An introduction to NMR-based approaches for measuring protein dynamics

PubMed Central

Kleckner, Ian R; Foster, Mark P

2010-01-01

Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. PMID:21059410

Nanoscopic length scale dependence of hydrogen bonded molecular associates’ dynamics in methanol

PubMed Central

Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.

2017-01-01

In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding. PMID:28527447

Ultra-Slow Dielectric Relaxation Process in Polyols

NASA Astrophysics Data System (ADS)

Yomogida, Yoshiki; Minoguchi, Ayumi; Nozaki, Ryusuke

2004-04-01

Dielectric relaxation processes with relaxation times larger than that for the structural α process are reported for glycerol, xylitol, sorbitol and their mixtures for the first time. Appearance of this ultra-slow process depends on cooling rate. More rapid cooling gives larger dielectric relaxation strength. However, relaxation time is not affected by cooling rate and shows non-Arrhenius temperature dependence with correlation to the α process. It can be considered that non-equilibrium dynamic structure causes the ultra-slow process. Scale of such structure would be much larger than that of the region for the cooperative molecular orientations for the α process.

Femtosecond coherent nuclear dynamics of excited tetraphenylethylene: Ultrafast transient absorption and ultrafast Raman loss spectroscopic studies

NASA Astrophysics Data System (ADS)

Kayal, Surajit; Roy, Khokan; Umapathy, Siva

2018-01-01

Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy. TA measurements on the S1 state reveal step-wise population relaxation from the Franck-Condon (FC) state → relaxed state → twisted state, while the URLS study provides insights on the vibrational dynamics during the course of the reaction. The TA spectral dynamics and vibrational Raman amplitudes within 1 ps reveal vibrational wave packet propagating from the FC state to the relaxed state. Fourier transformation of this oscillation leads to a ˜130 cm-1 low-frequency phenyl torsional mode. Two vibrational marker bands, Cet=Cet stretching (˜1512 cm-1) and Cph=Cph stretching (˜1584 cm-1) modes, appear immediately after photoexcitation in the URLS spectra. The initial red-shift of the Cph=Cph stretching mode with a time constant of ˜400 fs (in butyronitrile) is assigned to the rate of planarization of excited TPE. In addition, the Cet=Cet stretching mode shows initial blue-shift within 1 ps followed by frequency red-shift, suggesting that on the sub-picosecond time scale, structural relaxation is dominated by phenyl torsion rather than the central Cet=Cet twist. Furthermore, the effect of the solvent on the structural dynamics is discussed in the context of ultrafast nuclear dynamics and solute-solvent coupling.

Femtosecond coherent nuclear dynamics of excited tetraphenylethylene: Ultrafast transient absorption and ultrafast Raman loss spectroscopic studies.

PubMed

Kayal, Surajit; Roy, Khokan; Umapathy, Siva

2018-01-14

Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy. TA measurements on the S 1 state reveal step-wise population relaxation from the Franck-Condon (FC) state → relaxed state → twisted state, while the URLS study provides insights on the vibrational dynamics during the course of the reaction. The TA spectral dynamics and vibrational Raman amplitudes within 1 ps reveal vibrational wave packet propagating from the FC state to the relaxed state. Fourier transformation of this oscillation leads to a ∼130 cm -1 low-frequency phenyl torsional mode. Two vibrational marker bands, C et =C et stretching (∼1512 cm -1 ) and C ph =C ph stretching (∼1584 cm -1 ) modes, appear immediately after photoexcitation in the URLS spectra. The initial red-shift of the C ph =C ph stretching mode with a time constant of ∼400 fs (in butyronitrile) is assigned to the rate of planarization of excited TPE. In addition, the C et =C et stretching mode shows initial blue-shift within 1 ps followed by frequency red-shift, suggesting that on the sub-picosecond time scale, structural relaxation is dominated by phenyl torsion rather than the central C et =C et twist. Furthermore, the effect of the solvent on the structural dynamics is discussed in the context of ultrafast nuclear dynamics and solute-solvent coupling.

The static structure and dynamics of cadmium sulfide nanoparticles within poly(styrene- block-isoprene) diblock copolymer melts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jang, Woo -Sik; Koo, Peter; Bryson, Kyle

Here, the static structure and dynamic behavior of cadmium sulfide nanoparticles suspended in block copolymer matrix are investigated using transmission electron microscopy, small-angle X-ray scattering, and X-ray photon correlation spectroscopy. The transmission electron micro- scopy study shows that cadmium sulfide nanoparticles are preferentially segregated within the polyisoprene domain of a poly(styrene- block-isoprene) diblock copolymer. For the dynamics study, X-ray photon correlation spectroscopy captures the relaxation process of cadmium sulfide nanoparticles. The measured characteristic relaxation time reveals that the observed dynamics are hyperdiffusive. The characteristic velocity and corresponding activation energy, which are hallmarks of a hyperdiffusive system, are determined from themore » relationship between the characteristic relaxation time and the wavevector.« less

The static structure and dynamics of cadmium sulfide nanoparticles within poly(styrene- block-isoprene) diblock copolymer melts

DOE PAGES

Jang, Woo -Sik; Koo, Peter; Bryson, Kyle; ...

2015-12-20

Here, the static structure and dynamic behavior of cadmium sulfide nanoparticles suspended in block copolymer matrix are investigated using transmission electron microscopy, small-angle X-ray scattering, and X-ray photon correlation spectroscopy. The transmission electron micro- scopy study shows that cadmium sulfide nanoparticles are preferentially segregated within the polyisoprene domain of a poly(styrene- block-isoprene) diblock copolymer. For the dynamics study, X-ray photon correlation spectroscopy captures the relaxation process of cadmium sulfide nanoparticles. The measured characteristic relaxation time reveals that the observed dynamics are hyperdiffusive. The characteristic velocity and corresponding activation energy, which are hallmarks of a hyperdiffusive system, are determined from themore » relationship between the characteristic relaxation time and the wavevector.« less

Nonequilibrium self-organization of colloidal particles on substrates: adsorption, relaxation, and annealing.

PubMed

Araújo, Nuno A M; Dias, Cristóvão S; Telo da Gama, Margarida M

2017-01-11

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate (mesoscopic) structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. Here we discuss the self-organization of functionalized colloids (also known as patchy colloids) on attractive substrates. We review our recent results on the adsorption and relaxation and explore the use of annealing cycles to overcome kinetic barriers and drive the relaxation towards the targeted structures.

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

NASA Astrophysics Data System (ADS)

Lindner, Benjamin; Yi, Zheng; Prinz, Jan-Hendrik; Smith, Jeremy C.; Noé, Frank

2013-11-01

The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffin, Philip J., E-mail: pgrif@seas.upenn.edu; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-28

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range—indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffin, Phillip J.; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-01

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range-indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

PubMed

De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

2014-12-09

A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

PubMed

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

Relationship between local structure and relaxation in out-of-equilibrium glassy systems

DOE PAGES

Schoenholz, Samuel S.; Cubuk, Ekin D.; Kaxiras, Efthimios; ...

2016-12-27

The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the dynamical glass transition, such as viscosity, can change by many orders of magnitude over long periods of time following external perturbation. During this progress toward equilibrium, glassy systems exhibit a history dependence that has complicated their study. In previous work, we bridged the gap between structure and dynamics in glassy liquids above their dynamical glass transition temperatures by introducing a scalar field calledmore » “softness,” a quantity obtained using machine-learning methods. Softness is designed to capture the hidden patterns in relative particle positions that correlate strongly with dynamical rearrangements of particle positions. Here we show that the out-of-equilibrium behavior of a model glass-forming system can be understood in terms of softness. We first demonstrate that the evolution of behavior following a temperature quench is a primarily structural phenomenon: The structure changes considerably, but the relationship between structure and dynamics remains invariant. We then show that the relaxation time can be robustly computed from structure as quantified by softness, with the same relation holding both in equilibrium and as the system ages. Together, these results show that the history dependence of the relaxation time in glasses requires knowledge only of the softness in addition to the usual state variables.« less

Relationship between local structure and relaxation in out-of-equilibrium glassy systems.

PubMed

Schoenholz, Samuel S; Cubuk, Ekin D; Kaxiras, Efthimios; Liu, Andrea J

2017-01-10

The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the dynamical glass transition, such as viscosity, can change by many orders of magnitude over long periods of time following external perturbation. During this progress toward equilibrium, glassy systems exhibit a history dependence that has complicated their study. In previous work, we bridged the gap between structure and dynamics in glassy liquids above their dynamical glass transition temperatures by introducing a scalar field called "softness," a quantity obtained using machine-learning methods. Softness is designed to capture the hidden patterns in relative particle positions that correlate strongly with dynamical rearrangements of particle positions. Here we show that the out-of-equilibrium behavior of a model glass-forming system can be understood in terms of softness. To do this we first demonstrate that the evolution of behavior following a temperature quench is a primarily structural phenomenon: The structure changes considerably, but the relationship between structure and dynamics remains invariant. We then show that the relaxation time can be robustly computed from structure as quantified by softness, with the same relation holding both in equilibrium and as the system ages. Together, these results show that the history dependence of the relaxation time in glasses requires knowledge only of the softness in addition to the usual state variables.

Glass transition and relaxation dynamics of propylene glycol-water solutions confined in clay

NASA Astrophysics Data System (ADS)

Elamin, Khalid; Björklund, Jimmy; Nyhlén, Fredrik; Yttergren, Madeleine; Mârtensson, Lena; Swenson, Jan

2014-07-01

The molecular dynamics of aqueous solutions of propylene glycol (PG) and propylene glycol methylether (PGME) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy and differential scanning calorimetry. As typical for liquids in confined geometries the intensity of the cooperative α-relaxation becomes considerably more suppressed than the more local β-like relaxation processes. In fact, at high water contents the calorimetric glass transition and related structural α-relaxation cannot even be observed, due to the confinement. Thus, the intensity of the viscosity related α-relaxation is dramatically reduced, but its time scale as well as the related glass transition temperature Tg are for both systems only weakly influenced by the confinement. In the case of the PGME-water solutions it is an important finding since in the corresponding bulk system a pronounced non-monotonic concentration dependence of the glass transition related dynamics has been observed due to the growth of hydrogen bonded relaxing entities of water bridging between PGME molecules [J. Sjöström, J. Mattsson, R. Bergman, and J. Swenson, Phys. Chem. B 115, 10013 (2011)]. The present results suggest that the same type of structural entities are formed in the quasi-two-dimensional space between the clay platelets. It is also observed that the main water relaxation cannot be distinguished from the β-relaxation of PG or PGME in the concentration range up to intermediate water contents. This suggests that these two processes are coupled and that the water molecules affect the time scale of the β-relaxation. However, this is most likely true also for the corresponding bulk solutions, which exhibit similar time scales of this combined relaxation process below Tg. Finally, it is found that at higher water contents the water relaxation does not merge with, or follow, the α-relaxation above Tg, but instead crosses the α-relaxation, indicating that the two relaxation processes are independent of each other. This can only occur if the two processes do not occur in the same parts of the confined solutions. Most likely the hydration shell of the interlayer Na+ ions is causing this water relaxation, which does not participate in the α-relaxation at any temperature.

Glass transition and relaxation dynamics of propylene glycol-water solutions confined in clay.

PubMed

Elamin, Khalid; Björklund, Jimmy; Nyhlén, Fredrik; Yttergren, Madeleine; Mårtensson, Lena; Swenson, Jan

2014-07-21

The molecular dynamics of aqueous solutions of propylene glycol (PG) and propylene glycol methylether (PGME) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy and differential scanning calorimetry. As typical for liquids in confined geometries the intensity of the cooperative α-relaxation becomes considerably more suppressed than the more local β-like relaxation processes. In fact, at high water contents the calorimetric glass transition and related structural α-relaxation cannot even be observed, due to the confinement. Thus, the intensity of the viscosity related α-relaxation is dramatically reduced, but its time scale as well as the related glass transition temperature Tg are for both systems only weakly influenced by the confinement. In the case of the PGME-water solutions it is an important finding since in the corresponding bulk system a pronounced non-monotonic concentration dependence of the glass transition related dynamics has been observed due to the growth of hydrogen bonded relaxing entities of water bridging between PGME molecules [J. Sjöström, J. Mattsson, R. Bergman, and J. Swenson, Phys. Chem. B 115, 10013 (2011)]. The present results suggest that the same type of structural entities are formed in the quasi-two-dimensional space between the clay platelets. It is also observed that the main water relaxation cannot be distinguished from the β-relaxation of PG or PGME in the concentration range up to intermediate water contents. This suggests that these two processes are coupled and that the water molecules affect the time scale of the β-relaxation. However, this is most likely true also for the corresponding bulk solutions, which exhibit similar time scales of this combined relaxation process below Tg. Finally, it is found that at higher water contents the water relaxation does not merge with, or follow, the α-relaxation above Tg, but instead crosses the α-relaxation, indicating that the two relaxation processes are independent of each other. This can only occur if the two processes do not occur in the same parts of the confined solutions. Most likely the hydration shell of the interlayer Na(+) ions is causing this water relaxation, which does not participate in the α-relaxation at any temperature.

Dynamics of Block Copolymer Nanocomposites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mochrie, Simon G. J.

2014-09-09

A detailed study of the dynamics of cadmium sulfide nanoparticles suspended in polystyrene homopolymer matrices was carried out using X-ray photon correlation spectroscopy for temperatures between 120 and 180 °C. For low molecular weight polystyrene homopolymers, the observed dynamics show a crossover from diffusive to hyper-diffusive behavior with decreasing temperatures. For higher molecular weight polystyrene, the nanoparticle dynamics appear hyper-diffusive at all temperatures studied. The relaxation time and characteristic velocity determined from the measured hyper-diffusive dynamics reveal that the activation energy and underlying forces determined are on the order of 2.14 × 10-19 J and 87 pN, respectively. We alsomore » carried out a detailed X-ray scattering study of the static and dynamic behavior of a styrene– isoprene diblock copolymer melt with a styrene volume fraction of 0.3468. At 115 and 120 °C, we observe splitting of the principal Bragg peak, which we attribute to phase coexistence of hexagonal cylindrical and cubic double- gyroid structure. In the disordered phase, above 130 °C, we have characterized the dynamics of composition fluctuations via X-ray photon correlation spectroscopy. Near the peak of the static structure factor, these fluctuations show stretched-exponential relaxations, characterized by a stretching exponent of about 0.36 for a range of temperatures immediately above the MST. The corresponding characteristic relaxation times vary exponentially with temperature, changing by a factor of 2 for each 2 °C change in temperature. At low wavevectors, the measured relaxations are diffusive with relaxation times that change by a factor of 2 for each 8 °C change in temperature.« less

A dynamical study of Galactic globular clusters under different relaxation conditions

NASA Astrophysics Data System (ADS)

Zocchi, A.; Bertin, G.; Varri, A. L.

2012-03-01

Aims: We perform a systematic combined photometric and kinematic analysis of a sample of globular clusters under different relaxation conditions, based on their core relaxation time (as listed in available catalogs), by means of two well-known families of spherical stellar dynamical models. Systems characterized by shorter relaxation time scales are expected to be better described by isotropic King models, while less relaxed systems might be interpreted by means of non-truncated, radially-biased anisotropic f(ν) models, originally designed to represent stellar systems produced by a violent relaxation formation process and applied here for the first time to the study of globular clusters. Methods: The comparison between dynamical models and observations is performed by fitting simultaneously surface brightness and velocity dispersion profiles. For each globular cluster, the best-fit model in each family is identified, along with a full error analysis on the relevant parameters. Detailed structural properties and mass-to-light ratios are also explicitly derived. Results: We find that King models usually offer a good representation of the observed photometric profiles, but often lead to less satisfactory fits to the kinematic profiles, independently of the relaxation condition of the systems. For some less relaxed clusters, f(ν) models provide a good description of both observed profiles. Some derived structural characteristics, such as the total mass or the half-mass radius, turn out to be significantly model-dependent. The analysis confirms that, to answer some important dynamical questions that bear on the formation and evolution of globular clusters, it would be highly desirable to acquire larger numbers of accurate kinematic data-points, well distributed over the cluster field. Appendices are available in electronic form at http://www.aanda.org

Anomalously large isotope effect in the glass transition of water

DOE PAGES

Gainaru, Catalin; Agapov, Alexander L.; Fuentes-Landete, Violeta; ...

2014-11-24

Here we present the discovery of an unusually large isotope effect in the structural relaxation and the glass transition temperature T g of water. Dielectric relaxation spectroscopy of low-density as well as of vapor deposited amorphous water reveal T g differences of 10±2K between H 2O and D 2O, sharply contrasting with other hydrogen bonded liquids for which H/D exchange increases T g by typically less than 1K. We show that the large isotope effect and the unusual variation of relaxation times in water at low temperatures can be explained in terms of quantum effects. Thus, our findings shed newmore » light on water's peculiar low-temperature dynamics and the possible role of quantum effects in its structural relaxation, and possibly in dynamics of other low molecular weight liquids.« less

Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

DOE PAGES

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...

2016-11-10

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics.

PubMed

Shim, Y; Choi, M Y; Kim, Hyung J

2005-01-22

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids. (c) 2005 American Institute of Physics.

Surfactant mediated polyelectrolyte self-assembly

DOE PAGES

Goswami, Monojoy; Borreguero Calvo, Jose M.; Pincus, Phillip A.; ...

2015-11-25

Self-assembly and dynamics of polyelectrolyte (PE) surfactant complex (PES) is investigated using molecular dynamics simulations. The complexation is systematically studied for five different PE backbone charge densities. At a fixed surfactant concentration the PES complexation exhibits pearl-necklace to agglomerated double spherical structures with a PE chain decorating the surfactant micelles. The counterions do not condense on the complex, but are released in the medium with a random distribution. The relaxation dynamics for three different length scales, polymer chain, segmental and monomer, show distinct features of the charge and neutral species; the counterions are fastest followed by the PE chain andmore » surfactants. The surfactant heads and tails have the slowest relaxation due to their restricted movement inside the agglomerated structure. At the shortest length scale, all the charge and neutral species show similar relaxation dynamics confirming Rouse behavior at monomer length scales. Overall, the present study highlights the structure-property relationship for polymer-surfactant complexation. These results will help improve the understanding of PES complex and should aid in the design of better materials for future applications.« less

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

NASA Astrophysics Data System (ADS)

Schubert, Alexander; Falvo, Cyril; Meier, Christoph

2016-08-01

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the "surfaces" for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

Engineering and Scaling the Spontaneous Magnetization Reversal of Faraday Induced Magnetic Relaxation in Nano-Sized Amorphous Ni Coated on Crystalline Au.

PubMed

Li, Wen-Hsien; Lee, Chi-Hung; Kuo, Chen-Chen

2016-05-28

We report on the generation of large inverse remanent magnetizations in nano-sized core/shell structure of Au/Ni by turning off the applied magnetic field. The remanent magnetization is very sensitive to the field reduction rate as well as to the thermal and field processes before the switching off of the magnetic field. Spontaneous reversal in direction and increase in magnitude of the remanent magnetization in subsequent relaxations over time were found. All of the various types of temporal relaxation curves of the remanent magnetizations are successfully scaled by a stretched exponential decay profile, characterized by two pairs of relaxation times and dynamic exponents. The relaxation time is used to describe the reduction rate, while the dynamic exponent describes the dynamical slowing down of the relaxation through time evolution. The key to these effects is to have the induced eddy current running beneath the amorphous Ni shells through Faraday induction.

Conductivity-Relaxation Relations in Nanocomposite Polymer Electrolytes Containing Ionic Liquid.

PubMed

Shojaatalhosseini, Mansoureh; Elamin, Khalid; Swenson, Jan

2017-10-19

In this study, we have used nanocomposite polymer electrolytes, consisting of poly(ethylene oxide) (PEO), δ-Al 2 O 3 nanoparticles, and lithium bis(trifluoromethanesolfonyl)imide (LiTFSI) salt (with 4 wt % δ-Al 2 O 3 and PEO:Li ratios of 16:1 and 8:1), and added different amounts of the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethanesolfonyl)imide (BMITFSI). The aim was to elucidate whether the ionic liquid is able to dissociate the Li-ions from the ether oxygens and thereby decouple the ionic conductivity from the segmental polymer dynamics. The results from DSC and dielectric spectroscopy show that the ionic liquid speeds up both the segmental polymer dynamics and the motion of the Li + ions. However, a close comparison between the structural (α) relaxation process, given by the segmental polymer dynamics, and the ionic conductivity shows that the motion of the Li + ions decouples from the segmental polymer dynamics at higher concentrations of the ionic liquid (≥20 wt %) and instead becomes more related to the viscosity of the ionic liquid. This decoupling increases with decreasing temperature. In addition to the structural α-relaxation, two more local relaxation processes, denoted β and γ, are observed. The β-relaxation becomes slightly faster at the highest concentration of the ionic liquid (at least for the lower salt concentration), whereas the γ-relaxation is unaffected by the ionic liquid, over the whole concentration range 0-40 wt %.

Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

PubMed Central

Schanda, Paul; Ernst, Matthias

2016-01-01

Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution. PMID:27110043

DOE Office of Scientific and Technical Information (OSTI.GOV)

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Tian, Shubo; Zeng, Chenjie

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE PAGES

Zhou, Meng; Tian, Shubo; Zeng, Chenjie; ...

2016-12-22

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Fundamentals of ionic conductivity relaxation gained from study of procaine hydrochloride and procainamide hydrochloride at ambient and elevated pressure.

PubMed

Wojnarowska, Z; Swiety-Pospiech, A; Grzybowska, K; Hawelek, L; Paluch, M; Ngai, K L

2012-04-28

The pharmaceuticals, procaine hydrochloride and procainamide hydrochloride, are glass-forming as well as ionically conducting materials. We have made dielectric measurements at ambient and elevated pressures to characterize the dynamics of the ion conductivity relaxation in these pharmaceuticals, and calorimetric measurements for the structural relaxation. Perhaps due to their special chemical and physical structures, novel features are found in the ionic conductivity relaxation of these pharmaceuticals. Data of conductivity relaxation in most ionic conductors when represented by the electric loss modulus usually show a single resolved peak in the electric modulus loss M(")(f) spectra. However, in procaine hydrochloride and procainamide hydrochloride we find in addition another resolved loss peak at higher frequencies over a temperature range spanning across T(g). The situation is analogous to many non-ionic glass-formers showing the presence of the structural α-relaxation together with the Johari-Goldstein (JG) β-relaxation. Naturally the analogy leads us to name the slower and faster processes resolved in procaine hydrochloride and procainamide hydrochloride as the primary α-conductivity relaxation and the secondary β-conductivity relaxation, respectively. The analogy of the β-conductivity relaxation in procaine HCl and procainamide HCl with JG β-relaxation in non-ionic glass-formers goes further by the finding that the β-conductivity is strongly related to the α-conductivity relaxation at temperatures above and below T(g). At elevated pressure but compensated by raising temperature to maintain α-conductivity relaxation time constant, the data show invariance of the ratio between the β- and the α-conductivity relaxation times to changes of thermodynamic condition. This property indicates that the β-conductivity relaxation has fundamental importance and is indispensable as the precursor of the α-conductivity relaxation, analogous to the relation found between the Johari-Goldstein β-relaxation and the structural α-relaxation in non-ionic glass-forming systems. The novel features of the ionic conductivity relaxation are brought out by presenting the measurements in terms of the electric modulus or permittivity. If presented in terms of conductivity, the novel features are lost. This warns against insisting that a log-log plot of conductivity vs. frequency is optimal to reveal and interpret the dynamics of ionic conductors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jianping, E-mail: jwang@iccas.ac.cn; Yang, Fan; Zhao, Juan

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH{sub 3}CN, CHCl{sub 3}, and CCl{sub 4}), were examined using the N—H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics ofmore » NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N—H stretching mode was observed.« less

Pressure dependence of excited-state charge-carrier dynamics in organolead tribromide perovskites

NASA Astrophysics Data System (ADS)

Liu, X. C.; Han, J. H.; Zhao, H. F.; Yan, H. C.; Shi, Y.; Jin, M. X.; Liu, C. L.; Ding, D. J.

2018-05-01

Excited-state charge-carrier dynamics governs the performance of organometal trihalide perovskites (OTPs) and is strongly influenced by the crystal structure. Characterizing the excited-state charge-carrier dynamics in OTPs under high pressure is imperative for providing crucial insights into structure-property relations. Here, we conduct in situ high-pressure femtosecond transient absorption spectroscopy experiments to study the excited-state carrier dynamics of CH3NH3PbBr3 (MAPbBr3) under hydrostatic pressure. The results indicate that compression is an effective approach to modulate the carrier dynamics of MAPbBr3. Across each pressure-induced phase, carrier relaxation, phonon scattering, and Auger recombination present different pressure-dependent properties under compression. Responsiveness is attributed to the pressure-induced variation in the lattice structure, which also changes the electronic band structure. Specifically, simultaneous prolongation of carrier relaxation and Auger recombination is achieved in the ambient phase, which is very valuable for excess energy harvesting. Our discussion provides clues for optimizing the photovoltaic performance of OTPs.

Quantum effects in the dynamics of deeply supercooled water

DOE PAGES

Agapov, Alexander L.; Kolesnikov, Alexander I.; Novikov, Vladimir N.; ...

2015-02-26

In spite of its simple chemical structure, water remains one of the most puzzling liquids with many anomalies at low temperatures. Combining neutron scattering and dielectric relaxation spectroscopy, we show that quantum fluctuations are not negligible in deeply supercooled water. Our dielectric measurements reveal the anomalously weak temperature dependence of structural relaxation in vapor-deposited water close to the glass transition temperature T g~136K. We demonstrate that this anomalous behavior can be explained well by quantum effects. In conclusion, these results have significant implications for our understanding of water dynamics.

Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR.

PubMed

Walinda, Erik; Morimoto, Daichi; Sugase, Kenji

2018-04-26

Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ∼0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R 2 and R 1ρ , discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.

2005-06-01

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of H2 spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of H2 T1 relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4±1×10-8cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Ultrafast electronic dynamics in unipolar n-doped indium gallium arsenide/gallium arsenide self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Wu, Zong-Kwei J.

2006-12-01

Photodetectors based on intraband infrared absorption in the quantum dots have demonstrated improved performance over its quantum well counterpart by lower dark current, relative temperature insensitivity, and its ability for normal incidence operation. Various scattering processes, including phonon emission/absorption and carrier-carrier scattering, are critical in understanding device operation on the fundamental level. In previous studies, our group has investigated carrier dynamics in both low- and high-density regime. Ultrafast electron-hole scattering and the predicted phonon bottleneck effect in intrinsic quantum dots have been observed. Further examination on electron dynamics in unipolar structures is presented in this thesis. We used n-doped quantum dot in mid-infrared photodetector device structure to study the electron dynamics in unipolar structure. Differential transmission spectroscopy with mid-infrared intraband pump and optical interband probe was implemented to measure the electron dynamics directly without creating extra electron-hole pair, Electron relaxation after excitation was measured under various density and temperature conditions. Rapid capture into quantum dot within ˜ 10 ps was observed due to Auger-type electron-electron scattering. Intradot relaxation from the quantum dot excited state to the ground state was also observed on the time scale of 100 ps. With highly doped electron density in the structure, the inter-sublevel relaxation is dominated by Auger-type electron-electron scattering and the phonon bottleneck effect is circumvented. Nanosecond-scale recovery in larger-sized quantum dots was observed, not intrinsic to electron dynamics but due to band-bending and built-in voltage drift. An ensemble Monte Carlo simulation was also established to model the dynamics in quantum dots and in goad agreement with the experimental results. We presented a comprehensive picture of electron dynamics in the unipolar quantum dot structure. Although the phonon bottleneck is circumvented with high doped electron density, relaxation processes in unipolar quantum dots have been measured with time scales longer than that of bipolar systems. The results explain the operation principles of the quantum dot infrared photodetector on a microscopic level and provide basic understanding for future applications and designs.

Relaxation and physical aging in network glasses: a review.

PubMed

Micoulaut, Matthieu

2016-06-01

Recent progress in the description of glassy relaxation and aging are reviewed for the wide class of network-forming materials such as GeO2, Ge x Se1-x , silicates (SiO2-Na2O) or borates (B2O3-Li2O), all of which have an important usefulness in domestic, geological or optoelectronic applications. A brief introduction of the glass transition phenomenology is given, together with the salient features that are revealed both from theory and experiments. Standard experimental methods used for the characterization of the slowing down of the dynamics are reviewed. We then discuss the important role played by aspects of network topology and rigidity for the understanding of the relaxation of the glass transition, while also permitting analytical predictions of glass properties from simple and insightful models based on the network structure. We also emphasize the great utility of computer simulations which probe the dynamics at the molecular level, and permit the calculation of various structure-related functions in connection with glassy relaxation and the physics of aging which reveal the non-equilibrium nature of glasses. We discuss the notion of spatial variations of structure which leads to the concept of 'dynamic heterogeneities', and recent results in relation to this important topic for network glasses are also reviewed.

Self-assembly and structural relaxation in a model ionomer melt

DOE PAGES

Goswami, Monojoy; Borreguero, Jose M.; Sumpter, Bobby G.

2015-02-26

Molecular dynamics simulations are used to understand the self-assembly and structural relaxation in ionomer melts containing less than 10% degree of ionization on the backbone. We study the self-assembly of charged sites and counterions that show structural ordering and agglomeration with a range of structures that can be achieved by changing the dielectric constant of the medium. The intermediate scattering function shows a decoupling of charge and counterion relaxation at longer length scales for only high dielectric constant and at shorter length scales for all dielectric constants. Finally, the slow structural decay of counterions in the strongly correlated ionomer systemmore » closely resembles transport properties of semi-flexible polymers.« less

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr; Meier, Christoph; Falvo, Cyril

2016-08-07

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking themore » molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.« less

Dynamics and structure of hydrogen-bonding glass formers: Comparison between hexanetriol and sugar alcohols based on dielectric relaxation

NASA Astrophysics Data System (ADS)

Nakanishi, Masahiro; Nozaki, Ryusuke

2010-04-01

Broadband dielectric spectra of supercooled 1,2,6-hexanetriol are presented in order to reveal physical picture behind a glass transition of polyhydric alcohols. It has been reported so far that temperature dependences of α relaxation time for sugar alcohols exhibit systematic trend against number of carbon atoms or OH groups per molecule. However, because each molecule is composed of equal number of carbon atoms and OH groups in the case of the reported sugar alcohols, the more dominant parameter to govern the α relaxation dynamics has not been discussed. By using a chemical structure of the hexanetriol composed of the deferent number of carbon and OH, it is possible to determine the dominant parameter. From temperature dependence of α relaxation times, it is strongly supported that the number of OH groups is the dominant parameter. Furthermore, from an analysis of static dielectric constant, it is suggested that local hydrogen-bonding structure is similar among all polyhydric alcohols. From these two results, a simple picture of the origin of the systematic character is proposed.

Dynamics and structure of hydrogen-bonding glass formers: comparison between hexanetriol and sugar alcohols based on dielectric relaxation.

PubMed

Nakanishi, Masahiro; Nozaki, Ryusuke

2010-04-01

Broadband dielectric spectra of supercooled 1,2,6-hexanetriol are presented in order to reveal physical picture behind a glass transition of polyhydric alcohols. It has been reported so far that temperature dependences of alpha relaxation time for sugar alcohols exhibit systematic trend against number of carbon atoms or OH groups per molecule. However, because each molecule is composed of equal number of carbon atoms and OH groups in the case of the reported sugar alcohols, the more dominant parameter to govern the alpha relaxation dynamics has not been discussed. By using a chemical structure of the hexanetriol composed of the deferent number of carbon and OH, it is possible to determine the dominant parameter. From temperature dependence of alpha relaxation times, it is strongly supported that the number of OH groups is the dominant parameter. Furthermore, from an analysis of static dielectric constant, it is suggested that local hydrogen-bonding structure is similar among all polyhydric alcohols. From these two results, a simple picture of the origin of the systematic character is proposed.

Presence of global and local α-relaxations in an alkyl phosphate glass former

NASA Astrophysics Data System (ADS)

Wu, Tao; Jin, Xiao; Saini, Manoj K.; Liu, Ying Dan; Ngai, K. L.; Wang, Li-Min

2017-10-01

The dynamics of a molecular glass former, tributyl phosphate (TBP), with an alkyl phosphate structure (three alkyl branches emanating from a polar core of PO4) is studied in the supercooled regime by dielectric and thermal (or enthalpic) relaxations. The dielectric fragility index md and the stretching exponent βd of the Kohlrausch-Williams-Watts correlation function are determined. Analyses of the enthalpic relaxation data by the Tool-Narayanaswamy-Moynihan-Hodge formalism yield the enthalpic fragility index mH and stretching exponent βH. The large difference between the dielectric md and the enthalpic mH, as well as between βd and βH, is a remarkable finding. The differences are interpreted by the formation of molecular self-assemblies. The interpretation is supported by the quite comparable fragility determined by viscosity and the enthalpic relaxation. The Kirkwood factor calculated at low temperatures is also consistent with the interpretation. The results suggest that the enthalpic relaxation involving the motions of all parts of TBP is global, while the dielectric relaxation detects the local rotation, which might originate from the rotation of the dipole moment of the core. The presence of two structural α-relaxations, one global and one local, with a large difference in dynamics is revealed for the first time in a molecular glass former.

Analysis/test correlation using VAWT-SDS on a step-relaxation test for the rotating Sandia 34 m test bed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argueello, J.G.; Dohrmann, C.R.; Carne, T.G.

The combined analysis/test effort described in this paper compares predictions with measured data from a step-relaxation test in the absence of significant wind-driven aerodynamic loading. The process described here is intended to illustrate a method for validation of time domain codes for structural analysis of wind turbine structures. Preliminary analyses were performed to investigate the transient dynamic response that the rotating Sandia 34 m Vertical Axis Wind Turbine (VAWT) would undergo when one of the two blades was excited by step-relaxation. The calculations served two purposes. The first was for pretest planning to evaluate the relative importance of the variousmore » forces that would be acting on the structure during the test and to determine if the applied force in the step-relaxation would be sufficient to produce an excitation that was distinguishable from that produced by the aerodynamic loads. The second was to provide predictions that could subsequently be compared to the data from the test. The test was carried out specifically to help in the validation of the time-domain structural dynamics code, VAWT-SDS, which predicts the dynamic response of VAWTs subject to transient events. Post-test comparisons with the data were performed and showed a qualitative agreement between pretest predictions and measured response. However, they also showed that there was significantly more damping in the measurements than included in the predictions. Efforts to resolve this difference, including post-test analyses, were undertaken and are reported herein. The overall effort described in this paper represents a major step in the process of arriving at a validated structural dynamics code.« less

Crystallization dynamics on curved surfaces

NASA Astrophysics Data System (ADS)

García, Nicolás A.; Register, Richard A.; Vega, Daniel A.; Gómez, Leopoldo R.

2013-07-01

We study the evolution from a liquid to a crystal phase in two-dimensional curved space. At early times, while crystal seeds grow preferentially in regions of low curvature, the lattice frustration produced in regions with high curvature is rapidly relaxed through isolated defects. Further relaxation involves a mechanism of crystal growth and defect annihilation where regions with high curvature act as sinks for the diffusion of domain walls. The pinning of grain boundaries at regions of low curvature leads to the formation of a metastable structure of defects, characterized by asymptotically slow dynamics of ordering and activation energies dictated by the largest curvatures of the system. These glassylike ordering dynamics may completely inhibit the appearance of the ground-state structures.

Relaxation mode analysis of a peptide system: comparison with principal component analysis.

PubMed

Mitsutake, Ayori; Iijima, Hiromitsu; Takano, Hiroshi

2011-10-28

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.

Isolating long-wavelength fluctuation from structural relaxation in two-dimensional glass: cage-relative displacement

NASA Astrophysics Data System (ADS)

Shiba, Hayato; Keim, Peter; Kawasaki, Takeshi

2018-03-01

It has recently been revealed that long-wavelength fluctuation exists in two-dimensional (2D) glassy systems, having the same origin as that given by the Mermin-Wagner theorem for 2D crystalline solids. In this paper, we discuss how to characterise quantitatively the long-wavelength fluctuation in a molecular dynamics simulation of a lightly supercooled liquid. We employ the cage-relative mean-square displacement (MSD), defined on relative displacement to its cage, to quantitatively separate the long-wavelength fluctuation from the original MSD. For increasing system size the amplitude of acoustic long wavelength fluctuations not only increases but shifts to later times causing a crossover with structural relaxation of caging particles. We further analyse the dynamic correlation length using the cage-relative quantities. It grows as the structural relaxation becomes slower with decreasing temperature, uncovering an overestimation by the four-point correlation function due to the long-wavelength fluctuation. These findings motivate the usage of cage-relative MSD as a starting point for analysis of 2D glassy dynamics.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Self-Healing Nanocomposite Hydrogel with Well-Controlled Dynamic Mechanics

NASA Astrophysics Data System (ADS)

Li, Qiaochu; Mishra, Sumeet; Chen, Pangkuan; Tracy, Joseph; Holten-Andersen, Niels

Network dynamics is a crucial factor that determines the macroscopic self-healing rate and efficiency in polymeric hydrogel materials, yet its controllability is seldom studied in most reported self-healing hydrogel systems. Inspired by mussel's adhesion chemistry, we developed a novel approach to assemble inorganic nanoparticles and catechol-decorated PEG polymer into a hydrogel network. When utilized as reversible polymer-particle crosslinks, catechol-metal coordination bonds yield a unique gel network with dynamic mechanics controlled directly by interfacial crosslink structure. Taking advantage of this structure-property relationship at polymer-particle interfaces, we next designed a hierarchically structured hybrid gel with two distinct relaxation timescales. By tuning the relative contribution of the two hierarchical relaxation modes, we are able to finely control the gel's dynamic mechanical behavior from a viscoelastic fluid to a stiff solid, yet preserving its fast self-healing property without the need for external stimuli.

Rapid Self-healing Nanocomposite Hydrogel with Tunable Dynamic Mechanics

NASA Astrophysics Data System (ADS)

Li, Qiaochu; Mishra, Sumeet; Chapman, Brian; Chen, Pangkuan; Tracy, Joseph; Holten-Andersen, Niels

The macroscopic healing rate and efficiency in self-repairing hydrogel materials are largely determined by the dissociation dynamics of their polymer network, which is hardly achieved in a controllable manner. Inspired by mussel's adhesion chemistry, we developed a novel approach to assemble inorganic nanoparticles and catechol-decorated PEG polymer into a hydrogel network. When utilized as reversible polymer-particle crosslinks, catechol-metal coordination bonds yield a unique gel network with dynamic mechanics controlled directly by interfacial crosslink structure. Taking advantage of this structure-property relationship at polymer-particle interfaces, we designed a hierarchically structured hybrid gel with two distinct relaxation timescales. By tuning the relative contribution of the two relaxation modes, we are able to finely control the gel's dynamic mechanical behavior from a viscoelastic fluid to a stiff solid, yet preserving its rapid self-healing property without the need for external stimuli.

High pressure studies on structural and secondary relaxation dynamics in silyl derivative of D-glucose

NASA Astrophysics Data System (ADS)

Minecka, Aldona; Kamińska, Ewa; Tarnacka, Magdalena; Dzienia, Andrzej; Madejczyk, Olga; Waliłko, Patrycja; Kasprzycka, Anna; Kamiński, Kamil; Paluch, Marian

2017-08-01

In this paper, broadband dielectric spectroscopy was applied to investigate molecular dynamics of 1,2,3,4,6-penta-O-(trimethylsilyl)-D-glucopyranose (S-GLU) at ambient and elevated pressures. Our studies showed that apart from the structural relaxation, one well resolved asymmetric secondary process (initially labeled as β) is observed in the spectra measured at p = 0.1 MPa. Analysis with the use of the coupling model and criterion proposed by Ngai and Capaccioli indicated that the β-process in S-GLU is probably a Johari-Goldstein relaxation of intermolecular origin. Further high pressure experiments demonstrated that there are in fact two secondary processes contributing to the β-relaxation. Therefore, one can postulate that the coupling model is a necessary, but not sufficient criterion to identify the true nature of the given secondary relaxation process. The role of pressure experiments in better understanding of the molecular origin of local mobility seems to be much more important. Interestingly, our research also revealed that the structural relaxation in S-GLU is very sensitive to compression. It was reflected in an extremely high pressure coefficient of the glass transition temperature (dTg/dp = 412 K/GPa). According to the literature data, such a high value of dTg/dp has not been obtained so far for any H-bonded, van der Waals, or polymeric glass-formers.

Determination of Protein Surface Hydration by Systematic Charge Mutations

NASA Astrophysics Data System (ADS)

Yang, Jin; Jia, Menghui; Qin, Yangzhong; Wang, Dihao; Pan, Haifeng; Wang, Lijuan; Xu, Jianhua; Zhong, Dongping; Dongping Zhong Collaboration; Jianhua Xu Collaboration

Protein surface hydration is critical to its structural stability, flexibility, dynamics and function. Recent observations of surface solvation on picosecond time scales have evoked debate on the origin of such relatively slow motions, from hydration water or protein charged sidechains, especially with molecular dynamics simulations. Here, we used a unique nuclease with a single tryptophan as a local probe and systematically mutated neighboring three charged residues to differentiate the contributions from hydration water and charged sidechains. By mutations of alternative one and two and all three charged residues, we observed slight increases in the total tryptophan Stokes shifts with less neighboring charged residue(s) and found insensitivity of charged sidechains to the relaxation patterns. The dynamics is correlated with hydration water relaxation with the slowest time in a dense charged environment and the fastest time at a hydrophobic site. On such picosecond time scales, the protein surface motion is restricted. The total Stokes shifts are dominantly from hydration water relaxation and the slow dynamics is from water-driven relaxation, coupled with local protein fluctuations.

Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering

NASA Astrophysics Data System (ADS)

Gallina, M. E.; Comez, L.; Morresi, A.; Paolantoni, M.; Perticaroli, S.; Sassi, P.; Fioretto, D.

2010-06-01

High resolution depolarized light scattering spectra, extended from 0.5 to 2×104 GHz by the combined used of a dispersive and an interferometric setup, give evidence of separated solute and solvent dynamics in diluted trehalose aqueous solutions. The slow relaxation process, located in the gigahertz frequency region, is analyzed as a function of temperature and concentration and assigned to the rotational diffusion of the sugar molecule. The results are discussed in comparison with the data obtained on glucose solutions and they are used to clarify the molecular origin of some among the several relaxation processes reported in literature for oligosaccharides solutions. The concentration dependence of relaxation time and of shear viscosity are also discussed, suggesting that the main effect of carbohydrate molecules on the structural relaxation of diluted aqueous solutions is the perturbation induced on the dynamics of the first hydration shell of each solute molecule.

Confined dynamics of grafted polymer chains in solutions of linear polymer

DOE PAGES

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh; ...

2017-09-11

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less

Confined dynamics of grafted polymer chains in solutions of linear polymer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less

Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

PubMed

Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

2015-12-01

Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

Memory Effect Manifested by a Boson Peak in Metallic Glass.

PubMed

Luo, P; Li, Y Z; Bai, H Y; Wen, P; Wang, W H

2016-04-29

We explore the correlation between a boson peak and structural relaxation in a typical metallic glass. Consistent with enthalpy recovery, a boson peak shows a memory effect in an aging-and-scan procedure. Single-step isothermal aging produces a monotonic decrease of enthalpy and boson peak intensity; for double-step isothermal aging, both enthalpy and boson peak intensity experience, coincidently, an incipient increase to a maximum and a subsequent decrease toward the equilibrium state. Our results indicate a direct link between slow structural relaxation and fast boson peak dynamics, which presents a profound understanding of the two dynamic behaviors in glass.

Communication: Effect of density on the physical aging of pressure-densified polymethylmethacrylate

NASA Astrophysics Data System (ADS)

Casalini, R.; Roland, C. M.

2017-09-01

The rate of physical aging of glassy polymethylmethacrylate (PMMA), followed from the change in the secondary relaxation with aging, is found to be independent of the density, the latter controlled by the pressure during glass formation. Thus, the aging behavior of the secondary relaxation is the same whether the glass is more compacted or less dense than the corresponding equilibrium liquid. This equivalence in aging of glasses formed under different pressures indicates that local packing is the dominant variable governing the glassy dynamics. The fact that pressure densification yields different glass structures is at odds with a model for non-associated materials having dynamic properties exhibited by PMMA, such as density scaling of the relaxation time and isochronal superposition of the relaxation dispersion.

Hyperdiffusive dynamics in Newtonian nanoparticle fluids [Hyperdiffusive dynamics in equilibrated nanoparticle fluids

DOE PAGES

Srivastava, Samanvaya; Agarwal, Praveen; Mangal, Rahul; ...

2015-09-24

Hyperdiffusive relaxations in soft glassy materials are typically associated with out-of-equilibrium states, and non-equilibrium physics and aging are often invoked in explaining their origins. Here, we report on hyperdiffusive motion in a model, equilibrium soft material comprised of single-component polymer-tethered-nanoparticles. In these materials, polymer mediated interactions lead to strong nanoparticle correlations, hyperdiffusive relaxations, and unusual variations of properties with temperature. Our experimental observations complement the current hypothesis that hyperdiffusive relaxations in soft materials require the material to exist in out–of–equilibrium states capable of driving structural rearrangements. Lastly, we propose alternatively that hyperdiffusive relaxations in our materials can arise naturally frommore » volume fluctuations brought about by equilibrium thermal forces.« less

Interpreting the nonlinear dielectric response of glass-formers in terms of the coupling model

NASA Astrophysics Data System (ADS)

Ngai, K. L.

2015-03-01

Nonlinear dielectric measurements at high electric fields of glass-forming glycerol and propylene carbonate initially were carried out to elucidate the dynamic heterogeneous nature of the structural α-relaxation. Recently, the measurements were extended to sufficiently high frequencies to investigate the nonlinear dielectric response of faster processes including the so-called excess wing (EW), appearing as a second power law at high frequencies in the loss spectra of many glass formers without a resolved secondary relaxation. While a strong increase of dielectric constant and loss is found in the nonlinear dielectric response of the α-relaxation, there is a lack of significant change in the EW. A surprise to the experimentalists finding it, this difference in the nonlinear dielectric properties between the EW and the α-relaxation is explained in the framework of the coupling model by identifying the EW investigated with the nearly constant loss (NCL) of caged molecules, originating from the anharmonicity of the intermolecular potential. The NCL is terminated at longer times (lower frequencies) by the onset of the primitive relaxation, which is followed sequentially by relaxation processes involving increasing number of molecules until the terminal Kohlrausch α-relaxation is reached. These intermediate faster relaxations, combined to form the so-called Johari-Goldstein (JG) β-relaxation, are spatially and dynamically heterogeneous, and hence exhibit nonlinear dielectric effects, as found in glycerol and propylene carbonate, where the JG β-relaxation is not resolved and in D-sorbitol where it is resolved. Like the linear susceptibility, χ1(f), the frequency dispersion of the third-order dielectric susceptibility, χ3(f), was found to depend primarily on the α-relaxation time, and independent of temperature T and pressure P. I show this property of the frequency dispersions of χ1(f) and χ3(f) is the characteristic of the many-body relaxation dynamics of interacting systems which are governed solely by the intermolecular potential, and thermodynamic condition plays no role in this respect. Although linked to χ3(f), dynamic heterogeneity is one of the parallel consequences of the many-body dynamics, and it should not be considered as the principal control parameter for the other dynamic properties of glassforming systems. Results same as χ3(f) at elevated pressures had been obtained before by molecular dynamics simulations from the four-points correlation function and the intermediate scattering function. Naturally all properties obtained from the computer experiment, including dynamics heterogeneity, frequency dispersion, the relation between the α- and JG β-relaxation, and the breakdown of the Stokes-Einstein relation, are parallel consequences of the many-body relaxation dynamics governed by the intermolecular potential.

Viscoelastic relaxations of high alcohols and alkanes: Effects of heterogeneous structure and translation-orientation coupling

NASA Astrophysics Data System (ADS)

Yamaguchi, Tsuyoshi

2017-03-01

The frequency-dependent shear viscosity of high alcohols and linear alkanes, including 1-butanol, 1-octanol, 1-dodecanol, n-hexane, n-decane, and n-tetradecane, was calculated using molecular dynamics simulation. The relaxation of all the liquids was bimodal. The correlation functions of the collective orientation were also evaluated. The analysis of these functions showed that the slower relaxation mode of alkanes is assigned to the translation-orientation coupling, while that of high alcohols is not. The X-ray structure factors of all the alcohols showed prepeaks, as have been reported in the literature, and the intermediate scattering functions were calculated at the prepeak. Comparing the intermediate scattering function with the frequency-dependent shear viscosity based on the mode-coupling theory, it was demonstrated that the slower viscoelastic relaxation of the alcohols is assigned to the relaxation of the heterogeneous structure described by the prepeak.

Association in ethylammonium nitrate-dimethyl sulfoxide mixtures: First structural and dynamical evidences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russina, Olga; Macchiagodena, Marina; Kirchner, Barbara

2015-01-01

Here we report the first structural and dynamic investigation on ethylammonium nitrate, a representative protic Ionic liquid, and dimethylsulfoxide. By using joined x/ray and neutron diffraction, we exploit the EPSR approach to extract structural information at atomistic level. EAN/DMSO turns out to be homogeneous at microscopic scales and indications for the existence of a structural leit motiv with stoichiometric composition 2DMSO:1EAN are found. Dielectric spectroscopy is used to access the relaxation map of the DMSO:EAN = 60:40 mixture. No crystallisation is detected and three relaxation processes could be characterised. Overall this study provides new indications of strict analogies between watermore » and ethylammonium nitrate. (c) 2014 Elsevier B.V. All rights reserved.« less

Ion Transport via Structural Relaxations in Polymerized Ionic Liquids

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Mogurampelly, Santosh

We study the mechanisms underlying ion transport in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymer electrolytes. We consider polymer electrolytes of varying polymerized ionic liquid to ionic liquid (polyIL:IL) ratios and use atomistic molecular dynamics (MD) simulations to probe the dynamical and structural characteristics of the electrolyte. Our results reveal that anion diffusion along polymer backbone occurs primarily viathe formation and breaking of ion-pairs involving threepolymerized cationic monomers of twodifferent polymer chains. Moreover, we observe that the ionic diffusivities exhibit a direct correlation with the structural relaxation times of the ion-pairs and hydrogen bonds (H-bonds). These results provide new insights into the mechanisms underlying ion transport in polymerized ionic liquid electrolytes.

Mechanical, structural, and dynamical modifications of cholesterol exposed porcine aortic elastin.

PubMed

Bilici, Kubra; Morgan, Steven W; Silverstein, Moshe C; Wang, Yunjie; Sun, Hyung Jin; Zhang, Yanhang; Boutis, Gregory S

2016-11-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2 H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13 C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin is more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical, Structural, and Dynamical Modifications of Cholesterol Exposed Porcine Aortic Elastin

PubMed Central

Bilici, Kubra; Morgan, Steven W.; Silverstein, Moshe C.; Wang, Yunjie; Sun, Hyung Jin; Zhang, Katherine; Boutis, Gregory S.

2016-01-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin appears more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. PMID:27648754

Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

NASA Astrophysics Data System (ADS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein.

Dynamics of Lithium Polymer Electrolytes using X-ray Photon Correlation Spectroscopy and Rheology

NASA Astrophysics Data System (ADS)

Oparaji, Onyekachi; Narayanan, Suresh; Sandy, Alec; Hallinan, Daniel, Jr.

Polymer electrolytes are promising materials for high energy density rechargeable batteries. Battery fade can be caused by structural evolution in the battery electrode and loss of electrode/electrolyte adhesion during cycling. Both of these effects are dependent on polymer mechanical properties. In addition, cycling rate is dictated by the ion mobility of the polymer electrolyte. Lithium ion mobility is expected to be strongly coupled to polymer dynamics. Therefore, we investigate polymer dynamics as a function of salt concentration using X-ray Photon Correlation Spectroscopy (XPCS) and rheology. We report the influence of lithium salt concentration on the structural relaxation time (XPCS) and stress relaxation time (rheology) of high molecular weight poly(styrene - ethylene oxide) block copolymer membranes.

Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

NASA Astrophysics Data System (ADS)

Separdar, L.; Davatolhagh, S.

2016-12-01

Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

Femtosecond dynamics of a cardiotonic medicine (milrinone) in neutral water

NASA Astrophysics Data System (ADS)

Gil, M.; Douhal, A.

2006-09-01

Milrinone is a medicine used to attenuate heart attack disease. Understanding its interaction with water is of importance for the knowledge of its stability and related phenomena. This intimate information requires the unraveling of the dynamics under the physiological conditions. Here we report the first study of ultrafast processes of this medicine. We show that S 2 relaxation of the keto structure (K) occurs in ˜150 fs and the intramolecular-charge transfer reaction in less than 100 fs to produce a relaxed CT-K state. An observed ˜10 ps decay is assigned to vibrational relaxation/cooling and twisting in the formed CT-K.

Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport

DOE PAGES

Gruss, Daniel; Velizhanin, Kirill A.; Zwolak, Michael

2016-04-20

Landauer’s formula is the standard theoretical tool to examine ballistic transport in nano- and meso-scale junctions, but it necessitates that any variation of the junction with time must be slow compared to characteristic times of the system, e.g., the relaxation time of local excitations. Transport through structurally dynamic junctions is, however, increasingly of interest for sensing, harnessing fluctuations, and real-time control. Here, we calculate the steady-state current when relaxation of electrons in the reservoirs is present and demonstrate that it gives rise to three regimes of behavior: weak relaxation gives a contact-limited current; strong relaxation localizes electrons, distorting their naturalmore » dynamics and reducing the current; and in an intermediate regime the Landauer view of the system only is recovered. Lastly, we also demonstrate that a simple equation of motion emerges, which is suitable for efficiently simulating time-dependent transport.« less

Relaxation processes in disaccharide sugar glasses

NASA Astrophysics Data System (ADS)

Hwang, Yoon-Hwae; Kwon, Hyun-Joung; Seo, Jeong-Ah; Shin, Dong-Myeong; Ha, Ji-Hye; Kim, Hyung-Kook

2013-02-01

We represented relaxation processes of disaccharide sugars (anhydrous trehalose and maltose) in supercooled and glassy states by using several spectroscopy techniques which include a broadband dielectric loss spectroscopy, photon correlation spectroscopy and X-ray diffraction (Retvield analysis) methods which are powerful tools to measure the dynamics in glass forming materials. In a dielectric loss spectroscopy study, we found that anhydrous trehalose and maltose glasses have an extra relaxation process besides α-, JG β- and γ-relaxations which could be related to a unique property of glycoside bond in disaccharides. In photon correlation spectroscopy study, we found an interesting compressed exponential relaxation at temperatures above 140°C. The q-1 dependence of its relaxation time corresponds to an ultraslow ballistic motion due to the local structure rearrangements. In the same temperature range, we found the glycosidic bond structure changes in trehalose molecule from the Raman and the Retvield X-ray diffraction measurements indicating that the observed compressed exponential relaxation in supercooled liquid trehalose could be resulted in the glycosidic bond structure change. Therefore, the overall results from this study might support the fact that the superior bioprotection ability of disaccharide sugar glasses might originate from this unique relaxation process of glycosidic bond.

Atomic Scale Medium Range Order and Relaxation Dynamics in Metallic Glass

NASA Astrophysics Data System (ADS)

Zhang, Pei

We studied the atomic scale structure of bulk metallic glass (BMG) with the combination of fluctuation electron microscopy (FEM) and hybrid reverse Monte Carlo (HRMC) simulation. Medium range order (MRO), which occupies the length scale between short range order (SRO) and long-range order, plays an important role on the properties of metallic glass, but the characterization of MRO in experiment is difficult because conventional techniques are not sensitive to the structure at MRO scale. Compared with the X-ray and neutron which can measure SRO by two-body correlation functions, FEM is an effective way to detect MRO structure through three and four-body correlation functions, providing information about the size, distribution, and internal structure of MRO combing HRMC modeling. Thickness estimation is necessary in FEM experiment and HRMC calculation, so in Chapter 3, we measured the elastic and inelastic mean free paths of metallic glass alloys based on focused ion beam prepared thin samples with measured thickness gradients. We developed a model based on the Wentzel atomic model to predict the elastic mean free path for other amorphous materials. In Chapter 4, we studied the correlation of MRO and glass forming ability ZrCuAl alloy. Results from Variable resolution fluctuation microscopy show that in Zr50Cu35Al15 the crystal-like clusters shrink but become more ordered, while icosahedral-like clusters grow. Compared with Zr50Cu45Al5, Zr50Cu35Al15 with poorer glass forming ability exhibits more stable crystal-like structure under annealing, indicating that destabilizing crystal-like structures is important to achieve better glass forming ability in this alloy. In Chapter 5, we studied the crystallization and MRO structural in deformed and quenched Ni60Nb40 metallic glass. The deformed Ni60Nb40 contains fewer icosahedral-like Voronoi clusters and more crystal-like and bcc-like Voronoi clusters. The crystal-like and bcc-like medium range order clusters may be the structural origin for its lower crystallization temperature compared with quenched alloy. Dynamics heterogeneity is proposed to be the microscopic origin of the dynamic nature of glass transition. Some experimental evidence and simulation have indicated that different regions of materials indeed relax at fast or slow rate. However, the spatial distribution of relaxation time visualized from the experiment as the direct evidence of heterogeneous dynamics is still challenging. We proposed to measure the structural dynamics of supercooled metallic glasses with electron correlation microscopy (ECM) technique at the nanometer scale. ECM was developed as a way to measure structural relaxation times of liquids with nanometer-scale spatial resolution using the coherent electron scattering equivalent of photon correlation spectroscopy. In chapter 6, we studied the experimental requirements of ECM to obtain reliable results. For example, the trajectory length must be at least 40 times the relaxation time to obtain a well-converged g2( t), and the time per frame must be less than 0.1 time the relaxation time to obtain sufficient sampling. ECM experiment was firstly realized in scanning transmission electron microscopy (STEM) mode and applied to measure the structural relaxation time of Pd based metallic glass. In order to overcome the drift problem and capture the spatial information, we developed ECM experiment in dark field (DF) mode. In Chapter 7, through DF-ECM, we visualized the spatially heterogeneous dynamics by in-situ heating Pt57.5Cu14.7Ni 5.3P22.5 nanowire into supercooled liquid state, and quantify the size of the heterogeneity by four-point correlation function. The thickness effect and temporal evolution of the heterogeneous domain were also discussed. Additionally, a fast near-surface dynamics was discovered, providing an effective mechanism for surface crystallization of liquids by homogeneous nucleation.

Structural, electrical properties and dielectric relaxations in Na+-ion-conducting solid polymer electrolyte.

PubMed

Arya, Anil; Sharma, A L

2018-04-25

In this paper, we have studied the structural, microstructural, electrical, dielectric properties and ion dynamics of a sodium-ion-conducting solid polymer electrolyte film comprising PEO 8 -NaPF 6 +  x wt. % succinonitrile. The structural and surface morphology properties have been investigated, respectively using x-ray diffraction and field emission scanning electron microscopy. The complex formation was examined using Fourier transform infrared spectroscopy, and the fraction of free anions/ion pairs obtained via deconvolution. The complex dielectric permittivity and loss tangent has been analyzed across the whole frequency window, and enables us to estimate the DC conductivity, dielectric strength, double layer capacitance and relaxation time. The presence of relaxing dipoles was determined by the addition of succinonitrile (wt./wt.) and the peak shift towards high frequency indicates the decrease of relaxation time. Further, relations among various relaxation times ([Formula: see text]) have been elucidated. The complex conductivity has been examined across the whole frequency window; it obeys the Universal Power Law, and displays strong dependency on succinonitrile content. The sigma representation ([Formula: see text]) was introduced in order to explore the ion dynamics by highlighting the dispersion region in the Cole-Cole plot ([Formula: see text]) in the lower frequency window; increase in the semicircle radius indicates a decrease of relaxation time. This observation is accompanied by enhancement in ionic conductivity and faster ion transport. A convincing, logical scheme to justify the experimental data has been proposed.

Interplay of Structure and Dynamics in Biomaterials

NASA Astrophysics Data System (ADS)

Vodnala, Preeti

Study of structure and dynamic behavior is essential to understand molecular motions in biological systems. In this work, two biomaterials were studied to address membrane properties and protein diffusion. For the first project, we studied the structure of liposomes, artificial vesicles that are used for drug encapsulation and administration of pharmaceuticals or cellular nutrients. Small-angle x-ray scattering (SAXS) was used to determine the structural properties of different liposomes composed of egg-PC and cholesterol bilayer. We examined the location of cholesterol by labelling cholesterol with bromine molecule and reveal that cholesterol is located one side of the leaflet adjusting itself to the curvature of a liposome. In my second project, we studied the dynamics of concentrated suspensions of alpha crystallin, one of the most abundant proteins in the human eye lens using X-ray photon correlation spectroscopy (XPCS). An improved understanding of dynamics could point the way towards treatments presbyopia and cataract. The dynamics were measured at volume fraction close to the critical volume fraction for the glass transition, where the intermediate scattering function, ƒ(q,T) could be well fit using a double exponential decay. The measured relaxation is in reasonable agreement with published molecular dynamics simulations for the relaxation times of hard-sphere colloids.

Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

NASA Astrophysics Data System (ADS)

Giordano, V. M.; Ruta, B.

2016-01-01

Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization.

Recasting a model atomistic glassformer as a system of icosahedra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinney, Rhiannon; Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TS; Liverpool, Tanniemola B.

2015-12-28

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling, these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model, we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation timemore » remains finite for non-zero temperature.« less

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

PubMed

Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

2012-07-10

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

A simple model of entropy relaxation for explaining effective activation energy behavior below the glass transition temperature.

PubMed

Bisquert, Juan; Henn, François; Giuntini, Jean-Charles

2005-03-01

Strong changes in relaxation rates observed at the glass transition region are frequently explained in terms of a physical singularity of the molecular motions. We show that the unexpected trends and values for activation energy and preexponential factor of the relaxation time tau, obtained at the glass transition from the analysis of the thermally stimulated current signal, result from the use of the Arrhenius law for treating the experimental data obtained in nonstationary experimental conditions. We then demonstrate that a simple model of structural relaxation based on a time dependent configurational entropy and Adam-Gibbs relaxation time is sufficient to explain the experimental behavior, without invoking a kinetic singularity at the glass transition region. The pronounced variation of the effective activation energy appears as a dynamic signature of entropy relaxation that governs the change of relaxation time in nonstationary conditions. A connection is demonstrated between the peak of apparent activation energy measured in nonequilibrium dielectric techniques, with the overshoot of the dynamic specific heat that is obtained in calorimetry techniques.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

PubMed

Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

2011-06-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

Structural Effects on the Spin Dynamics of Potential Molecular Qubits.

PubMed

Atzori, Matteo; Benci, Stefano; Morra, Elena; Tesi, Lorenzo; Chiesa, Mario; Torre, Renato; Sorace, Lorenzo; Sessoli, Roberta

2018-01-16

Control of spin-lattice magnetic relaxation is crucial to observe long quantum coherence in spin systems at reasonable temperatures. Such a control is most often extremely difficult to achieve, because of the coexistence of several relaxation mechanisms, that is direct, Raman, and Orbach. These are not always easy to relate to the energy states of the investigated system, because of the contribution to the relaxation of additional spin-phonon coupling phenomena mediated by intramolecular vibrations. In this work, we have investigated the effect of slight changes on the molecular structure of four vanadium(IV)-based potential spin qubits on their spin dynamics, studied by alternate current (AC) susceptometry. The analysis of the magnetic field dependence of the relaxation time correlates well with the low-energy vibrational modes experimentally detected by time-domain THz spectroscopy. This confirms and extends our preliminary observations on the role played by spin-vibration coupling in determining the fine structure of the spin-lattice relaxation time as a function of the magnetic field, for S = 1 / 2 potential spin qubits. This study represents a step forward in the use of low-energy vibrational spectroscopy as a prediction tool for the design of molecular spin qubits with long-lived quantum coherence. Indeed, quantum coherence times of ca. 4.0-6.0 μs in the 4-100 K range are observed for the best performing vanadyl derivatives identified through this multitechnique approach.

Local viscosity and solvent relaxation experienced by rod-like fluorophores in AOT/4-chlorophenol/m-xylene organogels

NASA Astrophysics Data System (ADS)

Dandapat, Manika; Mandal, Debabrata

2017-01-01

Organogels prepared from AOT/4-chlorophenol/m-xylene are immobile in the macroscopic sense, with a well-characterized internal structure. However, the molecular level dynamics inside the gels is not too clear, although a very slow structural relaxation has been reported previously. Using a set of rod-like fluorophores, we find that the rotational mobility of a small guest molecule inside the gel can be extremely fast, indicating presence of sufficiently low-microviscosity domains. These domains consist of m-xylene solvent molecules trapped in the interstices of fiber bundles comprising columnar stacks of 4-chlorophenol surrounded by AOT molecules. However, interstitial trapping of m-xylene does retard its own dynamics, which explains the slow solvent relaxation inside the gels. Hence, the state of m-xylene in the organogel may be characterized as "bound", in contrast to the "free" state in neat m-xylene.

Ultrafast exciton fine structure relaxation dynamics in lead chalcogenide nanocrystals.

PubMed

Johnson, Justin C; Gerth, Kathrine A; Song, Qing; Murphy, James E; Nozik, Arthur J; Scholes, Gregory D

2008-05-01

The rates of fine structure relaxation in PbS, PbSe, and PbTe nanocrystals were measured on a femtosecond time scale as a function of temperature with no applied magnetic field by cross-polarized transient grating spectroscopy (CPTG) and circularly polarized pump-probe spectroscopy. The relaxation rates among exciton fine structure states follow trends with nanocrystal composition and size that are consistent with the expected influence of material dependent spin-orbit coupling, confinement enhanced electron-hole exchange interaction, and splitting between L valleys that are degenerate in the bulk. The size dependence of the fine structure relaxation rate is considerably different from what is observed for small CdSe nanocrystals, which appears to result from the unique material properties of the highly confined lead chalcogenide quantum dots. Modeling and qualitative considerations lead to conclusions about the fine structure of the lowest exciton absorption band, which has a potentially significant bearing on photophysical processes that make these materials attractive for practical purposes.

Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations.

PubMed

Emperador, Agusti; Solernou, Albert; Sfriso, Pedro; Pons, Carles; Gelpi, Josep Lluis; Fernandez-Recio, Juan; Orozco, Modesto

2013-02-12

Protein-protein interactions are responsible for the transfer of information inside the cell and represent one of the most interesting research fields in structural biology. Unfortunately, after decades of intense research, experimental approaches still have difficulties in providing 3D structures for the hundreds of thousands of interactions formed between the different proteins in a living organism. The use of theoretical approaches like docking aims to complement experimental efforts to represent the structure of the protein interactome. However, we cannot ignore that current methods have limitations due to problems of sampling of the protein-protein conformational space and the lack of accuracy of available force fields. Cases that are especially difficult for prediction are those in which complex formation implies a non-negligible change in the conformation of the interacting proteins, i.e., those cases where protein flexibility plays a key role in protein-protein docking. In this work, we present a new approach to treat flexibility in docking by global structural relaxation based on ultrafast discrete molecular dynamics. On a standard benchmark of protein complexes, the method provides a general improvement over the results obtained by rigid docking. The method is especially efficient in cases with large conformational changes upon binding, in which structure relaxation with discrete molecular dynamics leads to a predictive success rate double that obtained with state-of-the-art rigid-body docking.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Atomistic details of protein dynamics and the role of hydration water

DOE PAGES

Khodadadi, Sheila; Sokolov, Alexei P.

2016-05-04

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Atomistic details of protein dynamics and the role of hydration water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khodadadi, Sheila; Sokolov, Alexei P.

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Viscoelastic properties of addition-cured polyimides used in high temperature polymer matrix composites

NASA Technical Reports Server (NTRS)

Roberts, Gary D; Malarik, Diane C.; Robaidek, Jerrold O.

1991-01-01

Viscoelastic properties of the addition cured polyimide, PMR-15, were studied using dynamic mechanical and stress relaxation tests. For temperatures below the glass transition temperature, T sub g, the dynamic mechanical properties measured using a temperature scan rate of 10 C/min were strongly affected by the presence of absorbed moisture in the resin. Dynamic mechanical properties measured as a function of time during an isothermal hold provided an indication of chemical changes occurring in the resin. For temperatures above (T sub g + 20 C), the storage modulus increased continuously as a function of time indicating that additional crosslinking is occurring in the resin. Because of these changes in chemical structures, the stress relaxation modulus could not be measured over any useful time interval for temperatures above T sub g. For temperatures below T sub g, dynamic mechanical properties appeared to be unaffected by chemical changes for times exceeding 1 hr. Since the duration of the stress relaxation tests was less than 1 hr, the stress relaxation modulus could be measured. As long as the moisture content of the resin was less than 2 pct, stress relaxation curves measured at different temperatures could be superimposed using horizontal shifts along the log(time) axis with only small shifts along the vertical axis.

Thermomechanical Properties and Glass Dynamics of Polymer-Tethered Colloidal Particles and Films

PubMed Central

2017-01-01

Polymer-tethered colloidal particles (aka “particle brush materials”) have attracted interest as a platform for innovative material technologies and as a model system to elucidate glass formation in complex structured media. In this contribution, Brillouin light scattering is used to sequentially evaluate the role of brush architecture on the dynamical properties of brush particles in both the individual and assembled (film) state. In the former state, the analysis reveals that brush–brush interactions as well as global chain relaxation sensitively depend on grafting density; i.e., more polymer-like behavior is observed in sparse brush systems. This is interpreted to be a consequence of more extensive chain entanglement. In contrast, the local relaxation of films does not depend on grafting density. The results highlight that relaxation processes in particle brush-based materials span a wider range of time and length scales as compared to linear chain polymers. Differentiation between relaxation on local and global scale is necessary to reveal the influence of molecular structure and connectivity on the aging behavior of these complex systems. PMID:29755139

Thermomechanical Properties and Glass Dynamics of Polymer-Tethered Colloidal Particles and Films.

PubMed

Cang, Yu; Reuss, Anna N; Lee, Jaejun; Yan, Jiajun; Zhang, Jianan; Alonso-Redondo, Elena; Sainidou, Rebecca; Rembert, Pascal; Matyjaszewski, Krzysztof; Bockstaller, Michael R; Fytas, George

2017-11-14

Polymer-tethered colloidal particles (aka "particle brush materials") have attracted interest as a platform for innovative material technologies and as a model system to elucidate glass formation in complex structured media. In this contribution, Brillouin light scattering is used to sequentially evaluate the role of brush architecture on the dynamical properties of brush particles in both the individual and assembled (film) state. In the former state, the analysis reveals that brush-brush interactions as well as global chain relaxation sensitively depend on grafting density; i.e., more polymer-like behavior is observed in sparse brush systems. This is interpreted to be a consequence of more extensive chain entanglement. In contrast, the local relaxation of films does not depend on grafting density. The results highlight that relaxation processes in particle brush-based materials span a wider range of time and length scales as compared to linear chain polymers. Differentiation between relaxation on local and global scale is necessary to reveal the influence of molecular structure and connectivity on the aging behavior of these complex systems.

Dielectric relaxation of guest molecules in a clathrate structure of syndiotactic polystyrene.

PubMed

Urakawa, Osamu; Kaneko, Fumitoshi; Kobayashi, Hideo

2012-12-13

Structure and dynamics of semicrystalline polymer films composed of syndiotactic polystyrene (sPS) and 2-butanone were examined through X-ray diffraction, polarized FTIR, and dielectric relaxation measurements. The X-ray and FTIR measurements revealed its crystal structure to be δ-clathrate containing 2-butanone molecules inside. The carbonyl group of 2-butanone in the crystal was found to orient preferentially parallel to the ac plane of the crystal through the polarized ATR FTIR measurements. Dielectric measurements were also conducted on these film samples to see only the relaxation dynamics of 2-butanone thanks to the high dielectric intensity of 2-butanone compared to sPS. Two relaxation modes denoted by slow and fast modes appeared. The former was assigned to the motion of 2-butanone molecules entrapped in the cavities of the crystalline (δ-form) and the latter to those in the amorphous region. We focused on the slow mode in order to elucidate the specific dynamics of the guest molecule confined in the crystalline region. The relaxation time of the slow mode was about 4 orders of magnitude longer than that of liquid 2-butanone. This suggests that the dynamics of guest molecules is highly restricted due to the high barrier to conformational and/or orientational change of the guest molecule in the cavity of δ-crystal. Furthermore, the dielectric intensity Δε of the slow mode was much smaller than the one calculated from that of bulk liquid 2-butanone and the guest concentration in the crystalline region (the intensity was only 10% of the estimated value from the bulk liquid data). This result also indicates that the free rotational motion of 2-butanone molecules is restricted inside the crystal. This will be consistently related to the weak uniplanar orientation of the carbonyl group of 2-butanone parallel to the ac plane revealed by the X-ray and polarized ATR FTIR measurements.

Effects of the bond polarity on the structural and dynamical properties of silica-like liquids

NASA Astrophysics Data System (ADS)

Pafong Sanjon, E.; Drossel, B.; Vogel, M.

2018-03-01

Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity. Moreover, we find that the density maximum and the fragile-to-strong transition move to lower temperatures until they eventually vanish when the partial charges are decreased below approximately 75% of their regular value. Irrespective of whether strong or fragile behavior exists, structural relaxation is governed by hopping motion at sufficiently low temperatures. As long as there is a strong regime, the energy barrier associated with strong dynamics decreases with decreasing partial charges, but the dependence on the bond polarity differs from that of the activation energy in the Arrhenius regime at high temperatures. We show that the fragile-to-strong transition is associated with structural changes occurring between the first and second coordination shells that lead to a decrease in density and an increase in tetrahedral order. In particular, independent of the value of the partial charges, the distribution of the local structures is the same at this dynamic crossover, but we find no evidence that the effect occurs upon crossing the Widom line. In the fragile regime at intermediate temperatures, the relaxation times are well described by a previously proposed model which decomposes the apparent activation energy into a constant single-particle contribution and a temperature-dependent collective contribution. However, our results for silica-like melts do not obey several common relations of the model parameters reported for molecular glass formers.

Structure and dynamics of the conserved protein GPI anchor core inserted into detergent micelles.

PubMed

Chevalier, Franck; Lopez-Prados, Javier; Groves, Patrick; Perez, Serge; Martín-Lomas, Manuel; Nieto, Pedro M

2006-10-01

A suitable approach which combines nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have been used to study the structure and the dynamics of the glycosylphosphatidylinositol (GPI) anchor Manalphal-2Manalpha1-6Manalphal -4GlcNalpha1-6myo-inositol-1-OPO(3)-sn-1,2-dimyristoylglycerol (1) incorporated into dodecylphosphatidylcholine (DPC) micelles. The results have been compared to those previously obtained for the products obtainable from (1) after phospholipase cleavage, in aqueous solution. Relaxation and diffusion NMR experiments were used to establish the formation of stable aggregates and the insertion of (1) into the micelles. MD calculations were performed including explicit water, sodium and chloride ions and using the Particle Mesh Ewald approach for the evaluation of the electrostatic energy term. The MD predicted three dimensional structure and dynamics were substantiated by nuclear overhauser effect (NOE) measurements and relaxation data. The pseudopentasaccharide structure, which was not affected by incorporation of (1) into the micelle, showed a complex dynamic behaviour with a faster relative motion at the terminal mannopyranose unit and decreased mobility close to the micelle. This motion may be better described as an oscillation relative to the membrane rather than a folding event.

Theory of Cooperative Activated Structural Relaxation in Polymer Nanocomposites Composed of Small and Sticky Particles

NASA Astrophysics Data System (ADS)

Xie, Shijie; Schweizer, Kenneth

Recently, Cheng, Sokolov and coworkers have discovered qualitatively new dynamic behavior (exceptionally large Tg and fragility increases, unusual thermal and viscoelastic responses) in polymer nanocomposites composed of nanoparticles comparable in size to a polymer segment which form physical bonds with both themselves and segments. We generalize the Elastically Collective Nonlinear Langevin Equation theory of deeply supercooled molecular and polymer liquids to study the cooperative activated hopping dynamics of this system based on the dynamic free energy surface concept. The theoretical calculations are consistent with segmental relaxation time measurements as a function of temperature and nanoparticle volume fraction, and also the nearly linear growth of Tg with NP loading; predictions are made for the influence of nonuniversal chemical effects. The theory suggests the alpha process involves strongly coupled activated motion of segments and nanoparticles, consistent with the observed negligible change of the heat capacity jump with filler loading. Based on cohesive energy calculations and transient network ideas, full structural relaxation is suggested to involve a second, slower bond dissociation process with distinctive features and implications.

Stochastic tools hidden behind the empirical dielectric relaxation laws

NASA Astrophysics Data System (ADS)

Stanislavsky, Aleksander; Weron, Karina

2017-03-01

The paper is devoted to recent advances in stochastic modeling of anomalous kinetic processes observed in dielectric materials which are prominent examples of disordered (complex) systems. Theoretical studies of dynamical properties of ‘structures with variations’ (Goldenfield and Kadanoff 1999 Science 284 87-9) require application of such mathematical tools—by means of which their random nature can be analyzed and, independently of the details distinguishing various systems (dipolar materials, glasses, semiconductors, liquid crystals, polymers, etc), the empirical universal kinetic patterns can be derived. We begin with a brief survey of the historical background of the dielectric relaxation study. After a short outline of the theoretical ideas providing the random tools applicable to modeling of relaxation phenomena, we present probabilistic implications for the study of the relaxation-rate distribution models. In the framework of the probability distribution of relaxation rates we consider description of complex systems, in which relaxing entities form random clusters interacting with each other and single entities. Then we focus on stochastic mechanisms of the relaxation phenomenon. We discuss the diffusion approach and its usefulness for understanding of anomalous dynamics of relaxing systems. We also discuss extensions of the diffusive approach to systems under tempered random processes. Useful relationships among different stochastic approaches to the anomalous dynamics of complex systems allow us to get a fresh look at this subject. The paper closes with a final discussion on achievements of stochastic tools describing the anomalous time evolution of complex systems.

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

PubMed Central

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

2008-01-01

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

Structural, electrical properties and dielectric relaxations in Na+-ion-conducting solid polymer electrolyte

NASA Astrophysics Data System (ADS)

Arya, Anil; Sharma, A. L.

2018-04-01

In this paper, we have studied the structural, microstructural, electrical, dielectric properties and ion dynamics of a sodium-ion-conducting solid polymer electrolyte film comprising PEO8-NaPF6+  x wt. % succinonitrile. The structural and surface morphology properties have been investigated, respectively using x-ray diffraction and field emission scanning electron microscopy. The complex formation was examined using Fourier transform infrared spectroscopy, and the fraction of free anions/ion pairs obtained via deconvolution. The complex dielectric permittivity and loss tangent has been analyzed across the whole frequency window, and enables us to estimate the DC conductivity, dielectric strength, double layer capacitance and relaxation time. The presence of relaxing dipoles was determined by the addition of succinonitrile (wt./wt.) and the peak shift towards high frequency indicates the decrease of relaxation time. Further, relations among various relaxation times ({{τ }{{\\varepsilon \\prime}}}>~{{τ }tanδ }>{{τ }z}>{{τ }m} ) have been elucidated. The complex conductivity has been examined across the whole frequency window; it obeys the Universal Power Law, and displays strong dependency on succinonitrile content. The sigma representation ({{σ }\\prime\\prime}~versus~{{σ }\\prime} ) was introduced in order to explore the ion dynamics by highlighting the dispersion region in the Cole–Cole plot ({{\\varepsilon }\\prime\\prime}~versus~{{\\varepsilon }\\prime} ) in the lower frequency window; increase in the semicircle radius indicates a decrease of relaxation time. This observation is accompanied by enhancement in ionic conductivity and faster ion transport. A convincing, logical scheme to justify the experimental data has been proposed.

Mode-coupling theoretical analysis of transport and relaxation properties of liquid dimethylimidazolium chloride

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Koda, S.

2010-03-01

The mode-coupling theory for molecular liquids based on the interaction-site model is applied to a representative molecular ionic liquid, dimethylimidazolium chloride, and dynamic properties such as shear viscosity, self-diffusion coefficients, reorientational relaxation time, electric conductivity, and dielectric relaxation spectrum are analyzed. Molecular dynamics (MD) simulation is also performed on the same system for comparison. The theory captures the characteristics of the dynamics of the ionic liquid qualitatively, although theoretical relaxation times are several times larger than those from the MD simulation. Large relaxations are found in the 100 MHz region in the dispersion of the shear viscosity and the dielectric relaxation, in harmony with various experiments. The relaxations of the self-diffusion coefficients are also found in the same frequency region. The dielectric relaxation spectrum is divided into the contributions of the translational and reorientational modes, and it is demonstrated that the relaxation in the 100 MHz region mainly stems from the translational modes. The zero-frequency electric conductivity is close to the value predicted by the Nernst-Einstein equation in both MD simulation and theoretical calculation. However, the frequency dependence of the electric conductivity is different from those of self-diffusion coefficients in that the former is smaller than the latter in the gigahertz-terahertz region, which is compensated by the smaller dispersion of the former in the 100 MHz region. The analysis of the theoretical calculation shows that the difference in their frequency dependence is due to the different contribution of the short- and long-range liquid structures.

Structure and dynamics of a silica melt in neutral confinement

NASA Astrophysics Data System (ADS)

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-01

We analyze the effects of spatial confinement on viscous silica using molecular dynamics simulations. For this purpose, we prepare a silica melt in a cylindrical pore, which is produced by pinning appropriate fractions of silicon and oxygen atoms in a bulk system after an equilibration period. In this way, the structure of the confined silica melt remains unaffected, while the confinement has a strong impact on the dynamics. We find that the structural relaxation of viscous silica is slowed down according to a double exponential law when approaching the pore wall. Moreover, we observe that static density correlations exist in the vicinity of the pore wall. Based on these effects, we determine dynamical and structural length scales of the silica melt. Both length scales show a similar increase upon cooling, with values on the order of the next-neighbor distances in the studied temperature range. Interestingly, we find no evidence that the growth of the length scales is affected by a fragile-to-strong transition of the silica melt. This observation casts serious doubts on the relevance of these length scales for the structural relaxation, at least for the studied glass former.

Structure and dynamics of a silica melt in neutral confinement.

PubMed

Geske, Julian; Drossel, Barbara; Vogel, Michael

2017-04-07

We analyze the effects of spatial confinement on viscous silica using molecular dynamics simulations. For this purpose, we prepare a silica melt in a cylindrical pore, which is produced by pinning appropriate fractions of silicon and oxygen atoms in a bulk system after an equilibration period. In this way, the structure of the confined silica melt remains unaffected, while the confinement has a strong impact on the dynamics. We find that the structural relaxation of viscous silica is slowed down according to a double exponential law when approaching the pore wall. Moreover, we observe that static density correlations exist in the vicinity of the pore wall. Based on these effects, we determine dynamical and structural length scales of the silica melt. Both length scales show a similar increase upon cooling, with values on the order of the next-neighbor distances in the studied temperature range. Interestingly, we find no evidence that the growth of the length scales is affected by a fragile-to-strong transition of the silica melt. This observation casts serious doubts on the relevance of these length scales for the structural relaxation, at least for the studied glass former.

From elemental tellurium to Ge2Sb2Te5 melts: High temperature dynamic and relaxation properties in relationship with the possible fragile to strong transition

NASA Astrophysics Data System (ADS)

Flores-Ruiz, H.; Micoulaut, M.

2018-01-01

We investigate the dynamic properties of Ge-Sb-Te phase change melts using first principles molecular dynamics with a special emphasis on the effect of tellurium composition on melt dynamics. From structural models and trajectories established previously [H. Flores-Ruiz et al., Phys. Rev. B 92, 134205 (2015)], we calculate the diffusion coefficients for the different species, the activation energies for diffusion, the Van Hove correlation, and the intermediate scattering functions able to substantiate the dynamics and relaxation behavior of the liquids as a function of temperature and composition that is also compared to experiment whenever possible. We find that the diffusion is mostly Arrhenius-like and that the addition of Ge/Sb atoms leads to a global decrease of the jump probability and to an increase in activated dynamics for diffusion. Relaxation behavior is analyzed and used in order to evaluate the possibility of a fragile to strong transition that is evidenced from the calculated high fragility (M = 129) of Ge2Sb2Te5 at high temperatures.

Structure of Boron Nitride Nanotubes: Tube Closing Vs. Chirality

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu

1998-01-01

The structure of boron nitride nanotubes is investigated using a generalized tight-binding molecular dynamics method. It is shown that dynamic relaxation results in a wavelike or "rippled" surface in which the B atoms rotate inward and the N atoms move outward, reminiscent of the surface relaxation of the III-V semiconductors. More importantly, the three different morphologies of the tube closing with flat, conical and amorphous ends, as observed in experiments, are shown to be directly related to the tube chiralities. The abundance of flat end tubes observed in experiments is, thus, shown to be an indication of the greater stability of "zig-zag" BN tubes over the "arm-chair" tubes under experimental conditions.

Local orientational mobility in regular hyperbranched polymers.

PubMed

Dolgushev, Maxim; Markelov, Denis A; Fürstenberg, Florian; Guérin, Thomas

2016-07-01

We study the dynamics of local bond orientation in regular hyperbranched polymers modeled by Vicsek fractals. The local dynamics is investigated through the temporal autocorrelation functions of single bonds and the corresponding relaxation forms of the complex dielectric susceptibility. We show that the dynamic behavior of single segments depends on their remoteness from the periphery rather than on the size of the whole macromolecule. Remarkably, the dynamics of the core segments (which are most remote from the periphery) shows a scaling behavior that differs from the dynamics obtained after structural average. We analyze the most relevant processes of single segment motion and provide an analytic approximation for the corresponding relaxation times. Furthermore, we describe an iterative method to calculate the orientational dynamics in the case of very large macromolecular sizes.

Ameba-like diffusion in two-dimensional polymer melts: how critical exponents determine the structural relaxation

NASA Astrophysics Data System (ADS)

Kreer, Torsten; Meyer, Hendrik; Baschnagel, Joerg

2008-03-01

By means of numerical investigations we demonstrate that the structural relaxation of linear polymers in two dimensional (space-filling) melts is characterized by ameba-like diffusion, where the chains relax via frictional dissipation at their interfacial contact lines. The perimeter length of the contact line determines a new length scale, which does not exist in three dimensions. We show how this length scale follows from the critical exponents, which hence characterize not only the static but also the dynamic properties of the melt. Our data is in agreement with recent theoretical predictions, concerning the time-dependence of single-monomer mean-square displacements and the scaling of concomitant relaxation times with the degree of polymerization. For the latter we demonstrate a density crossover-scaling as an additional test for ameba-like relaxation. We compare our results to the conceptually different Rouse model, which predicts numerically close exponents. Our data can clearly rule out the classical picture as the relevant relaxation mechanism in two-dimensional polymer melts.

Aging of Johari-Goldstein Relaxation in Structural Glasses

NASA Astrophysics Data System (ADS)

Yardimci, Hasan; Leheny, Robert L.

2006-03-01

Using frequency-dependent dielectric susceptibility measurements we characterize the aging in two supercooled liquids, sorbitol and xylitol, below their calorimetric glass transition temperatures, Tg. In addition to the alpha relaxation that tracks the structural dynamics, the susceptibilities of both liquids possess a secondary Johari-Goldstein relaxation at higher frequencies. Following a quench below Tg, the susceptibility slowly approaches equilibrium behavior. For both liquids, features of the Johari-Goldstein relaxation display a dependence on the time since the quench, or aging time, that is very similar to the age dependence of the alpha peak. However, one can not assign a single fictive temperature to both the alpha and Johari-Goldstein relaxations. For example, the peak frequency of the Johari-Goldstein relaxation remains constant during aging for sorbitol while it increases with age for xylitol, inconsistent with a decreasing fictive temperature. This behavior contrasts with that of the high frequency tail of the alpha peak whose shape and position track the aging of the main part of the peak.

Transient slowing down relaxation dynamics of the supercooled dusty plasma liquid after quenching.

PubMed

Su, Yen-Shuo; Io, Chong-Wai; I, Lin

2012-07-01

The spatiotemporal evolutions of microstructure and motion in the transient relaxation toward the steady supercooled liquid state after quenching a dusty plasma Wigner liquid, formed by charged dust particles suspended in a low pressure discharge, are experimentally investigated through direct optical microscopy. It is found that the quenched liquid slowly evolves to a colder state with more heterogeneities in structure and motion. Hopping particles and defects appear in the form of clusters with multiscale cluster size distributions. Via the structure rearrangement induced by the reduced thermal agitation from the cold thermal bath after quenching, the temporarily stored strain energy can be cascaded through the network to different newly distorted regions and dissipated after transferring to nonlinearly coupled motions with different scales. It leads to the observed self-similar multiscale slowing down relaxation with power law increases of structural order and structural relaxation time, the similar power law decreases of particle motions at different time scales, and the stronger and slower fluctuations with increasing waiting time toward the new steady state.

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Smith, Grant D.

1994-01-01

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Delayed plastic relaxation limit in SiGe islands grown by Ge diffusion from a local source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanacore, G. M.; Zani, M.; Tagliaferri, A., E-mail: alberto.tagliaferri@polimi.it

2015-03-14

The hetero-epitaxial strain relaxation in nano-scale systems plays a fundamental role in shaping their properties. Here, the elastic and plastic relaxation of self-assembled SiGe islands grown by surface-thermal-diffusion from a local Ge solid source on Si(100) are studied by atomic force and transmission electron microscopies, enabling the simultaneous investigation of the strain relaxation in different dynamical regimes. Islands grown by this technique remain dislocation-free and preserve a structural coherence with the substrate for a base width as large as 350 nm. The results indicate that a delay of the plastic relaxation is promoted by an enhanced Si-Ge intermixing, induced by themore » surface-thermal-diffusion, which takes place already in the SiGe overlayer before the formation of a critical nucleus. The local entropy of mixing dominates, leading the system toward a thermodynamic equilibrium, where non-dislocated, shallow islands with a low residual stress are energetically stable. These findings elucidate the role of the interface dynamics in modulating the lattice distortion at the nano-scale, and highlight the potential use of our growth strategy to create composition and strain-controlled nano-structures for new-generation devices.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Siqi; Senses, Erkan; Jiao, Yang

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Dephasing dynamics in confined myoglobin

NASA Astrophysics Data System (ADS)

Goj, Anne; Loring, Roger F.

2007-11-01

Confinement of a solution can slow solvent dynamics and in turn influence the reactivity and structure of the solute. Encapsulating a protein in an aqueous pore affects its binding properties, stability to degradation, interconversion between conformational states, and energy relaxation. We perform molecular dynamics simulations of H64V-CO mutant myoglobin solvated by varying amounts of liquid water, and in turn enclosed by a matrix of immobilized solvent, to mimic differing degrees of confinement of H64V-CO in a glass. We calculate the three-pulse vibrational echo signal of the CO ligand from the autocorrelation function of fluctuations in the CO vibrational frequency. When the first solvation layer alone is free to relax, the correlation function displays only fast relaxation reminiscent of the case of a protein in a fixed, immobilized solvent matrix. However the vibrational echo signal in this case decays significantly more rapidly than for a static solvent. With two solvation layers mobile, the correlation function displays long time relaxation characteristic of the unconfined protein and the echo signal decays rapidly. The echo signal of the protein with two mobile solvation layers is nearly identical to that of the unconfined protein, despite the substantially constrained solvent dynamics in the confined case.

Characterization of Dynamics in Complex Lyophilized Formulations: I. Comparison of Relaxation Times Measured by Isothermal Calorimetry with Data Estimated from the Width of the Glass Transition Temperature Region

PubMed Central

Chieng, Norman; Mizuno, Masayasu; Pikal, Michael

2013-01-01

The purposes of this study are to characterize the relaxation dynamics in complex freeze dried formulations and to investigate the quantitative relationship between the structural relaxation time as measured by thermal activity monitor (TAM) and that estimated from the width of the glass transition temperature (ΔTg). The latter method has advantages over TAM because it is simple and quick. As part of this objective, we evaluate the accuracy in estimating relaxation time data at higher temperatures (50°C and 60°C) from TAM data at lower temperature (40°C) and glass transition region width (ΔTg) data obtained by differential scanning calorimetry. Formulations studied here were hydroxyethyl starch (HES)-disaccharide, HES-polyol and HES-disaccharide-polyol at various ratios. We also re-examine, using TAM derived relaxation times, the correlation between protein stability (human growth hormone, hGH) and relaxation times explored in a previous report, which employed relaxation time data obtained from ΔTg. Results show that most of the freeze dried formulations exist in single amorphous phase, and structural relaxation times were successfully measured for these systems. We find a reasonably good correlation between TAM measured relaxation times and corresponding data obtained from estimates based on ΔTg, but the agreement is only qualitative. The comparison plot showed that TAM data is directly proportional to the 1/3 power of ΔTg data, after correcting for an offset. Nevertheless, the correlation between hGH stability and relaxation time remained qualitatively the same as found with using ΔTg derived relaxation data, and it was found that the modest extrapolation of TAM data to higher temperatures using ΔTg method and TAM data at 40°C resulted in quantitative agreement with TAM measurements made at 50 °C and 60 °C, provided the TAM experiment temperature is well below the Tg of the sample. PMID:23608636

Secondary relaxation dynamics in rigid glass-forming molecular liquids with related structures.

PubMed

Li, Xiangqian; Wang, Meng; Liu, Riping; Ngai, Kia L; Tian, Yongjun; Wang, Li-Min; Capaccioli, Simone

2015-09-14

The dielectric relaxation in three glass-forming molecular liquids, 1-methylindole (1MID), 5H-5-Methyl-6,7-dihydrocyclopentapyrazine (MDCP), and Quinaldine (QN) is studied focusing on the secondary relaxation and its relation to the structural α-relaxation. All three glass-formers are rigid and more or less planar molecules with related chemical structures but have dipoles of different strengths at different locations. A strong and fast secondary relaxation is detected in the dielectric spectra of 1MID, while no resolved β-relaxation is observed in MDCP and QN. If the observed secondary relaxation in 1MID is identified with the Johari-Goldstein (JG) β-relaxation, then apparently the relation between the α- and β-relaxation frequencies of 1MID is not in accord with the Coupling Model (CM). The possibility of the violation of the prediction in 1MID as due to either the formation of hydrogen-bond induced clusters or the involvement of intramolecular degree of freedom is ruled out. The violation is explained by the secondary relaxation originating from the in-plane rotation of the dipole located on the plane of the rigid molecule, contributing to dielectric loss at higher frequencies and more intense than the JG β-relaxation generated by the out-of-plane rotation. MDCP has smaller dipole moment located in the plane of the molecule; however, presence of the change of curvature of dielectric loss, ε″(f), at some frequency on the high-frequency flank of the α-relaxation reveals the JG β-relaxation in MDCP and which is in accord with the CM prediction. QN has as large an in-plane dipole moment as 1MID, and the absence of the resolved secondary relaxation is explained by the smaller coupling parameter than the latter in the framework of the CM.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Y.W.; Labouriau, A.; Taylor, C.M.

Dynamics and structure of tri-n-butyltin fluoride in n-hexane solutions were probed using (tin-119) nuclear magnetic resonance spin relaxation methodologies. Significant relaxation-induced polarization transfer effects were observed and exploited. The experimental observations indicate that the tri-n-butyl fluoride exists in a polymeric form in solution. For a 0.10% (w/w) solution at 25 [degree]C, NMR reveals significant orientational/exchange relaxation on both the microsecond and nanosecond time scales. Solution-state and solid-state parameters are compared and contrasted. 26 refs., 3 figs., 1 tab.

Dynamic anomalies in a supercooled liquid: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Wahnström, Göran

1991-07-01

Molecular-dynamics simulations have been carried out on a two-component Lennard-Jones system, quenched into supercooled and amorphous states. Careful attention is paid to proper equilibration of the system in the supercooled liquid regime and long production runs are performed in order to reveal slow structural relaxation processes. The results for the time-dependence of the self-part of the density autocorrelation function Fqs(t) show two different slow relaxation processes, where the slowest (α relaxation) can be represented by a stretched exponential, A exp[- (t/τrel)ß]. In frequency domain this gives rise to a quasi-elastic peak and it is found that its area, the nonergodicity parameter fqs, shows an anomalous decrease when increasing the temperature towards a critical value Tc. This happens in the supercooled liquid regime and it is one of the basic predictions of the recent mode-coupling theory for the liquid-glass transition problem.

Computer simulations of structural transitions in large ferrofluid aggregates

NASA Astrophysics Data System (ADS)

Yoon, Mina; Tomanek, David

2003-03-01

We have developed a quaternion molecular dynamics formalism to study structural transitions in systems of ferrofluid particles in colloidal suspensions. Our approach takes advantage of the viscous damping provided by the surrounding liquid and enables us to study the time evolution of these systems over milli-second time periods as a function of the number of particles, initial geometry, and an externally applied magnetic field. Our computer simulations for aggregates containing tens to hundreds of ferrofluid particles suggest that these systems relax to the global optimum structure in a step-wise manner. During the relaxation process, the potential energy decreases by two mechanisms, which occur on different time scales. Short time periods associated with structural relaxations within a given morphology are followed by much slower processes that generally lead to a simpler morphology. We discuss possible applications of these externally driven structural transitions for targeted medication delivery.

Changes in the Coherent Dynamics of Nanoconfined Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Vallejo, Kevin; Cano, Melissa; Li, Song; Rotner, Gernot; Faraone, Antonio; Banuelos, Jose

Confinement and temperature effects on the coherent dynamics of the room temperature ionic liquid (RTIL) [C10MPy+] [Tf2N-] were investigated using neutron spin-echo (NSE) in two silica matrices with different pore size. Several intermolecular forces give rise to the bulk molecular structure between anions and cations. NSE provided dynamics (via the coherent intermediate scattering function) in the time range of 0.004 to 10 ns, and at Q-values corresponding to intermediate range ordering and inter- and intra-molecular length scales of the RTIL. Pore wall effects were delineated by comparing bulk RTIL dynamics with those of the confined fluid in 2.8 nm and 8 nm pores. Analytical models were applied to the experimental data to extract decay times and amplitudes of each component. We find a fast relaxation outside the experiment time window, a primary relaxation, and slow, surface-induced dynamics, which all speed up with increased temperature, however, the temperature dependence differs between bulk and confinement. This study sheds light on the structure and dynamics of RTILs and is relevant to the optimization of RTILs for green technologies and applications.

Collective relaxation dynamics of small-world networks

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N , average degree k , and topological randomness q . We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q , including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

Collective relaxation dynamics of small-world networks.

PubMed

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N, average degree k, and topological randomness q. We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q, including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics.

PubMed

Liu, Xu; Shepherd, Tyson R; Murray, Ann M; Xu, Zhen; Fuentes, Ernesto J

2013-03-05

PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity, structure, and dynamics of Tiam1 PDZ domain/ligand interactions. We show that the PDZ domain specifically binds syndecan1 (SDC1), phosphorylated SDC1 (pSDC1), and SDC3 but not other syndecan isoforms. The crystal structure of the PDZ/SDC1 complex indicates that syndecan affinity is derived from amino acids beyond the four C-terminal residues. Remarkably, the crystal structure of the PDZ/pSDC1 complex reveals a binding pocket that accommodates the phosphoryl group. Methyl relaxation experiments of PDZ/SCD1 and PDZ/pSDC1 complexes reveal that PDZ-phosphoryl interactions dampen dynamic motions in a distal region of the PDZ domain by decoupling them from the ligand-binding site. Our data are consistent with a selection model by which specificity and phosphorylation regulate PDZ/syndecan interactions and signaling events. Importantly, our relaxation data demonstrate that PDZ/phospho-ligand interactions regulate protein dynamics and their coupling to distal sites. Copyright © 2013 Elsevier Ltd. All rights reserved.

Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth S.; Saltzman, Erica J.

2004-07-01

A statistical mechanical theory of collective dynamic barriers, slow segmental relaxation, and the glass transition of polymer melts is developed by combining, and in some aspects extending, methods of mode coupling, density functional, and activated hopping transport theories. A coarse-grained description of polymer chains is adopted and the melt is treated as a liquid of segments. The theory is built on the idea that collective density fluctuations on length scales considerably longer than the local cage scale are of primary importance in the deeply supercooled regime. The barrier hopping or segmental relaxation time is predicted to be a function primarily of a single parameter that is chemical structure, temperature, and pressure dependent. This parameter depends on the material-specific dimensionless amplitude of thermal density fluctuations (compressibility) and a reduced segmental density determined by the packing length and backbone characteristic ratio. Analytic results are derived for a crossover temperature Tc, collective barrier, and glass transition temperature Tg. The relation of these quantities to structural and thermodynamic properties of the polymer melt is established. A universal power-law scaling behavior of the relaxation time below Tc is predicted based on identification of a reduced temperature variable that quantifies the breadth of the supercooled regime. Connections between the ratio Tc/Tg, two measures of dynamic fragility, and the magnitude of the local relaxation time at Tg logically follow. Excellent agreement with experiment is found for these generic aspects, and the crucial importance of the experimentally observed near universality of the dynamic crossover time is established. Extensions of the theory to treat the full chain dynamics, heterogeneity, barrier fluctuations, and nonpolymeric thermal glass forming liquids are briefly discussed.

Diffusion-controlled and "diffusionless" crystal growth near the glass transition temperature: relation between liquid dynamics and growth kinetics of seven ROY polymorphs.

PubMed

Sun, Ye; Xi, Hanmi; Ediger, M D; Richert, Ranko; Yu, Lian

2009-08-21

The liquid dynamics of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, named ROY for its red, orange, and yellow crystal polymorphs, was characterized by dielectric spectroscopy and differential scanning calorimetry. Four of these polymorphs show fast "diffusionless" crystal growth at low temperatures while three others do not. ROY was found to be a typical fragile organic liquid. Its alpha relaxation process has time-temperature superposition symmetry across the viscous range (tau(alpha)=100 s-100 ns) with the width of the relaxation peak characterized by a constant beta(KWW) of 0.73. No secondary relaxation peak was observed, even with glasses made by fast quenching. For the polymorphs not showing fast crystal growth in the glassy state, the growth rate has a power-law relation with tau(alpha), u proportional to tau(alpha)(-xi), where xi approximately = 0.7. For the polymorphs showing fast crystal growth in the glassy state, the growth is so fast near and below the glass transition temperature T(g) that thousands of molecular layers can be added to the crystalline phase during one structural relaxation time of the liquid. In the glassy state, this mode of growth slows slightly over time. This slowdown is not readily explained by the effect of physical aging on the thermodynamic driving force of crystallization, the glass vapor pressure, or the rate of structural relaxation. This study demonstrates that from the same liquid or glass, the growth of some polymorphs is accurately described as being limited by the rate of structural relaxation or bulk diffusion, whereas the growth of other polymorphs is too fast to be under such control.

Static Modulation Wave of Arrays of Halogen Interactions Transduced to a Hierarchy of Nanoscale Change Stimuli of Crystalline Rotors Dynamics.

PubMed

Simonov, Sergey; Zorina, Leokadiya; Wzietek, Pawel; Rodríguez-Fortea, Antonio; Canadell, Enric; Mézière, Cécile; Bastien, Guillaume; Lemouchi, Cyprien; Garcia-Garibay, Miguel A; Batail, Patrick

2018-06-13

Here we present a study where what can be seen as a static modulation wave encompassing four successive arrays of interacting iodine atoms in crystalline 1,4-Bis((4'-(iodoethynyl)phenyl) ethynyl)bicyclo[2,2,2]octane rotors changes the structure from one-half molecule to three-and-a-half molecules in the asymmetric unit below a phase transition at 105 K. The remarkable finding is that the total 1 H spin-lattice relaxation rate, T 1 -1 , of unprecedented complexity to date in molecular rotors, is the weighted sum of the relaxation rates of the four contributing rotors relaxation rates, each with distinguishable exchange frequencies reflecting Arrhenius parameters with different activation barriers ( E a ) and attempt frequencies (τ o -1 ). This allows us to show in tandem with rotor-environment interaction energy calculations how the dynamics of molecular rotors are able to decode structural information from their surroundings with remarkable nanoscale precision.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-01

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

PubMed

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Characterization of the Electric Double Layer Formation Dynamics of a Metal/Ionic Liquid/Metal Structure.

PubMed

Schmidt, Elliot; Shi, Sha; Ruden, P Paul; Frisbie, C Daniel

2016-06-15

Although ionic liquids (ILs) have been used extensively in recent years as a high-capacitance "dielectric" in electric double layer transistors, the dynamics of the double layer formation have remained relatively unexplored. Better understanding of the dynamics and relaxation processes involved in electric double layer formation will guide device optimization, particularly with regard to switching speed. In this paper, we explore the dynamical characteristics of an IL in a metal/ionic liquid/metal (M/IL/M) capacitor. In particular, we examine a Au/IL/Au structure where the IL is 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate. The experiments consist of frequency-dependent impedance measurements and time-dependent current vs voltage measurements for applied linear voltage ramps and abrupt voltage steps. The parameters of an equivalent circuit model are determined by fits to the impedance vs frequency data and subsequently verified by calculating the current vs voltage characteristics for the applied potential profiles. The data analysis indicates that the dynamics of the structure are characterized by a wide distribution of relaxation times spanning the range of less than microseconds to longer than seconds. Possible causes for these time scales are discussed.

Nonlinear dielectric spectroscopy of propylene carbonate derivatives

NASA Astrophysics Data System (ADS)

Casalini, R.; Roland, C. M.

2018-04-01

Nonlinear dielectric measurements were carried out on two strongly polar liquids, 4-vinyl-1,3-dioxolan-2-one (VPC) and 4-ethyl-1,3-dioxolan-2-one (EPC), having chemical structures differing from propylene carbonate (PC) only by the presence of a pendant group. Despite their polarity, the compounds are all non-associated, "simple" liquids. From the linear component of the dielectric response, the α relaxation peak breadth was found to be invariant at a fixed value of the relaxation time, τα. From spectra from the nonlinear component, the number of dynamically correlated molecules was determined; it was also constant at fixed τα. Thus, two manifestations of dynamic heterogeneity depend only on the time constant for structural reorientation. More broadly, the cooperativity of molecular motions for non-associated glass-forming materials is connected to (i.e., reciprocally governs) the time scale. The equation of state for the two liquids was also obtained from density measurements made over a broad range of pressures and temperatures. Using these data, it was determined that the relaxation times of both liquids conform to density scaling. The effect of density, relative to thermal effects, on the α relaxation increases going from PC < VPC < EPC.

Dynamics of one-state downhill protein folding.

PubMed

Li, Peng; Oliva, Fabiana Y; Naganathan, Athi N; Muñoz, Victor

2009-01-06

The small helical protein BBL has been shown to fold and unfold in the absence of a free energy barrier according to a battery of quantitative criteria in equilibrium experiments, including probe-dependent equilibrium unfolding, complex coupling between denaturing agents, characteristic DSC thermogram, gradual melting of secondary structure, and heterogeneous atom-by-atom unfolding behaviors spanning the entire unfolding process. Here, we present the results of nanosecond T-jump experiments probing backbone structure by IR and end-to-end distance by FRET. The folding dynamics observed with these two probes are both exponential with common relaxation times but have large differences in amplitude following their probe-dependent equilibrium unfolding. The quantitative analysis of amplitude and relaxation time data for both probes shows that BBL folding dynamics are fully consistent with the one-state folding scenario and incompatible with alternative models involving one or several barrier crossing events. At 333 K, the relaxation time for BBL is 1.3 micros, in agreement with previous folding speed limit estimates. However, late folding events at room temperature are an order of magnitude slower (20 micros), indicating a relatively rough underlying energy landscape. Our results in BBL expose the dynamic features of one-state folding and chart the intrinsic time-scales for conformational motions along the folding process. Interestingly, the simple self-averaging folding dynamics of BBL are the exact dynamic properties required in molecular rheostats, thus supporting a biological role for one-state folding.

Role of quantum fluctuations in structural dynamics of liquids of light molecules

DOE PAGES

Agapov, A.; Novikov, V. N.; Kisliuk, A.; ...

2016-12-16

A possible role of quantum effects, such as tunneling and zero-point energy, in the structural dynamics of supercooled liquids is studied by dielectric spectroscopy. Our results demonstrate that the liquids, bulk 3-methyl pentane and confined normal and deuterated water, have low glass transition temperature and unusually low for their class of materials steepness of the temperature dependence of structural relaxation (fragility). Although we do not find any signs of tunneling in the structural relaxation of these liquids, their unusually low fragility can be well described by the influence of the quantum fluctuations. Confined water presents an especially interesting case inmore » comparison to the earlier data on bulk low-density amorphous and vapor deposited water. Confined water exhibits a much weaker isotope effect than bulk water, although the effect is still significant. Here, we show that it can be ascribed to the change of the energy barrier for relaxation due to a decrease in the zeropoint energy upon D/H substitution. We observed a difference in the behavior of confined and bulk water demonstrates high sensitivity of quantum effects to the barrier heights and structure of water. Moreover, these results demonstrate that extrapolation of confined water properties to the bulk water behavior is questionable.« less

Cooperativity in Molecular Dynamics Structural Models and the Dielectric Spectra of 1,2-Ethanediol

NASA Astrophysics Data System (ADS)

Usacheva, T. M.

2018-05-01

Linear relationships are established between the experimental equilibrium correlation factor and the molecular dynamics (MD) mean value of the O-H···O bond angle and the longitudinal component of the unit vector of the mean statistical dipole moment of the cluster in liquid 1,2-ethanediol (12ED). The achievements of modern MD models in describing the experimental dispersion of the permittivity of 12ED by both continuous and discrete relaxation time spectra are analyzed. The advantage computer MD experiments have over dielectric spectroscopy for calculating relaxation time and determining the molecular diffusion mechanisms of the rearrangement of the network 12ED structure, which is more complex than water, is demonstrated.

Quantum Emitters in Two-Dimensional Structured Reservoirs in the Nonperturbative Regime

NASA Astrophysics Data System (ADS)

González-Tudela, A.; Cirac, J. I.

2017-10-01

We show that the coupling of quantum emitters to a two-dimensional reservoir with a simple band structure gives rise to exotic quantum dynamics with no analogue in other scenarios and which cannot be captured by standard perturbative treatments. In particular, for a single quantum emitter with its transition frequency in the middle of the band, we predict an exponential relaxation at a rate different from that predicted by Fermi's golden rule, followed by overdamped oscillations and slow relaxation decay dynamics. This is accompanied by directional emission into the reservoir. This directionality leads to a modification of the emission rate for few emitters and even perfect subradiance, i.e., suppression of spontaneous emission, for four quantum emitters.

Ultrafast 25-fs relaxation in highly excited states of methyl azide mediated by strong nonadiabatic coupling.

PubMed

Peters, William K; Couch, David E; Mignolet, Benoit; Shi, Xuetao; Nguyen, Quynh L; Fortenberry, Ryan C; Schlegel, H Bernhard; Remacle, Françoise; Kapteyn, Henry C; Murnane, Margaret M; Li, Wen

2017-12-26

Highly excited electronic states are challenging to explore experimentally and theoretically-due to the large density of states and the fact that small structural changes lead to large changes in electronic character with associated strong nonadiabatic dynamics. They can play a key role in astrophysical and ionospheric chemistry, as well as the detonation chemistry of high-energy density materials. Here, we implement ultrafast vacuum-UV (VUV)-driven electron-ion coincidence imaging spectroscopy to directly probe the reaction pathways of highly excited states of energetic molecules-in this case, methyl azide. Our data, combined with advanced theoretical simulations, show that photoexcitation of methyl azide by a 10-fs UV pulse at 8 eV drives fast structural changes and strong nonadiabatic coupling that leads to relaxation to other excited states on a surprisingly fast timescale of 25 fs. This ultrafast relaxation differs from dynamics occurring on lower excited states, where the timescale required for the wavepacket to reach a region of strong nonadiabatic coupling is typically much longer. Moreover, our theoretical calculations show that ultrafast relaxation of the wavepacket to a lower excited state occurs along one of the conical intersection seams before reaching the minimum energy conical intersection. These findings are important for understanding the unique strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules. Although such observations have been predicted for many years, this study represents one of the few where such strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules have been conclusively observed directly, making it possible to identify the ultrafast reaction pathways.

Dynamics of glass-forming liquids. XVIII. Does entropy control structural relaxation times?

NASA Astrophysics Data System (ADS)

Samanta, Subarna; Richert, Ranko

2015-01-01

We study the dielectric dynamics of viscous glycerol in the presence of a large bias field. Apart from dielectric saturation and polarization anisotropy, we observe that the steady state structural relaxation time is longer by 2.7% in the presence of a 225 kV/cm dc-field relative to the linear response counterpart, equivalent to a field induced glass transition (Tg) shift of +84 mK. This result compares favorably with the 3.0% time constant increase predicted on the basis of a recent report [G. P. Johari, J. Chem. Phys. 138, 154503 (2013)], where the field induced reduction of the configurational entropy translates into slower dynamics by virtue of the Adam-Gibbs relation. Other models of field dependent glass transition temperatures are also discussed. Similar to observations related to the electro-optical Kerr effect, the rise time of the field induced effect is much longer than its collapse when the field is removed again. The orientational relaxation time of the plastic crystal cyclo-octanol is more sensitive to a bias field, showing a 13.5% increase at a field of 150 kV/cm, equivalent to an increase of Tg by 0.58 K.

Unveiling the molecular mechanism of self-healing in a telechelic, supramolecular polymer network

PubMed Central

Yan, Tingzi; Schröter, Klaus; Herbst, Florian; Binder, Wolfgang H.; Thurn-Albrecht, Thomas

2016-01-01

Reversible polymeric networks can show self-healing properties due to their ability to reassemble after application of stress and fracture, but typically the relation between equilibrium molecular dynamics and self-healing kinetics has been difficult to disentangle. Here we present a well-characterized, self-assembled bulk network based on supramolecular assemblies, that allows a clear distinction between chain dynamics and network relaxation. Small angle x-ray scattering and rheological measurements provide evidence for a structurally well-defined, dense network of interconnected aggregates giving mechanical strength to the material. Different from a covalent network, the dynamic character of the supramolecular bonds enables macroscopic flow on a longer time scale and the establishment of an equilibrium structure. A combination of linear and nonlinear rheological measurements clearly identifies the terminal relaxation process as being responsible for the process of self-healing. PMID:27581380

Structural steady states and relaxation oscillations in a two-phase fluid under shear flow: Experiments and phenomenological model

NASA Astrophysics Data System (ADS)

Courbin, L.; Benayad, A.; Panizza, P.

2006-01-01

By means of several rheophysics techniques, we report on an extensive study of the couplings between flow and microstructures in a two-phase fluid made of lamellar (Lα) and sponge (L3) phases. Depending on the nature of the imposed dynamical parameter (stress or shear rate) and on the experimental conditions (brine salinity or temperature), we observe several different structural steady states consisting of either multilamellar droplets (with or without a long range order) or elongated (L3) phase domains. Two different astonishing phenomena, shear-induced phase inversion and relaxation oscillations, are observed. We show that (i) phase inversion is related to a shear-induced topological change between monodisperse multilamellar droplets and elongated structures and (ii) droplet size relaxation oscillations result from a shear-induced change of the surface tension between both coexisting (Lα) and (L3) phases. To explain these relaxation oscillations, we present a phenomenological model and compare its numerical predictions to our experimental results.

Relaxation dynamics of C60

NASA Astrophysics Data System (ADS)

Walsh, Tiffany R.; Wales, David J.

1998-10-01

The relaxation dynamics of C60 from high-energy isomers to Buckminsterfullerene is examined using a master equation approach. An exhaustive catalog of the C60 fullerene isomers containing only five- and six-membered rings is combined with knowledge of the Stone-Wales rearrangements that connect all such isomers. Full geometry optimizations have been performed for all the minima and the transition states which connect them up to six Stone-Wales steps away from the global minimum. A density-functional tight-binding potential was employed to provide a quantum mechanical description of the bonding. The resulting picture of the potential energy landscape reveals a "weeping willow" structure which offers a clear explanation for the relatively long relaxation times observed experimentally. We also predict the most important transient local minima on the annealing pathway.

Structure and component dynamics in binary mixtures of poly(2-(dimethylamino)ethyl methacrylate) with water and tetrahydrofuran: A diffraction, calorimetric, and dielectric spectroscopy study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goracci, G., E-mail: sckgorag@ehu.es; Arbe, A.; Alegría, A.

2016-04-21

We have combined X-ray diffraction, neutron diffraction with polarization analysis, small angle neutron scattering, differential scanning calorimetry, and broad band dielectric spectroscopy to investigate the structure and dynamics of binary mixtures of poly (2-(dimethylamino)ethyl methacrylate) with either water or tetrahydrofuran (THF) at different concentrations. Aqueous mixtures are characterized by a highly heterogeneous structure where water clusters coexist with an underlying nano-segregation of main chains and side groups of the polymeric matrix. THF molecules are homogeneously distributed among the polymeric nano-domains for concentrations of one THF molecule/monomer or lower. A more heterogeneous situation is found for higher THF amounts, but withoutmore » evidences for solvent clusters. In THF-mixtures, we observe a remarkable reduction of the glass-transition temperature which is enhanced with increasing amount of solvent but seems to reach saturation at high THF concentrations. Adding THF markedly reduces the activation energy of the polymer β-relaxation. The presence of THF molecules seemingly hinders a slow component of this process which is active in the dry state. The aqueous mixtures present a strikingly broad glass-transition feature, revealing a highly heterogeneous behavior in agreement with the structural study. Regarding the solvent dynamics, deep in the glassy state all data can be described by an Arrhenius temperature dependence with a rather similar activation energy. However, the values of the characteristic times are about three orders of magnitude smaller for THF than for water. Water dynamics display a crossover toward increasingly higher apparent activation energies in the region of the onset of the glass transition, supporting its interpretation as a consequence of the freezing of the structural relaxation of the surrounding matrix. The absence of such a crossover (at least in the wide dynamic window here accessed) in THF is attributed to the lack of cooperativity effects in the relaxation of these molecules within the polymeric matrix.« less

Slow Debye-type peak observed in the dielectric response of polyalcohols

NASA Astrophysics Data System (ADS)

Bergman, Rikard; Jansson, Helén; Swenson, Jan

2010-01-01

Dielectric relaxation spectroscopy of glass forming liquids normally exhibits a relaxation scenario that seems to be surprisingly general. However, the relaxation dynamics is more complicated for hydrogen bonded liquids. For instance, the dielectric response of monoalcohols is dominated by a mysterious Debye-like process at lower frequencies than the structural α-relaxation that is normally dominating the spectra of glass formers. For polyalcohols this process has been thought to be absent or possibly obscured by a strong contribution from conductivity and polarization effects at low frequencies. We here show that the Debye-like process, although much less prominent, is also present in the response of polyalcohols. It can be observed in the derivative of the real part of the susceptibility or directly in the imaginary part if the conductivity contribution is reduced by covering the upper electrode with a thin Teflon layer. We report on results from broadband dielectric spectroscopy studies of several polyalcohols: glycerol, xylitol, and sorbitol. The findings are discussed in relation to other experimental observations of ultraslow (i.e., slower than the viscosity related α-relaxation) dynamics in glass formers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mamontov, Eugene; Zolnierczuk, Piotr A.; Ohl, Michael E.

Using neutron spin-echo and backscattering spectroscopy, we have found that at low temperatures water molecules in an aqueous solution engage in center-of-mass dynamics that are different from both the main structural relaxations and the well-known localized motions in the transient cages of the nearest neighbor molecules. While the latter localized motions are known to take place on the picosecond time scale and Angstrom length scale, the slower motions that we have observed are found on the nanosecond time scale and nanometer length scale. They are associated with the slow secondary relaxations, or excess wing dynamics, in glass-forming liquids. Our approach,more » therefore, can be applied to probe the characteristic length scale of the dynamic entities associated with slow dynamics in glass-forming liquids, which presently cannot be studied by other experimental techniques.« less

On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr

Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFGmore » tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.« less

Tight-binding molecular-dynamics study of point defects in GaAs

NASA Astrophysics Data System (ADS)

Seong, Hyangsuk; Lewis, Laurent J.

1995-08-01

Tight-binding molecular-dynamics simulations at 0 K have been performed in order to study the effect of defects (vacancies and antisites) in different states of charge on the electronic and structural properties of GaAs. Relaxations are fully included in the model, and for each defect we calculate the local atomic structure, the volume change upon relaxing, the formation energy (including chemical potential contributions), and the ionization levels. We find Ga vacancies to relax by an amount which is independent of the state of charge, consistent with positron lifetime measurements. Our calculations also predict Ga vacancies to exhibit a negative-U effect, and to assume a triply negative charge state for most values of the electron chemical potential. The relaxation of As vacancies, on the contrary, depends sensitively on the state of charge. The model confirms the two experimentally observed ionization levels for this defect, just below the conduction-band minimum. Likewise, Ga antisites exhibit large relaxations. In fact, in the neutral state, relaxation is so large that it leads to a ``broken-bond'' configuration, in excellent accord with the first-principles calculations of Zhang and Chadi [Phys. Rev. Lett. 64, 1789 (1990)]. This system also exhibits a negative-U effect, for values of the electron chemical potential near midgap. For As antisites, we find only a weak relaxation, independent of the charge. The model predicts the neutral state of the defect to be the ground state for values of the electron chemical potential near and above midgap, which supports the view that the EL2 defect is a neutral As antisite. Upon comparing the formation energies of the various defects we finally find that, for all values of the atomic chemical potentials, antisites are most likely to occur than vacancies.

Glass transition of polymers in bulk, confined geometries, and near interfaces

NASA Astrophysics Data System (ADS)

Napolitano, Simone; Glynos, Emmanouil; Tito, Nicholas B.

2017-03-01

When cooled or pressurized, polymer melts exhibit a tremendous reduction in molecular mobility. If the process is performed at a constant rate, the structural relaxation time of the liquid eventually exceeds the time allowed for equilibration. This brings the system out of equilibrium, and the liquid is operationally defined as a glass—a solid lacking long-range order. Despite almost 100 years of research on the (liquid/)glass transition, it is not yet clear which molecular mechanisms are responsible for the unique slow-down in molecular dynamics. In this review, we first introduce the reader to experimental methodologies, theories, and simulations of glassy polymer dynamics and vitrification. We then analyse the impact of connectivity, structure, and chain environment on molecular motion at the length scale of a few monomers, as well as how macromolecular architecture affects the glass transition of non-linear polymers. We then discuss a revised picture of nanoconfinement, going beyond a simple picture based on interfacial interactions and surface/volume ratio. Analysis of a large body of experimental evidence, results from molecular simulations, and predictions from theory supports, instead, a more complex framework where other parameters are relevant. We focus discussion specifically on local order, free volume, irreversible chain adsorption, the Debye-Waller factor of confined and confining media, chain rigidity, and the absolute value of the vitrification temperature. We end by highlighting the molecular origin of distributions in relaxation times and glass transition temperatures which exceed, by far, the size of a chain. Fast relaxation modes, almost universally present at the free surface between polymer and air, are also remarked upon. These modes relax at rates far larger than those characteristic of glassy dynamics in bulk. We speculate on how these may be a signature of unique relaxation processes occurring in confined or heterogeneous polymeric systems.

Probing equilibrium by nonequilibrium dynamics: Aging in Co/Cr superlattices

NASA Astrophysics Data System (ADS)

Binek, Christian

2013-03-01

Magnetic aging phenomena are investigated in a structurally ordered Co/Cr superlattice through measurements of magnetization relaxation, magnetic susceptibility, and hysteresis at various temperatures above and below the onset of collective magnetic order. We take advantage of the fact that controlled growth of magnetic multilayer thin films via molecular beam epitaxy allows tailoring the intra and inter-layer exchange interaction and thus enables tuning of magnetic properties including the spin-fluctuation spectra. Tailored nanoscale periodicity in Co/Cr multilayers creates mesoscopic spatial magnetic correlations with slow relaxation dynamics when quenching the system into a nonequilibrium state. Magnetization relaxation in weakly correlated spin systems depends on the microscopic spin-flip time of about 10 ns and is therefore a fast process. The spin correlations in our Co/Cr superlattice bring the magnetization dynamics to experimentally better accessible time scales of seconds or hours. In contrast to spin-glasses, where slow dynamics due to disorder and frustration is a well-known phenomenon, we tune and increase relaxation times in ordered structures. This is achieved by increasing spin-spin correlation between mesoscopically correlated regions rather than individual atomic spins, a concept with some similarity to block spin renormalization. Magnetization transients are measured after exposing the Co/Cr heterostructure to a magnetic set field for various waiting times. Scaling analysis reveals an asymptotic power-law behavior in accordance with a full aging scenario. The temperature dependence of the relaxation exponent shows pronounced anomalies at the equilibrium phase transitions of the antiferromagnetic superstructure and the ferromagnetic to paramagnetic transition of the Co layers. The latter leaves only weak fingerprints in the equilibrium magnetic behavior but gives rise to a prominent change in nonequilibrium properties. Our findings suggest that scaling analysis of nonequilibrium data can serve as a probe for weak equilibrium phase transitions. Financial support by NRI, and NSF through EPSCoR, and MRSEC 0820521 is greatly acknowledged.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Fluoropolymer Microstructure and Dynamics: Influence of Molecular Orientation Induced by Uniaxial Drawing

NASA Astrophysics Data System (ADS)

Miranda, Daniel; Yin, Chaoqing; Runt, James

Fluorinated semi-crystalline polymer films are attractive for dielectric film applications due to their chemical inertness, heat resistance, and high thermal stability. In the present investigation we explore the influence of orientation induced by uniaxial drawing on the crystalline microstructure and relaxation processes of poly(ethylene-tetrafluoroethylene) (ETFE), in order to ascertain how morphological control can benefit polymer dielectric design. When drawn below or near the Tg, the crystallinity of the drawn films is unchanged, and oriented amorphous structures and crystalline microfibrils form at high draw ratios. This orientation slows segmental relaxation, reflected by an increase in the dynamic Tg, and also delays the transition to the high temperature crystalline form of ETFE. When drawing above the Tg, the films undergo strain-induced crystallization at high draw ratios. For these films an increase in the dynamic Tg is also observed, in addition to a second segmental relaxation process, appearing as a shoulder on the primary process. We propose that this represents a contribution from a rigid amorphous fraction, having slowed chain dynamics. Supported by Office of Naval Research.

Characterization of dynamics in complex lyophilized formulations: I. Comparison of relaxation times measured by isothermal calorimetry with data estimated from the width of the glass transition temperature region.

PubMed

Chieng, Norman; Mizuno, Masayasu; Pikal, Michael

2013-10-01

The purposes of this study are to characterize the relaxation dynamics in complex freeze dried formulations and to investigate the quantitative relationship between the structural relaxation time as measured by thermal activity monitor (TAM) and that estimated from the width of the glass transition temperature (ΔT(g)). The latter method has advantages over TAM because it is simple and quick. As part of this objective, we evaluate the accuracy in estimating relaxation time data at higher temperatures (50 °C and 60 °C) from TAM data at lower temperature (40 °C) and glass transition region width (ΔT(g)) data obtained by differential scanning calorimetry. Formulations studied here were hydroxyethyl starch (HES)-disaccharide, HES-polyol, and HES-disaccharide-polyol at various ratios. We also re-examine, using TAM derived relaxation times, the correlation between protein stability (human growth hormone, hGH) and relaxation times explored in a previous report, which employed relaxation time data obtained from ΔT(g). Results show that most of the freeze dried formulations exist in single amorphous phase, and structural relaxation times were successfully measured for these systems. We find a reasonably good correlation between TAM measured relaxation times and corresponding data obtained from estimates based on ΔT(g), but the agreement is only qualitative. The comparison plot showed that TAM data are directly proportional to the 1/3 power of ΔT(g) data, after correcting for an offset. Nevertheless, the correlation between hGH stability and relaxation time remained qualitatively the same as found with using ΔT(g) derived relaxation data, and it was found that the modest extrapolation of TAM data to higher temperatures using ΔT(g) method and TAM data at 40 °C resulted in quantitative agreement with TAM measurements made at 50 °C and 60 °C, provided the TAM experiment temperature, is well below the Tg of the sample. Copyright © 2013 Elsevier B.V. All rights reserved.

Limits of metastability in amorphous ices: the neutron scattering Debye-Waller factor.

PubMed

Amann-Winkel, Katrin; Löw, Florian; Handle, Philip H; Knoll, Wiebke; Peters, Judith; Geil, Burkhard; Fujara, Franz; Loerting, Thomas

2012-12-21

Recently, it became clear that relaxation effects in amorphous ices play a very important role that has previously been overlooked. The thermodynamic history of amorphous samples strongly affects their transition behavior. In particular, well-relaxed samples show higher thermal stability, thereby providing a larger window to investigate their glass transitions. We here present neutron scattering experiments using fixed elastic window scans on relaxed forms of amorphous ice, namely expanded high density amorphous ice (eHDA), a variant of low density amorphous ice (LDA-II) and hyperquenched glassy water (HGW). These amorphous ices are expected to be true glassy counterparts of deeply supercooled liquid water, therefore fast precursor dynamics of structural relaxation are expected to appear below the calorimetric glass transition temperature. The Debye-Waller factor shows a very weak sub-T(g) anomaly in some of the samples, which might be the signature of such fast precursor dynamics. However, we cannot find this behavior consistently in all samples at all reciprocal length scales of momentum transfer.

Structural relaxation in a binary metallic melt: Molecular dynamics computer simulation of undercooled Al80Ni20

NASA Astrophysics Data System (ADS)

Das, Subir K.; Horbach, Jürgen; Voigtmann, Thomas

2008-08-01

Molecular dynamics computer simulations are performed to study structure and structural relaxation in the glassforming metallic alloy Al80Ni20 . The interactions between the particles are modeled by an effective potential of the embedded atom type. Our model of Al80Ni20 exhibits chemical short-range order (CSRO) that is reflected in a broad prepeak around a wave number of 1.8Å-1 in the partial static structure factor for the Ni-Ni correlations. The CSRO is due to the preference of Ni atoms to have Al rather than Ni atoms as nearest neighbors. By analyzing incoherent and coherent intermediate scattering functions as well as self-diffusion constants and shear viscosity, we discuss how the chemical ordering is reflected in the dynamics of the deeply undercooled melt. The q dependence of the α relaxation time as well as the Debye-Waller factor for the Al-Al correlations show oscillations at the location of the prepeak in the partial static structure factor for the Ni-Ni correlations. The latter feature of the Debye-Waller factor is well reproduced by a calculation in the framework of the mode coupling theory (MCT) of the glass transition, using the partial static structure factors from the simulation as input. We also check the validity of the Stokes-Einstein-Sutherland formula that relates the self-diffusion coefficients with the shear viscosity. We show that it breaks down already far above the mode coupling critical temperature Tc . The failure of the Stokes-Einstein-Sutherland relation is not related to the specific chemical ordering in Al80Ni20 .

Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions.

PubMed

Chen, Pan; Terenzi, Camilla; Furó, István; Berglund, Lars A; Wohlert, Jakob

2018-05-15

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13 C NMR longitudinal relaxation times ( T 1 ) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.

Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

NASA Astrophysics Data System (ADS)

Mitric, Roland

The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

Why many polymers are so fragile: A new perspective

DOE PAGES

Dalle-Ferrier, C.; Kisliuk, A.; Hong, L.; ...

2016-10-21

Many polymers exhibit much steeper temperature dependence of their structural relaxation time (higher fragility) than liquids of small molecules, and the mechanism of this unusually high fragility in polymers remains a puzzle. To reveal additional hints for understanding the underlying mechanism, we analyzed correlation of many properties of polymers to their fragility on example of model polymer polystyrene with various molecular weights (MWs). Here, we demonstrate that these correlations work for short chains (oligomers), but fail progressively with increase in MW. Our surprising discovery is that the steepness of the temperature dependence (fragility) of the viscosity that is determined bymore » chain relaxation follows the correlations at all molecular weights. These results suggest that the molecular level relaxation still follows the behavior usual for small molecules even in polymers, and its fragility (chain fragility) falls in the range usual for molecular liquids. It is the segmental relaxation that has this unusually high fragility. We also speculate that many polymers cannot reach an ergodic state on the time scale of segmental dynamics due to chain connectivity and rigidity. This leads to sharper decrease in accessible configurational entropy upon cooling and results in steeper temperature dependence of segmental relaxation. Our proposed scenario provides a new important insight into the specifics of polymer dynamics: the role of ergodicity time and length scale. At the end, we suggest that a similar scenario can be applicable also to other molecular systems with slow intra-molecular degrees of freedom and to chemically complex systems where the time scale of chemical fluctuations can be longer than the time scale of structural relaxation.« less

Why many polymers are so fragile: A new perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalle-Ferrier, C.; Kisliuk, A.; Hong, L.

Many polymers exhibit much steeper temperature dependence of their structural relaxation time (higher fragility) than liquids of small molecules, and the mechanism of this unusually high fragility in polymers remains a puzzle. To reveal additional hints for understanding the underlying mechanism, we analyzed correlation of many properties of polymers to their fragility on example of model polymer polystyrene with various molecular weights (MWs). Here, we demonstrate that these correlations work for short chains (oligomers), but fail progressively with increase in MW. Our surprising discovery is that the steepness of the temperature dependence (fragility) of the viscosity that is determined bymore » chain relaxation follows the correlations at all molecular weights. These results suggest that the molecular level relaxation still follows the behavior usual for small molecules even in polymers, and its fragility (chain fragility) falls in the range usual for molecular liquids. It is the segmental relaxation that has this unusually high fragility. We also speculate that many polymers cannot reach an ergodic state on the time scale of segmental dynamics due to chain connectivity and rigidity. This leads to sharper decrease in accessible configurational entropy upon cooling and results in steeper temperature dependence of segmental relaxation. Our proposed scenario provides a new important insight into the specifics of polymer dynamics: the role of ergodicity time and length scale. At the end, we suggest that a similar scenario can be applicable also to other molecular systems with slow intra-molecular degrees of freedom and to chemically complex systems where the time scale of chemical fluctuations can be longer than the time scale of structural relaxation.« less

Spatially and temporally resolved exciton dynamics and transport in single nanostructures and assemblies

NASA Astrophysics Data System (ADS)

Huang, Libai

2015-03-01

The frontier in solar energy conversion now lies in learning how to integrate functional entities across multiple length scales to create optimal devices. To address this new frontier, I will discuss our recent efforts on elucidating multi-scale energy transfer, migration, and dissipation processes with simultaneous femtosecond temporal resolution and nanometer spatial resolution. We have developed ultrafast microscopy that combines ultrafast spectroscopy with optical microscopy to map exciton dynamics and transport with simultaneous ultrafast time resolution and diffraction-limited spatial resolution. We have employed pump-probe transient absorption microscopy to elucidate morphology and structure dependent exciton dynamics and transport in single nanostructures and molecular assemblies. More specifically, (1) We have applied transient absorption microscopy (TAM) to probe environmental and structure dependent exciton relaxation pathways in sing-walled carbon nanotubes (SWNTs) by mapping dynamics in individual pristine SWNTs with known structures. (2) We have systematically measured and modeled the optical properties of the Frenkel excitons in self-assembled porphyrin tubular aggregates that represent an analog to natural photosynthetic antennae. Using a combination of ultrafast optical microscopy and stochastic exciton modeling, we address exciton transport and relaxation pathways, especially those related to disorder.

Glycerol in micellar confinement with tunable rigidity

NASA Astrophysics Data System (ADS)

Lannert, Michael; Müller, Allyn; Gouirand, Emmanuel; Talluto, Vincenzo; Rosenstihl, Markus; Walther, Thomas; Stühn, Bernd; Blochowicz, Thomas; Vogel, Michael

2016-12-01

We investigate the glassy dynamics of glycerol in the confinement of a microemulsion system, which is stable on cooling down to the glass transition of its components. By changing the composition, we vary the viscosity of the matrix, while keeping the confining geometry intact, as is demonstrated by small angle X-ray scattering. By means of 2H NMR, differential scanning calorimetry, and triplet solvation dynamics we, thus, probe the dynamics of glycerol in confinements of varying rigidity. 2H NMR results show that, at higher temperatures, the dynamics of confined glycerol is unchanged compared to bulk behavior, while the reorientation of glycerol molecules becomes significantly faster than in the bulk in the deeply supercooled regime. However, comparison of different 2H NMR findings with data from calorimetry and solvation dynamics reveals that this acceleration is not due to the changed structural relaxation of glycerol, but rather due to the rotational motion of essentially rigid glycerol droplets or of aggregates of such droplets in a more fluid matrix. Thus, independent of the matrix mobility, the glycerol dynamics remains unchanged except for the smallest droplets, where an increase of Tg and, thus, a slowdown of the structural relaxation is observed even in a fluid matrix.

Electronic and Structural Elements That Regulate the Excited-State Dynamics in Purine Nucleobase Derivatives

PubMed Central

2015-01-01

The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited 1nπ* state. Following vibrational and conformational relaxation, the 1nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the 1nπ* state while simultaneously facilitating access to the 1ππ*(La)/S0 conical intersection, such that population of the 1nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position. PMID:25763596

Resonantly enhanced spin-lattice relaxation of Mn2 + ions in diluted magnetic (Zn,Mn)Se/(Zn,Be)Se quantum wells

NASA Astrophysics Data System (ADS)

Debus, J.; Ivanov, V. Yu.; Ryabchenko, S. M.; Yakovlev, D. R.; Maksimov, A. A.; Semenov, Yu. G.; Braukmann, D.; Rautert, J.; Löw, U.; Godlewski, M.; Waag, A.; Bayer, M.

2016-05-01

The dynamics of spin-lattice relaxation in the magnetic Mn2 + ion system of (Zn,Mn)Se/(Zn,Be)Se quantum-well structures are studied using optical methods. Pronounced cusps are found in the giant Zeeman shift of the quantum-well exciton photoluminescence at specific magnetic fields below 10 T, when the Mn spin system is heated by photogenerated carriers. The spin-lattice relaxation time of the Mn ions is resonantly accelerated at the cusp magnetic fields. Our theoretical analysis demonstrates that a cusp occurs at a spin-level mixing of single Mn2 + ions and a quick-relaxing cluster of nearest-neighbor Mn ions, which can be described as intrinsic cross-relaxation resonance within the Mn spin system.

Rotational Dynamics of Solutes with Multiple Single Bond Axes Studied by Infrared Pump-Probe Spectroscopy.

PubMed

Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

2018-02-01

To investigate the relationship between the structural degrees of freedom around a vibrational probe and the rotational relaxation process of a solute in solution, we studied the anisotropy decays of three different N 3 -derivatized amino acids in primary alcohol solutions. By performing polarization-controlled IR pump-probe measurements, we reveal that the anisotropy decays of the vibrational probe molecules in 1-alcohol solutions possess two decay components, at subpicosecond and picosecond time scales. On the basis of results showing that the fast relaxation component is insensitive to the vibrational probe molecule, we suggest that the anisotropy decay of the N 3 group on a subpicosecond time scale results from a local, small-amplitude fluctuation of the flexible vibrational probe, which does not depend on the details of its molecular structure. However, the slow relaxation component depends on the solute: with longer alkyl chains attached to the N 3 group, the anisotropy decay of the slow component is faster. Consequently, we conclude that the slow relaxation component corresponds to the reorientational motion of the N 3 group correlated with other intramolecular rotational motions (e.g., rotational motions of the neighboring alkyl chain). Our experimental results provide important insight into understanding the rotational dynamics of solutes with multiple single bond axes in solution.

High pressure study of molecular dynamics of protic ionic liquid lidocaine hydrochloride.

PubMed

Swiety-Pospiech, A; Wojnarowska, Z; Pionteck, J; Pawlus, S; Grzybowski, A; Hensel-Bielowka, S; Grzybowska, K; Szulc, A; Paluch, M

2012-06-14

In this paper, we investigate the effect of pressure on the molecular dynamics of protic ionic liquid lidocaine hydrochloride, a commonly used pharmaceutical, by means of dielectric spectroscopy and pressure-temperature-volume methods. We observed that near T(g) the pressure dependence of conductivity relaxation times reveals a peculiar behavior, which can be treated as a manifestation of decoupling between ion migration and structural relaxation times. Moreover, we discuss the validity of thermodynamic scaling in lidocaine HCl. We also employed the temperature-volume Avramov model to determine the value of pressure coefficient of glass transition temperature, dT(g)/dP|(P = 0.1). Finally, we investigate the role of thermal and density fluctuations in controlling of molecular dynamics of the examined compound.

Stokes-Einstein relation of the liquid metal rubidium and its relationship to changes in the microscopic dynamics with increasing temperature

NASA Astrophysics Data System (ADS)

Demmel, F.; Tani, A.

2018-06-01

For liquid rubidium the Stokes-Einstein (SE) relation is well fulfilled near the melting point with an effective hydrodynamic diameter, which agrees well with a value from structural investigations. A wealth of thermodynamic and microscopic data exists for a wide range of temperatures for liquid rubidium and hence it represents a good test bed to challenge the SE relation with rising temperature from an experimental point of view. We performed classical molecular dynamics simulations to complement the existing experimental data using a pseudopotential, which describes perfectly the structure and dynamics of liquid rubidium. The derived SE relation from combining experimental shear viscosity data with simulated diffusion coefficients reveals a weak violation at about 1.3 Tmelting≈400 K. The microscopic relaxation dynamics on nearest neighbor distances from neutron spectroscopy demonstrate distinct changes in the amplitude with rising temperature. The derived average relaxation time for density fluctuations on this length scale shows a non-Arrhenius behavior, with a slope change around 1.5 Tmelting≈450 K. Combining the simulated macroscopic self-diffusion coefficient with that microscopic average relaxation time, a distinct violation of the SE relation in the same temperature range can be demonstrated. One can conclude that the changes in the collective dynamics, a mirror of the correlated movements of the particles, are at the origin for the violation of the SE relation. The changes in the dynamics can be understood as a transition from a more viscous liquid metal to a more fluid-like liquid above the crossover temperature range of 1.3-1.5 Tmelting. The decay of the amplitude of density fluctuations in liquid aluminium, lead, and rubidium demonstrates a remarkable agreement and points to a universal thermal crossover in the dynamics of liquid metals.

Elastically driven intermittent microscopic dynamics in soft solids

NASA Astrophysics Data System (ADS)

Bouzid, Mehdi; Colombo, Jader; Barbosa, Lucas Vieira; Del Gado, Emanuela

2017-06-01

Soft solids with tunable mechanical response are at the core of new material technologies, but a crucial limit for applications is their progressive aging over time, which dramatically affects their functionalities. The generally accepted paradigm is that such aging is gradual and its origin is in slower than exponential microscopic dynamics, akin to the ones in supercooled liquids or glasses. Nevertheless, time- and space-resolved measurements have provided contrasting evidence: dynamics faster than exponential, intermittency and abrupt structural changes. Here we use 3D computer simulations of a microscopic model to reveal that the timescales governing stress relaxation, respectively, through thermal fluctuations and elastic recovery are key for the aging dynamics. When thermal fluctuations are too weak, stress heterogeneities frozen-in upon solidification can still partially relax through elastically driven fluctuations. Such fluctuations are intermittent, because of strong correlations that persist over the timescale of experiments or simulations, leading to faster than exponential dynamics.

Molecular dynamics simulation of the polymer electrolyte poly(ethylene oxide)/LiClO(4). II. Dynamical properties.

PubMed

Siqueira, Leonardo J A; Ribeiro, Mauro C C

2006-12-07

The dynamical properties of the polymer electrolyte poly(ethylene oxide) (PEO)LiClO(4) have been investigated by molecular dynamics simulations. The effect of changing salt concentration and temperature was evaluated on several time correlation functions. Ionic displacements projected on different directions reveal anisotropy in short-time (rattling) and long-time (diffusive) dynamics of Li(+) cations. It is shown that ionic mobility is coupled to the segmental motion of the polymeric chain. Structural relaxation is probed by the intermediate scattering function F(k,t) at several wave vectors. Good agreement was found between calculated and experimental F(k,t) for pure PEO. A remarkable slowing down of polymer relaxation is observed upon addition of the salt. The ionic conductivity estimated by the Nernst-Einstein equation is approximately ten times higher than the actual conductivity calculated by the time correlation function of charge current.

Ultraslow dielectric relaxation process in supercooled polyhydric alcohols

NASA Astrophysics Data System (ADS)

Yomogida, Yoshiki; Minoguchi, Ayumi; Nozaki, Ryusuke

2006-04-01

Complex permittivity was obtained on glycerol, xylitol, sorbitol and sorbitol-xylitol mixtures in the supercooled liquid state in the frequency range between 10μHz and 500MHz at temperatures near and above the glass transition temperature. For all the materials, a dielectric relaxation process was observed in addition to the well-known structural α and Johari-Goldstein β relaxation process [G. P. Johari and M. Goldstein, J. Chem. Phys. 53, 2372 (1970)]. The relaxation time for the new process is always larger than that for the α process. The relaxation time shows non-Arrhenius temperature dependence with correlation to the behavior of the α process and it depends on the molecular size systematically. The dielectric relaxation strength for the new process shows the effect of thermal history and decreases exponentially with time at a constant temperature. It can be considered that a nonequilibrium dynamics causes the new process.

Flux-split algorithms for flows with non-equilibrium chemistry and vibrational relaxation

NASA Technical Reports Server (NTRS)

Grossman, B.; Cinnella, P.

1990-01-01

The present consideration of numerical computation methods for gas flows with nonequilibrium chemistry thermodynamics gives attention to an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Flux-splitting procedures are developed for the fully-coupled inviscid equations encompassing fluid dynamics and both chemical and internal energy-relaxation processes. A fully coupled and implicit large-block structure is presented which embodies novel forms of flux-vector split and flux-difference split algorithms valid for nonequilibrium flow; illustrative high-temperature shock tube and nozzle flow examples are given.

Granular materials flow like complex fluids

NASA Astrophysics Data System (ADS)

Kou, Binquan; Cao, Yixin; Li, Jindong; Xia, Chengjie; Li, Zhifeng; Dong, Haipeng; Zhang, Ang; Zhang, Jie; Kob, Walter; Wang, Yujie

2017-11-01

Granular materials such as sand, powders and foams are ubiquitous in daily life and in industrial and geotechnical applications. These disordered systems form stable structures when unperturbed, but in the presence of external influences such as tapping or shear they `relax', becoming fluid in nature. It is often assumed that the relaxation dynamics of granular systems is similar to that of thermal glass-forming systems. However, so far it has not been possible to determine experimentally the dynamic properties of three-dimensional granular systems at the particle level. This lack of experimental data, combined with the fact that the motion of granular particles involves friction (whereas the motion of particles in thermal glass-forming systems does not), means that an accurate description of the relaxation dynamics of granular materials is lacking. Here we use X-ray tomography to determine the microscale relaxation dynamics of hard granular ellipsoids subject to an oscillatory shear. We find that the distribution of the displacements of the ellipsoids is well described by a Gumbel law (which is similar to a Gaussian distribution for small displacements but has a heavier tail for larger displacements), with a shape parameter that is independent of the amplitude of the shear strain and of the time. Despite this universality, the mean squared displacement of an individual ellipsoid follows a power law as a function of time, with an exponent that does depend on the strain amplitude and time. We argue that these results are related to microscale relaxation mechanisms that involve friction and memory effects (whereby the motion of an ellipsoid at a given point in time depends on its previous motion). Our observations demonstrate that, at the particle level, the dynamic behaviour of granular systems is qualitatively different from that of thermal glass-forming systems, and is instead more similar to that of complex fluids. We conclude that granular materials can relax even when the driving strain is weak.

Dynamical properties in supercooling liquid of trehalose aqueous solution studied by Brillouin scattering

NASA Astrophysics Data System (ADS)

Shibata, Tomohiko; Tominaga, Ayane; Takayama, Haruki; Kojima, Seiji

2013-02-01

Brillouin scattering spectroscopy has been applied to study the dynamical properties of glass transition of trehalose aqueous solutions in a high-frequency gigahertz range and in the temperature range (-190°C ≤ T ≤ 100°C). The temperature variations of sound velocity and attenuation were accurately determined using the refractive index measured by a prism-coupling method. The temperature dependence of relaxation time of the structural relaxation process was determined by the Debye model. Its temperature dependence shows Arrhenius behavior in a liquid state. The parameters of Arrhenius law were also determined as a function of trehalose concentration.

Preparation and Relaxation of Very Stable Glassy States of a Simulated Liquid

NASA Astrophysics Data System (ADS)

Jack, Robert L.; Hedges, Lester O.; Garrahan, Juan P.; Chandler, David

2011-12-01

We prepare metastable glassy states in a model glass former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose “fast” vibrational degrees of freedom are maintained at thermal equilibrium by contact with a heat bath, while the “slow” structural degrees of freedom are located in deep valleys of the energy landscape. We examine the relaxation to equilibrium and the vibrational properties of these metastable states. The glassy states we prepare by our trajectory sampling method are very stable to thermal fluctuations and also more mechanically rigid than low-temperature equilibrated configurations.

Structural relaxation in supercooled orthoterphenyl.

PubMed

Chong, S-H; Sciortino, F

2004-05-01

We report molecular-dynamics simulation results performed for a model of molecular liquid orthoterphenyl in supercooled states, which we then compare with both experimental data and mode-coupling-theory (MCT) predictions, aiming at a better understanding of structural relaxation in orthoterphenyl. We pay special attention to the wave number dependence of the collective dynamics. It is shown that the simulation results for the model share many features with experimental data for real system, and that MCT captures the simulation results at the semiquantitative level except for intermediate wave numbers connected to the overall size of the molecule. Theoretical results at the intermediate wave number region are found to be improved by taking into account the spatial correlation of the molecule's geometrical center. This supports the idea that unusual dynamical properties at the intermediate wave numbers, reported previously in simulation studies for the model and discernible in coherent neutron-scattering experimental data, are basically due to the coupling of the rotational motion to the geometrical-center dynamics. However, there still remain qualitative as well as quantitative discrepancies between theoretical prediction and corresponding simulation results at the intermediate wave numbers, which call for further theoretical investigation.

Effect of pressure on decoupling of ionic conductivity from structural relaxation in hydrated protic ionic liquid, lidocaine HCl.

PubMed

Swiety-Pospiech, A; Wojnarowska, Z; Hensel-Bielowka, S; Pionteck, J; Paluch, M

2013-05-28

Broadband dielectric spectroscopy and pressure-temperature-volume methods are employed to investigate the effect of hydrostatic pressure on the conductivity relaxation time (τσ), both in the supercooled and glassy states of protic ionic liquid lidocaine hydrochloride monohydrate. Due to the decoupling between the ion conductivity and structural dynamics, the characteristic change in behavior of τσ(T) dependence, i.e., from Vogel-Fulcher-Tammann-like to Arrhenius-like behavior, is observed. This crossover is a manifestation of the liquid-glass transition of lidocaine HCl. The similar pattern of behavior was also found for pressure dependent isothermal measurements. However, in this case the transition from one simple volume activated law to another was noticed. Additionally, by analyzing the changes of conductivity relaxation times during isothermal densification of the sample, it was found that compression enhances the decoupling of electrical conductivity from the structural relaxation. Herein, we propose a new parameter, dlogRτ∕dP, to quantify the pressure sensitivity of the decoupling phenomenon. Finally, the temperature and volume dependence of τσ is discussed in terms of thermodynamic scaling concept.

Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics.

PubMed

Stirnemann, Guillaume; Laage, Damien

2012-07-21

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.

Comparison of Structural Relaxation Behavior in As-Cast and Pre-Annealed Zr-Based Bulk Metallic Glasses Just below Glass Transition

DOE PAGES

Haruyama, Osami; Yoshikawa, Kazuyoshi; Yamazaki, Yoshikatsu; ...

2015-04-25

In this paper, the α-relaxation of pre-annealed Zr 55Cu 30Ni 5Al 10 bulk metallic glasses (BMGs) was compared with that of as-cast Zr-based BMGs including Zr 55Cu 30Ni 5Al 10. The α-relaxation was investigated by volume relaxation. The relaxation behavior was well described by a stretched exponential relaxation function, Φ (t) ≈ exp [ - (t/τ α ) β α ], with the isothermal relaxation time, τ α, and the Kohlrausch exponent, β α. The β α exhibited the strong temperature dependence for the pre-annealed BMG, while the weak temperature dependence was visualized for the as-cast BMG similar to themore » dynamic relaxation. The τ α’s were modified by Moynihan and Narayanaswamy-Tool-Moynihan methods that reduce the difference in the thermal history of sample. Finally, as a result, the relaxation kinetics in the glass resembled that of a liquid deduced from the behavior of viscosity in the supercooled liquid.« less

Characterization of local motions in proteins detected by nuclear magnetic resonance relaxation studies

NASA Astrophysics Data System (ADS)

Fischer, Mark William Frederick

1998-08-01

The study of protein structure and function is incomplete without an understanding of protein dynamics. We use nuclear magnetic resonance (NMR) relaxation studies to probe pico and nano second dynamics in E. coli flavodoxin, measuring both 15N and 13C/sp/prime relaxation. Observing poor correlation between the generalized order parameters, S2, for the N-NH and C'-Cα vectors in this nearly spherical molecule, we conclude that local or semi-local anisotropic motions are present. A new experiment is introduced from which the cross correlation, Rcc, between the carbonyl chemical shift anisotropy relaxation and the C'- Cα dipole-dipole relaxation is obtained. Theoretical modeling of the behavior of S2 N- NH,/ S2C/sp/prime-C/sb[α], and Rcc under specific anisotropic motions allows the construction of motional restriction maps. Analyzing our experimental data in terms of these motional maps allows for the identification of local motions which might otherwise have gone undetected and, more importantly, allows for the nature of the motions to be characterized. This is demonstrated for several helices of flavodoxin which appear to be executing concerted limited rotations about their helical axes.

Effects of cross correlation on the relaxation time of a bistable system driven by cross-correlated noise

NASA Astrophysics Data System (ADS)

Mei, Dongcheng; Xie, Chongwei; Zhang, Li

2003-11-01

We study the effects of correlations between additive and multiplicative noise on relaxation time in a bistable system driven by cross-correlated noise. Using the projection-operator method, we derived an analytic expression for the relaxation time Tc of the system, which is the function of additive (α) and multiplicative (D) noise intensities, correlation intensity λ of noise, and correlation time τ of noise. After introducing a noise intensity ratio and a dimensionless parameter R=D/α, and then performing numerical computations, we find the following: (i) For the case of R<1, the relaxation time Tc increases as R increases. (ii) For the cases of R⩾1, there is a one-peak structure on the Tc-R plot and the effects of cross-correlated noise on the relaxation time are very notable. (iii) For the case of R<1, Tc almost does not change with both λ and τ, and for the cases of R⩾1, Tc decreases as λ increases, however Tc increases as τ increases. λ and τ play opposite roles in Tc, i.e., λ enhances the fluctuation decay of dynamical variable and τ slows down the fluctuation decay of dynamical variable.

Dynamics of a bilayer membrane coupled to a two-dimensional cytoskeleton: Scale transfers of membrane deformations

NASA Astrophysics Data System (ADS)

Okamoto, Ryuichi; Komura, Shigeyuki; Fournier, Jean-Baptiste

2017-07-01

We theoretically investigate the dynamics of a floating lipid bilayer membrane coupled with a two-dimensional cytoskeleton network, taking into account explicitly the intermonolayer friction, the discrete lattice structure of the cytoskeleton, and its prestress. The lattice structure breaks lateral continuous translational symmetry and couples Fourier modes with different wave vectors. It is shown that within a short time interval a long-wavelength deformation excites a collection of modes with wavelengths shorter than the lattice spacing. These modes relax slowly with a common renormalized rate originating from the long-wavelength mode. As a result, and because of the prestress, the slowest relaxation is governed by the intermonolayer friction. Conversely, and most interestingly, forces applied at the scale of the cytoskeleton for a sufficiently long time can cooperatively excite large-scale modes.

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses

PubMed Central

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-01-01

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation. PMID:28223697

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

PubMed

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hao; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4; Zhong, Cheng

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 Cumore » 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.« less

Mechanism of vibrational energy dissipation of free OH groups at the air-water interface.

PubMed

Hsieh, Cho-Shuen; Campen, R Kramer; Okuno, Masanari; Backus, Ellen H G; Nagata, Yuki; Bonn, Mischa

2013-11-19

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air-water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air-H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces.

Excitations and relaxation dynamics in multiferroic GeV4S8 studied by terahertz and dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Reschke, S.; Wang, Zhe; Mayr, F.; Ruff, E.; Lunkenheimer, P.; Tsurkan, V.; Loidl, A.

2017-10-01

We report on THz time-domain spectroscopy on multiferroic GeV4S8 , which undergoes orbital ordering at a Jahn-Teller transition at 30.5 K and exhibits antiferromagnetic order below 14.6 K. The THz experiments are complemented by dielectric experiments at audio and radio frequencies. We identify a low-lying excitation close to 0.5 THz, which is only weakly temperature dependent and probably corresponds to a molecular excitation within the electronic level scheme of the V4 clusters. In addition, we detect complex temperature-dependent behavior of a low-lying phononic excitation, closely linked to the onset of orbitally driven ferroelectricity. In the high-temperature cubic phase, which is paramagnetic and orbitally disordered, this excitation is of relaxational character becomes an overdamped Lorentzian mode in the orbitally ordered phase below the Jahn-Teller transition, and finally appears as well-defined phonon excitation in the antiferromagnetic state. Abrupt changes in the real and imaginary parts of the complex dielectric permittivity show that orbital ordering appears via a structural phase transition with strong first-order character and that the onset of antiferromagnetic order is accompanied by significant structural changes, which are of first-order character, too. Dielectric spectroscopy documents that at low frequencies, significant dipolar relaxations are present in the orbitally ordered, paramagnetic phase only. In contrast to the closely related GaV4S8 , this relaxation dynamics that most likely mirrors coupled orbital and polar fluctuations does not seem to be related to the dynamic processes detected in the THz regime.

Mechanism of vibrational energy dissipation of free OH groups at the air–water interface

PubMed Central

Hsieh, Cho-Shuen; Campen, R. Kramer; Okuno, Masanari; Backus, Ellen H. G.; Nagata, Yuki; Bonn, Mischa

2013-01-01

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air–water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air–H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces. PMID:24191016

Brillouin-scattering study of liquid-glass transitions in ternary mixtures of water, trehalose, and an ionic liquid

NASA Astrophysics Data System (ADS)

Takayama, Haruki; Shibata, Tomohiko; Ishii, Takahiro; Kojima, Seiji

2013-04-01

Ternary mixtures of water, sugar, and ionic liquid have been studied as new candidates for bioprotectants. To clarify the elastic properties and relaxation dynamics of the supercooled liquid and glassy states at low temperatures, the liquid-glass transitions were investigated by using a micro-Brillouin-scattering technique. The refractive index was measured accurately as a function of content and temperature to determine the sound velocity and the attenuation from Brillouin frequency shift and peak width. The relaxation times of structural relaxations related to liquidglass transitions were determined as functions of temperature. The Meyer-Neldel rule was found to hold for the activation energy and the prefactor of the Arrhenius law for the relaxation time.

A logic-based method for integer programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hooker, J.; Natraj, N.R.

1994-12-31

We propose a logic-based approach to integer programming that replaces traditional branch-and-cut techniques with logical analogs. Integer variables are regarded as atomic propositions. The constraints give rise to logical formulas that are analogous to separating cuts. No continuous relaxation is used. Rather, the cuts are selected so that they can be easily solved as a discrete relaxation. (In fact, defining a relaxation and generating cuts are best seen as the same problem.) We experiment with relaxations that have a k-tree structure and can be solved by nonserial dynamic programming. We also present logic-based analogs of facet-defining cuts, Chv{acute a}tal rank,more » etc. We conclude with some preliminary computational results.« less

Adiabatic Coupling Constant of Nitrobenzene- n-Alkane Critical Mixtures. Evidence from Ultrasonic Spectra and Thermodynamic Data

NASA Astrophysics Data System (ADS)

Mirzaev, Sirojiddin Z.; Kaatze, Udo

2016-09-01

Ultrasonic spectra of mixtures of nitrobenzene with n-alkanes, from n-hexane to n-nonane, are analyzed. They feature up to two Debye-type relaxation terms with discrete relaxation times and, near the critical point, an additional relaxation term due to the fluctuations in the local concentration. The latter can be well represented by the dynamic scaling theory. Its amplitude parameter reveals the adiabatic coupling constant of the mixtures of critical composition. The dependence of this thermodynamic parameter upon the length of the n-alkanes corresponds to that of the slope in the pressure dependence of the critical temperature and is thus taken another confirmation of the dynamic scaling model. The change in the variation of the coupling constant and of several other mixture parameters with alkane length probably reflects a structural change in the nitrobenzene- n-alkane mixtures when the number of carbon atoms per alkane exceeds eight.

Flow acceleration structure of Aurelia aurita: implications on propulsion

NASA Astrophysics Data System (ADS)

Kim, Jin-Tae; Piper, Matthew; Chamorro, Leonardo P.

2017-11-01

The jetting and paddling mechanisms used by Aurelia aurita jellyfish allows for one of the most efficient propulsion among other metazoans. Characterization of the induced flow acceleration is critical to uncover distinctive patterns. We found four acceleration structures using 3D measurements of body and flow dynamics in Lagrangian frame of reference. Two intense structures occur near the bell margin and are generated by paddling; the other two around the center of the jellyfish and half magnitude are a result of jetting. Their interaction leads to the maximum flow velocity in the middle of the relaxation, where relatively straight flow trajectories occur. The jellyfish achieves an efficient relaxation by generating flow deceleration with minor body deceleration.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

NASA Astrophysics Data System (ADS)

Peccati, Francesca; Mai, Sebastian; González, Leticia

2017-03-01

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

PubMed Central

2017-01-01

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C–Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320905

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

1H NMR relaxometry and quadrupole relaxation enhancement as a sensitive probe of dynamical properties of solids—[C(NH2)3]3Bi2I9 as an example

NASA Astrophysics Data System (ADS)

Florek-Wojciechowska, M.; Wojciechowski, M.; Jakubas, R.; Brym, Sz.; Kruk, D.

2016-02-01

1H nuclear magnetic resonance relaxometry has been applied to reveal information on dynamics and structure of Gu3Bi2I9 ([Gu = C(NH2)3] denotes guanidinium cation). The data have been analyzed in terms of a theory of quadrupole relaxation enhancement, which has been extended here by including effects associated with quadrupole (14N) spin relaxation caused by a fast fluctuating component of the electric field gradient tensor. Two motional processes have been identified: a slow one occurring on a timescale of about 8 × 10-6 s which has turned out to be (almost) temperature independent, and a fast process in the range of 10-9 s. From the 1H-14N relaxation contribution (that shows "quadrupole peaks") the quadrupole parameters, which are a fingerprint of the arrangement of the anionic network, have been determined. It has been demonstrated that the magnitude of the quadrupole coupling considerably changes with temperature and the changes are not caused by phase transitions. At the same time, it has been shown that there is no evidence of abrupt changes in the cationic dynamics and the anionic substructure upon the phase transitions.

Desolvation-Driven 100-Fold Slow-down of Tunneling Relaxation Rate in Co(II)-Dy(III) Single-Molecule Magnets through a Single-Crystal-to-Single-Crystal Process

NASA Astrophysics Data System (ADS)

Liu, Jun-Liang; Wu, Jie-Yi; Huang, Guo-Zhang; Chen, Yan-Cong; Jia, Jian-Hua; Ungur, Liviu; Chibotaru, Liviu F.; Chen, Xiao-Ming; Tong, Ming-Liang

2015-11-01

Single-molecule magnets (SMMs) are regarded as a class of promising materials for spintronic and ultrahigh-density storage devices. Tuning the magnetic dynamics of single-molecule magnets is a crucial challenge for chemists. Lanthanide ions are not only highly magnetically anisotropic but also highly sensitive to the changes in the coordination environments. We developed a feasible approach to understand parts of the magneto-structure correlations and propose to regulate the relaxation behaviors via rational design. A series of Co(II)-Dy(III)-Co(II) complexes were obtained using in situ synthesis; in this system of complexes, the relaxation dynamics can be greatly improved, accompanied with desolvation, via single-crystal to single-crystal transformation. The effective energy barrier can be increased from 293 cm-1 (422 K) to 416 cm-1 (600 K), and the tunneling relaxation time can be grown from 8.5 × 10-4 s to 7.4 × 10-2 s. These remarkable improvements are due to the change in the coordination environments of Dy(III) and Co(II). Ab initio calculations were performed to better understand the magnetic dynamics.

Diffusive dynamics during the high-to-low density transition in amorphous ice

DOE PAGES

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix; ...

2017-06-26

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

NASA Astrophysics Data System (ADS)

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkühler, Felix; Sprung, Michael; Mariedahl, Daniel; Sellberg, Jonas A.; Pathak, Harshad; Späh, Alexander; Cavalca, Filippo; Schlesinger, Daniel; Ricci, Alessandro; Jain, Avni; Massani, Bernhard; Aubree, Flora; Benmore, Chris J.; Loerting, Thomas; Grübel, Gerhard; Pettersson, Lars G. M.; Nilsson, Anders

2017-08-01

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

Relaxation processes of the liquid crystal ME6N in the isotropic phase studied by Raman scattering experiments

NASA Astrophysics Data System (ADS)

Giorgini, Maria Grazia; Arcioni, Alberto; Polizzi, Ciro; Musso, Maurizio; Ottaviani, Paolo

2004-03-01

We have investigated the Raman profiles of the ν(C≡N) and ν(C=O) vibrational modes of the nematic liquid crystal ME6N (4-cyanophenyl-4'-hexylbenzoate) in the isotropic phase at different temperatures and used them as probes of the dynamics and structural organization of this liquid. The vibrational time correlation functions of the ν(C≡N) mode, rather adequately interpreted within the assumption of exponential modulation function (the Kubo-Rothschild theory), indicate that the system experiences an intermediate dynamical regime that gets only slightly faster with increasing temperature. However, this theory fails in predicting the non-exponential behavior that the time correlation functions manifest in the long time range (t>3 ps). For this reason we have additionally approached the interpretation of vibrational correlation functions in terms of the theory formulated by Rothschild and co-workers for locally structured liquids. The application of this theory reveals that the molecular dynamics in this liquid crystal in the isotropic phase is that deriving from a distribution of differently sized clusters, which narrows as the temperature increases. Even at the highest temperature reached in this study (87 °C above the nematic-isotropic transition), the liquid has not yet achieved the structure of the simple liquid and the dynamics has not reached the limit of the single channel process. The vibrational and orientational relaxations occur in very different time scales. The temperature independence of the orientational dynamics in the whole range from 55 °C to 135 °C has been referred to the nonhydrodynamic behavior of the system, arising when local pseudonematic structures persist for times longer than the orientational relaxation. The occurrence of the process of resonant vibrational energy transfer between the C=O groups of adjacent molecules has been revealed in the isotropic phase by a slightly positive Raman noncoincidence effect in the band associated with the ν(C=O) mode. A qualitative interpretation is tentatively given in terms of partial cancellation of contributions deriving from structures having opposite orientations of their C=O groups.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

Dynamics of Photoexcited State of Semiconductor Quantum Dots

NASA Astrophysics Data System (ADS)

Trivedi, Dhara J.

In this thesis, non-adiabatic molecular dynamics (NAMD) of excited states in semiconductor quantum dots are investigated. Nanoscale systems provide important opportunities for theory and computation for research because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial in understanding what is being measured. The simulation of NAMD is an indispensable tool for understanding complex ultrafast photoinduced processes such as charge and energy transfer, thermal relaxation, and charge recombination. Based on the state-of-the-art ab initio approaches in both the energy and time domains, the thesis presents a comprehensive discussion of the dynamical processes in quantum dots, ranging from the initial photon absorption to the final emission. We investigate the energy relaxation and transfer rates in pure and surface passivated quantum dots of different sizes. The study establishes the fundamental mechanisms of the electron and hole relaxation processes with and without hole traps. We develop and implement more accurate and efficient methods for NAMD. These methods are advantageous over the traditional ones when one encounters classically forbidden transitions. We also explore the effect of decoherence and non-adiabatic couplings on the dynamics. The results indicate significant influence on the accuracy and related computational cost of the simulated dynamics.

Ultrafast carrier dynamics of titanic acid nanotubes investigated by transient absorption spectroscopy.

PubMed

Wang, Li; Zhao, Hui; Pan, Lin Yun; Weng, Yu Xiang; Nakato, Yoshihiro; Tamai, Naoto

2010-12-01

Carrier dynamics of titanic acid nanotubes (phase of H2Ti2O5.H2O) deposited on a quartz plate was examined by visible/near-IR transient absorption spectroscopy with an ultraviolet excitation. The carrier dynamics of titanic acid nanotubes follows the fast trapping process which attributed to the intrinsic tubular structure, the relaxation of shallow trapped carriers and the recombination as a second-order kinetic process. Transient absorption of titanic acid nanotubes was dominated by the absorption of surface-trapped holes in visible region around 500 nm, which was proved by the faster decay dynamics in the presence of polyvinyl alcohol as a hole-scavenger. However, the slow relaxation of free carriers was much more pronounced in the TiO2 single crystals, as compared with the transient absorption spectra of titanic acid nanotubes under the similar excitation.

Structural inhomogeneity of interfacial water at lipid monolayers revealed by surface-specific vibrational pump-probe spectroscopy.

PubMed

Bonn, Mischa; Bakker, Huib J; Ghosh, Avishek; Yamamoto, Susumu; Sovago, Maria; Campen, R Kramer

2010-10-27

We report vibrational lifetime measurements of the OH stretch vibration of interfacial water in contact with lipid monolayers, using time-resolved vibrational sum frequency (VSF) spectroscopy. The dynamics of water in contact with four different lipids are reported and are characterized by vibrational relaxation rates measured at 3200, 3300, 3400, and 3500 cm(-1). We observe that the water molecules with an OH frequency ranging from 3300 to 3500 cm(-1) all show vibrational relaxation with a time constant of T(1) = 180 ± 35 fs, similar to what is found for bulk water. Water molecules with OH groups near 3200 cm(-1) show distinctly faster relaxation dynamics, with T(1) < 80 fs. We successfully model the data by describing the interfacial water containing two distinct subensembles in which spectral diffusion is, respectively, rapid (3300-3500 cm(-1)) and absent (3200 cm(-1)). We discuss the potential biological implications of the presence of the strongly hydrogen-bonded, rapidly relaxing water molecules at 3200 cm(-1) that are decoupled from the bulk water system.

Entropic Elastic Processes in Protein Mechanisms. Part 1. Elastic Structure Due to an Inverse Temperature Transition and Elasticity Due to Internal Chain Dynamics,

DTIC Science & Technology

1986-01-01

Bungenberg de Jong , H . G . and Kruyt, H . R. (1930). Kolloid-Z 50, 39-48. Bungenberg de Jong , H . G . and Kruyt, H . R. (1929). Proc. Kon. Ned. Adak...Submitted). Bungenbery de Jong , H . G . (1949). In Colloid Science, Vol. 2 (Kruyt, H . R., ed.) Elsevier/North Holland Publishers, Amsterdam, pp. 232...Resonance Relaxation Studies g . Dielectric Relaxation Studies h . Temperature Dependence

Excited-State Deactivation of Branched Phthalocyanine Compounds.

PubMed

Zhu, Huaning; Li, Yang; Chen, Jun; Zhou, Meng; Niu, Yingli; Zhang, Xinxing; Guo, Qianjin; Wang, Shuangqing; Yang, Guoqiang; Xia, Andong

2015-12-21

The excited-state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis- and trisphthalocyanines) are studied by using steady-state and femtosecond transient absorption spectral measurements, where the excited-state energy-transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis-Pc). In trisphthalocyanine (tris-Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre-associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady-state spectra also show a face-to-face conformation in bis-Pc, whereas in tris-Pc, two of the three phthalocyanine branches form a pre-associated face-to-face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure-property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn

2015-12-14

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motionmore » of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.« less

Interrelated structures of the transport shock and collisional relaxation layer in a multitemperature, multilevel ionized gas

NASA Technical Reports Server (NTRS)

Vinolo, A. R.; Clarke, J. H.

1972-01-01

The gas dynamic structures of the transport shock and the downstream collisional relaxation layer are evaluated for partially ionized monatomic gases. Elastic and inelastic collisional nonequilibrium effects are taken into consideration. Three electronic levels are accounted for in the microscopic model of the atom. Nonequilibrium processes with respect to population of levels and species plus temperature are considered. By using an asymptotic technique the shock morphology is found on a continuum flow basis. The asymptotic procedure gives two distinct layers in which the nonequilibrium effects to be considered are different. A transport shock appears as the inner solution to an outer collisional relaxation layer in which the gas reaches local equilibrium. A family of numerical examples is displayed for different flow regimes. Argon and helium models are used in these examples.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

NASA Astrophysics Data System (ADS)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20-40ps for tendamistat and 80-120ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30-40ps and 150-200ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time.

Electron spin dynamics and spin–lattice relaxation of trityl radicals in frozen solutions†

PubMed Central

Chen, Hanjiao; Maryasov, Alexander G.; Rogozhnikova, Olga Yu.; Trukhin, Dmitry V.; Tormyshev, Victor M.

2017-01-01

Electron spin–lattice relaxation of two trityl radicals, d24-OX063 and Finland trityl, were studied under conditions relevant to their use in dissolution dynamic nuclear polarization (DNP). The dependence of relaxation kinetics on temperature up to 100 K and on concentration up to 60 mM was obtained at X- and W-bands (0.35 and 3.5 Tesla, respectively). The relaxation is quite similar at both bands and for both trityl radicals. At concentrations typical for DNP, relaxation is mediated by excitation transfer and spin-diffusion to fast-relaxing centers identified as triads of trityl radicals that spontaneously form in the frozen samples. These centers relax by an Orbach–Aminov mechanism and determine the relaxation, saturation and electron spin dynamics during DNP. PMID:27560644

A Surrogate for Debye-Waller Factors from Dynamic Stokes Shifts

PubMed Central

Zhong, Qin; Johnson, Jerainne; Aamer, Khaled A.; Tyagi, Madhusudan

2011-01-01

We show that the short-time behavior of time-resolved fluorescence Stokes shifts (TRSS) are similar to that of the intermediate scattering function obtained from neutron scattering at q near the peak in the static structure factor for glycerol. This allows us to extract a Debye-Waller (DW) factor analog from TRSS data at times as short as 1 ps in a relatively simple way. Using the time-domain relaxation data obtained by this method we show that DW factors evaluated at times ≥ 40 ps can be directly influenced by α relaxation and thus should be used with caution when evaluating relationships between fast and slow dynamics in glassforming systems. PMID:21701673

Combined phosphorescence-holographic approach for singlet oxygen detection in biological media

NASA Astrophysics Data System (ADS)

Semenova, I. V.; Belashov, A. V.; Beltukova, D. M.; Petrov, N. V.; Vasyutinskii, O. S.

2015-06-01

The paper presents a novel combined approach aimed to detect and monitor singlet oxygen molecules in biological specimens by means of the simultaneous recording and monitoring of their deactivation dynamics in the two complementary channels: radiative and nonradiative. The approach involves both the direct registration of phosphorescence at the wavelength of about 1270 nm caused by radiative relaxation of excited singlet oxygen molecules and holographic recording of thermal disturbances in the medium produced by their nonradiative relaxation. The data provides a complete set of information on singlet oxygen location and dynamics in the medium. The approach was validated in the case study of photosensitized generation of singlet oxygen in onion cell structures.

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

PubMed

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probemore » solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.« less

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-01

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Large-amplitude jumps and non-Gaussian dynamics in highly concentrated hard sphere fluids.

PubMed

Saltzman, Erica J; Schweizer, Kenneth S

2008-05-01

Our microscopic stochastic nonlinear Langevin equation theory of activated dynamics has been employed to study the real-space van Hove function of dense hard sphere fluids and suspensions. At very short times, the van Hove function is a narrow Gaussian. At sufficiently high volume fractions, such that the entropic barrier to relaxation is greater than the thermal energy, its functional form evolves with time to include a rapidly decaying component at small displacements and a long-range exponential tail. The "jump" or decay length scale associated with the tail increases with time (or particle root-mean-square displacement) at fixed volume fraction, and with volume fraction at the mean alpha relaxation time. The jump length at the alpha relaxation time is predicted to be proportional to a measure of the decoupling of self-diffusion and structural relaxation. At long times corresponding to mean displacements of order a particle diameter, the volume fraction dependence of the decay length disappears. A good superposition of the exponential tail feature based on the jump length as a scaling variable is predicted at high volume fractions. Overall, the theoretical results are in good accord with recent simulations and experiments. The basic aspects of the theory are also compared with a classic jump model and a dynamically facilitated continuous time random-walk model. Decoupling of the time scales of different parts of the relaxation process predicted by the theory is qualitatively similar to facilitated dynamics models based on the concept of persistence and exchange times if the elementary event is assumed to be associated with transport on a length scale significantly smaller than the particle size.

Ultrafast Hydration Dynamics and Coupled Water-Protein Fluctuations in Apomyoglobin

NASA Astrophysics Data System (ADS)

Yang, Yi; Zhang, Luyuan; Wang, Lijuan; Zhong, Dongping

2009-06-01

Protein hydration dynamics are of fundamental importance to its structure and function. Here, we characterize the global solvation dynamics and anisotropy dynamics around the apomyoglobin surface in different conformational states (native and molten globule) by measuring the Stokes shift and anisotropy decay of tryptophan with femtosecond-resolved fluorescence upconversion. With site-directed mutagenesis, we designed sixteen mutants with one tryptophan in each, and placed the probe at a desirable position ranging from buried in the protein core to fully solvent-exposed on the protein surface. In all protein sites studied, two distinct solvation relaxations (1-8 ps and 20-200 ps) were observed, reflecting the initial collective water relaxation and subsequent hydrogen-bond network restructuring, respectively, and both are strongly correlated with protein's local structures and chemical properties. The hydration dynamics of the mutants in molten globule state are faster than those observed in native state, indicating that the protein becomes more flexible and less structured when its conformation is converted from fully-folded native state to partially-folded molten globule state. Complementary, fluorescence anisotropy dynamics of all mutants in native state show an increasing trend of wobbling times (40-260 ps) when the location of the probe is changed from a loop, to a lateral helix, and then, to the compact protein core. Such an increase in wobbling times is related to the local protein structural rigidity, which relates the interaction of water with side chains. The ultrafast hydration dynamics and related side-chain motion around the protein surface unravel the coupled water-protein fluctuations on the picosecond time scales and indicate that the local protein motions are slaved by hydrating water fluctuations.

The Relationship of Dynamical Heterogeneity to the Adam-Gibbs and Random First-Order Transition Theories of Glass Formation

NASA Astrophysics Data System (ADS)

Starr, Francis; Douglas, Jack; Sastry, Srikanth

2013-03-01

We examine measures of dynamical heterogeneity for a bead-spring polymer melt and test how these scales compare with the scales hypothesized by the Adam and Gibbs (AG) and random first-order transition (RFOT) theories. We show that the time scale of the high-mobility clusters and strings is associated with a diffusive time scale, while the low-mobility particles' time scale relates to a structural relaxation time. The difference of the characteristic times naturally explains the decoupling of diffusion and structural relaxation time scales. We examine the appropriateness of identifying the size scales of mobile particle clusters or strings with the size of cooperatively rearranging regions (CRR) in the AG and RFOT theories. We find that the string size appears to be the most consistent measure of CRR for both the AG and RFOT models. Identifying strings or clusters with the``mosaic'' length of the RFOT model relaxes the conventional assumption that the``entropic droplet'' are compact. We also confirm the validity of the entropy formulation of the AG theory, constraining the exponent values of the RFOT theory. This constraint, together with the analysis of size scales, enables us to estimate the characteristic exponents of RFOT.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaminski, K.; Adrjanowicz, K.; Paluch, M.

Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the {beta} process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the {gamma} relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determinemore » structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noe, F; Diadone, Isabella; Lollmann, Marc

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observedmore » relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.« less

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

PubMed

Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

2008-02-01

We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

Non-monotonic dynamics of water in its binary mixture with 1,2-dimethoxy ethane: A combined THz spectroscopic and MD simulation study.

PubMed

Das Mahanta, Debasish; Patra, Animesh; Samanta, Nirnay; Luong, Trung Quan; Mukherjee, Biswaroop; Mitra, Rajib Kumar

2016-10-28

A combined experimental (mid- and far-infrared FTIR spectroscopy and THz time domain spectroscopy (TTDS) (0.3-1.6 THz)) and molecular dynamics (MD) simulation technique are used to understand the evolution of the structure and dynamics of water in its binary mixture with 1,2-dimethoxy ethane (DME) over the entire concentration range. The cooperative hydrogen bond dynamics of water obtained from Debye relaxation of TTDS data reveals a non-monotonous behaviour in which the collective dynamics is much faster in the low X w region (where X w is the mole fraction of water in the mixture), whereas in X w ∼ 0.8 region, the dynamics gets slower than that of pure water. The concentration dependence of the reorientation times of water, calculated from the MD simulations, also captures this non-monotonous character. The MD simulation trajectories reveal presence of large amplitude angular jumps, which dominate the orientational relaxation. We rationalize the non-monotonous, concentration dependent orientational dynamics by identifying two different physical mechanisms which operate at high and low water concentration regimes.

Structure of the two-dimensional relaxation spectra seen within the eigenmode perturbation theory and the two-site exchange model.

PubMed

Bytchenkoff, Dimitri; Rodts, Stéphane

2011-01-01

The form of the two-dimensional (2D) NMR-relaxation spectra--which allow to study interstitial fluid dynamics in diffusive systems by correlating spin-lattice (T(1)) and spin-spin (T(2)) relaxation times--has given rise to numerous conjectures. Herein we find analytically a number of fundamental structural properties of the spectra: within the eigen-modes formalism, we establish relationships between the signs and intensities of the diagonal and cross-peaks in spectra obtained by various 1 and 2D NMR-relaxation techniques, reveal symmetries of the spectra and uncover interdependence between them. We investigate more specifically a practically important case of porous system that has sets of T(1)- and T(2)-eigenmodes and eigentimes similar to each other by applying the perturbation theory. Furthermore we provide a comparative analysis of the application of the, mathematically more rigorous, eigen-modes formalism and the, rather more phenomenological, first-order two-site exchange model to diffusive systems. Finally we put the results that we could formulate analytically to the test by comparing them with computer-simulations for 2D porous model systems. The structural properties, in general, are to provide useful clues for assignment and analysis of relaxation spectra. The most striking of them--the presence of negative peaks--underlines an urgent need for improvement of the current 2D Inverse Laplace Transform (ILT) algorithm used for calculation of relaxation spectra from NMR raw data. Copyright © 2010 Elsevier Inc. All rights reserved.

How Do Organic Vapors Swell Ultrathin Films of Polymer of Intrinsic Microporosity PIM-1?

PubMed

Ogieglo, Wojciech; Rahimi, Khosorov; Rauer, Sebastian Bernhard; Ghanem, Bader; Ma, Xiaohua; Pinnau, Ingo; Wessling, Matthias

2017-07-27

Dynamic sorption of ethanol and toluene vapor into ultrathin supported films of polymer of intrinsic microporosity PIM-1 down to a thickness of 6 nm are studied with a combination of in situ spectroscopic ellipsometry and in situ X-ray reflectivity. Both ethanol and toluene significantly swell the PIM-1 matrix and, at the same time, induce persistent structural relaxations of the frozen-in glassy PIM-1 morphology. For ethanol below 20 nm, three effects were identified. First, the swelling magnitude at high vapor pressures is reduced by about 30% as compared to that of thicker films. Second, at low penetrant activities (below 0.3p/p 0 ), films below 20 nm are able to absorb slightly more penetrant as compared with thicker films despite a similar swelling magnitude. Third, for the ultrathin films, the onset of the dynamic penetrant-induced glass transition P g has been found to shift to higher values, indicating higher resistance to plasticization. All of these effects are consistent with a view where immobilization of the superglassy PIM-1 at the substrate surface leads to an arrested, even more rigid, and plasticization-resistant, yet still very open, microporous structure. PIM-1 in contact with the larger and more condensable toluene shows very complex, heterogeneous swelling dynamics, and two distinct penetrant-induced relaxation phenomena, probably associated with the film outer surface and the bulk, are detected. Following the direction of the penetrant's diffusion, the surface seems to plasticize earlier than the bulk, and the two relaxations remain well separated down to 6 nm film thickness, where they remarkably merge to form just a single relaxation.

Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

PubMed Central

Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

2009-01-01

15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

Pinch-off dynamics, extensional viscosity and relaxation time of dilute and ultradilute aqueous polymer solutions

NASA Astrophysics Data System (ADS)

Biagioli, Madeleine; Dinic, Jelena; Jimenez, Leidy Nallely; Sharma, Vivek

Free surface flows and drop formation processes present in printing, jetting, spraying, and coating involve the development of columnar necks that undergo spontaneous surface-tension driven instability, thinning, and pinch-off. Stream-wise velocity gradients that arise within the thinning neck create and extensional flow field, which induces micro-structural changes within complex fluids that contribute elastic stresses, changing the thinning and pinch-off dynamics. In this contribution, we use dripping-onto-substrate (DoS) extensional rheometry technique for visualization and analysis of the pinch-off dynamics of dilute and ultra-dilute aqueous polyethylene oxide (PEO) solutions. Using a range of molecular weights, we study the effect of both elasticity and finite extensibility. Both effective relaxation time and the transient extensional viscosity are found to be strongly concentration-dependent even for highly dilute solutions.

Interrelated structures of the transport shock and collisional relaxation layer in a multitemperature, multilevel ionized gas

NASA Technical Reports Server (NTRS)

Vinolo, A. R.; Clarke, J. H.

1973-01-01

The gas dynamic structures of the transport shock and the downstream collisional relaxation layer are evaluated for partially ionized monatomic gases. Elastic and inelastic collisional nonequilibrium effects are taken into consideration. In the microscopic model of the atom, three electronic levels are accounted for. By using an asymptotic technique, the shock morphology is found on a continuum flow basis. This procedure gives two distinct layers in which the nonequilibrium effects to be considered are different. A transport shock appears as the inner solution to an outer collisional relaxation layer. The results show four main interesting points: (1) on structuring the transport shock, ionization and excitation rates must be included in the formulation, since the flow is not frozen with respect to the population of the different electronic levels; (2) an electron temperature precursor appears at the beginning of the transport shock; (3) the collisional layer is rationally reduced to quadrature for special initial conditions, which (4) are obtained from new Rankine-Hugoniot relations for the inner shock.

Energy landscape in frustrated systems: Cation hopping in pyrochlores

NASA Astrophysics Data System (ADS)

Brooks Hinojosa, Beverly; Asthagiri, Aravind; Nino, Juan C.

2013-07-01

We investigate the dynamics of the local environment and electronic structure in inherently dipolar frustrated pyrochlore compounds to help identify the fundamental nature of dipolar disorder in pyrochlore systems and determine the necessary and sufficient conditions for dielectric relaxation. We map out the energy landscape associated with cation hopping events in three compounds and correlate the hopping pathway with experimental dielectric response. Comprehensive analysis of the calculations allows us to postulate rules to predict the occurrence of relaxation and cation hopping pathways.

A Polyhedral Outer-approximation, Dynamic-discretization optimization solver, 1.x

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bent, Rusell; Nagarajan, Harsha; Sundar, Kaarthik

2017-09-25

In this software, we implement an adaptive, multivariate partitioning algorithm for solving mixed-integer nonlinear programs (MINLP) to global optimality. The algorithm combines ideas that exploit the structure of convex relaxations to MINLPs and bound tightening procedures

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine.

PubMed

Kotur, Marija; Weinacht, Thomas C; Zhou, Congyi; Kistler, Kurt A; Matsika, Spiridoula

2011-05-14

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.

Multiple-decker phthalocyaninato dinuclear lanthanoid(III) single-molecule magnets with dual-magnetic relaxation processes.

PubMed

Katoh, Keiichi; Horii, Yoji; Yasuda, Nobuhiro; Wernsdorfer, Wolfgang; Toriumi, Koshiro; Breedlove, Brian K; Yamashita, Masahiro

2012-11-28

The SMM behaviour of dinuclear Ln(III)-Pc multiple-decker complexes (Ln = Tb(3+) and Dy(3+)) with energy barriers and slow-relaxation behaviour were explained by using X-ray crystallography and static and dynamic susceptibility measurements. In particular, interactions among the 4f electrons of several dinuclear Ln(III)-Pc type SMMs have never been discussed on the basis of the crystal structure. For dinuclear Tb(III)-Pc complexes, a dual magnetic relaxation process was observed. The relaxation processes are due to the anisotropic centres. Our results clearly show that the two Tb(3+) ion sites are equivalent and are consistent with the crystal structure. On the other hand, the mononuclear Tb(III)-Pc complex exhibited only a single magnetic relaxation process. This is clear evidence that the magnetic relaxation mechanism depends heavily on the dipole-dipole (f-f) interactions between the Tb(3+) ions in the dinuclear systems. Furthermore, the SMM behaviour of dinuclear Dy(III)-Pc type SMMs with smaller energy barriers compared with that of Tb(III)-Pc and slow-relaxation behaviour was explained. Dinuclear Dy(III)-Pc SMMs exhibited single-component magnetic relaxation behaviour. The results indicate that the magnetic relaxation properties of dinuclear Ln(III)-Pc multiple-decker complexes are affected by the local molecular symmetry and are extremely sensitive to tiny distortions in the coordination geometry. In other words, the spatial arrangement of the Ln(3+) ions (f-f interactions) in the crystal is important. Our work shows that the SMM properties can be fine-tuned by introducing weak intermolecular magnetic interactions in a controlled SMM spatial arrangement.

Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

PubMed

Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle Aulikki; Güntert, Peter; Riek, Roland

2014-04-01

Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space. Copyright © 2013 Elsevier Inc. All rights reserved.

Water Dynamics in the Hydration Shells of Biomolecules

PubMed Central

2017-01-01

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water. PMID:28248491

Thermally induced magnetic relaxation in square artificial spin ice.

PubMed

Andersson, M S; Pappas, S D; Stopfel, H; Östman, E; Stein, A; Nordblad, P; Mathieu, R; Hjörvarsson, B; Kapaklis, V

2016-11-24

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system - square artificial spin ice - we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Using time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.

Thermally induced magnetic relaxation in square artificial spin ice

NASA Astrophysics Data System (ADS)

Andersson, M. S.; Pappas, S. D.; Stopfel, H.; Östman, E.; Stein, A.; Nordblad, P.; Mathieu, R.; Hjörvarsson, B.; Kapaklis, V.

2016-11-01

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system - square artificial spin ice - we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Using time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.

In-situ atomic force microscopy observation revealing gel-like plasticity on a metallic glass surface

NASA Astrophysics Data System (ADS)

Lu, Y. M.; Zeng, J. F.; Huang, J. C.; Kuan, S. Y.; Nieh, T. G.; Wang, W. H.; Pan, M. X.; Liu, C. T.; Yang, Y.

2017-03-01

It has been decade-long and enduring efforts to decipher the structural mechanism of plasticity in metallic glasses; however, it still remains a challenge to directly reveal the structural change, if any, that precedes; and dominant plastics flow in them. Here, by using the dynamic atomic force microscope as an "imaging" as well as a "forcing" tool, we unfold a real-time sequence of structural evolution occurring on the surface of an Au-Si thin film metallic glass. In sharp contrast to the common notion that plasticity comes along with mechanical softening in bulk metallic glasses, our experimental results directly reveal three types of nano-sized surface regions, which undergo plasticity but exhibit different characters of structural evolution following the local plasticity events, including stochastic structural rearrangement, unusual local relaxation and rejuvenation. As such, yielding on the metallic-glass surface manifests as a dynamic equilibrium between local relaxation and rejuvenation as opposed to shear instability in bulk metallic-glasses. Our finding demonstrates that plasticity on the metallic glass surface of Au-Si metallic glass bears much resemblance to that of the colloidal gels, of which nonlinear rheology rather than shear instability governs the constitutive behavior of plasticity.

Dynamic Relaxation: A Technique for Detailed Thermo-Elastic Structural Analysis of Transportation Structures

NASA Astrophysics Data System (ADS)

Shoukry, Samir N.; William, Gergis W.; Riad, Mourad Y.; McBride, Kevyn C.

2006-08-01

Dynamic relaxation is a technique developed to solve static problems through an explicit integration in finite element. The main advantage of such a technique is the ability to solve a large problem in a relatively short time compared with the traditional implicit techniques, especially when using nonlinear material models. This paper describes the use of such a technique in analyzing large transportation structures as dowel jointed concrete pavements and 306-m-long, reinforced concrete bridge superstructure under the effect of temperature variations. The main feature of the pavement model is the detailed modeling of dowel bars and their interfaces with the surrounding concrete using extremely fine mesh of solid elements, while in the bridge structure it is the detailed modeling of the girder-deck interface as well as the bracing members between the girders. The 3DFE results were found to be in a good agreement with experimentally measured data obtained from an instrumented pavements sections and a highway bridge constructed in West Virginia. Thus, such a technique provides a good tool for analyzing the response of large structures to static loads in a fraction of the time required by traditional, implicit finite element methods.

Dynamics of Ice/Water Confined in Nanoporous Alumina.

PubMed

Suzuki, Yasuhito; Steinhart, Martin; Graf, Robert; Butt, Hans-Jürgen; Floudas, George

2015-11-19

Dielectric (DS), IR spectroscopy, and (1)H MAS NMR are employed in the study of ice/water confined in nanoporous alumina with pore diameters ranging from 400 nm down to 25 nm. Within nanoporous alumina there is a transformation from heterogeneous nucleation of hexagonal ice in the larger pores to homogeneous nucleation of cubic ice in the smaller pores. DS and IR show excellent agreement in the temperature interval and pore size dependence of the transformation. DS further revealed two dynamic processes under confinement. The "fast" and "slow" processes with an Arrhenius temperature dependence are attributed to ice and supercooled water relaxation, respectively. The main relaxation process of ice under confinement ("slow" process) has an activation energy of 44 ± 2 kJ/mol. The latter is in agreement with the reported relaxation times and activation energy of cubic ice prepared following a completely different route (by pressure). (1)H MAS NMR provided new insight in the state of ice structures as well as of supercooled water. Under confinement, a layer of liquid-like water coexists with ice structures. In addition, both ice structures under confinement appear to be more ordered than bulk hexagonal ice. Supercooled water in the smaller pores is different from bulk water. It shows a shift of the signal toward higher chemical shift values which may suggest stronger hydrogen bonding between the water molecules or increasing interactions with the AAO walls.

Ultrafast relaxation dynamics of nitric oxide synthase studied by visible broadband transient absorption spectroscopy

NASA Astrophysics Data System (ADS)

Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S.

2017-09-01

Ultrafast dynamics of endothelial nitric oxide synthase (eNOS) oxygenase domain was studied by transient absorption spectroscopy pumping at Soret band. The broadband visible probe spectrum has visualized the relaxation dynamics from the Soret band to Q-band and charge transfer (CT) band. Supported by two-dimensional correlation spectroscopy, global fitting analysis has successfully concluded the relaxation dynamics from the Soret band to be (1) electronic transition to Q-band (0.16 ps), (2) ligand dissociation and CT (0.94 ps), (3) relaxation of the CT state (4.0 ps), and (4) ligand rebinding (59 ps).

Water types and their relaxation behavior in partially rehydrated CaFe-mixed binary oxide obtained from CaFe-layered double hydroxide in the 155-298 K temperature range.

PubMed

Bugris, Valéria; Haspel, Henrik; Kukovecz, Ákos; Kónya, Zoltán; Sipiczki, Mónika; Sipos, Pál; Pálinkó, István

2013-10-29

Heat-treated CaFe-layered double hydroxide samples were equilibrated under conditions of various relative humidities (11%, 43% and 75%). Measurements by FT-IR and dielectric relaxation spectroscopies revealed that partial to full reconstruction of the layered structure took place. Water types taking part in the reconstruction process were identified via dielectric relaxation measurements either at 298 K or on the flash-cooled (to 155 K) samples. The dynamics of water molecules at the various positions was also studied by this method, allowing the flash-cooled samples to warm up to 298 K.

{sup 1}H NMR relaxometry and quadrupole relaxation enhancement as a sensitive probe of dynamical properties of solids—[C(NH{sub 2}){sub 3}]{sub 3}Bi{sub 2}I{sub 9} as an example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Florek-Wojciechowska, M.; Wojciechowski, M.; Brym, Sz.

{sup 1}H nuclear magnetic resonance relaxometry has been applied to reveal information on dynamics and structure of Gu{sub 3}Bi{sub 2}I{sub 9} ([Gu = C(NH{sub 2}){sub 3}] denotes guanidinium cation). The data have been analyzed in terms of a theory of quadrupole relaxation enhancement, which has been extended here by including effects associated with quadrupole ({sup 14}N) spin relaxation caused by a fast fluctuating component of the electric field gradient tensor. Two motional processes have been identified: a slow one occurring on a timescale of about 8 × 10{sup −6} s which has turned out to be (almost) temperature independent, andmore » a fast process in the range of 10{sup −9} s. From the {sup 1}H-{sup 14}N relaxation contribution (that shows “quadrupole peaks”) the quadrupole parameters, which are a fingerprint of the arrangement of the anionic network, have been determined. It has been demonstrated that the magnitude of the quadrupole coupling considerably changes with temperature and the changes are not caused by phase transitions. At the same time, it has been shown that there is no evidence of abrupt changes in the cationic dynamics and the anionic substructure upon the phase transitions.« less

Nonadiabatic Dynamics for Electrons at Second-Order: Real-Time TDDFT and OSCF2.

PubMed

Nguyen, Triet S; Parkhill, John

2015-07-14

We develop a new model to simulate nonradiative relaxation and dephasing by combining real-time Hartree-Fock and density functional theory (DFT) with our recent open-systems theory of electronic dynamics. The approach has some key advantages: it has been systematically derived and properly relaxes noninteracting electrons to a Fermi-Dirac distribution. This paper combines the new dissipation theory with an atomistic, all-electron quantum chemistry code and an atom-centered model of the thermal environment. The environment is represented nonempirically and is dependent on molecular structure in a nonlocal way. A production quality, O(N(3)) closed-shell implementation of our theory applicable to realistic molecular systems is presented, including timing information. This scaling implies that the added cost of our nonadiabatic relaxation model, time-dependent open self-consistent field at second order (OSCF2), is computationally inexpensive, relative to adiabatic propagation of real-time time-dependent Hartree-Fock (TDHF) or time-dependent density functional theory (TDDFT). Details of the implementation and numerical algorithm, including factorization and efficiency, are discussed. We demonstrate that OSCF2 approaches the stationary self-consistent field (SCF) ground state when the gap is large relative to k(b)T. The code is used to calculate linear-response spectra including the effects of bath dynamics. Finally, we show how our theory of finite-temperature relaxation can be used to correct ground-state DFT calculations.

Local structural order and relaxation effects in metal-chalcogenide glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saleh, Z.M.

1990-01-01

Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) have been employed to study the local structural order and the relaxation mechanisms in metal-arsenic-chalcogenide glasses for metal concentrations within the glass forming region. The glass forming region in the Cu-As-S and Cu-As-se glassy systems extends approximately to 6 and 25 at. % copper, respectively. In the composition Cu[sub x](As[sub 2/5]Ch[sub 3/5])[sub 1[minus]x], where Ch = S or Se, there is evidence of dramatic changes in the local structure as copper is added to the system. One important change is the formation of As-As bonds which are absent in As[sub 2]Ch[submore » 3]. The [sup 75]As NQR measurements indicate that the density of these bonds increases with copper concentration x. These results are consistent with the predictions of a model proposed recently to explain the local structural order in glassy metal chalcogenides. While NQR data show that arsenic atoms are threefold coordinated, EXAFs measurements have shown that copper is fourfold coordinated within the glass forming ranges in both systems. The NMR measurements confirm this result and quantitatively determine the local environment around the copper nuclei. For the naturally occurring mineral luzonite (Cu[sub 3]AsS[sub 4]) copper is fourfold coordinated. The known structure of this mineral has been used as a guide to understanding the local structure in the glasses. Copper and arsenic nuclear relaxation measurements were used to study the dynamics of these systems. The temperature and frequency dependence of the spin-lattice and spin-spin relaxation times have been carefully measured to determine the relaxation mechanisms.« less

Unravelling the mechanisms of vibrational relaxation in solution.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Orr-Ewing, Andrew J; Ashfold, Michael N R

2017-04-01

We present a systematic study of the mode-specific vibrational relaxation of NO 2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO 2 fragments produced from the 340 nm photolysis of N 2 O 4 → NO 2 (X) + NO 2 (A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO 2 bending and stretching modes, even at energies as high as 7000 cm -1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20-1100 ps. NO 2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO 2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO 2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution.

Branching, Superdiffusion and Stress Relaxation in Surfactant Micelles

NASA Astrophysics Data System (ADS)

Sureshkumar, R.; Dhakal, S.; Syracuse University Team

2016-11-01

We investigate the mechanism of branch formation and its effects on the dynamics and rheology of a model cationic micellar fluid using molecular dynamics (MD) simulations. Branched structures are formed upon increasing counter ion density. A sharp decrease in the solution viscosity with increasing salinity has long been attributed to the sliding motion of micellar branches along the main chain. Simulations not only provide firm evidence of branch sliding in real time, but also show enhanced diffusion of surfactants by virtue of such motion. Insights into the mechanism of stress relaxation associated with branch sliding will be discussed. Specifically, an externally imposed stress damps out more quickly in a branched system compared to that in an unbranched one. NSF Grants 1049489, 1049454.

Anti-correlated spectral motion in bisphthalocyanines: evidence for vibrational modulation of electronic mixing.

PubMed

Prall, Bradley S; Parkinson, Dilworth Y; Ishikawa, Naoto; Fleming, Graham R

2005-12-08

We exploit a coherently excited nuclear wave packet to study nuclear motion modulation of electronic structure in a metal bridged phthalocyanine dimer, lutetium bisphthalocyanine, which displays two visible absorption bands. We find that the nuclear coordinate influences the energies of the underlying exciton and charge resonance states as well as their interaction; the interplay of the various couplings creates unusual anti-correlated spectral motion in the two bands. Excited state relaxation dynamics are the same regardless of which transition is pumped, with decay time constants of 1.5 and 11 ps. The dynamics are analyzed using a three-state kinetic model after relaxation from one or two additional states faster than the experimental time resolution of 50-100 fs.

Subpicosecond surface dynamics in genomic DNA from in vitro-grown plant species: a SERS assessment.

PubMed

Muntean, Cristina M; Bratu, Ioan; Leopold, Nicolae; Morari, Cristian; Buimaga-Iarinca, Luiza; Purcaru, Monica A P

2015-09-07

In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.

Contrasting dynamics of fragile and non-fragile polyalcohols through the glass, and dynamical, transitions: A comparison of neutron scattering and dielectric relaxation data for sorbitol and glycerol.

PubMed

Migliardo, F; Angell, C A; Magazù, S

2017-01-01

Glycerol and sorbitol are glass-forming hydrogen-bonded systems characterized by intriguing properties which make these systems very interesting also from the applications point of view. The goal of this work is to relate the hydrogen-bonded features, relaxation dynamics, glass transition properties and fragility of these systems, in particular to seek insight into their very different liquid fragilities. The comparison between glycerol and sorbitol is carried out by collecting the elastic incoherent neutron scattering (EINS) intensity as a function of temperature and of the instrumental energy resolution. Intensity data vs temperature and resolution are analyzed in terms of thermal restraint and Resolution Elastic Neutron Scattering (RENS) approaches. The number of OH groups, which are related to the connecting sites, is a significant parameter both in the glass transition and in the dynamical transition. On the other hand, the disordered nature of sorbitol is confirmed by the existence of different relaxation processes. From the applications point of view, glycerol and sorbitol have remarkable bioprotectant properties which make these systems useful in different technological and industrial fields. Furthermore, polyols are rich in glassforming liquid phenomenology and highly deserving of study in their own right. The comparison of EINS and calorimetric data on glycerol and sorbitol helps provide a connection between structural relaxation, dynamical transition, glass transition, and fragility. The evaluation of the inflection point in the elastic intensity behavior as a function of temperature and instrumental energy resolution provides a confirmation of the validity of the RENS approach. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016. Published by Elsevier B.V.

Anomalous Debye-like dielectric relaxation of water in micro-sized confined polymeric systems.

PubMed

Colosi, C; Costantini, M; Barbetta, A; Cametti, C; Dentini, M

2013-12-14

While it is well known that spatial confinement on a nm scale affects the molecular dynamics of water resulting in a hindered dipolar reorientation, question of whether these effects could result at length scales larger than these, i.e., in confined regions of the order of μm or more, is still under debate. Here we use dielectric relaxation spectroscopy techniques to study the relaxation orientation dynamics of water entrapped in different polymeric matrices with pore sizes of the order of 100 μm, analyzing the frequency relaxation behaviour of the dielectric response. Our results show that, contrary to what has been generally thought, even in confinements which are not particularly high such as those realized here, regions typically hundred micrometers in size can affect the water structure, inducing a water phase with properties different from those of bulk water. In particular, we observe a dielectric dispersion centered in the range 10(5)-10(7) Hz, in between the one characteristic of ice (8.3 kHz at T = 0 °C) and the one of bulk water (19.2 GHz at T = 25 °C). The analysis of the dependence on temperature of the relaxation time of this unexpected contribution rules out the possibility that it can be attributed to an interfacial polarization (Maxwell-Wagner effect) and suggests a dipolar Debye-like origin due to a slow-down of the hydrogen-bonded network orientational polarization. Also at these scales, the confinement alters the structure of water, leading to a hindered reorientation. These properties imply that water confined within these polymeric porous matrices is more ordered than bulk water. These findings may be important in order to understand biological processes in cells and in different biological compartments, where water is physiologically confined.

Dynamics of aqueous binary glass-formers confined in MCM-41.

PubMed

Elamin, Khalid; Jansson, Helén; Swenson, Jan

2015-05-21

Dielectric permittivity measurements were performed on water solutions of propylene glycol (PG) and propylene glycol monomethyl ether (PGME) confined in 21 Å pores of the silica matrix MCM-41 C10 in wide frequency (10(-2)-10(6) Hz) and temperature (130-250 K) ranges. The aim was to elucidate how the formation of large hydrogen bonded structural entities, found in bulk solutions of PGME, was affected by the confined geometry, and to make comparisons with the dynamic behavior of the PG-water system. For all solutions the measurements revealed four almost concentration independent relaxation processes. The intensity of the fastest process is low compared to the other relaxation processes and might be caused by both hydroxyl groups of the pore surfaces and by local motions of water and solute molecules. The second fastest process contains contributions from both the main water relaxation as well as the intrinsic β-relaxation of the solute molecules. The third fastest process is the viscosity related α-relaxation. Its concentration independency is very different compared to the findings for the corresponding bulk systems, particularly for the PGME-water system. The experimental data suggests that the surface interactions induce a micro-phase separation of the two liquids, resulting in a full molecular layer of water molecules coordinating to the hydrophilic hydroxyl groups on the surfaces of the silica pores. This, in turn, increases the geometrical confinement effect for the remaining solution even more and prevents the building up of the same type of larger structural entities in the PGME-water system as in the corresponding bulk solutions. The slowest process is mainly hidden in the high conductivity contribution at low frequencies, but its temperature dependence can be extracted for the PGME-water system. However, its origin is not fully clear, as will be discussed.

Epoxy-based hydrogels investigated by high-frequency dielectric relaxation spectroscopy.

PubMed

Krakovský, Ivan; Shikata, Toshiyuki; Hasegawa, Ryuta

2013-11-14

Using high-frequency dielectric relaxation spectroscopy, nanophase-separated structures of epoxy-based hydrogels were investigated as a function of water content at 25 °C. The dielectric spectra resulting from the hydrogels were reasonably decomposed into two Debye-type and two Cole-Cole-type relaxation modes. The fastest Debye-type mode, found at 8.3 ps, was attributed to the rotational relaxation process of free water molecules in the bulk state. The other Debye-type mode, at ca. 20-34 ps, originates from the exchange process of water molecules that are hydrogen-bonded to the hydrophilic epoxy network portions for free bulk ones. The first Cole-Cole-type mode observed, at ca. 20-370 ps, was assigned to the complicated dynamics for electric dipole moments of the hydrophilic groups in the epoxy networks (mainly monomeric oxyethylene units). The slowest major Cole-Cole-type mode, at 5-29 ns, was attributed to the Maxwell-Wagner-Sillars polarization process and confirmed the presence of the nanophase-separated structures as revealed by the previous small-angle neutron scattering experiments.

Relaxation dynamics of internal segments of DNA chains in nanochannels

NASA Astrophysics Data System (ADS)

Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team

We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.

Glassy dynamics of dense particle assemblies on a spherical substrate.

PubMed

Vest, Julien-Piera; Tarjus, Gilles; Viot, Pascal

2018-04-28

We study by molecular dynamics simulation a dense one-component system of particles confined on a spherical substrate. We more specifically investigate the evolution of the structural and dynamical properties of the system when changing the control parameters, the temperature and the curvature of the substrate. We find that the dynamics become glassy at low temperature, with a strong slowdown of the relaxation and the emergence of dynamical heterogeneity. The prevalent local 6-fold order is frustrated by curvature and we analyze in detail the role of the topological defects in the statics and the dynamics of the particle assembly.

Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r).

PubMed

Otten, Renee; Villali, Janice; Kern, Dorothee; Mulder, Frans A A

2010-12-01

To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ (1)H Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [(1)H, (13)C]-d-glucose in ∼100% D(2)O, which yields CHD(2) methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using (13)C TOCSY NMR spectroscopy, as was recently demonstrated (Otten, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure (1)H CPMG relaxation dispersion profiles for CHD(2) methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-δ1 and Thr-γ2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong (13)C scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone (15)N CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the (1)H line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 ± 0.5) × 10(3) per second (i.e., τ(ex) = 64.7 ± 1.9 μs). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by (1)H CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone (15)N relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins.

Dynamic phase coexistence in glass-forming liquids.

PubMed

Pastore, Raffaele; Coniglio, Antonio; Ciamarra, Massimo Pica

2015-07-09

One of the most controversial hypotheses for explaining the heterogeneous dynamics of glasses postulates the temporary coexistence of two phases characterized by a high and by a low diffusivity. In this scenario, two phases with different diffusivities coexist for a time of the order of the relaxation time and mix afterwards. Unfortunately, it is difficult to measure the single-particle diffusivities to test this hypothesis. Indeed, although the non-Gaussian shape of the van-Hove distribution suggests the transient existence of a diffusivity distribution, it is not possible to infer from this quantity whether two or more dynamical phases coexist. Here we provide the first direct observation of the dynamical coexistence of two phases with different diffusivities, by showing that in the deeply supercooled regime the distribution of the single-particle diffusivities acquires a transient bimodal shape. We relate this distribution to the heterogeneity of the dynamics and to the breakdown of the Stokes-Einstein relation, and we show that the coexistence of two dynamical phases occurs up to a timescale growing faster than the relaxation time on cooling, for some of the considered models. Our work offers a basis for rationalizing the dynamics of supercooled liquids and for relating their structural and dynamical properties.

Pushing the glass transition towards random close packing using self-propelled hard spheres

NASA Astrophysics Data System (ADS)

Ni, Ran; Stuart, Martien A. Cohen; Dijkstra, Marjolein

2013-10-01

Although the concept of random close packing with an almost universal packing fraction of approximately 0.64 for hard spheres was introduced more than half a century ago, there are still ongoing debates. The main difficulty in searching the densest packing is that states with packing fractions beyond the glass transition at approximately 0.58 are inherently non-equilibrium systems, where the dynamics slows down with a structural relaxation time diverging with density; hence, the random close packing is inaccessible. Here we perform simulations of self-propelled hard spheres, and we find that with increasing activity the relaxation dynamics can be sped up by orders of magnitude. The glass transition shifts to higher packing fractions upon increasing the activity, allowing the study of sphere packings with fluid-like dynamics at packing fractions close to RCP. Our study opens new possibilities of investigating dense packings and the glass transition in systems of hard particles.

Dynamics of poroelastic foams

NASA Astrophysics Data System (ADS)

Forterre, Yoel; Sobac, Benjamin

2010-11-01

Soft poroelastic structures are widespread in biological tissues such as cartilaginous joints in bones, blood-filled placentae or plant organs. Here we investigate the dynamics of open elastic foams immersed in viscous fluids, as model soft poroelastic materials. The experiment consists in slowly compacting blocs of polyurethane solid foam embedded in silicon oil-tanks and studying their relaxation to equilibrium when the confining stress is suddenly released. Measurements of the local fluid pressure and foam velocity field are compared with a simple two-phase flow approach. For small initial compactions, the results show quantitative agreement with the classical diffusion theory of soil consolidation (Terzaghi, Biot). On the other hand, for large initial compactions, the dynamics exhibits long relaxation times and decompaction fronts, which are mainly controlled by the highly non-linear mechanical response of the foam. The analogy between this process and the evaporation of a polymer melt close to the glass transition will be briefly discussed.

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

NASA Astrophysics Data System (ADS)

Hu, Xiaohu; Hong, Liang; Dean Smith, Micholas; Neusius, Thomas; Cheng, Xiaolin; Smith, Jeremy C.

2016-02-01

Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behaviour with effective relaxation times existing over many decades in time, from ps up to ~102 s (refs ,,,). Here, using molecular dynamics simulations, we show that, on timescales from 10-12 to 10-5 s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behaviour persists up to timescales approaching the in vivo lifespan of individual protein molecules.

Static and dynamic properties of two-dimensional Coulomb clusters.

PubMed

Ash, Biswarup; Chakrabarti, J; Ghosal, Amit

2017-10-01

We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional confinements across the crossover from solid- to liquid-like behaviors. While static correlations that investigate the translational and bond orientational order in the confinements show the footprints of hexatic-like phase at low temperatures, dynamics of the particles slow down considerably in this phase, reminiscent of a supercooled liquid. Using density correlations, we probe long-lived heterogeneities arising from the interplay of the irregularity in the confinement and long-range Coulomb interactions. The relaxation at multiple time scales show stretched-exponential decay of spatial correlations in irregular traps. Temperature dependence of characteristic time scales, depicting the structural relaxation of the system, show striking similarities with those observed for the glassy systems, indicating that some of the key signatures of supercooled liquids emerge in confinements with lower spatial symmetries.

Ultrafast dynamics of multi-exciton state coupled to coherent vibration in zinc chlorin aggregates for artificial photosynthesis.

PubMed

Shi, Tongchao; Liu, Zhengzheng; Miyatake, Tomohiro; Tamiaki, Hitoshi; Kobayashi, Takayoshi; Zhang, Zeyu; Du, Juan; Leng, Yuxin

2017-11-27

Ultrafast vibronic dynamics induced by the interaction of the Frenkel exciton with the coherent molecular vibrations in a layer-structured zinc chlorin aggregates prepared for artificial photosynthesis have been studied by 7.1 fs real-time vibrational spectroscopy with multi-spectrum detection. The fast decay of 100 ± 5fs is ascribed to the relaxation from the higher multi-exciton state (MES) to the one-exciton state, and the slow one of 863 ± 70fs is assigned to the relaxation from Q-exciton state to the dark nonfluorescent charge-transfer (CT) state, respectively. In addition, the wavelength dependences of the exciton-vibration coupling strength are found to follow the zeroth derivative of the transient absorption spectra of the exciton. It could be explained in term of the transition dipole moment modulated by dynamic intensity borrowing between the B transition and the Q transition through the vibronic interactions.

Ultrafast coherence transfer in DNA-templated silver nanoclusters

PubMed Central

Thyrhaug, Erling; Bogh, Sidsel Ammitzbøll; Carro-Temboury, Miguel R; Madsen, Charlotte Stahl; Vosch, Tom; Zigmantas, Donatas

2017-01-01

DNA-templated silver nanoclusters of a few tens of atoms or less have come into prominence over the last several years due to very strong absorption and efficient emission. Applications in microscopy and sensing have already been realized, however little is known about the excited-state structure and dynamics in these clusters. Here we report on a multidimensional spectroscopy investigation of the energy-level structure and the early-time relaxation cascade, which eventually results in the population of an emitting state. We find that the ultrafast intramolecular relaxation is strongly coupled to a specific vibrational mode, resulting in the concerted transfer of population and coherence between excited states on a sub-100 fs timescale. PMID:28548085

A Finite-Element Method Model of Soft Tissue Response to Impulsive Acoustic Radiation Force

PubMed Central

Palmeri, Mark L.; Sharma, Amy C.; Bouchard, Richard R.; Nightingale, Roger W.; Nightingale, Kathryn R

2010-01-01

Several groups are studying acoustic radiation force and its ability to image the mechanical properties of tissue. Acoustic radiation force impulse (ARFI) imaging is one modality using standard diagnostic ultrasound scanners to generate localized, impulsive, acoustic radiation forces in tissue. The dynamic response of tissue is measured via conventional ultrasonic speckle-tracking methods and provides information about the mechanical properties of tissue. A finite-element method (FEM) model has been developed that simulates the dynamic response of tissues, with and without spherical inclusions, to an impulsive acoustic radiation force excitation from a linear array transducer. These FEM models were validated with calibrated phantoms. Shear wave speed, and therefore elasticity, dictates tissue relaxation following ARFI excitation, but Poisson’s ratio and density do not significantly alter tissue relaxation rates. Increased acoustic attenuation in tissue increases the relative amount of tissue displacement in the near field compared with the focal depth, but relaxation rates are not altered. Applications of this model include improving image quality, and distilling material and structural information from tissue’s dynamic response to ARFI excitation. Future work on these models includes incorporation of viscous material properties and modeling the ultrasonic tracking of displaced scatterers. PMID:16382621

Direct Nanoscale Characterization of Submolecular Mobility in Complex Organic Non-linear Optical Systems

NASA Astrophysics Data System (ADS)

Knorr, Daniel; Gray, Tomoko; Kim, Tae-Dong; Luo, Jingdong; Jen, Alex; Overney, Rene

2008-03-01

For organic non-linear optical (NLO) materials composed of intricate molecular building blocks, the challenge is to deduce meaningful molecular scale mobility information to understand complex relaxation and phase behavior. This is crucial, as the process of achieving a robust acentric alignment strongly depends on the availability of inter- and intra-molecular mobilities outside the temperature range of the device operation window. Here, we introduce a nanoscale methodology based on scanning probe microscopy that provides direct insight into structural relaxations and shows great potential to direct material design of sophisticated macromolecules. It also offers a means by which mesoscale dynamics and cooperativity involved in relaxation processes can be quantified in terms of dynamic entropy and enthalpy. This study demonstrates this methodology to describe the mesocale dynamics of two systems (1) organic networking dendronized NLO molecular glasses that self-assemble into physically linked polymers due to quadrupolar phenyl-perfluorophenyl interactions and (2) dendronized side-chain electro-optic (EO) polymers. For the self assembling glasses, the degree of intermolecular cooperativity can be deduced using this methodology, while for the dendronized side-chain polymers, specific side chain mobilities are exploited to improve EO properties.

Dynamics and relaxation of charge carriers in poly(methylmethacrylate)-lithium salt based polymer electrolytes plasticized with ethylene carbonate

NASA Astrophysics Data System (ADS)

Pal, P.; Ghosh, A.

2016-07-01

In this paper, we have studied the dynamics and relaxation of charge carriers in poly(methylmethacrylate)-lithium salt based polymer electrolytes plasticized with ethylene carbonate. Structural and thermal properties have been examined using X-ray diffraction and differential scanning calorimetry, respectively. We have analyzed the complex conductivity spectra by using power law model coupled with the contribution of electrode polarization at low frequencies and high temperatures. The temperature dependence of the ionic conductivity and crossover frequency exhibits Vogel-Tammann-Fulcher type behavior indicating a strong coupling between the ionic and the polymer chain segmental motions. The scaling of the ac conductivity indicates that relaxation dynamics of charge carriers follows a common mechanism for all temperatures and ethylene carbonate concentrations. The analysis of the ac conductivity also shows the existence of a nearly constant loss in these polymer electrolytes at low temperatures and high frequencies. The fraction of free anions and ion pairs in polymer electrolyte have been obtained from the analysis of Fourier transform infrared spectra. It is observed that these quantities influence the behavior of the composition dependence of the ionic conductivity.

Diffusive dynamics of nanoparticles in ultra-confined media

DOE PAGES

Jacob, Jack Deodato; Conrad, Jacinta; Krishnamoorti, Ramanan; ...

2015-08-10

Differential dynamic microscopy (DDM) was used to investigate the diffusive dynamics of nanoparticles of diameter 200 400 nm that were strongly confined in a periodic square array of cylindrical nanoposts. The minimum distance between posts was 1.3 5 times the diameter of the nanoparticles. The image structure functions obtained from the DDM analysis were isotropic and could be fit by a stretched exponential function. The relaxation time scaled diffusively across the range of wave vectors studied, and the corresponding scalar diffusivities decreased monotonically with increased confinement. The decrease in diffusivity could be described by models for hindered diffusion that accountedmore » for steric restrictions and hydrodynamic interactions. The stretching exponent decreased linearly as the nanoparticles were increasingly confined by the posts. Altogether, these results are consistent with a picture in which strongly confined nanoparticles experience a heterogeneous spatial environment arising from hydrodynamics and volume exclusion on time scales comparable to cage escape, leading to multiple relaxation processes and Fickian but non-Gaussian diffusive dynamics.« less

Dynamic spin filtering at the Co/Alq3 interface mediated by weakly coupled second layer molecules.

PubMed

Droghetti, Andrea; Thielen, Philip; Rungger, Ivan; Haag, Norman; Großmann, Nicolas; Stöckl, Johannes; Stadtmüller, Benjamin; Aeschlimann, Martin; Sanvito, Stefano; Cinchetti, Mirko

2016-08-31

Spin filtering at organic-metal interfaces is often determined by the details of the interaction between the organic molecules and the inorganic magnets used as electrodes. Here we demonstrate a spin-filtering mechanism based on the dynamical spin relaxation of the long-living interface states formed by the magnet and weakly physisorbed molecules. We investigate the case of Alq3 on Co and, by combining two-photon photoemission experiments with electronic structure theory, show that the observed long-time spin-dependent electron dynamics is driven by molecules in the second organic layer. The interface states formed by physisorbed molecules are not spin-split, but acquire a spin-dependent lifetime, that is the result of dynamical spin-relaxation driven by the interaction with the Co substrate. Such spin-filtering mechanism has an important role in the injection of spin-polarized carriers across the interface and their successive hopping diffusion into successive molecular layers of molecular spintronics devices.

Dynamic spin filtering at the Co/Alq3 interface mediated by weakly coupled second layer molecules

PubMed Central

Droghetti, Andrea; Thielen, Philip; Rungger, Ivan; Haag, Norman; Großmann, Nicolas; Stöckl, Johannes; Stadtmüller, Benjamin; Aeschlimann, Martin; Sanvito, Stefano; Cinchetti, Mirko

2016-01-01

Spin filtering at organic-metal interfaces is often determined by the details of the interaction between the organic molecules and the inorganic magnets used as electrodes. Here we demonstrate a spin-filtering mechanism based on the dynamical spin relaxation of the long-living interface states formed by the magnet and weakly physisorbed molecules. We investigate the case of Alq3 on Co and, by combining two-photon photoemission experiments with electronic structure theory, show that the observed long-time spin-dependent electron dynamics is driven by molecules in the second organic layer. The interface states formed by physisorbed molecules are not spin-split, but acquire a spin-dependent lifetime, that is the result of dynamical spin-relaxation driven by the interaction with the Co substrate. Such spin-filtering mechanism has an important role in the injection of spin-polarized carriers across the interface and their successive hopping diffusion into successive molecular layers of molecular spintronics devices. PMID:27578395

From viscous to elastic sheets: Dynamics of smectic freely floating films

NASA Astrophysics Data System (ADS)

Harth, Kirsten; May, Kathrin; Trittel, Torsten; Stannarius, Ralf

2015-03-01

Oscillations and rupture of bubbles, composed of an inner fluid separated from an outer fluid by a membrane, represent an old but still immensely active field of research. Membrane properties except surface tension are often neglected for simple fluid films (e.g. soap bubbles), whereas they govern the dynamics in systems with more complex membranes (e.g. vesicles). Due to their layered phase structure, smectic liquid crystals can form stable, uniform and easy-to handle fluid films of immense aspect ratios. Recently, freely floating bubbles detached from a support were prepared. We analyze the relaxation from strongly non-spherical shapes and the rupture dynamics of such bubbles using high-speed video recordings. Peculiar dynamics intermediate between those of simple viscous fluid films and an elastic response emerge: Oscillations, slowed relaxation and even the formation of wrinkles and extrusions. We characterize these phenomena and propose explanations. We acknowledge funding by the German Aerospace Center DLR within Project OASIS-CO and German Science Foundation Project STA 425-28.

Dynamic spin filtering at the Co/Alq3 interface mediated by weakly coupled second layer molecules

NASA Astrophysics Data System (ADS)

Droghetti, Andrea; Thielen, Philip; Rungger, Ivan; Haag, Norman; Großmann, Nicolas; Stöckl, Johannes; Stadtmüller, Benjamin; Aeschlimann, Martin; Sanvito, Stefano; Cinchetti, Mirko

2016-08-01

Spin filtering at organic-metal interfaces is often determined by the details of the interaction between the organic molecules and the inorganic magnets used as electrodes. Here we demonstrate a spin-filtering mechanism based on the dynamical spin relaxation of the long-living interface states formed by the magnet and weakly physisorbed molecules. We investigate the case of Alq3 on Co and, by combining two-photon photoemission experiments with electronic structure theory, show that the observed long-time spin-dependent electron dynamics is driven by molecules in the second organic layer. The interface states formed by physisorbed molecules are not spin-split, but acquire a spin-dependent lifetime, that is the result of dynamical spin-relaxation driven by the interaction with the Co substrate. Such spin-filtering mechanism has an important role in the injection of spin-polarized carriers across the interface and their successive hopping diffusion into successive molecular layers of molecular spintronics devices.

Real-time observation of cascaded electronic relaxation processes in p-Fluorotoluene

NASA Astrophysics Data System (ADS)

Hao, Qiaoli; Deng, Xulan; Long, Jinyou; Wang, Yanmei; Abulimiti, Bumaliya; Zhang, Bing

2017-08-01

Ultrafast electronic relaxation processes following two photoexcitation of 400 nm in p-Fluorotoluene (pFT) have been investigated utilizing time-resolved photoelectron imaging coupled with time-resolved mass spectroscopy. Cascaded electronic relaxation processes started from the electronically excited S2 state are directly imaged in real time and well characterized by two distinct time constants of 85 ± 10 fs and 2.4 ± 0.3 ps. The rapid component corresponds to the lifetime of the initially excited S2 state, including the structure relaxation from the Franck-Condon region to the conical intersection of S2/S1 and the subsequent internal conversion to the highly excited S1 state. While, the slower relaxation constant is attributed to the further internal conversion to the high levels of S0 from the secondarily populated S1 locating in the channel three region. Moreover, dynamical differences with benzene and toluene of analogous structures, including, specifically, the slightly slower relaxation rate of S2 and the evidently faster decay of S1, are also presented and tentatively interpreted as the substituent effects. In addition, photoelectron kinetic energy and angular distributions reveal the feature of accidental resonances with low-lying Rydberg states (the 3p, 4s and 4p states) during the multi-photon ionization process, providing totally unexpected but very interesting information for pFT.

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Thermally induced magnetic relaxation in square artificial spin ice

DOE PAGES

Andersson, M. S.; Pappas, S. D.; Stopfel, H.; ...

2016-11-24

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here in this paper, we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system $-$ square artificial spin ice $-$ we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Usingmore » time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.« less

Thermally induced magnetic relaxation in square artificial spin ice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, M. S.; Pappas, S. D.; Stopfel, H.

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here in this paper, we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system $-$ square artificial spin ice $-$ we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Usingmore » time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.« less

Mismatch in cation size causes rapid anion dynamics in solid electrolytes: the role of the Arrhenius pre-factor.

PubMed

Breuer, Stefan; Wilkening, Martin

2018-03-28

Crystalline ion conductors exhibiting fast ion dynamics are of utmost importance for the development of, e.g., sensors or rechargeable batteries. In some layer-structured or nanostructured compounds fluorine ions participate in remarkably fast self-diffusion processes. As has been shown earlier, F ion dynamics in nanocrystalline, defect-rich BaF 2 is much higher than that in the coarse-grained counterpart BaF 2 . The thermally metastable fluoride (Ba,Ca)F 2 , which can be prepared by joint high-energy ball milling of the binary fluorides, exhibits even better ion transport properties. While long-range ion dynamics has been studied recently, less information is known about local ion hopping processes to which 19 F nuclear magnetic resonance (NMR) spin-lattice relaxation is sensitive. The present paper aims at understanding ion dynamics in metastable, nanocrystalline (Ba,Ca)F 2 by correlating short-range ion hopping with long-range transport properties. Variable-temperature NMR line shapes clearly indicate fast and slow F spin reservoirs. Surprisingly, from an atomic-scale point of view increased ion dynamics at intermediate values of composition is reflected by increased absolute spin-lattice relaxation rates rather than by a distinct minimum in activation energy. Hence, the pre-factor of the underlying Arrhenius relation, which is determined by the number of mobile spins, the attempt frequency and entropy effects, is identified as the parameter that directly enhances short-range ion dynamics in metastable (Ba,Ca)F 2 . Concerted ion migration could also play an important role to explain the anomalies seen in NMR spin-lattice relaxation.

Linear rheology and structure of molecular bottlebrushes with short side chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com; Brant, Patrick; Crowther, Donna J.

We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M{sub w}/M{sub n} 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M{sub e,aPP}= 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition,more » reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.« less

13C, 2H NMR Studies of Structural and Dynamical Modifications of Glucose-Exposed Porcine Aortic Elastin

PubMed Central

Silverstein, Moshe C.; Bilici, Kübra; Morgan, Steven W.; Wang, Yunjie; Zhang, Yanhang; Boutis, Gregory S.

2015-01-01

Elastin, the principal component of the elastic fiber of the extracellular matrix, imparts to vertebrate tissues remarkable resilience and longevity. This work focuses on elucidating dynamical and structural modifications of porcine aortic elastin exposed to glucose by solid-state NMR spectroscopic and relaxation methodologies. Results from macroscopic stress-strain tests are also presented and indicate that glucose-treated elastin is mechanically stiffer than the same tissue without glucose treatment. These measurements show a large hysteresis in the stress-strain behavior of glucose-treated elastin—a well-known signature of viscoelasticity. Two-dimensional relaxation NMR methods were used to investigate the correlation time, distribution, and population of water in these samples. Differences are observed between the relative populations of water, whereas the measured correlation times of tumbling motion of water across the samples were similar. 13C magic-angle-spinning NMR methods were applied to investigate structural and dynamical modifications after glucose treatment. Although some overall structure is preserved, the process of glucose exposure results in more heterogeneous structures and slower mobility. The correlation times of tumbling motion of the 13C-1H internuclear vectors in the glucose-treated sample are larger than in untreated samples, pointing to their more rigid structure. The 13C cross-polarization spectra reveal a notably increased α-helical character in the alanine motifs after glucose exposure. Results from molecular dynamics simulations are provided that add further insight into dynamical and structural changes of a short repeat, [VPGVG]5, an alanine pentamer, desmosine, and isodesmosine sites with and without glucose. The simulations point to changes in the entropic and energetic contributions in the retractive forces of VPGVG and AAAAA motifs. The most notable change is the increase of the energetic contribution in the retractive force due to peptide-glucose interactions of the VPGVG motif, which may play an important role in the observed stiffening in glucose-treated elastin. PMID:25863067

Transition to exponential relaxation in weakly disordered electron glasses

NASA Astrophysics Data System (ADS)

Ovadyahu, Z.

2018-06-01

The out-of-equilibrium excess conductance of electron-glasses Δ G (t ) typically relaxes with a logarithmic time dependence. Here it is shown that the log(t ) relaxation of a weakly disordered InxO film crosses over asymptotically to an exponential dependence Δ G (t )∝exp {-[t /τ (∞ )]} . This allows for assigning a well-defined relaxation-time τ (∞ ) for a given system disorder (characterized by the Ioffe-Regel parameter kFℓ ). Near the metal-insulator transition, τ (∞ ) obeys the scaling relation τ (∞ ) ∝[(kFℓ)C-kFℓ ] with the same critical disorder (kFℓ)C where the zero-temperature conductivity of this system vanishes. The latter defines the position of the disorder-driven metal-to-insulator transition which is a quantum-phase transition. In this regard the electron glass differs from classical glasses, such as the structural glass and spin glass. The ability to experimentally assign an unambiguous relaxation time allows us to demonstrate the steep dependence of the electron-glass dynamics on carrier concentration.

Accidental Kähler moduli inflation

NASA Astrophysics Data System (ADS)

Maharana, Anshuman; Rummel, Markus; Sumitomo, Yoske

2015-09-01

We study a model of accidental inflation in type IIB string theory where inflation occurs near the inflection point of a small Kähler modulus. A racetrack structure helps to alleviate the known concern that string-loop corrections may spoil Kähler Moduli Inflation unless having a significant suppression via the string coupling or a special brane setup. Also, the hierarchy of gauge group ranks required for the separation between moduli stabilization and inflationary dynamics is relaxed. The relaxation becomes more significant when we use the recently proposed D-term generated racetrack model.

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

NASA Astrophysics Data System (ADS)

He, Jianbin; Zhang, Zhiyong; Shi, Yunyu; Liu, Haiyan

2003-08-01

We describe a method for efficient sampling of the energy landscape of a protein in atomic molecular dynamics simulations. A simulation is divided into alternatively occurring relaxation phases and excitation phases. In the relaxation phase (conventional simulation), we use a frequently updated reference structure and deviations from this reference structure to mark whether the system has been trapped in a local minimum. In that case, the simulation enters the excitation phase, during which a few slow collective modes of the system are coupled to a higher temperature bath. After the system has escaped from the minimum (also judged by deviations from the reference structure) the simulation reenters the relaxation phase. The collective modes are obtained from a coarse-grained Gaussian elastic network model. The scheme, which we call ACM-AME (amplified collective motion-assisted minimum escaping), is compared with conventional simulations as well as an alternative scheme that elevates the temperature of all degrees of freedom during the excitation phase (amplified overall motion-assisted minimum escaping, or AOM-AME). Comparison is made using simulations on four peptides starting from non-native extended or all helical structures. In terms of sampling low energy conformations and continuously sampling new conformations throughout a simulation, the ACM-AME scheme demonstrates very good performance while the AOM-AME scheme shows little improvement upon conventional simulations. Limited success is achieved in producing structures close to the native structures of the peptides: for an S-peptide analog, the ACM-AME approach is able to reproduce its native helical structure, and starting from an all-helical structure of the villin headpiece subdomain (HP-36) in implicit solvent, two out of three 150 ns ACM-AME runs are able to sample structures with 3-4 Å backbone root-mean-square deviations from the nuclear magnetic resonance structure of the protein.

Glass transition and relaxation processes of nanocomposite polymer electrolytes.

PubMed

Money, Benson K; Hariharan, K; Swenson, Jan

2012-07-05

This study focus on the effect of δ-Al(2)O(3) nanofillers on the dc-conductivity, glass transition, and dielectric relaxations in the polymer electrolyte (PEO)(4):LiClO(4). The results show that there are three dielectric relaxation processes, α, β, and γ, in the systems, although the structural α-relaxation is hidden in the strong conductivity contribution and could therefore not be directly observed. However, by comparing an enhanced dc-conductivity, by approximately 2 orders of magnitude with 4 wt % δ-Al(2)O(3) added, with a decrease in calorimetric glass transition temperature, we are able to conclude that the dc-conductivity is directly coupled to the hidden α-relaxation, even in the presence of nanofillers (at least in the case of δ-Al(2)O(3) nanofillers at concentrations up to 4 wt %). This filler induced speeding up of the segmental polymer dynamics, i.e., the α-relaxation, can be explained by the nonattractive nature of the polymer-filler interactions, which enhance the "free volume" and mobility of polymer segments in the vicinity of filler surfaces.

Multiscale polar theory of microtubule and motor-protein assemblies

DOE PAGES

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; ...

2015-01-27

Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new “bioactive” liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics. It is not yet well understood how microscopic activity, which involves polarity-dependent interactions between motor proteins and microtubules, yields such larger-scale dynamical structures. In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by cross-linking motors allow us to study microscopic organization and stresses. Polarity sorting and cross-link relaxation emerge as two polar-specificmore » sources of active destabilizing stress. On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses. Finally, the results connect local polar structure to flow structures and defect dynamics.« less

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

PubMed

Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

2017-03-21

To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

NMR investigations of molecular dynamics

NASA Astrophysics Data System (ADS)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Cooling rate effects in sodium silicate glasses: Bridging the gap between molecular dynamics simulations and experiments

NASA Astrophysics Data System (ADS)

Li, Xin; Song, Weiying; Yang, Kai; Krishnan, N. M. Anoop; Wang, Bu; Smedskjaer, Morten M.; Mauro, John C.; Sant, Gaurav; Balonis, Magdalena; Bauchy, Mathieu

2017-08-01

Although molecular dynamics (MD) simulations are commonly used to predict the structure and properties of glasses, they are intrinsically limited to short time scales, necessitating the use of fast cooling rates. It is therefore challenging to compare results from MD simulations to experimental results for glasses cooled on typical laboratory time scales. Based on MD simulations of a sodium silicate glass with varying cooling rate (from 0.01 to 100 K/ps), here we show that thermal history primarily affects the medium-range order structure, while the short-range order is largely unaffected over the range of cooling rates simulated. This results in a decoupling between the enthalpy and volume relaxation functions, where the enthalpy quickly plateaus as the cooling rate decreases, whereas density exhibits a slower relaxation. Finally, we show that, using the proper extrapolation method, the outcomes of MD simulations can be meaningfully compared to experimental values when extrapolated to slower cooling rates.

Enhanced ultrafast relaxation rate in the Weyl semimetal phase of MoTe2 measured by time- and angle-resolved photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Crepaldi, A.; Autès, G.; Gatti, G.; Roth, S.; Sterzi, A.; Manzoni, G.; Zacchigna, M.; Cacho, C.; Chapman, R. T.; Springate, E.; Seddon, E. A.; Bugnon, Ph.; Magrez, A.; Berger, H.; Vobornik, I.; Kalläne, M.; Quer, A.; Rossnagel, K.; Parmigiani, F.; Yazyev, O. V.; Grioni, M.

2017-12-01

MoTe2 has recently been shown to realize in its low-temperature phase the type-II Weyl semimetal (WSM). We investigated by time- and angle- resolved photoelectron spectroscopy (tr-ARPES) the possible influence of the Weyl points on the electron dynamics above the Fermi level EF, by comparing the ultrafast response of MoTe2 in the trivial and topological phases. In the low-temperature WSM phase, we report an enhanced relaxation rate of electrons optically excited to the conduction band, which we interpret as a fingerprint of the local gap closure when Weyl points form. By contrast, we find that the electron dynamics of the related compound WTe2 is slower and temperature independent, consistent with a topologically trivial nature of this material. Our results shows that tr-ARPES is sensitive to the small modifications of the unoccupied band structure accompanying the structural and topological phase transition of MoTe2.

Local dynamics of glass-forming polystyrene thin films from atomistic simulation

NASA Astrophysics Data System (ADS)

Zhou, Yuxing; Milner, Scott

Despite a wide technological application ranging from protective coatings to organic solar cells, there still no consensus on the mechanism for the glass transition in polymer thin films a manifestation of the infamous glass problem under confinement. Many experimental and computational studies have observed a large deviation of nanoscale dynamical properties in thin films from the corresponding properties in bulk. In this work, we perform extensive united-atom simulations on atactic polystyrene free-standing thin films near the glass transition temperature and focus on the effect of free surface on the local dynamics. We study the segmental dynamics as a function of distance from the surface for different temperatures, from which relaxation time and thereby local Tg is obtained for each layer. We find the dynamics near free surface is not only enhanced but becomes less strongly temperature dependent as Tg is approached compared to the bulk. We find an increasing length scale associated with mobility propagation from the free surface as temperature decreases, but no correlation between local structure and enhanced relaxation rates near the surface, consistent with studies on bead-spring chains.

Multi-field C-13 NMR Relaxation Study of the Tripeptide Glycine-Proline-Glycine-NH2

NASA Astrophysics Data System (ADS)

Shibata, John; Forrester, Mary

2010-03-01

T1 and T2 C-13 NMR relaxation measurements were performed on the tripeptide Gly-Pro-Gly-NH2 on 300 MHz, 500 MHz, and 800 MHz NMR instruments (1). T1 and T2 data at different field strengths were analyzed to reveal the internal dynamics of this tripeptide. The results are compared to the classification scheme of rigidity by Anishetty, et al. (2). The dynamics of the tripeptide at different carbons in the molecule probe the site-specificity of the motions. We compare the dynamics revealed at the glycines with the dynamics in the proline ring. These motions are also being studied by molecular dynamics using the molecular modeling program Tinker (3). (1) Measurements at 500 MHz and 800 MHz were performed at the Alabama High Field NMR Center, University of Alabama at Huntsville, Huntsville, AL. (2) Anishetty, S., Pennathur, G., Anishetty, R. BMC Structural Biology 2:9 (2002). http://www.biomedcentral.com/1472-6807/2/9. (3) Dudek, M. J., Ramnarayan, K., Ponder, J. W. J. Comput. Chem. 19, 548 (1996). http://dasher.wustl.edu/tinker.

Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

NASA Astrophysics Data System (ADS)

Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

2004-05-01

The spin dynamics in the helical chain Co(hfac) 2NITPhOMe has been investigated by 1H NMR and μSR relaxation. In the temperature range 15

Shock wave structure in rarefied polyatomic gases with large relaxation time for the dynamic pressure

NASA Astrophysics Data System (ADS)

Taniguchi, Shigeru; Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

2018-05-01

The shock wave structure in rarefied polyatomic gases is analyzed based on extended thermodynamics (ET). In particular, the case with large relaxation time for the dynamic pressure, which corresponds to large bulk viscosity, is considered by adopting the simplest version of extended thermodynamics with only 6 independent fields (ET6); the mass density, the velocity, the temperature and the dynamic pressure. Recently, the validity of the theoretical predictions by ET was confirmed by the numerical analysis based on the kinetic theory in [S Kosuge and K Aoki: Phys. Rev. Fluids, Vol. 3, 023401 (2018)]. It was shown that numerical results using the polyatomic version of ellipsoidal statistical model agree with the theoretical predictions by ET for small or moderately large Mach numbers. In the present paper, first, we compare the theoretical predictions by ET6 with the ones by kinetic theory for large Mach number under the same assumptions, that is, the gas is polytropic and the bulk viscosity is proportional to the temperature. Second, the shock wave structure for large Mach number in a non-polytropic gas is analyzed with the particular interest in the effect of the temperature dependence of specific heat and the bulk viscosity on the shock wave structure. Through the analysis of the case of a rarefied carbon dioxide (CO2) gas, it is shown that these temperature dependences play important roles in the precise analysis of the structure for strong shock waves.

Probing the solvation structure and dynamics in ionic liquids by time-resolved infrared spectroscopy of 4-(dimethylamino)benzonitrile.

PubMed

Ando, Rômulo A; Brown-Xu, Samantha E; Nguyen, Lisa N Q; Gustafson, Terry L

2017-09-20

In this work we demonstrate the use of the push-pull model system 4-(dimethylamino)benzonitrile (DMABN) as a convenient molecular probe to investigate the local solvation structure and dynamics by means of time-resolved infrared spectroscopy (TRIR). The photochemical features associated with this system provide several advantages due to the high charge separation between the ground and charge transfer states involving the characteristic nitrile bond, and an excited state lifetime that is long enough to observe the slow solvation dynamics in organic solvents and ionic liquids. The conversion from a locally excited state to an intramolecular charge transfer state (LE-ICT) in ionic liquids shows similar kinetic lifetimes in comparison to organic solvents. This similarity confirms that such conversion depends solely on the intramolecular reorganization of DMABN in the excited state, and not by the dynamics of solvation. In contrast, the relative shift of the ν(CN) vibration during the relaxation of the ICT state reveals two distinct lifetimes that are sensitive to the solvent environment. This study reveals a fast time component which is attributed to the dipolar relaxation of the solvent and a slower time component related to the rotation of the dimethylamino group of DMABN.

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

NASA Astrophysics Data System (ADS)

Ochoa, D. A.; Levit, R.; Fancher, C. M.; Esteves, G.; Jones, J. L.; E García, J.

2017-05-01

Ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot be associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel-Fulcher-Tammann phenomenological equation. Results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.

Monolithic multigrid methods for two-dimensional resistive magnetohydrodynamics

DOE PAGES

Adler, James H.; Benson, Thomas R.; Cyr, Eric C.; ...

2016-01-06

Magnetohydrodynamic (MHD) representations are used to model a wide range of plasma physics applications and are characterized by a nonlinear system of partial differential equations that strongly couples a charged fluid with the evolution of electromagnetic fields. The resulting linear systems that arise from discretization and linearization of the nonlinear problem are generally difficult to solve. In this paper, we investigate multigrid preconditioners for this system. We consider two well-known multigrid relaxation methods for incompressible fluid dynamics: Braess--Sarazin relaxation and Vanka relaxation. We first extend these to the context of steady-state one-fluid viscoresistive MHD. Then we compare the two relaxationmore » procedures within a multigrid-preconditioned GMRES method employed within Newton's method. To isolate the effects of the different relaxation methods, we use structured grids, inf-sup stable finite elements, and geometric interpolation. Furthermore, we present convergence and timing results for a two-dimensional, steady-state test problem.« less

Optimal Ge/SiGe nanofin geometries for hole mobility enhancement: Technology limit from atomic simulations

NASA Astrophysics Data System (ADS)

Vedula, Ravi Pramod; Mehrotra, Saumitra; Kubis, Tillmann; Povolotskyi, Michael; Klimeck, Gerhard; Strachan, Alejandro

2015-05-01

We use first principles simulations to engineer Ge nanofins for maximum hole mobility by controlling strain tri-axially through nano-patterning. Large-scale molecular dynamics predict fully relaxed, atomic structures for experimentally achievable nanofins, and orthogonal tight binding is used to obtain the corresponding electronic structure. Hole transport properties are then obtained via a linearized Boltzmann formalism. This approach explicitly accounts for free surfaces and associated strain relaxation as well as strain gradients which are critical for quantitative predictions in nanoscale structures. We show that the transverse strain relaxation resulting from the reduction in the aspect ratio of the fins leads to a significant enhancement in phonon limited hole mobility (7× over unstrained, bulk Ge, and 3.5× over biaxially strained Ge). Maximum enhancement is achieved by reducing the width to be approximately 1.5 times the height and further reduction in width does not result in additional gains. These results indicate significant room for improvement over current-generation Ge nanofins, provide geometrical guidelines to design optimized geometries and insight into the physics behind the significant mobility enhancement.

Ion dynamics in a new class of materials: nanoglassy lithium alumosilicates

NASA Astrophysics Data System (ADS)

Stanje, B.; Bottke, P.; Breuer, S.; Hanzu, I.; Heitjans, P.; Wilkening, M.

2018-03-01

In many cases nanocrystalline materials, prepared through high-energy ball milling, reveal enhanced ion dynamics when compared to the situation in the coarse-grained analogues. This effect, which has particularly been seen for lithium alumosilicates, has been ascribed to structural disorder, i.e., the introduction of defect sites during mechanical treatment. Much less is, however, known about ion transport in nanostructured amorphous materials, e.g., nanoglassy compounds, which are regarded as a new class of functional materials. Following earlier studies on nanoglassy lithium alumosilicates and borates, here we studied ion dynamics in nanoglassy petalite LiAlSi4O10. While conductivity spectroscopy unequivocally reveals that long-range ion dynamics in nanoglassy LiAlSi4O10 decreases upon milling, local dynamics, sensed by 7Li nuclear magnetic resonance (NMR) spin-lattice relaxation, points to enhanced Li ion mobility compared to the non-treated glass. Most likely, as for nanocrystalline ceramics also for nanoglassy samples a heterogeneous structure, consisting of bulk and interfacial regions, is formed. For LiAlSi4O10 these interfacial regions, characterized by a higher degree of free volume, might act as hosts for spins experiencing fast longitudinal NMR relaxation. Obviously, these regions do not form a through-going network, which would allow the ions to move over long distances as quickly as in the unmilled glass.

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

Global dynamics of a stochastic neuronal oscillator

NASA Astrophysics Data System (ADS)

Yamanobe, Takanobu

2013-11-01

Nonlinear oscillators have been used to model neurons that fire periodically in the absence of input. These oscillators, which are called neuronal oscillators, share some common response structures with other biological oscillations such as cardiac cells. In this study, we analyze the dependence of the global dynamics of an impulse-driven stochastic neuronal oscillator on the relaxation rate to the limit cycle, the strength of the intrinsic noise, and the impulsive input parameters. To do this, we use a Markov operator that both reflects the density evolution of the oscillator and is an extension of the phase transition curve, which describes the phase shift due to a single isolated impulse. Previously, we derived the Markov operator for the finite relaxation rate that describes the dynamics of the entire phase plane. Here, we construct a Markov operator for the infinite relaxation rate that describes the stochastic dynamics restricted to the limit cycle. In both cases, the response of the stochastic neuronal oscillator to time-varying impulses is described by a product of Markov operators. Furthermore, we calculate the number of spikes between two consecutive impulses to relate the dynamics of the oscillator to the number of spikes per unit time and the interspike interval density. Specifically, we analyze the dynamics of the number of spikes per unit time based on the properties of the Markov operators. Each Markov operator can be decomposed into stationary and transient components based on the properties of the eigenvalues and eigenfunctions. This allows us to evaluate the difference in the number of spikes per unit time between the stationary and transient responses of the oscillator, which we show to be based on the dependence of the oscillator on past activity. Our analysis shows how the duration of the past neuronal activity depends on the relaxation rate, the noise strength, and the impulsive input parameters.

Global dynamics of a stochastic neuronal oscillator.

PubMed

Yamanobe, Takanobu

2013-11-01

Nonlinear oscillators have been used to model neurons that fire periodically in the absence of input. These oscillators, which are called neuronal oscillators, share some common response structures with other biological oscillations such as cardiac cells. In this study, we analyze the dependence of the global dynamics of an impulse-driven stochastic neuronal oscillator on the relaxation rate to the limit cycle, the strength of the intrinsic noise, and the impulsive input parameters. To do this, we use a Markov operator that both reflects the density evolution of the oscillator and is an extension of the phase transition curve, which describes the phase shift due to a single isolated impulse. Previously, we derived the Markov operator for the finite relaxation rate that describes the dynamics of the entire phase plane. Here, we construct a Markov operator for the infinite relaxation rate that describes the stochastic dynamics restricted to the limit cycle. In both cases, the response of the stochastic neuronal oscillator to time-varying impulses is described by a product of Markov operators. Furthermore, we calculate the number of spikes between two consecutive impulses to relate the dynamics of the oscillator to the number of spikes per unit time and the interspike interval density. Specifically, we analyze the dynamics of the number of spikes per unit time based on the properties of the Markov operators. Each Markov operator can be decomposed into stationary and transient components based on the properties of the eigenvalues and eigenfunctions. This allows us to evaluate the difference in the number of spikes per unit time between the stationary and transient responses of the oscillator, which we show to be based on the dependence of the oscillator on past activity. Our analysis shows how the duration of the past neuronal activity depends on the relaxation rate, the noise strength, and the impulsive input parameters.

Nanoscale cluster dynamics in the martensitic phase of Ni-Mn-Sn shape-memory alloys

NASA Astrophysics Data System (ADS)

Hoch, Michael; Yuan, Shaojie; Kuhns, Phillip; Reyes, Arneil; Brooks, James; Phelan, Daniel; Srivastava, Vijay; James, Richard; Leighton, Chris

2015-03-01

The martensitic phases of Ni-Mn-Sn magnetic shape memory alloys exhibit interesting low temperature magnetic properties, including intrinsic superparamagnetism and exchange bias effects, which have previously been rationalized in terms of spin clusters. We show here that spin-echo NMR, involving 55Mn hyperfine fields, permits ferromagnetic and antiferromagnetic nanoregions to be directly identified in these materials and yields estimates of their size distributions. Nuclear relaxation rate measurements, made as a function of temperature, provide information on both the dynamics and on the electronic structure of the nanoregions. The relaxation rates are analyzed using a combination of Redfield and Korringa mechanisms, the Korringa procedure providing information on the density of states at the Fermi level. Results will be presented for a number of these alloys. DMR-1309463.

Mapping hydration dynamics around a protein surface

PubMed Central

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2007-01-01

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (≈1–8 ps) and tens to hundreds of picoseconds (≈20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

Team dynamics in isolated, confined environments - Saturation divers and high altitude climbers

NASA Technical Reports Server (NTRS)

Kanki, Barbara G.; Gregorich, Steven E.

1992-01-01

The effects of leadership dynamics and social organization factors on team performance under conditions of high altitude climbing and deep sea diving are studied. Teams of two to four members that know each other well and have a relaxed informal team structure with much sharing of responsibilities are found to do better than military teams with more than four members who do not know each other well and have a formal team structure with highly specialized rules. Professionally guided teams with more than four members, a formally defined team structure, and clearly designated role assignments did better than 'club' teams of more than four members with a fairly informal team structure and little role specialization.

Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.

PubMed

Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R

2015-07-08

We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.

Shear banding leads to accelerated aging dynamics in a metallic glass

NASA Astrophysics Data System (ADS)

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; Shin, Jeremy; Maaß, Robert

2018-01-01

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. Using site-specific x-ray photon correlation spectroscopy, we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretched exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. These insights highlight how a ubiquitous nanoscale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.

Significant difference in the dynamics between strong and fragile glass formers.

PubMed

Furukawa, Akira; Tanaka, Hajime

2016-11-01

Glass-forming liquids are often classified into strong glass formers with nearly Arrhenius behavior and fragile ones with super-Arrhenius behavior. We reveal a significant difference in the dynamics between these two types of glass formers through molecular dynamics simulations: In strong glass formers, the relaxation dynamics of density fluctuations is nondiffusive, whereas in fragile glass formers it exhibits diffusive behavior. We demonstrate that this distinction is a direct consequence of the fundamental difference in the underlying elementary relaxation process between these two dynamical classes of glass formers. For fragile glass formers, a density-exchange process proceeds the density relaxation, which takes place locally at the particle level in normal states but is increasingly cooperative and nonlocal as the temperature is lowered in supercooled states. On the other hand, in strong glass formers, such an exchange process is not necessary for density relaxation due to the presence of other local relaxation channels. Our finding provides a novel insight into Angell's classification scheme from a hydrodynamic perspective.

Shear banding leads to accelerated aging dynamics in a metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

Shear banding leads to accelerated aging dynamics in a metallic glass

DOE PAGES

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; ...

2018-01-11

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

Femtosecond Heterodyne Transient Grating Detection of Conformational Dynamics in the S0 (11Ag-) State of Carotenoids After Nonradiative Decay of the S2 (11Bu+) State

NASA Astrophysics Data System (ADS)

Roscioli, Jerome D.; Ghosh, Soumen; Bishop, Michael M.; Lafountain, Amy M.; Frank, Harry A.; Beck, Warren F.

Transient grating spectroscopy was used to study the dynamics of nonradiative decay of the S1 (21Ag-) state in ß-carotene and peridinin after optical preparation of the S2) state. The kinetics of the recovery of the absorption and dispersion components of the third-order signal exhibit significantly different time constants. For β-carotene in benzonitrile, the absorption and dispersion recovery time constants are 11.6 and 10.2 ps. For peridinin in methanol, the time constants are 9.9 and 7.4 ps. These results indicate that the initial product of the decay of the S1 state is a conformationally displaced structure. The decay rate for the S1 state and the conformational relaxation rate are both slowed in peridinin as the polarity of the solvent decreases; in ethyl acetate, the conformational relaxation time constant is 45 ps, which rules out a dominant contribution from vibrational cooling. These results indicate that the S1 state develops intramolecular charge transfer character owing to distortions along torsional and out-of-plane coordinates, with a pyramidal structure favored as the most stable conformation. Recovery of the photoselected ground state conformation involves a reverse charge-transfer event followed by relaxation to a planar structure. Work supported by Photosynthetic Systems Program of the U.S. Department of Energy under Grant DE-SC0010847.

Time scales of relaxation dynamics during transient conditions in two-phase flow: RELAXATION DYNAMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schlüter, Steffen; Berg, Steffen; Li, Tianyi

2017-06-01

The relaxation dynamics toward a hydrostatic equilibrium after a change in phase saturation in porous media is governed by fluid reconfiguration at the pore scale. Little is known whether a hydrostatic equilibrium in which all interfaces come to rest is ever reached and which microscopic processes govern the time scales of relaxation. Here we apply fast synchrotron-based X-ray tomography (X-ray CT) to measure the slow relaxation dynamics of fluid interfaces in a glass bead pack after fast drainage of the sample. The relaxation of interfaces triggers internal redistribution of fluids, reduces the surface energy stored in the fluid interfaces, andmore » relaxes the contact angle toward the equilibrium value while the fluid topology remains unchanged. The equilibration of capillary pressures occurs in two stages: (i) a quick relaxation within seconds in which most of the pressure drop that built up during drainage is dissipated, a process that is to fast to be captured with fast X-ray CT, and (ii) a slow relaxation with characteristic time scales of 1–4 h which manifests itself as a spontaneous imbibition process that is well described by the Washburn equation for capillary rise in porous media. The slow relaxation implies that a hydrostatic equilibrium is hardly ever attained in practice when conducting two-phase experiments in which a flux boundary condition is changed from flow to no-flow. Implications for experiments with pressure boundary conditions are discussed.« less

Role of thermal history in atomic dynamics of chalcogenide glass: A case study on Ge{sub 20}Te{sub 80} glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Yashika; Kalra, Geetanjali; Murugavel, Sevi, E-mail: murug@physics.du.ac.in

The non-existence of thermodynamic equilibrium in glasses, their thermal history plays a very crucial role in explaining the relaxation behavior in various time scales and its configurational states. More importantly, the associated relaxation behavior is related mainly to the structural phenomenon of the glasses. Here, we report the dependence of quenching rate on the variation of structural units. The local structures of these glasses are monitored by recording the Raman spectroscopy and related to the different configurational states. The observed variations in structural differences are reflected in the measured density of the corresponding glasses. The quenching rate dependent of themore » relative fractions of edge-shared and corner-shared GeTe{sub 4} tetrahedral units are shown to be consistent with the corresponding variations in the measured density values.« less

Aging of the Johari-Goldstein relaxation in the glass-forming liquids sorbitol and xylitol

NASA Astrophysics Data System (ADS)

Yardimci, Hasan; Leheny, Robert L.

2006-06-01

Employing frequency-dependent dielectric susceptibility we characterize the aging in two supercooled liquids, sorbitol and xylitol, below their calorimetric glass transition temperatures. In addition to the alpha relaxation that tracks the structural dynamics, the susceptibility of both liquids possesses a secondary Johari-Goldstein relaxation at higher frequencies. Following a quench through the glass transition, the susceptibility slowly approaches the equilibrium behavior. For both liquids, the magnitude of the Johari-Goldstein relaxation displays a dependence on the time since the quench, or aging time, that is quantitatively very similar to the age dependence of the alpha peak frequency. The Johari-Goldstein relaxation time remains constant during aging for sorbitol while it decreases slightly with age for xylitol. Hence, one cannot sensibly assign a fictive temperature to the Johari-Goldstein relaxation. This behavior contrasts with that of liquids lacking distinct Johari-Goldstein peaks for which the excess wing of the alpha peak tracks the main part of the peak during aging, enabling the assignment of a single fictive temperature to the entire spectrum. The aging behavior of the Johari-Goldstein relaxation time further calls into question the possibility that the relaxation time possesses stronger temperature dependence in equilibrium than is observed in the out-of-equilibrium state below the glass transition.

Aging kinetics of levoglucosan orientational glass as a rate dispersion process and consequences for the heterogeneous dynamics view

DOE Office of Scientific and Technical Information (OSTI.GOV)

Righetti, Maria Cristina; Tombari, Elpidio; Johari, G. P., E-mail: joharig@mcmaster.ca

Aging kinetics of a glass is currently modeled in terms of slowing of its α-relaxation dynamics, whose features are interpreted in terms of dynamic heterogeneity, i.e., formation and decay of spatially and temporally distinct nm-size regions. To test the merits of this view, we studied the calorimetric effects of aging an orientational glass of levoglucosan crystal in which such regions would not form in the same way as they form in liquids, and persist in structural glasses, because there is no liquid-like molecular diffusion in the crystal. By measuring the heat capacity, C{sub p}, we determined the change in themore » enthalpy, H, and the entropy, S, during two aging-protocols: (a) keeping the samples isothermally at temperature, T{sub a}, and measuring the changes after different aging times, t{sub a}, and (b) keeping the samples at different T{sub a}s and measuring the changes after the same t{sub a}. A model-free analysis of the data shows that as t{sub a} is increased (procedure (a)), H and S decrease according to a dispersive rate kinetics, and as T{sub a} is increased (procedure (b)), H and S first increase, reach a local maximum at a certain T{sub a}, and then decrease. Even though there is no translational diffusion to produce (liquid-like) free volume, and no translational-rotational decoupling, the aging features are indistinguishable from those of structural glasses. We also find that the Kohlrausch parameter, originally fitted to the glass-aging data, decreases with decrease in T{sub a}, which is incompatible with the current use of the aging data for estimating the α-relaxation time. We argue that the vibrational state of a glass is naturally incompatible with its configurational state, and both change on aging until they are compatible, in the equilibrium liquid. So, dipolar fluctuations seen as the α-relaxation would not be the same motions that cause aging. We suggest that aging kinetics is intrinsically dispersive with its own characteristic rate constant and it does not yield the α-relaxation rate. In this view, thermodynamic and other properties define the fictive temperature; the real or imaginary components of a dynamic property do not define it. While particles’ overall motions may still play a crucial role in (structural) glass physics, we conclude that translational diffusion alone is not a requirement for structure stabilization on aging of a kinetically frozen state.« less

Testing the paradigms of the glass transition in colloids

NASA Astrophysics Data System (ADS)

Zia, Roseanna; Wang, Jialun; Peng, Xiaoguang; Li, Qi; McKenna, Gregory

2017-11-01

Many molecular liquids freeze upon fast enough cooling. This so-called glass state is path dependent and out of equilibrium, as measured by the Kovacs signature experiments, i.e. intrinsic isotherms, asymmetry of approach and memory effect. The reasons for this path- and time-dependence are not fully understood, due to fast molecular relaxations. Colloids provide a natural way to model such behavior, owing to disparity in colloidal versus solvent time scales that can slow dynamics. To shed light on the ambiguity of glass transition, we study via large-scale dynamic simulation of hard-sphere colloidal glass after volume-fraction jumps, where particle size increases at fixed system volume followed by protocols of the McKenna-Kovacs signature experiments. During and following each jump, the positions, velocities, and particle-phase stress are tracked and utilized to characterize relaxation time scales. The impact of both quench depth and quench rate on arrested dynamics and ``state'' variables is explored. In addition, we expand our view to various structural signatures, and rearrangement mechanism is proposed. The results provide insight into not only the existence of an ``ideal'' glass transition, but also the role of structure in such a dense amorphous system.

Identifying time scales for violation/preservation of Stokes-Einstein relation in supercooled water

PubMed Central

Kawasaki, Takeshi; Kim, Kang

2017-01-01

The violation of the Stokes-Einstein (SE) relation D ~ (η/T)−1 between the shear viscosity η and the translational diffusion constant D at temperature T is of great importance for characterizing anomalous dynamics of supercooled water. Determining which time scales play key roles in the SE violation remains elusive without the measurement of η. We provide comprehensive simulation results of the dynamic properties involving η and D in the TIP4P/2005 supercooled water. This enabled the thorough identification of the appropriate time scales for the SE relation Dη/T. In particular, it is demonstrated that the temperature dependence of various time scales associated with structural relaxation, hydrogen bond breakage, stress relaxation, and dynamic heterogeneities can be definitely classified into only two classes. That is, we propose the generalized SE relations that exhibit “violation” or “preservation.” The classification depends on the examined time scales that are coupled or decoupled with the diffusion. On the basis of the classification, we explain the physical origins of the violation in terms of the increase in the plateau modulus and the nonexponentiality of stress relaxation. This implies that the mechanism of SE violation is attributed to the attained solidity upon supercooling, which is in accord with the growth of non-Gaussianity and spatially heterogeneous dynamics. PMID:28835918

The relationship of dynamical heterogeneity to the Adam-Gibbs and random first-order transition theories of glass formation.

PubMed

Starr, Francis W; Douglas, Jack F; Sastry, Srikanth

2013-03-28

We carefully examine common measures of dynamical heterogeneity for a model polymer melt and test how these scales compare with those hypothesized by the Adam and Gibbs (AG) and random first-order transition (RFOT) theories of relaxation in glass-forming liquids. To this end, we first analyze clusters of highly mobile particles, the string-like collective motion of these mobile particles, and clusters of relative low mobility. We show that the time scale of the high-mobility clusters and strings is associated with a diffusive time scale, while the low-mobility particles' time scale relates to a structural relaxation time. The difference of the characteristic times for the high- and low-mobility particles naturally explains the well-known decoupling of diffusion and structural relaxation time scales. Despite the inherent difference of dynamics between high- and low-mobility particles, we find a high degree of similarity in the geometrical structure of these particle clusters. In particular, we show that the fractal dimensions of these clusters are consistent with those of swollen branched polymers or branched polymers with screened excluded-volume interactions, corresponding to lattice animals and percolation clusters, respectively. In contrast, the fractal dimension of the strings crosses over from that of self-avoiding walks for small strings, to simple random walks for longer, more strongly interacting, strings, corresponding to flexible polymers with screened excluded-volume interactions. We examine the appropriateness of identifying the size scales of either mobile particle clusters or strings with the size of cooperatively rearranging regions (CRR) in the AG and RFOT theories. We find that the string size appears to be the most consistent measure of CRR for both the AG and RFOT models. Identifying strings or clusters with the "mosaic" length of the RFOT model relaxes the conventional assumption that the "entropic droplets" are compact. We also confirm the validity of the entropy formulation of the AG theory, constraining the exponent values of the RFOT theory. This constraint, together with the analysis of size scales, enables us to estimate the characteristic exponents of RFOT.

Ultrafast hole carrier relaxation dynamics in p-type CuO nanowires

PubMed Central

2011-01-01

Ultrafast hole carrier relaxation dynamics in CuO nanowires have been investigated using transient absorption spectroscopy. Following femtosecond pulse excitation in a non-collinear pump-probe configuration, a combination of non-degenerate transmission and reflection measurements reveal initial ultrafast state filling dynamics independent of the probing photon energy. This behavior is attributed to the occupation of states by photo-generated carriers in the intrinsic hole region of the p-type CuO nanowires located near the top of the valence band. Intensity measurements indicate an upper fluence threshold of 40 μJ/cm2 where carrier relaxation is mainly governed by the hole dynamics. The fast relaxation of the photo-generated carriers was determined to follow a double exponential decay with time constants of 0.4 ps and 2.1 ps. Furthermore, time-correlated single photon counting measurements provide evidence of three exponential relaxation channels on the nanosecond timescale. PMID:22151927

Normal modes of weak colloidal gels

NASA Astrophysics Data System (ADS)

Varga, Zsigmond; Swan, James W.

2018-01-01

The normal modes and relaxation rates of weak colloidal gels are investigated in calculations using different models of the hydrodynamic interactions between suspended particles. The relaxation spectrum is computed for freely draining, Rotne-Prager-Yamakawa, and accelerated Stokesian dynamics approximations of the hydrodynamic mobility in a normal mode analysis of a harmonic network representing several colloidal gels. We find that the density of states and spatial structure of the normal modes are fundamentally altered by long-ranged hydrodynamic coupling among the particles. Short-ranged coupling due to hydrodynamic lubrication affects only the relaxation rates of short-wavelength modes. Hydrodynamic models accounting for long-ranged coupling exhibit a microscopic relaxation rate for each normal mode, λ that scales as l-2, where l is the spatial correlation length of the normal mode. For the freely draining approximation, which neglects long-ranged coupling, the microscopic relaxation rate scales as l-γ, where γ varies between three and two with increasing particle volume fraction. A simple phenomenological model of the internal elastic response to normal mode fluctuations is developed, which shows that long-ranged hydrodynamic interactions play a central role in the viscoelasticity of the gel network. Dynamic simulations of hard spheres that gel in response to short-ranged depletion attractions are used to test the applicability of the density of states predictions. For particle concentrations up to 30% by volume, the power law decay of the relaxation modulus in simulations accounting for long-ranged hydrodynamic interactions agrees with predictions generated by the density of states of the corresponding harmonic networks as well as experimental measurements. For higher volume fractions, excluded volume interactions dominate the stress response, and the prediction from the harmonic network density of states fails. Analogous to the Zimm model in polymer physics, our results indicate that long-ranged hydrodynamic interactions play a crucial role in determining the microscopic dynamics and macroscopic properties of weak colloidal gels.

Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

PubMed

Choudhuri, Jyoti Roy; Chandra, Amalendu

2014-10-07

We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

Principal Component Relaxation Mode Analysis of an All-Atom Molecular Dynamics Simulation of Human Lysozyme

NASA Astrophysics Data System (ADS)

Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi

2013-02-01

A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2017-02-01

We use all atom molecular dynamics simulations to investigate the influence of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6) ionic liquid on the structure and transport properties of poly(ethylene oxide) (PEO) polymer electrolytes doped with LiPF6 salt. We observe enhanced diffusivities of the Li+, PF6-, and BMIM+ ions with increasing loading of the ionic liquid. Interplay between the different ion-ion and ion-polymer interactions is seen to lead to a destabilization of the Li-PF6 coordination and increase in the strength of association between the Li+ cations and the polymer backbone. As a consequence, the polymer segmental relaxation times are shown to be only moderately affected by the addition of ionic liquids. The ionic-liquid induced changes in the mobilities of Li+ ions are seen to be correlated to polymer segmental relaxation times. However, the mobilities of BMIM+ ions are seen to be more strongly correlated to the BMIM-PF6 ion-pair relaxation times.

Quantitative analysis of backbone dynamics in a crystalline protein from nitrogen-15 spin-lattice relaxation.

PubMed

Giraud, Nicolas; Blackledge, Martin; Goldman, Maurice; Böckmann, Anja; Lesage, Anne; Penin, François; Emsley, Lyndon

2005-12-28

A detailed analysis of nitrogen-15 longitudinal relaxation times in microcrystalline proteins is presented. A theoretical model to quantitatively interpret relaxation times is developed in terms of motional amplitude and characteristic time scale. Different averaging schemes are examined in order to propose an analysis of relaxation curves that takes into account the specificity of MAS experiments. In particular, it is shown that magic angle spinning averages the relaxation rate experienced by a single spin over one rotor period, resulting in individual relaxation curves that are dependent on the orientation of their corresponding carousel with respect to the rotor axis. Powder averaging thus leads to a nonexponential behavior in the observed decay curves. We extract dynamic information from experimental decay curves, using a diffusion in a cone model. We apply this study to the analysis of spin-lattice relaxation rates of the microcrystalline protein Crh at two different fields and determine differential dynamic parameters for several residues in the protein.

Effect of pressure on β relaxation in La60Ni15Al25 metallic glass

NASA Astrophysics Data System (ADS)

Xu, H. Y.; Sheng, H. W.; Li, M. Z.

2018-03-01

The effect of pressure on β relaxation in La60Ni15Al25 metallic glass (MG) was investigated by activation-relaxation technique in combination with molecular dynamics simulation. It is found that the β relaxation behavior and the potential energy landscape are significantly modulated by pressure. With increasing pressure, the atomic motion in β relaxation in La60Ni15Al25 MG changes from hopping-dominated to the string-like-dominated motion with increased activation energy. Moreover, while the hopping motion is gradually suppressed as pressure is increased, the cooperative rearrangements with more atoms involved but very low activation energies are significantly enhanced by pressure. It is further found that the "subbasins" in the potential energy landscape in La60Ni15Al25 MG become deeper and steeper with increasing pressure, leading to the increase of activation energy. Meanwhile, some neighboring "subbasins" merge under pressure accompanied by the disappearance of energy barriers in-between, leading to events with very low activation energies in the β relaxation. The atomic structure analysis reveals that the transformation of atomic motions in β relaxation in La60Ni15Al25 MG under pressure is strongly correlated with the decrease of pentagon-rich atomic clusters and the increase of clusters with fewer pentagons. These findings provide a new understanding of the β relaxation mechanism and some clues for tuning β relaxation in MGs.

Structural, optical and Carrier dynamics of self-assembled InGaN nanocolumns on Si(111)

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Devi, Pooja; Soto Rodriguez, P. E. D.; Jain, Rishabh; Jaggi, Neena; Sinha, R. K.; Kumar, Mahesh

2018-05-01

We investigated the morphological, structural, optical, electrical and carrier relaxation dynamic changes on the self-assembled grown InGaN nanocolumns (NCs) directly on p-Si(111) substrate at two different substrate temperature, namely 580 °C (A) and 500 °C (B). The emission wavelength of comparably low temperature (LT) grown NCs was red-shifted from 3.2eV to 2.4eV. First observations on the charge carrier dynamics of these directly grown NCs show comparable broad excited state absorption (ESA) for LT gown NCs, which manifest bi-exponential decay due to the radiative defects generated during the coalescence of these NCs.

Dynamical Heterogeneity in Granular Fluids and Structural Glasses

NASA Astrophysics Data System (ADS)

Avila, Karina E.

Our current understanding of the dynamics of supercooled liquids and other similar slowly evolving (glassy) systems is rather limited. One aspect that is particularly poorly understood is the origin and behavior of the strong non trivial fluctuations that appear in the relaxation process toward equilibrium. Glassy systems and granular systems both present regions of particles moving cooperatively and at different rates from other regions. This phenomenon is known as spatially heterogeneous dynamics. A detailed explanation of this phenomenon may lead to a better understanding of the slow relaxation process, and perhaps it could even help to explain the presence of the glass transition. This dissertation concentrates on studying dynamical heterogeneity by analyzing simulation data for models of granular materials and structural glasses. For dissipative granular fluids, the growing behavior of dynamical heterogeneities is studied for different densities and different degrees of inelasticity in the particle collisions. The correlated regions are found to grow rapidly as the system approaches dynamical arrest. Their geometry is conserved even when probing at different cutoff length in the correlation function or when the energy dissipation in the system is increased. For structural glasses, I test a theoretical framework that models dynamical heterogeneity as originated in the presence of Goldstone modes, which emerge from a broken continuous time reparametrization symmetry. This analysis is based on quantifying the size and the spatial correlations of fluctuations in the time variable and of other kinds of fluctuations. The results obtained here agree with the predictions of the hypothesis. In particular, the fluctuations associated to the time reparametrization invariance become stronger for low temperatures, long timescales, and large coarse graining lengths. Overall, this research points to dynamical heterogeneity to be described for granular systems similarly than for other glassy systems and it provides evidence in favor of a particular theory for the origin of dynamical heterogeneity.

Optical studies of dynamical processes in disordered materials

NASA Astrophysics Data System (ADS)

Yen, William M.

1990-12-01

The research continues to focus on the study of the structure and the dynamic behavior of insulating solids which can be activated optically. The physical processes which produce relaxation and energy transfer in the optical excited states were of particular interest. The studies were based principally on optical laser spectroscopic techniques which reveal a more detailed view of the materials of interest and which will ultimately lead to the development of more efficient optoelectronic materials.

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2015-10-01

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratio for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Rui; Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu

2015-10-14

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratiomore » for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.« less

Star PolyMOCs with Diverse Structures, Dynamics, and Functions by Three-Component Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yufeng; Gu, Yuwei; Keeler, Eric G.

2016-12-05

We report star polymer metal–organic cage (polyMOC) materials whose structures, mechanical properties, functionalities, and dynamics can all be precisely tailored through a simple three-component assembly strategy. The star polyMOC network is composed of tetra-arm star polymers functionalized with ligands on the chain ends, small molecule ligands, and palladium ions; polyMOCs are formed via metal–ligand coordination and thermal annealing. The ratio of small molecule ligands to polymer-bound ligands determines the connectivity of the MOC junctions and the network structure. The use of large M12L24 MOCs enables great flexibility in tuning this ratio, which provides access to a rich spectrum of materialmore » properties including tunable moduli and relaxation dynamics.« less

Protein electron transfer: is biology (thermo)dynamic?

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.

2015-12-01

Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated kinetics, which extends the transition-state theory to dynamically dispersive media. Releasing the grip of thermodynamics in kinetic calculations through nonergodicity provides the mechanism for an efficient optimization between reaction rates and the spectrum of relaxation times of the protein-water thermal bath. Bath dynamics, it appears, play as important role as the free energy in optimizing biology’s performance.

XUV-induced reactions in benzene on sub-10 fs timescale: nonadiabatic relaxation and proton migration.

PubMed

Galbraith, M C E; Smeenk, C T L; Reitsma, G; Marciniak, A; Despré, V; Mikosch, J; Zhavoronkov, N; Vrakking, M J J; Kornilov, O; Lépine, F

2017-08-02

Unraveling ultrafast dynamical processes in highly excited molecular species has an impact on our understanding of chemical processes such as combustion or the chemical composition of molecular clouds in the universe. In this article we use short (<7 fs) XUV pulses to produce excited cationic states of benzene molecules and probe their dynamics using few-cycle VIS/NIR laser pulses. The excited states produced by the XUV pulses lie in an especially complex spectral region where multi-electronic effects play a dominant role. We show that very fast τ ≈ 20 fs nonadiabatic processes dominate the relaxation of these states, in agreement with the timescale expected for most excited cationic states in benzene. In the CH 3 + fragmentation channel of the doubly ionized benzene cation we identify pathways that involve structural rearrangement and proton migration to a specific carbon atom. Further, we observe non-trivial transient behavior in this fragment channel, which can be interpreted either in terms of propagation of the nuclear wavepacket in the initially excited electronic state of the cation or as a two-step electronic relaxation via an intermediate state.

Dynamics of Uncrystallized Water, Ice, and Hydrated Protein in Partially Crystallized Gelatin-Water Mixtures Studied by Broadband Dielectric Spectroscopy.

PubMed

Sasaki, Kaito; Panagopoulou, Anna; Kita, Rio; Shinyashiki, Naoki; Yagihara, Shin; Kyritsis, Apostolos; Pissis, Polycarpos

2017-01-12

The glass transition of partially crystallized gelatin-water mixtures was investigated using broadband dielectric spectroscopy (BDS) over a wide range of frequencies (10 mHz to 10 MHz), temperatures (113-298 K), and concentrations (10-45 wt %). Three dielectric relaxation processes (processes I, II, and III) were clearly observed. Processes I, II, and III originate from uncrystallized water (UCW) in the hydration shells of gelatin, ice, and hydrated gelatin, respectively. A dynamic crossover, called the Arrhenius to non-Arrhenius transition of UCW, was observed at the glass transition temperature of the relaxation process of hydrated gelatin for all mixtures. The amount of UCW increases with increasing gelatin content. However, above 35 wt % gelatin, the amount of UCW became more dependent on the gelatin concentration. This increase in UCW causes a decrease in the glass transition temperature of the cooperative motion of gelatin and UCW, which appears to result from a change in the aggregation structure of gelatin in the mixture at a gelatin concentration of approximately 35 wt %. The temperature dependence of the relaxation time of process II has nearly the same activation energy as pure ice made by slow crystallization of ice Ih. This implies that process II originates from the dynamics of slowly crystallized ice Ih.

Dynamics in supercooled polyalcohols: Primary and secondary relaxation

NASA Astrophysics Data System (ADS)

Döß, A.; Paluch, M.; Sillescu, H.; Hinze, G.

2002-10-01

We have studied details of the molecular dynamics in a series of pure polyalcohols by means of dielectric spectroscopy and 2H nuclear magnetic resonance (NMR). From glycerol to threitol, xylitol and sorbitol a systematic change in the dynamics of the primary and secondary relaxation is found. With increasing molecular weight and fragility an increase in the width of the α-peak is observed. Details of the molecular reorientation process responsible for the α-relaxation were exploited by two-dimensional NMR experiments. It is found that in the same sequence of polyalcohols the appearance of the secondary relaxation changes gradually from a wing type scenario to a pronounced β-peak. From NMR experiments using selectively deuterated samples the molecular origin of the secondary relaxation could be elucidated in more detail.

Relaxation Dynamics in Heme Proteins.

NASA Astrophysics Data System (ADS)

Scholl, Reinhard Wilhelm

A protein molecule possesses many conformational substates that are likely arranged in a hierarchy consisting of a number of tiers. A hierarchical organization of conformational substates is expected to give rise to a multitude of nonequilibrium relaxation phenomena. If the temperature is lowered, transitions between substates of higher tiers are frozen out, and relaxation processes characteristic of lower tiers will dominate the observational time scale. This thesis addresses the following questions: (i) What is the energy landscape of a protein? How does the landscape depend on the environment such as pH and viscosity, and how can it be connected to specific structural parts? (ii) What relaxation phenomena can be observed in a protein? Which are protein specific, and which occur in other proteins? How does the environment influence relaxations? (iii) What functional form best describes relaxation functions? (iv) Can we connect the motions to specific structural parts of the protein molecule, and are these motions important for the function of the protein?. To this purpose, relaxation processes after a pressure change are studied in carbonmonoxy (CO) heme proteins (myoglobin-CO, substrate-bound and substrate-free cytochrome P450cam-CO, chloroperoxidase-CO, horseradish peroxidase -CO) between 150 K and 250 K using FTIR spectroscopy to monitor the CO bound to the heme iron. Two types of p -relaxation experiments are performed: p-release (200 to ~eq40 MPa) and p-jump (~eq40 to 200 MPa) experiments. Most of the relaxations fall into one of three groups and are characterized by (i) nonexponential time dependence and non-Arrhenius temperature dependence (FIM1( nu), FIM1(Gamma)); (ii) exponential time dependence and non-Arrhenius temperature dependence (FIM0(A_{i}to A_{j})); exponential time dependence and Arrhenius temperature dependence (FIMX( nu)). The influence of pH is studied in myoglobin-CO and shown to have a strong influence on the substate population of the highest tier, tier 0, but not on the relaxation rates. Two different viscosities in myoglobin-CO are compared. The dependence of relaxations on the thermodynamic history of a sample is shown. For substrate-free P450cam-CO, relaxations after a p-jump are observed far above the glass transition of the protein-solvent system.

A practical approach to calculate the time evolutions of magnetic field effects on photochemical reactions in nano-structured materials.

PubMed

Yago, Tomoaki; Wakasa, Masanobu

2015-04-21

A practical method to calculate time evolutions of magnetic field effects (MFEs) on photochemical reactions involving radical pairs is developed on the basis of the theory of the chemically induced dynamic spin polarization proposed by Pedersen and Freed. In theory, the stochastic Liouville equation (SLE), including the spin Hamiltonian, diffusion motions of the radical pair, chemical reactions, and spin relaxations, is solved by using the Laplace and the inverse Laplace transformation technique. In our practical approach, time evolutions of the MFEs are successfully calculated by applying the Miller-Guy method instead of the final value theorem to the inverse Laplace transformation process. Especially, the SLE calculations are completed in a short time when the radical pair dynamics can be described by the chemical kinetics consisting of diffusions, reactions and spin relaxations. The SLE analysis with a short calculation time enables one to examine the various parameter sets for fitting the experimental date. Our study demonstrates that simultaneous fitting of the time evolution of the MFE and of the magnetic field dependence of the MFE provides valuable information on the diffusion motions of the radical pairs in nano-structured materials such as micelles where the lifetimes of radical pairs are longer than hundreds of nano-seconds and the magnetic field dependence of the spin relaxations play a major role for the generation of the MFE.

Spectra- and temperature-dependent dynamics of directly end-pumped holmium lasers

NASA Astrophysics Data System (ADS)

Ji, Encai; Shen, Yijie; Nie, Mingming; Fu, Xing; Liu, Qiang

2017-04-01

We develop a theoretical model with high accuracy for directly end-pumped Ho3+ laser system considering the influences of ground-state depletion, energy transfer up-conversion, temperature-dependent cross sections, and pump spectra shift. The heat generation in our model is precisely evaluated by calculating the transition rates of non-radiation relaxation processes among manifolds and in-band relaxation processes based on a detailed analysis of energy levels structure of holmium ions. A spatial dynamic thermal iteration method, just developed by our group, is applied to describe the coupled influences between spatial thermal effects and pump spectra. This model is verified to both adapt to the narrow-band good beam-quality pumped case and the broad-band bad beam-quality pumped case, which is in accordance with our previous reported experimental results.

Ultrafast carrier dynamics in the large-magnetoresistance material WTe 2

DOE PAGES

Dai, Y. M.; Bowlan, J.; Li, H.; ...

2015-10-07

In this study, ultrafast optical pump-probe spectroscopy is used to track carrier dynamics in the large-magnetoresistance material WTe 2. Our experiments reveal a fast relaxation process occurring on a subpicosecond time scale that is caused by electron-phonon thermalization, allowing us to extract the electron-phonon coupling constant. An additional slower relaxation process, occurring on a time scale of ~5–15 ps, is attributed to phonon-assisted electron-hole recombination. As the temperature decreases from 300 K, the time scale governing this process increases due to the reduction of the phonon population. However, below ~50 K, an unusual decrease of the recombination time sets in,more » most likely due to a change in the electronic structure that has been linked to the large magnetoresistance observed in this material.« less

Dielectric relaxation of 2-ethyl-1-hexanol around the glass transition by thermally stimulated depolarization currents.

PubMed

Arrese-Igor, S; Alegría, A; Colmenero, J

2015-06-07

We explore new routes for characterizing the Debye-like and α relaxation in 2-ethyl-1-hexanol (2E1H) monoalcohol by using low frequency dielectric techniques including thermally stimulated depolarization current (TSDC) techniques and isothermal depolarization current methods. In this way, we have improved the resolution of the overlapped processes making it possible the analysis of the data in terms of a mode composition as expected for a chain-like response. Furthermore the explored ultralow frequencies enabled to study dynamics at relatively low temperatures close to the glass transition (Tg). Results show, on the one hand, that Debye-like and α relaxation timescales dramatically approach to each other upon decreasing temperature to Tg. On the other hand, the analysis of partial polarization TSDC data confirms the single exponential character of the Debye-like relaxation in 2E1H and rules out the presence of Rouse type modes in the scenario of a chain-like response. Finally, on crossing the glass transition, the Debye-like relaxation shows non-equilibrium effects which are further emphasized by aging treatment and would presumably emerge as a result of the arrest of the structural relaxation below Tg.

The mechanical spectra of β-relaxation and spontaneous densification effects in an amorphous polymer

NASA Astrophysics Data System (ADS)

Muzeau, Elisabeth; Johari, G. P.

1990-12-01

The dynamic mechanical spectra of shear modulus of poly(methyl methacrylate) have been measured at several temperatures over the frequency range 10 -4-1 Hz in order to study localized diffusion of chain segments which appears as β-relaxation. The shape of the spectra of both the real and imaginary components has been analyzed. It is described by a stretched exponential decay function with exponent of 0.18 and it shows nearly 50% change in the modulus over this frequency range. This exponent and the rate of relaxation are remarkably similar to those observed by dielectric methods. A procedure for obtaining the exponent of the decay function and the relaxation strength of the β-process has been outlined. The strength of the β-relaxation, or equivalently the number of molecular segments undergoing a thermally activated localized diffusion, decreases on structural relaxation during the isothermal ageing, and the magnitude of the modulus increases. Qualitatively speaking, these effects seem comparable to the effects of an increase in density that normally occurs with decrease in temperature or increase in pressure, and demonstrate that isothermal ageing causes collapse of "soft sites" in a rigid amorphous matrix.

Glass transition of soft colloids

NASA Astrophysics Data System (ADS)

Philippe, Adrian-Marie; Truzzolillo, Domenico; Galvan-Myoshi, Julian; Dieudonné-George, Philippe; Trappe, Véronique; Berthier, Ludovic; Cipelletti, Luca

2018-04-01

We explore the glassy dynamics of soft colloids using microgels and charged particles interacting by steric and screened Coulomb interactions, respectively. In the supercooled regime, the structural relaxation time τα of both systems grows steeply with volume fraction, reminiscent of the behavior of colloidal hard spheres. Computer simulations confirm that the growth of τα on approaching the glass transition is independent of particle softness. By contrast, softness becomes relevant at very large packing fractions when the system falls out of equilibrium. In this nonequilibrium regime, τα depends surprisingly weakly on packing fraction, and time correlation functions exhibit a compressed exponential decay consistent with stress-driven relaxation. The transition to this novel regime coincides with the onset of an anomalous decrease in local order with increasing density typical of ultrasoft systems. We propose that these peculiar dynamics results from the combination of the nonequilibrium aging dynamics expected in the glassy state and the tendency of colloids interacting through soft potentials to refluidize at high packing fractions.

Origin of dielectric relaxor behavior in PVDF-based copolymer and terpolymer films

NASA Astrophysics Data System (ADS)

Pramanick, Abhijit; Osti, Naresh C.; Jalarvo, Niina; Misture, Scott T.; Diallo, Souleymane Omar; Mamontov, Eugene; Luo, Y.; Keum, Jong-Kahk; Littrell, Ken

2018-04-01

Relaxor ferroelectrics exhibit frequency-dispersion of their dielectric permittivity peak as a function of temperature, the origin of which has been widely debated. Microscopic understanding of such behavior for polymeric ferroelectrics has presented new challenges since unlike traditional ceramic ferroelectrics, dielectric relaxation in polymers is a consequence of short-range molecular dynamics that are difficult to measure directly. Here, through careful analysis of atomic-level H-atom dynamics as determined by Quasi-elastic Neutron Scattering (QENS), we show that short-range molecular dynamics within crystalline domains cannot explain the macroscopic frequency-dispersion of dielectric properties observed in prototypical polyvinylidene-fluoride (PVDF)-based relaxor ferroelectrics. Instead, from multiscale quantitative microstructural characterization, a clear correlation between the amount of crystalline-amorphous interfaces and dielectric relaxation is observed, which indicates that such interfaces play a central role. These results provide critical insights into the role of atomic and microscopic structures towards relaxor behavior in ferroelectric polymers, which will be important for their future design.

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

DOE PAGES

Hu, Xiaohu; Hong, Liang; Smith, Micholas Dean; ...

2015-11-23

Here, internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from ps up to ~10 2s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10 –12 to 10 –5s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of themore » energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.« less

Surface and interface effects on non-radiative exciton recombination and relaxation dynamics in CdSe/Cd,Zn,S nanocrystals

NASA Astrophysics Data System (ADS)

Walsh, Brenna R.; Saari, Jonathan I.; Krause, Michael M.; Nick, Robert; Coe-Sullivan, Seth; Kambhampati, Patanjali

2016-06-01

Excitonic state-resolved pump/probe spectroscopy and time correlate single photon counting were used to study exciton dynamics from the femtosecond to nanosecond time scales in CdSe/Cd,Zn,S nanocrystals. These measurements reveal the role of the core/shell interface as well as surface on non-radiative excitonic processes over three time regimes. Time resolved photoluminescence reports on how the interface controls slow non-radiative processes that dictate emission at the single excitonic level. Heterogeneity in decay is minimized by interfacial structure. Pump/probe measurements explore the non-radiative multiexcitonic recombination processes on the picosecond timescale. These Auger based non-radiative processes dictate lifetimes of multiexcitonic states. Finally state-resolved pump/probe measurements on the femtosecond timescale reveal the influence of the interface on electron and hole relaxation dynamics. We find that the interface has a profound influence on all three types of non-radiative processes which ultimately control light emission from nanocrystals.

Structural characteristics and properties of the regenerated silk fibroin prepared from formic acid.

PubMed

Um, I C; Kweon, H Y; Park, Y H; Hudson, S

2001-08-20

Structural characteristics and thermal and solution properties of the regenerated silk fibroin (SF) prepared from formic acid (FU) were compared with those of SF from water (AU). According to the turbidity and shear viscosity measurement, SF formic acid solution was stable and transparent, no molecular aggregations occurred. The sample FU exhibited the beta-sheet structure, while AU random coil conformation using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and differential scanning calorimetry. The effects of methanol treatment on samples were also examined. According to the measurement of crystallinity (XRD) and crystallinity index (FTIR), the concept of long/short-range ordered structure formation was proposed. Long-range ordered crystallites are predominantly formed for methanol treated SF film while SF film cast from formic acid favors the formation of short-range ordered structure. The relaxation temperatures of SF films measured by dynamic thermomechanical analysis supported the above mechanism due to the sensitivity of relaxation temperature on the short-range order.

Early-Time Excited-State Relaxation Dynamics of Iridium Compounds: Distinct Roles of Electron and Hole Transfer.

PubMed

Liu, Xiang-Yang; Zhang, Ya-Hui; Fang, Wei-Hai; Cui, Ganglong

2018-06-28

Excited-state and photophysical properties of Ir-containing complexes have been extensively studied because of their potential applications as organic light-emitting diode emitting materials. However, their early time excited-state relaxation dynamics are less explored computationally. Herein we have employed our recently implemented TDDFT-based generalized surface-hopping dynamics method to simulate excited-state relaxation dynamics of three Ir(III) compounds having distinct ligands. According to our multistate dynamics simulations including five excited singlet states i.e., S n ( n = 1-5) and ten excited triplet states, i.e., T n ( n = 1-10), we have found that the intersystem crossing (ISC) processes from the S n to T n are very efficient and ultrafast in these three Ir(III) compounds. The corresponding ISC rates are estimated to be 65, 81, and 140 fs, which are reasonably close to the experimentally measured ca. 80, 80, and 110 fs. In addition, the internal conversion (IC) processes within respective singlet and triplet manifolds are also ultrafast. These ultrafast IC and ISC processes are caused by large nonadiabatic and spin-orbit couplings, respectively, as well as small energy gaps. Importantly, although these Ir(III) complexes share similar macroscopic phenomena, i.e., ultrafast IC and ISC, their microscopic excited-state relaxation mechanism and dynamics are qualitatively distinct. Specifically, the dynamical behaviors of electron and hole and their roles are variational in modulating the excited-state relaxation dynamics of these Ir(III) compounds. In other words, the electronic properties of the ligands that are coordinated with the central Ir(III) atom play important roles in regulating the microscopic excited-state relaxation dynamics. These gained insights could be useful for rationally designing Ir(III) compounds with excellent photoluminescence.

Slowing hot-carrier relaxation in graphene using a magnetic field

NASA Astrophysics Data System (ADS)

Plochocka, P.; Kossacki, P.; Golnik, A.; Kazimierczuk, T.; Berger, C.; de Heer, W. A.; Potemski, M.

2009-12-01

A degenerate pump-probe technique is used to investigate the nonequilibrium carrier dynamics in multilayer graphene. Two distinctly different dynamics of the carrier relaxation are observed. A fast relaxation (˜50fs) of the carriers after the initial effect of phase-space filling followed by a slower relaxation (˜4ps) due to thermalization. Both relaxation processes are less efficient when a magnetic field is applied at low temperatures which is attributed to the suppression of the electron-electron Auger scattering due to the nonequidistant Landau-level spacing of the Dirac fermions in graphene.

Multiscale Relaxation Dynamics in Ultrathin Metallic Glass-Forming Films

NASA Astrophysics Data System (ADS)

Bi, Q. L.; Lü, Y. J.; Wang, W. H.

2018-04-01

The density layering phenomenon originating from a free surface gives rise to the layerlike dynamics and stress heterogeneity in ultrathin Cu-Zr glassy films, which facilitates the occurrence of multistep relaxations in the timescale of computer simulations. Taking advantage of this condition, we trace the relaxation decoupling and evolution with temperature simply via the intermediate scattering function. We show that the β relaxation hierarchically follows fast and slow modes in films, and there is a β -relaxation transition as the film is cooled close to the glass transition. We provide the direct observation of particle motions responsible for the β relaxation and reveal the dominant mechanism varying from the thermal activated to the cooperative jumps across the transition.

Detection of weak signals through nonlinear relaxation times for a Brownian particle in an electromagnetic field.

PubMed

Jiménez-Aquino, J I; Romero-Bastida, M

2011-07-01

The detection of weak signals through nonlinear relaxation times for a Brownian particle in an electromagnetic field is studied in the dynamical relaxation of the unstable state, characterized by a two-dimensional bistable potential. The detection process depends on a dimensionless quantity referred to as the receiver output, calculated as a function of the nonlinear relaxation time and being a characteristic time scale of our system. The latter characterizes the complete dynamical relaxation of the Brownian particle as it relaxes from the initial unstable state of the bistable potential to its corresponding steady state. The one-dimensional problem is also studied to complement the description.

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

PubMed

Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

2016-05-10

Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A numerical study of the South China Sea Warm Current during winter monsoon relaxation

NASA Astrophysics Data System (ADS)

Zhang, Cong; Ding, Yang; Bao, Xianwen; Bi, Congcong; Li, Ruixiang; Zhang, Cunjie; Shen, Biao; Wan, Kai

2018-03-01

Using a Finite-Volume Community Ocean Model, we investigated the dynamic mechanism of the South China Sea Warm Current (SCSWC) in the northern South China Sea (NSCS) during winter monsoon relaxation. The model reproduces the mean surface circulation of the NSCS during winter, while model-simulated subtidal currents generally capture its current pattern. The model shows that the current over the continental shelf is generally southwestward, under a strong winter monsoon condition, but a northeastward counter-wind current usually develops between 50-and 100-m isobaths, when the monsoon relaxes. Model experiments, focusing on the wind relaxation process, show that sea level is elevated in the northwestern South China Sea (SCS), related to the persistent northeasterly monsoon. Following wind relaxation, a high sea level band builds up along the mid-shelf, and a northeastward current develops, having an obvious vertical barotropic structure. Momentum balance analysis indicates that an along-shelf pressure gradient provides the initial driving force for the SCSWC during the first few days following wind relaxation. The SCSWC subsequently reaches a steady quasi-geostrophic balance in the cross-shelf direction, mainly linked to sea level adjustment over the shelf. Lagrangian particle tracking experiments show that both the southwestward coastal current and slope current contribute to the northeastward movement of the SCSWC during winter monsoon relaxation.

Relaxation of the structure of simple metal ion complexes in aqueous solutions at up to supercritical conditions

USGS Publications Warehouse

Mayanovic, Robert A.; Jayanetti, Sumedha; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2003-01-01

Recently x-ray absorption fine structure (XAFS) studies of various ions in aqueous solutions showed a variation of cation-ligand bond lengths, often coupled with other structure changes, with increasing temperatures. Thus, the variations of the structure of several metal ion complexes with temperature based on observations from the X-ray absorption fine structure (XAFS) studies in the hope that it will stimulate the development of either first- principles theory or molecular dynamics simulations that might adequately describes these results are discussed.

Ultrafast internal conversion dynamics of highly excited pyrrole studied with VUV/UV pump probe spectroscopy.

PubMed

Horton, Spencer L; Liu, Yusong; Chakraborty, Pratip; Matsika, Spiridoula; Weinacht, Thomas

2017-02-14

We study the relaxation dynamics of pyrrole after excitation with an 8 eV pump pulse to a state just 0.2 eV below the ionization potential using vacuum ultraviolet/ultraviolet pump probe spectroscopy. Our measurements in conjunction with electronic structure calculations indicate that pyrrole undergoes rapid internal conversion to the ground state in less than 300 fs. We find that internal conversion to the ground state dominates over dissociation.

Is Buffer a Good Proxy for a Crowded Cell-Like Environment? A Comparative NMR Study of Calmodulin Side-Chain Dynamics in Buffer and E. coli Lysate

PubMed Central

Latham, Michael P.; Kay, Lewis E.

2012-01-01

Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s) of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded “cell-like” environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca2+-bound and Ca2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed “test-tube” studies, experiments performed under conditions that are “cell-like” are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function. PMID:23118958

Quasi-elastic neutron scattering studies of the slow dynamics of supercooled and glassy aspirin

NASA Astrophysics Data System (ADS)

Zhang, Yang; Tyagi, Madhusudan; Mamontov, Eugene; Chen, Sow-Hsin

2012-02-01

Aspirin, also known as acetylsalicylic acid (ASA), is not only a wonderful drug, but also a good glass former. Therefore, it serves as an important molecular system to study the near-arrest and arrested phenomena. In this paper, a high-resolution quasi-elastic neutron scattering (QENS) technique is used to investigate the slow dynamics of supercooled liquid and glassy aspirin from 410 down to 350 K. The measured QENS spectra can be analyzed with a stretched exponential model. We find that (i) the stretched exponent β(Q) is independent of the wavevector transfer Q in the measured Q range and (ii) the structural relaxation time τ(Q) follows a power-law dependence on Q. Consequently, the Q-independent structural relaxation time τ0 can be extracted for each temperature to characterize the slow dynamics of aspirin. The temperature dependence of τ0 can be fitted with the mode-coupling power law, the Vogel-Fulcher-Tammann equation and a universal equation for fragile glass forming liquids recently proposed by Tokuyama in the measured temperature range. The calculated dynamic response function χT(Q, t) using the experimentally determined self-intermediate scattering function of the hydrogen atoms of aspirin shows direct evidence of the enhanced dynamic fluctuations as the aspirin is increasingly supercooled, in agreement with the fixed-time mean squared displacement langx2rang and the non-Gaussian parameter α2 extracted from the elastic scattering.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems

NASA Astrophysics Data System (ADS)

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; Del Giudice, Paolo

2015-10-01

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a ‘basin’ of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems.

PubMed

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; del Giudice, Paolo

2015-10-14

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a 'basin' of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering

NASA Astrophysics Data System (ADS)

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G.; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V.; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F.

2016-01-01

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth’s deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å-1 corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.

Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering.

PubMed

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F

2016-01-07

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth's deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å(-1) corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.

Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4] 2-

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kjær, Kasper S.; Kunnus, Kristjan; Harlang, Tobias C. B.

The excited state dynamics of solvated [Fe(bpy)(CN) 4] 2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN) 4] 2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile. Here, in the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN) 4] 2-more » in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet ( 3MC) character, unlike other reported six-coordinate Fe(II)-centered coordination compounds, which form MC quintet ( 5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN) 4] 2- allows us to infer the influence of the solvent on the electronic structure of the complex. Lastly, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.« less

Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4] 2-

DOE PAGES

Kjær, Kasper S.; Kunnus, Kristjan; Harlang, Tobias C. B.; ...

2018-01-19

The excited state dynamics of solvated [Fe(bpy)(CN) 4] 2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN) 4] 2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile. Here, in the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN) 4] 2-more » in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet ( 3MC) character, unlike other reported six-coordinate Fe(II)-centered coordination compounds, which form MC quintet ( 5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN) 4] 2- allows us to infer the influence of the solvent on the electronic structure of the complex. Lastly, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.« less

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c.

PubMed

Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro

2016-01-22

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23-28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction site for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. Copyright © 2015 Elsevier Inc. All rights reserved.

Ultrafast energy relaxation in single light-harvesting complexes

DOE PAGES

Maly, Pavel; Gruber, J. Michael; Cogdell, Richard J.; ...

2016-02-22

Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub–100-fs range. At the same time, much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work, we use a pump–probe-type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changesmore » in both its shape and position. The observed behavior agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from a single long-lived complex with the whole ensemble, we demonstrate that, regarding the relaxation times, the ensemble can be considered ergodic. Lastly, our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.« less

Ultrafast energy relaxation in single light-harvesting complexes.

PubMed

Malý, Pavel; Gruber, J Michael; Cogdell, Richard J; Mančal, Tomáš; van Grondelle, Rienk

2016-03-15

Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub-100-fs range. At the same time, much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work, we use a pump-probe-type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changes in both its shape and position. The observed behavior agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from a single long-lived complex with the whole ensemble, we demonstrate that, regarding the relaxation times, the ensemble can be considered ergodic. Our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.

Ultrafast energy relaxation in single light-harvesting complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maly, Pavel; Gruber, J. Michael; Cogdell, Richard J.

Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub–100-fs range. At the same time, much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work, we use a pump–probe-type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changesmore » in both its shape and position. The observed behavior agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from a single long-lived complex with the whole ensemble, we demonstrate that, regarding the relaxation times, the ensemble can be considered ergodic. Lastly, our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.« less

Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model.

PubMed

Ngai, K L; Habasaki, J; Prevosto, D; Capaccioli, S; Paluch, Marian

2012-07-21

By now it is well established that the structural α-relaxation time, τ(α), of non-associated small molecular and polymeric glass-formers obey thermodynamic scaling. In other words, τ(α) is a function Φ of the product variable, ρ(γ)/T, where ρ is the density and T the temperature. The constant γ as well as the function, τ(α) = Φ(ρ(γ)/T), is material dependent. Actually this dependence of τ(α) on ρ(γ)/T originates from the dependence on the same product variable of the Johari-Goldstein β-relaxation time, τ(β), or the primitive relaxation time, τ(0), of the coupling model. To support this assertion, we give evidences from various sources itemized as follows. (1) The invariance of the relation between τ(α) and τ(β) or τ(0) to widely different combinations of pressure and temperature. (2) Experimental dielectric and viscosity data of glass-forming van der Waals liquids and polymer. (3) Molecular dynamics simulations of binary Lennard-Jones (LJ) models, the Lewis-Wahnström model of ortho-terphenyl, 1,4 polybutadiene, a room temperature ionic liquid, 1-ethyl-3-methylimidazolium nitrate, and a molten salt 2Ca(NO(3))(2)·3KNO(3) (CKN). (4) Both diffusivity and structural relaxation time, as well as the breakdown of Stokes-Einstein relation in CKN obey thermodynamic scaling by ρ(γ)/T with the same γ. (5) In polymers, the chain normal mode relaxation time, τ(N), is another function of ρ(γ)/T with the same γ as segmental relaxation time τ(α). (6) While the data of τ(α) from simulations for the full LJ binary mixture obey very well the thermodynamic scaling, it is strongly violated when the LJ interaction potential is truncated beyond typical inter-particle distance, although in both cases the repulsive pair potentials coincide for some distances.

An immersed-shell method for modelling fluid–structure interactions

PubMed Central

Viré, A.; Xiang, J.; Pain, C. C.

2015-01-01

The paper presents a novel method for numerically modelling fluid–structure interactions. The method consists of solving the fluid-dynamics equations on an extended domain, where the computational mesh covers both fluid and solid structures. The fluid and solid velocities are relaxed to one another through a penalty force. The latter acts on a thin shell surrounding the solid structures. Additionally, the shell is represented on the extended domain by a non-zero shell-concentration field, which is obtained by conservatively mapping the shell mesh onto the extended mesh. The paper outlines the theory underpinning this novel method, referred to as the immersed-shell approach. It also shows how the coupling between a fluid- and a structural-dynamics solver is achieved. At this stage, results are shown for cases of fundamental interest. PMID:25583857

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Andrew Loyd

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ patternmore » of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T 1, T 2, and 15N/ 1H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.« less

Qualitative change in structural dynamics of some glass-forming systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novikov, Vladimir N.; Sokolov, Alexei P.

2015-12-14

Analysis of the temperature dependence of the structural relaxation time Τα(T) in supercooled liquids revealed a qualitatively distinct feature a sharp, cusplike maximum in the second derivative of log Τα(T) at some T max. It suggests that the super-Arrhenius temperature dependence of Τα(T) in glass-forming liquids eventually crosses over to an Arrhenius behavior at T < T max, and there is no divergence of Τα(T) at nonzero T . T max can be above or below T g, depending on the sensitivity of τ(T) to a change in the liquid's density quantified by the exponent γ in the scaling Τα(T)more » ~exp(A/Tρ –γ). Lastly, these results might turn the discussion of the glass transition in a different direction toward the origin of the limiting activation energy for structural relaxation at low T.« less

MYStIX: Dynamical evolution of young clusters

NASA Astrophysics Data System (ADS)

Kuhn, Michael A.

2014-08-01

The spatial structure of young stellar clusters in Galactic star-forming regions provides insight into these clusters’ dynamical evolution---a topic with implications for open questions in star-formation and cluster survival. The Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) provides a sample of >30,000 young stars in star-forming regions (d<3.6 kpc) that contain at least one O-type star. We use the finite mixture model analysis to identify subclusters of stars and determine their properties: including subcluster radii, intrinsic numbers of stars, central density, ellipticity, obscuration, and age. In 17 MYStIX regions we find 142 subclusters, with a diverse radii and densities and age spreads of up to ~1 Myr in a region. There is a strong negative correlation between subcluster radius and density, which indicates that embedded subclusters expand but also gain stars as they age. Subcluster expansion is also shown by a positive radius--age correlation, which indicates that subclusters are expanding at <1 km/s. The subcluster ellipticity distribution and number--density relation show signs of a hierarchical merger scenario, whereby young stellar clusters are built up through mergers of smaller clumps, causing evolution from a clumpy spatial distribution of stars (seen in some regions) to a simpler distribution of stars (seen in other regions). Many of the simple young stellar clusters show signs of dynamically relaxation, even though they are not old enough for this to have occurred through two-body interactions. However, this apparent contradiction might be explained if small subcluster, which have shorter dynamical relaxation times, can produce dynamically relaxed clusters through hierarchical mergers.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

State-Resolved Metal Nanoparticle Dynamics Viewed through the Combined Lenses of Ultrafast and Magneto-optical Spectroscopies.

PubMed

Zhao, Tian; Herbert, Patrick J; Zheng, Hongjun; Knappenberger, Kenneth L

2018-06-19

Electronic carrier dynamics play pivotal roles in the functional properties of nanomaterials. For colloidal metals, the mechanisms and influences of these dynamics are structure dependent. The coherent carrier dynamics of collective plasmon modes for nanoparticles (approximately 2 nm and larger) determine optical amplification factors that are important to applied spectroscopy techniques. In the nanocluster domain (sub-2 nm), carrier coupling to vibrational modes affects photoluminescence yields. The performance of photocatalytic materials featuring both nanoparticles and nanoclusters also depends on the relaxation dynamics of nonequilibrium charge carriers. The challenges for developing comprehensive descriptions of carrier dynamics spanning both domains are multifold. Plasmon coherences are short-lived, persisting for only tens of femtoseconds. Nanoclusters exhibit discrete carrier dynamics that can persist for microseconds in some cases. On this time scale, many state-dependent processes, including vibrational relaxation, charge transfer, and spin conversion, affect carrier dynamics in ways that are nonscalable but, rather, structure specific. Hence, state-resolved spectroscopy methods are needed for understanding carrier dynamics in the nanocluster domain. Based on these considerations, a detailed understanding of structure-dependent carrier dynamics across length scales requires an appropriate combination of spectroscopic methods. Plasmon mode-specific dynamics can be obtained through ultrafast correlated light and electron microscopy (UCLEM), which pairs interferometric nonlinear optical (INLO) with electron imaging methods. INLO yields nanostructure spectral resonance responses, which capture the system's homogeneous line width and coherence dynamics. State-resolved nanocluster dynamics can be obtained by pairing ultrafast with magnetic-optical spectroscopy methods. In particular, variable-temperature variable-field (VTVH) spectroscopies allow quantification of transient, excited states, providing quantification of important parameters such as spin and orbital angular momenta as well as the energy gaps that separate electronic fine structure states. Ultrafast two-dimensional electronic spectroscopy (2DES) can be used to understand how these details influence state-to-state carrier dynamics. In combination, VTVH and 2DES methods can provide chemists with detailed information regarding the structure-dependent and state-specific flow of energy through metal nanoclusters. In this Account, we highlight recent advances toward understanding structure-dependent carrier dynamics for metals spanning the sub-nanometer to tens of nanometers length scale. We demonstrate the use of UCLEM methods for arresting interband scattering effects. For sub-nanometer thiol-protected nanoclusters, we discuss the effectiveness of VTVH for distinguishing state-specific radiative recombination originating from a gold core versus organometallic protecting layers. This state specificity is refined further using femtosecond 2DES and two-color methods to isolate so-called superatom state dynamics and vibrationally mediated spin-conversion and emission processes. Finally, we discuss prospects for merging VTVH and 2DES methods into a single platform.

Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

PubMed

Berlin, Konstantin; Longhini, Andrew; Dayie, T Kwaku; Fushman, David

2013-12-01

To facilitate rigorous analysis of molecular motions in proteins, DNA, and RNA, we present a new version of ROTDIF, a program for determining the overall rotational diffusion tensor from single- or multiple-field nuclear magnetic resonance relaxation data. We introduce four major features that expand the program's versatility and usability. The first feature is the ability to analyze, separately or together, (13)C and/or (15)N relaxation data collected at a single or multiple fields. A significant improvement in the accuracy compared to direct analysis of R2/R1 ratios, especially critical for analysis of (13)C relaxation data, is achieved by subtracting high-frequency contributions to relaxation rates. The second new feature is an improved method for computing the rotational diffusion tensor in the presence of biased errors, such as large conformational exchange contributions, that significantly enhances the accuracy of the computation. The third new feature is the integration of the domain alignment and docking module for relaxation-based structure determination of multi-domain systems. Finally, to improve accessibility to all the program features, we introduced a graphical user interface that simplifies and speeds up the analysis of the data. Written in Java, the new ROTDIF can run on virtually any computer platform. In addition, the new ROTDIF achieves an order of magnitude speedup over the previous version by implementing a more efficient deterministic minimization algorithm. We not only demonstrate the improvement in accuracy and speed of the new algorithm for synthetic and experimental (13)C and (15)N relaxation data for several proteins and nucleic acids, but also show that careful analysis required especially for characterizing RNA dynamics allowed us to uncover subtle conformational changes in RNA as a function of temperature that were opaque to previous analysis.

Relaxation processes and physical aging in metallic glasses

NASA Astrophysics Data System (ADS)

Ruta, B.; Pineda, E.; Evenson, Z.

2017-12-01

Since their discovery in the 1960s, metallic glasses have continuously attracted much interest across the physics and materials science communities. In the forefront are their unique properties, which hold the alluring promise of broad application in fields as diverse as medicine, environmental science and engineering. However, a major obstacle to their wide-spread commercial use is their inherent temporal instability arising from underlying relaxation processes that can dramatically alter their physical properties. The result is a physical aging process which can bring about degradation of mechanical properties, namely through embrittlement and catastrophic mechanical failure. Understanding and controlling the effects of aging will play a decisive role in our on-going endeavor to advance the use of metallic glasses as structural materials, as well as in the more general comprehension of out-of-equilibrium dynamics in complex systems. This review presents an overview of the current state of the art in the experimental advances probing physical aging and relaxation processes in metallic glasses. Similarities and differences between other hard and soft matter glasses are highlighted. The topic is discussed in a multiscale approach, first presenting the key features obtained in macroscopic studies, then connecting them to recent novel microscopic investigations. Particular emphasis is put on the occurrence of distinct relaxation processes beyond the main structural process in viscous metallic melts and their fate upon entering the glassy state, trying to disentangle results and formalisms employed by the different groups of the glass-science community. A microscopic viewpoint is presented, in which physical aging manifests itself in irreversible atomic-scale processes such as avalanches and intermittent dynamics, ascribed to the existence of a plethora of metastable glassy states across a complex energy landscape. Future experimental challenges and the comparison with recent theoretical and numerical simulations are discussed as well.

Micro-Hall magnetometry on a Co-organic chain compound

NASA Astrophysics Data System (ADS)

Rolland, L.; Simonet, V.; Wernsdorfer, W.; Bogani, L.; Sessoli, R.

2004-05-01

The static and dynamical properties of Co-organic chains, with strong magnetic anisotropy, are studied by micro-Hall magnetometry. The low-temperature hysteresis cycles are discussed with respect to the helical structure of the chains. Thermally activated relaxation of the magnetization is observed, compatible with the Glauber model for a 1D Ising system.

Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

PubMed

Bureau, Hailey R; Merz, Dale R; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto

2015-01-01

Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD) or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD). Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

Theory of nonlinear elasticity, stress-induced relaxation, and dynamic yielding in dense fluids of hard nonspherical colloids

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2012-04-01

We generalize the microscopic naïve mode coupling and nonlinear Langevin equation theories of the coupled translation-rotation dynamics of dense suspensions of uniaxial colloids to treat the effect of applied stress on shear elasticity, cooperative cage escape, structural relaxation, and dynamic and static yielding. The key concept is a stress-dependent dynamic free energy surface that quantifies the center-of-mass force and torque on a moving colloid. The consequences of variable particle aspect ratio and volume fraction, and the role of plastic versus double glasses, are established in the context of dense, glass-forming suspensions of hard-core dicolloids. For low aspect ratios, the theory provides a microscopic basis for the recently observed phenomenon of double yielding as a consequence of stress-driven sequential unlocking of caging constraints via reduction of the distinct entropic barriers associated with the rotational and translational degrees of freedom. The existence, and breadth in volume fraction, of the double yielding phenomena is predicted to generally depend on both the degree of particle anisotropy and experimental probing frequency, and as a consequence typically occurs only over a window of (high) volume fractions where there is strong decoupling of rotational and translational activated relaxation. At high enough concentrations, a return to single yielding is predicted. For large aspect ratio dicolloids, rotation and translation are always strongly coupled in the activated barrier hopping event, and hence for all stresses only a single yielding process is predicted.

Reversible and Irreversible Behavior of Glass-forming Materials from the Standpoint of Hierarchical Dynamical Facilitation

NASA Astrophysics Data System (ADS)

Keys, Aaron

2013-03-01

Using molecular simulation and coarse-grained lattice models, we study the dynamics of glass-forming liquids above and below the glass transition temperature. In the supercooled regime, we study the structure, statistics, and dynamics of excitations responsible for structural relaxation for several atomistic models of glass-formers. Excitations (or soft spots) are detected in terms of persistent particle displacements. At supercooled conditions, we find that excitations are associated with correlated particle motions that are sparse and localized, and the statistics and dynamics of these excitations are facilitated and hierarchical. Excitations at one point in space facilitate the birth and death of excitations at neighboring locations, and space-time excitation structures are microcosms of heterogeneous dynamics at larger scales. Excitation-energy scales grow logarithmically with the characteristic size of the excitation, giving structural-relaxation times that can be predicted quantitatively from dynamics at short time scales. We demonstrate that these same physical principles govern the dynamics of glass-forming systems driven out-of-equilibrium by time-dependent protocols. For a system cooled and re-heated through the glass transition, non-equilibrium response functions, such as heat capacities, are notably asymmetric in time, and the response to melting a glass depends markedly on the cooling protocol by which the glass was formed. We introduce a quantitative description of this behavior based on the East model, with parameters determined from reversible transport data, that agrees well with irreversible differential scanning calorimetry. We find that the observed hysteresis and asymmetric response is a signature of an underlying dynamical transition between equilibrium melts with no trivial spatial correlations and non-equilibrium glasses with correlation lengths that are both large and dependent upon the rate at which the glass is prepared. The correlation length corresponds to the size of amorphous domains bounded by excitations that remain frozen on the observation time scale, thus forming stripes when viewed in space and time. We elucidate properties of the striped phase and show that glasses of this type, traditionally prepared through cooling, can be considered a finite-size realization of the inactive phase formed by the s-ensemble in the space-time thermodynamic limit.

Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation.

PubMed

Wang, Haobo; Yang, Lijiang; Niu, Xiaogang

2016-04-29

Protein absent in melanoma 2 (AIM2) is a double-strand DNA (ds DNA) sensor mainly located in cytoplasm of cell. It includes one N terminal PYD domain and one C terminal HIN domain. When the ds DNA such as DNA viruses and bacteria entered cytoplasm, the HIN domain of AIM2 will recognize and bind to DNA, and the PYD domain will bind to ASC protein which will result in the formation of AIM2 inflammasome. Three AIM2 PYD domain structures have been solved, but every structure yields a unique conformation around the α3 helix region. To understand why different AIM2 PYD structures show different conformations in this region, we use NMR relaxation techniques to study the backbone dynamics of mouse AIM2 PYD domain and perform molecular dynamics (MD) simulations on both mouse and human AIM2 PYD structures. Our results indicate that this region is highly flexible in both mouse and human AIM2 PYD domains, and the PYD domain may exist as a conformation ensemble in solution. Different environment makes the population vary among pre-existing conformational substrates of the ensemble, which may be the reason why different AIM2 PYD structures were observed under different conditions. Further docking analysis reveals that the conformation switching may be important for the autoinhibition of the AIM2 protein. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure and Dynamics of Interacting Nanoparticles in Semidilute Polymer Solutions

DOE PAGES

Pollng-Skutvik, Ryan; Mongcopa, Katrina Irene S.; Faraone, Antonio; ...

2016-08-17

We investigate the structure and dynamics of silica nanoparticles and polymer chains in semidilute solutions of high molecular weight polystyrene in 2-butanone to determine the effect of long-range interparticle interactions on the coupling between particle and polymer dynamics. Particles at concentrations of 1–10 wt % are well dispersed in the semidilute polymer solutions and exhibit long-range electrostatic repulsions between particles. Because the particles are comparably sized to the radius of gyration of the polymer, the particle dynamics is predicted to couple to that of the polymer. We verify that the polymer structure and dynamics are not significantly affected by themore » particles, indicating that the particle–polymer coupling does not change with increasing particle loading. We find that the coupling between the dynamics of comparably sized particles and polymer results in subdiffusive particle dynamics, as expected. Over the interparticle distance, however, the particle dynamics is hindered and not fully described by the relaxation of the surrounding polymer chains. Instead, the particle dynamics is inversely related to the structure factor, suggesting that physical particle–polymer coupling on short length scales and interparticle interactions on long length scales both present energetic barriers to particle motion that lead to subdiffusive dynamics and de Gennes narrowing, respectively.« less

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

DOE PAGES

Ochoa, D. A.; Levit, R.; Fancher, C. M.; ...

2017-04-05

We report that ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot bemore » associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel–Fulcher–Tammann phenomenological equation. Finally, results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.« less

Dynamic solvophobic effect and its cooperativity in the hydrogen-bonding liquids studied by dielectric and nuclear magnetic resonance relaxation.

PubMed

Yamaguchi, Tsuyoshi; Furuhashi, Hiroki; Matsuoka, Tatsuro; Koda, Shinobu

2008-12-25

The reorientational relaxation of solvent molecules in the mixture of nonpolar solutes and hydrogen-bonding liquids including water, alcohols, and amides are studied by dielectric and 2H-nuclear magnetic resonance (NMR) spin-lattice relaxations. The retardation of the reorientational motion of the solvent by weak solute-solvent interaction is observed in all the solvent systems. On the other hand, no clear correlation between the strength of the solute-solvent interaction and the slowing down of the solvent motion is found in N,N-dimethylacetamide, which suggests the importance of the hydrogen bonding in the dynamic solvophobic effect. The cooperativity of the reorientational relaxation is investigated by the comparison between the collective relaxation measured by the dielectric spectroscopy and the single-molecular reorientation determined by NMR. The modification of the dielectric relaxation time caused by the dissolution of the solute is larger than that of the single-molecular reorientational relaxation time in all the solvents studied here. The effect of the static correlation between the dipole moments of different molecules is calculated from the static dielectric constant, and the effect of the dynamic correlation is estimated. The difference in the effects of the solutes on the collective and single-molecular reorientational relaxation is mainly ascribed to the dynamic cooperativity in the cases of water and alcohols, which is consistent with the picture on the dynamic solvophobicity derived by our previous theoretical analysis (Yamaguchi, T.; Matsuoka, T.; Koda, S. J. Chem. Phys. 2004, 120, 7590). On the other hand, the static correlation plays the principal role in the case of N-methylformamide.

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Mode-coupling theory for active Brownian particles

NASA Astrophysics Data System (ADS)

Liluashvili, Alexander; Ónody, Jonathan; Voigtmann, Thomas

2017-12-01

We present a mode-coupling theory (MCT) for the slow dynamics of two-dimensional spherical active Brownian particles (ABPs). The ABPs are characterized by a self-propulsion velocity v0 and by their translational and rotational diffusion coefficients Dt and Dr, respectively. Based on the integration-through-transients formalism, the theory requires as input only the equilibrium static structure factors of the passive system (where v0=0 ). It predicts a nontrivial idealized-glass-transition diagram in the three-dimensional parameter space of density, self-propulsion velocity, and rotational diffusivity that arise because at high densities, the persistence length of active swimming ℓp=v0/Dr interferes with the interaction length ℓc set by the caging of particles. While the low-density dynamics of ABPs is characterized by a single Péclet number Pe=v02/DrDt , close to the glass transition the dynamics is found to depend on Pe and ℓp separately. At fixed density, increasing the self-propulsion velocity causes structural relaxation to speed up, while decreasing the persistence length slows down the relaxation. The active-MCT glass is a nonergodic state that is qualitatively different from the passive glass. In it, correlations of initial density fluctuations never fully decay, but also an infinite memory of initial orientational fluctuations is retained in the positions.

A Molecular Dynamics Study of the Structure-Dynamics Relationships of Supercooled Liquids and Glasses

NASA Astrophysics Data System (ADS)

Soklaski, Ryan

Central to the field of condensed matter physics is a decades old outstanding problem in the study of glasses -- namely explaining the extreme slowing of dynamics in a liquid as it is supercooled towards the so-called glass transition. Efforts to universally describe the stretched relaxation processes and heterogeneous dynamics that characteristically develop in supercooled liquids remain divided in both their approaches and successes. Towards this end, a consensus on the role that atomic and molecular structures play in the liquid is even more tenuous. However, mounting material science research efforts have culminated to reveal that the vast diversity of metallic glass species and their properties are rooted in an equally-broad set of structural archetypes. Herein lies the motivation of this dissertation: the detailed information available regarding the structure-property relationships of metallic glasses provides a new context in which one can study the evolution of a supercooled liquid by utilizing a structural motif that is known to dominate the glass. Cu64Zr36 is a binary alloy whose good glass-forming ability and simple composition makes it a canonical material to both empirical and numerical studies. Here, we perform classical molecular dynamics simulations and conduct a comprehensive analysis of the dynamical regimes of liquid Cu64Zr36, while focusing on the roles played by atomic icosahedral ordering -- a structural motif which ultimately percolates the glass' structure. Large data analysis techniques are leveraged to obtain uniquely detailed structural and dynamical information in this context. In doing so, we develop the first account of the origin of icosahedral order in this alloy, revealing deep connections between this incipient structural ordering, frustration-limited domain theory, and recent important empirical findings that are relevant to the nature of metallic liquids at large. Furthermore, important dynamical landmarks such as the breakdown of the Stokes-Einstein relationship, the decoupling of particle diffusivities, and the development of general "glassy" relaxation features are found to coincide with successive manifestation of icosahedral ordering that arise as the liquid is supercooled. Remarkably, we detect critical-like features in the growth of the icosahedron network, with signatures that suggest that a liquid-liquid phase transition may occur in the deeply supercooled regime to precede glass formation. Such a transition is predicted to occur in many supercooled liquids, although explicit evidence of this phenomenon in realistic systems is scarce. Ultimately this work concludes that icosahedral order characterizes all dynamical regimes of Cu64Zr 36, demonstrating the importance and utility of studying supercooled liquids in the context of locally-preferred structure. More broadly, it serves to confirm and inform recent theoretical and empirical findings that are central to understanding the physics underlying the glass transition.

Laser swelling of soft biological tissue by IR pulses

NASA Astrophysics Data System (ADS)

Malyshev, A.; Bityurin, N.

The temporal dynamics of biological tissue swelling under the effect of mid-IR laser radiation is considered theoretically following the experimental investigation published earlier. The probable mechanism of laser swelling is suggested. This mechanism consists of deformation of tissue protein base by vapor pressure, which appears due to evaporation of tissue water. The formation and relaxation of a hump on the surface was determined by both mechanical properties (elastic, plastic) and porosity of material providing water vapor transfer within tissue. It is found that these mechanisms can lead to the formation of both transient and stationary hump structures on the surface. To describe the hump relaxation, we consider a new, evaporation-condensation, mechanism of heat transfer within the region of biotissue with microchannels. This mechanism allows us to explain the value of relaxation time of the hump measured in experiment.

A theoretical model for the collective motion of proteins by means of principal component analysis

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2011-02-01

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2-0.4 ps and slow relaxation time of long diffusion about 1-2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from -0.746 to -0.938 for the real part and from -0.528 to -0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

On the structure-bounded growth processes in plant populations.

PubMed

Kilian, H G; Kazda, M; Király, F; Kaufmann, D; Kemkemer, R; Bartkowiak, D

2010-07-01

If growing cells in plants are considered to be composed of increments (ICs) an extended version of the law of mass action can be formulated. It evidences that growth of plants runs optimal if the reaction-entropy term (entropy times the absolute temperature) matches the contact energy of ICs. Since these energies are small, thermal molecular movements facilitate via relaxation the removal of structure disturbances. Stem diameter distributions exhibit extra fluctuations likely to be caused by permanent constraints. Since the signal-response system enables in principle perfect optimization only within finite-sized cell ensembles, plants comprising relatively large cell numbers form a network of size-limited subsystems. The maximal number of these constituents depends both on genetic and environmental factors. