Long-range Motion Research Articles

Activation of Nanoscale Allosteric Protein Domain Motion Revealed by Neutron Spin Echo Spectroscopy

NHERF1 is a multidomain scaffolding protein that assembles signaling complexes, and regulates the cell surface expression and endocytic recycling of a variety of membrane proteins. The ability of the two PDZ domains in NHERF1 to assemble protein complexes is allosterically modulated by the membrane-cytoskeleton linker protein ezrin, whose binding site is located as far as 110 Ångstroms away from the PDZ domains. Here, using neutron spin echo (NSE) spectroscopy, selective deuterium labeling, and theoretical analyses, we reveal the activation of interdomain motion in NHERF1 on nanometer length-scales and on submicrosecond timescales upon forming a complex with ezrin. We show that a much-simplified coarse-grained model suffices to describe interdomain motion of a multidomain protein or protein complex. We expect that future NSE experiments will benefit by exploiting our approach of selective deuteration to resolve the specific domain motions of interest from a plethora of global translational and rotational motions. Our results demonstrate that the dynamic propagation of allosteric signals to distal sites involves changes in long-range coupled domain motions on submicrosecond timescales, and that these coupled motions can be distinguished and characterized by NSE.

Grain Size Effect on Electrical and Dielectric Properties of the Nanostructured Dy-Doped Ceria ( Ce0.8Dy0.2O2 − δ )

Electrical and dielectric properties, and their correlations were discussed in the nanostructured materials with average grain sizes of 15, 35, and 58 nm using the dielectric functions such as dielectric permittivity , loss tangent , and electric modulus . The ionic transport mechanism varies with the grain size of the materials such that the material with an average grain size of 35 nm exhibited a higher value of ionic conductivity above (with at ), whereas the material with an average grain size of 15 nm shows higher value conductivity at lower temperatures. The oxygen vacancy in the material decreases with the decrease in grain size. The migration energy of oxygen ions also decreases with the decrease in grain size of the nanostructured material. The material with an average grain size of 35 nm shows a very low value association energy (i.e., 0.05 eV) compared to the others. At temperatures below , the local motion of oxygen vacancies around controls the conductivity of all the materials, and at higher temperatures, the conductivity in the materials with a larger grain size is mainly due to the long-range motion of vacancies.

High performance shape memory polymer networks based on rigid nanoparticle cores

Smart materials that can respond to external stimuli are of widespread interest in biomedical science. Thermal-responsive shape memory polymers, a class of intelligent materials that can be fixed at a temporary shape below their transition temperature (T(trans)) and thermally triggered to resume their original shapes on demand, hold great potential as minimally invasive self-fitting tissue scaffolds or implants. The intrinsic mechanism for shape memory behavior of polymers is the freezing and activation of the long-range motion of polymer chain segments below and above T(trans), respectively. Both T(trans) and the extent of polymer chain participation in effective elastic deformation and recovery are determined by the network composition and structure, which are also defining factors for their mechanical properties, degradability, and bioactivities. Such complexity has made it extremely challenging to achieve the ideal combination of a T(trans) slightly above physiological temperature, rapid and complete recovery, and suitable mechanical and biological properties for clinical applications. Here we report a shape memory polymer network constructed from a polyhedral oligomeric silsesquioxane nanoparticle core functionalized with eight polyester arms. The cross-linked networks comprising this macromer possessed a gigapascal-storage modulus at body temperature and a T(trans) between 42 and 48 degrees C. The materials could stably hold their temporary shapes for > 1 year at room temperature and achieve full shape recovery <or= 51 degrees C in a matter of seconds. Their versatile structures allowed for tunable biodegradability and biofunctionalizability. These materials have tremendous promise for tissue engineering applications.

Geometric context influences ambiguous apparent motion

How sensitive is the matching process in long-range apparent motion to contextual influences? The M points in N frames computational models make little accommodation for more general scene analysis constraints. Alternatively, if apparent motion perception is to be understood as generating a model of a scene transformation due to changing object/object and object/observer relationships, then other factors might affect one's interpretation. We examined the ability of contours to influence the interpretation of dynamic dot quartet motion. In the first two experiments, we measured the frequency of seeing horizontal vs. vertical quartet motion in the presence of flanking real or Kanizsa rectangles arranged outside the sides or top/bottom of the quartet. Most observers exhibited a significant change in quartet interpretation with the motion more frequently appearing to be along the contours. The biasing effect was greater for real contours than for cognitive contours. In some control conditions, the Pacman disks were oriented so that no virtual figure was seen, and no biasing effect was observed. In these experiments the observed along-the-contour bias was very sensitive to proximity. In contrast, a central “blocking” rectangle is also effective in biasing quartet motion, but in a way that is not proximity-dependent. A third experiment measured the influence of a central virtual blocker crossing either horizontal or vertical quartet paths. Virtual blockers were effective in all experienced observers, but only in some naive observers. Therefore the effect may depend on the observer being actively aware of the virtual contours and objects.

