattern of motion of discrete auroral forms is observed during positive interplanetary magnetic field (IMF) B(Z), i.e. equatorward motion into the cusp/cleft background arc from the poleward edge. Combined satellite and ground-based information for the latter cases indicate a source mechanism, poleward of the cusp at the high-latitude magnetopause or plasma mantle, giving rise to strong momentum transfer and electron precipitation structures within a approximately 200 km-wide latitudinal zone at the cusp/cleft poleward boundary. The striking similarities of auroral electrodynamics in the cleft/mantle region during northward and southward IMF indicate that a qualitatively similar solar wind-magnetosphere coupling mode is operating. It is suggested that, in both cases, the discrete auroral forms represent temporal/spatial structure of larger-scale convection over the polar magnetosphere.

The response of the magnetosphere-ionosphere system to solar wind dynamic pressure variations

We study the causal chain of events by which variations in the solar wind dynamic pressure cause the magnetopause boundary to move and excite magnetic perturbations at the ground. The observation of large ground magnetic transients is argued to be due to the coupling of the magnetohydrodynamic compressional wave to the field-guided Alfvén wave, which carrying current, can thereby transfer momentum to the ionosphere. The study highlights the similarity of the ionospheric signatures at a single station arising from the response of the coupled magnetosphere-ionosphere system to disparate impulsive processes at the magnetopause.

Dynamic effects of breakup on fusion reactions of weakly bound nuclei

The traditional reduction methods to represent the fusion cross sections of different systems are flawed when attempting to completely eliminate the geometrical aspects, such as the heights and radii of the barriers, and the static effects associated with the excess neutrons or protons in weakly bound nuclei. We remedy this by introducing a new dimensionless universal function, which allows the separation and disentanglement of the static and dynamic aspects of the breakup coupling effects connected with the excess nucleons. Applying this new reduction procedure to fusion data of several weakly bound systems, we find a systematic suppression of complete fusion above the Coulomb barrier and enhancement below it. Different behaviors are found for the total fusion cross sections. They are appreciably suppressed in collisions of neutron-halo nuclei, while they are practically not affected by the breakup coupling in cases of stable weakly bound nuclei. (C) 2009 Elsevier B.V. All rights reserved.

Disentangling static and dynamic effects of low breakup threshold in fusion reactions

A new technique to analyze fusion data is developed. From experimental cross sections and results of coupled-channel calculations a dimensionless function is constructed. In collisions of strongly bound nuclei this quantity is very close to a universal function of a variable related to the collision energy, whereas for weakly bound projectiles the effects of breakup coupling are measured by the deviations with respect to this universal function. This technique is applied to collisions of stable and unstable weakly bound isotopes.

Coupling rate measurement of a novel multi-actuated piezoelectric device using optical interferometry

The class of piezoelectric actuators considered in this paper consists of a multi-flexible structure actuated by two or more piezoceramic devices that must generate different output displacements and forces at different specified points of the domain and in different directions. The devices were modeled by finite element using the software ANSYS and the topology optimization method. The following XY actuators were build to achieve maximum displacement in the X and Y directions with a minimum crosstalk between them. The actuator prototypes are composed of an aluminum structure, manufactured by using a wire Electrical Discharge Machining, which are bonded to rectangular PZT5A piezoceramic blocks by using epoxy resin. Multi-actuator piezoelectric device displacements can be measured by using optical interferometry, since it allows dynamic measurements in the kHz range, which is of the order of the first resonance frequency of these piezomechanisms. A Michelson-type interferometer, with a He-Ne laser source, is used to measure the displacement amplitudes in nanometric range. A new optical phase demodulation technique is applied, based on the properties of the triangular waveform drive voltage applied to the XY piezoelectric nanopositioner. This is a low-phase-modulation-depth-like technique that allows the rapid interferometer auto-calibration. The measurements were performed at 100 Hz frequency, and revealed that the device is linear voltage range utilized in this work. The ratio between the generated and coupled output displacements and the drive voltages is equal to 10.97 nm/V and 1.76 nm/V, respectively, which corresponds to a 16% coupling rate. © 2010 IEEE.

Wide dynamic range homodyne interferometry method and its application for piezoactuator displacement measurements

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The dynamic behavior of a cantilever beam coupled to a non-ideal unbalanced motor through numerical and experimental analysis

An excitation force that is not influenced by the system state is said to be an ideal energy source. In real situations, a direct and feedback coupling between the excitation source and the system must always exist at a certain level. This manifestation of the law of conservation of energy is known as the Sommerfeld effect. In the case of obtaining a mathematical model for such a system, additional equations are usually necessary to describe the vibration sources with limited power and its coupling with the mechanical system. In this work, a cantilever beam and a non-ideal DC motor fixed to its free end are analyzed. The motor has an unbalanced mass that provides excitation to the system which is proportional to the current applied to the motor. During the coast up operation of the motor, if the drive power is increased slowly, making the excitation frequency pass through the first natural frequency of the beam, the DC motor speed will remain the same until it suddenly jumps to a much higher value (simultaneously its amplitude jumps to a much lower value) upon exceeding a critical input power. It was found that the Sommerfeld effect depends on some system parameters and the motor operational procedures. These parameters are explored to avoid the resonance capture in the Sommerfeld effect. Numerical simulations and experimental tests are used to help gather insight of this dynamic behavior. (C) 2014 Elsevier Ltd. All rights reserved.