The role of multi-area interactions for the computation of apparent motion

Apparent motion (AM) is a robust visual illusion, in which fast displays of static objects in successively different positions elicit the perception of object motion. Neurons in higher order areas 21 and 19 compute object motion under such conditions and send feedback to early visual areas 18 and 17, which is instrumental in eliciting computation of motion in those very areas. To explore the computational dynamics of AM, we made a neural field model consisting of two one-dimensional rings of simple neurons expressing firing rates, one for areas 17/18 and one for areas 19/21. The model neurons, without any orientation or direction selectivity, computed apparent motion for the range of space-timings of stimuli associated with short- and long-range AM in humans. The computation of long-range AM in 17/18 required two model areas and the presence of feedback and conduction/computation delays between those areas. As in the in vivo experiments of long-range AM, the stationary stimuli were initially mapped as stationary in model area 17/18, but after the feedback also these lower areas computed AM. The dynamics of the two-area network produces short-range and long-range apparent motion for a large range of feedback strengths and a small range of lateral excitation near the bifurcation to an amplitude instability. The computation of AM in higher order areas was due to the neurons in these areas having large receptive fields as a consequence of divergent feed-forward connectivity. This implies that these areas compute long-range AM when early areas 17 and 18 do not, and therefore higher order areas must enslave lower order areas to compute the same, if the whole network is to arrive at a coherent perceptual solution.

Differences and similarities in short- and long-range motion processing

Differences and similarities in short- and long-range motion processing

What does the Ternus display tell us about motion processing in human vision?

The Ternus display is a moving visual stimulus which elicits two very different percepts, according to the length of the interstimulus interval (ISI) between each frame of the motion sequence. These two percepts, referred to as element motion and group motion, have previously been analysed in terms of the operation of a low-level, dedicated short-range motion process (in the case of element motion), and of a higher-level, attentional long-range motion process (in the case of group motion). We used a novel Ternus configuration to show that both element and group motion are, in fact, mediated solely by a process sensitive to changes in the spatial appearance of the Ternus elements. In light of this, it appears that Ternus displays tell us nothing about low-level motion processing, implying that previous studies using Ternus displays, for instance those dealing with dyslexia, require reinterpretation. Further manipulations of the Ternus display revealed that the orientation and spatial-frequency discrimination of the process underlying the analysis of Ternus displays is far worse than thresholds for spatial vision. We conclude that Ternus displays are analysed via a long-range motion, or feature-tracking, process, and that this process is distinct from spatial vision.

Molecular Mechanism of Long-Range Diffusion in Phospholipid Membranes Studied by Quasielastic Neutron Scattering

The motion of phospholipids has previously been studied on many time scales due to the significance for living cells and technological applications. The motions on a pico- to nanosecond time scale were determined by quasielastic neutron scattering (QENS) to be much faster than the ones on the microsecond scale covered by fluorescence recovery after photobleaching (FRAP). This was explained by assuming that the molecules rattle fast in a cage of neighbors (observed with QENS) from which they escape once in a while; this escape was then the primary step of the slower diffusion measured by FRAP. However, nanosecond MD simulation studies could not observe any escape events; recent findings even suggested that the long-range motion in phospholipid membranes on short time scales is not diffusive but has flow-like characteristics. To check this novel view, we have repeated the QENS experiments with today's significantly improved instrumentation. By using the advantage of QENS that allows tuning of the observation time in the pico- to nanosecond range, it was possible to study the evolution of motions in this time frame. Localized motions, e.g., of the head and tail groups, appear separated from the long-range motion and do not obfuscate the analysis as they do in a mean squared displacement plot. The results for the long-range motion are indeed compatible with flow patterns, whereas the localized motions can account for the fast motions interpreted as motions in a cage before. Hereby, we give experimental evidence for a completely different mechanism of long-range motion on short time scales in phospholipid membranes.

Dynamics in Clays - Combining Neutron Scattering and Microscopic Simulation

AbstractMobility of ions and water in clays is at the heart of their remarkable properties of water retention and ion-exchange. It has been addressed here using two microscopic techniques: neutron scattering and molecular dynamics simulations. Neutron scattering gives access exclusively to water dynamics in clays, due to the exceptional sensitivity of neutrons to H atoms. The data interpretation can be challenging, especially for natural clays such as montmorillonite, with inhomogeneous swelling characteristics. A great improvement is achieved with the use of synthetic materials, as demonstrated here on the case of synthetic (fluoro)hectorite. The standard analytical models for long-range diffusive motion, isotropic translation and its derivative, powder averaged two dimensional translation, have been used to interpret the neutron scattering data. They both agree on the order of magnitude for the diffusion coefficient of water in monohydrated and bihydrated clays, 10−10m2s−1and 10−9m2s−1respectively. While the two-dimensional nature of water diffusion in clays is seen clearly from molecular dynamics simulations, its signature in neutron scattering data is obscured by the powder-averaging of the signal. A novel method, based on a multi-resolution analysis of scattering functions from powder samples, allows never-the-less a clear determination of the dimensionality of water motion in the system. Extracting information on local water motion is difficult on the basis of neutron scattering data only. Various models for localised motion, rotation on a sphere or jump diffusion, have been proposed and used to interpret the observed neutron data, however their applicability is questionable in light of information from molecular dynamics simulations. Aside from aiding the interpretation of neutron scattering data, MD simulations are most valuable in providing information on the behaviour of ions in clays. MD estimates the interlayer ion coefficients as of the some order of magnitude as water, even if the details of ionic motion are strikingly different between the two ions considered here, Na+and Cs+. Further, MD has also allowed to address the topic of ion exchange between clay interlayers and bulk aqueous solution. The microscopic picture of water and ion motion in clays, emerging from neutron scattering and MD simulations, should be treated as a building block of the overall modelling of macroscopic transport in clays, the ultimate property of interest for many clay applications.

Dielectric properties of block copolymers based on vinylidene fluoride and cyano comonomers

The syntheses of poly(vinylidene fluoride)- b-poly(AN, MAN, VCN) (PVDF- b-PM CN) block copolymers, using the iodine transfer polymerization (ITP) of acrylonitrile (AN), methacrylonitrile (MAN) and vinylidene cyanide (VCN), in the presence of PVDF-I, are presented. In a first step, the ITP of vinylidene fluoride (or 1,1-difluoroethylene, VDF) with C 6F 13I initiated by tert-butyl peroxypivalate is achieved. This ITP led to two different isomeric oligomers (PVDF-I) bearing either CH 2I or CF 2I end-groups. Second step, those fluorinated blocks were used latter as macromolecular chain transfer agents to achieve the ITP with cyanide monomers (M CN). The characterization of synthesized samples by 19F and 1H NMR spectroscopy allowed determining the average degree of polymerization. These block copolymers were characterized by SEC chromatography (4160–51100 g/mol) and by wide angle X-ray diffraction. Their thermal stabilities were studied using thermogravimetric analysis (TGA). The melting and glass transition temperatures as well as the degree of crystallinity were characterized by means of DSC. The influence of the copolymer compositions on dielectric properties has also been investigated. Dielectric analyses show several relaxations processes associated with long-range molecular motions, which are associated to the glass transition temperatures of both blocks (PVDF block and poly(cyano monomer blocks)). These behaviors are discussed in terms of dielectric proprieties as a function of molecular composition and mobility.

Crystallographic orientation and stress-amplitude dependence of damping in the martensite phase in textured Ti–Nb–Al shape memory alloy

The low-frequency damping (tanδ) of a strongly textured β-titanium shape memory alloy (SMA) was investigated by a dynamic mechanical analysis (DMA) in a tensile mode together with a tensile test and a crystallographic analysis of the transformation. In addition to the high background of tanδ in martensite, a broad tanδ peak with a relaxation-like character was found in the martensite phase similar to the Ti–Ni SMAs. There was a critical stress for the broad peak that corresponds to the stress to complete the martensite variant reorientation, whereas the high background of tanδ had no critical stress. This implies that the broad peak is generated through the long-range motion of twin boundaries. A guideline to estimate the orientation dependence of damping in textured SMAs is also proposed using the interaction energy between the external stress and the transformation.

Stress Amplitude Dependence of Internal Friction in TiNbAl Shape Memory Alloy

Stress amplitude dependence of internal friction (tanδ) of a Ti-base shape memory alloy, Ti-24mol%Nb-3mol%Al, with a well developed texture is investigated by a dynamic mechanical analyzer (DMA) in a tensile mode. In the martensite (C-orthorhombic) phase, tan was 0.01~0.05 and was much higher than that of the parent phase in all the test conditions. This means that the martensite/martensite interfaces move under the external sinusoidal stress. In addition to this high background, tanδ-peak appeared at around 153K. The tanδ-peak height clearly depended also on the stress amplitude (10~50MPa). In addition, a threshold stress for the appearance of the tanδ-peak existed in the DMA test and it was in good agreement with the yield stress (0.2% proof stress) in a tensile test at 153K. These results mean that a long-range motion of twin-boundaries is necessary for the appearance of the tanδ-peak.

Solvent Effects on Catalysis by Escherichia coli Dihydrofolate Reductase

Hydride transfer catalyzed by dihydrofolate reductase (DHFR) has been described previously within an environmentally coupled model of hydrogen tunneling, where protein motions control binding of substrate and cofactor to generate a tunneling ready conformation and modulate the width of the activation barrier and hence the reaction rate. Changes to the composition of the reaction medium are known to perturb protein motions. We have measured kinetic parameters of the reaction catalyzed by DHFR from Escherichia coli in the presence of various cosolvents and cosolutes and show that the dielectric constant, but not the viscosity, of the reaction medium affects the rate of reaction. Neither the primary kinetic isotope effect on the reaction nor its temperature dependence were affected by changes to the bulk solvent properties. These results are in agreement with our previous report on the effect of solvent composition on catalysis by DHFR from the hyperthermophile Thermotoga maritima. However, the effect of solvent on the temperature dependence of the kinetic isotope effect on hydride transfer catalyzed by E. coli DHFR is difficult to explain within a model, in which long-range motions couple to the chemical step of the reaction, but may indicate the existence of a short-range promoting vibration or the presence of multiple nearly isoenergetic conformational substates of enzymes with similar but distinct catalytic properties.

Four-dimensional deformable image registration using trajectory modeling

A four-dimensional deformable image registration (4D DIR) algorithm, referred to as 4D local trajectory modeling (4DLTM), is presented and applied to thoracic 4D computed tomography (4DCT) image sets. The theoretical framework on which this algorithm is built exploits the incremental continuity present in 4DCT component images to calculate a dense set of parameterized voxel trajectories through space as functions of time. The spatial accuracy of the 4DLTM algorithm is compared with an alternative registration approach in which component phase to phase (CPP) DIR is utilized to determine the full displacement between maximum inhale and exhale images. A publically available DIR reference database (http://www.dir-lab.com) is utilized for the spatial accuracy assessment. The database consists of ten 4DCT image sets and corresponding manually identified landmark points between the maximum phases. A subset of points are propagated through the expiratory 4DCT component images. Cubic polynomials were found to provide sufficient flexibility and spatial accuracy for describing the point trajectories through the expiratory phases. The resulting average spatial error between the maximum phases was 1.25 mm for the 4DLTM and 1.44 mm for the CPP. The 4DLTM method captures the long-range motion between 4DCT extremes with high spatial accuracy.

Event-chain Monte Carlo algorithms for hard-sphere systems

In this paper we present the event-chain algorithms, which are fast Markov-chain Monte Carlo methods for hard spheres and related systems. In a single move of these rejection-free methods, an arbitrarily long chain of particles is displaced, and long-range coherent motion can be induced. Numerical simulations show that event-chain algorithms clearly outperform the conventional Metropolis method. Irreversible versions of the algorithms, which violate detailed balance, improve the speed of the method even further. We also compare our method with a recent implementations of the molecular-dynamics algorithm.

Processing of Targets in Smooth or Apparent Motion Along the Vertical in the Human Brain: An fMRI Study

Neural substrates for processing constant speed visual motion have been extensively studied. Less is known about the brain activity patterns when the target speed changes continuously, for instance under the influence of gravity. Using functional MRI (fMRI), here we compared brain responses to accelerating/decelerating targets with the responses to constant speed targets. The target could move along the vertical under gravity (1g), under reversed gravity (-1g), or at constant speed (0g). In the first experiment, subjects observed targets moving in smooth motion and responded to a GO signal delivered at a random time after target arrival. As expected, we found that the timing of the motor responses did not depend significantly on the specific motion law. Therefore brain activity in the contrast between different motion laws was not related to motor timing responses. Average BOLD signals were significantly greater for 1g targets than either 0g or -1g targets in a distributed network including bilateral insulae, left lingual gyrus, and brain stem. Moreover, in these regions, the mean activity decreased monotonically from 1g to 0g and to -1g. In the second experiment, subjects intercepted 1g, 0g, and -1g targets either in smooth motion (RM) or in long-range apparent motion (LAM). We found that the sites in the right insula and left lingual gyrus, which were selectively engaged by 1g targets in the first experiment, were also significantly more active during 1g trials than during -1g trials both in RM and LAM. The activity in 0g trials was again intermediate between that in 1g trials and that in -1g trials. Therefore in these regions the global activity modulation with the law of vertical motion appears to hold for both RM and LAM. Instead, a region in the inferior parietal lobule showed a preference for visual gravitational motion only in LAM but not RM.

Relationship between free volume properties and structure of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) membranes via various crystallization conditions

The relationship between the crystalline structure and the free volume properties within the amorphous phase of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) membranes, which were prepared via isothermal crystallization processes at various crystallization temperatures, was investigated. From the data of positron annihilation lifetime (PAL) spectroscopy over a temperature range of 25–90°C, the temperature dependence of free volume size, amount, distribution, and relative fractional free volume and thermal expansion behaviors of free volume were discussed. The existence of a rigid-amorphous fraction (RAF) which constrained long-range motions in the semi-crystalline polymer was demonstrated by DSC trace and considered to interpret the temperature dependence of those free volume properties. Based on the crystallization conditions, the effect of the crystallization rate of PHBV polymer was proposed to explain the thermal expansion coefficients of free volume size. The membranes crystallized at faster crystallization rate would accompany higher thermal expansion coefficients of free volume size and the larger free volume size at higher temperatures. Larger distribution of the free volume size and higher thermal expansivity of o-Ps lifetime dispersion (dσ/dt) of isothermally melt-crystallized membranes were observed as a result of the bimodal distribution of the lamellar periodicity, which was obtained by small-angle X-ray scattering (SAXS), and less amount of RAF than that of a cold-crystallized membrane. Conclusively, free volume size and thermal expansion of the free volume in PHBV membranes were affected by the kinetics of crystallization; comparatively, the total amount of free volume and fractional free volume were determined by the final crystallinity. The size distribution of free volume was associated with the crystalline lamellar structure which was dominated by the crystallization conditions.

Electrical study and dielectric relaxation behavior in nanocrystalline Ce0.85Gd0.15O2−δ material at intermediate temperatures

The nanocrystalline material of 15 mol% Gd-doped ceria (Ce0.85Gd0.15O2−δ ) was prepared by citrate auto ignition method. The electrical study and dielectric relaxation technique were applied to investigate the ionic transport process in this nanocrystalline material with an average grain size of 13 nm and the dynamic relaxation parameters are deduced in the temperature range of 300–600°C. The ionic transference number in the material is found to be 0.85 at 500°C at ambient conditions. The oxygen ionic conduction in the nanocrystalline Ce0.85Gd0.15O2−δ material follows the hopping mechanism. The grain boundary relaxation is found to be associated with migration of charge carriers. The frequency spectra of modulus M″ exhibited a dielectric relaxation peak corresponding to defect associates \((\mathrm{Gd}\mbox{-}\mathrm{V}_{\mathrm{o}}^{_{_{{\blacksquare\,\blacksquare}}}})^{_{_{{\blacksquare}}}}\). The material exhibits very low values of migration energy and association energy of the oxygen vacancies in the long-range motion, i.e., 0.84 and 0.07 eV, respectively.

SIS model of epidemic spreading on dynamical networks with community

We present a new epidemic Susceptible-Infected-Susceptible (SIS) model to investigate the spreading behavior on networks with dynamical topology and community structure. Individuals in themodel are mobile agentswho are allowed to perform the inter-community (i.e., long-range) motion with the probability p. The mean-field theory is utilized to derive the critical threshold (λC) of epidemic spreading inside separate communities and the influence of the long-range motion on the epidemic spreading. The results indicate that λC is only related with the population density within the community, and the long-range motion will make the original disease-free community become the endemic state. Large-scale numerical simulations also demonstrate the theoretical approximations based on our new epidemic model. The current model and analysis will help us to further understand the propagation behavior of real epidemics taking place on social networks.

Displacement current analysis of carrier behavior in pentacene field effect transistor with poly(vinylidene fluoride and tetrafluoroethylene) gate insulator

The carrier injection mechanism was investigated using a field effect transistor (FET) system with a ferroelectric gate insulator: poly(vinylidene fluoride and tetrafluoroethylene). The carrier injection and the turnover voltage of the spontaneous polarization were measured by application of ramp gate voltage with various sweep rates. Three peaks appeared in the gate current-gate voltage characteristics (Ig-Vg) because of the turnover of the spontaneous polarization and the long-range carrier motion of injected carriers. We accounted for the peaks generated and analyzed the Ig-Vg characteristics. For FETs with Al electrodes, the increase in the sweep rate caused a larger turnover voltage. For FETs with Au electrodes, the turnover voltage was constant. Results show that the difference of the injection property well accounted for these results.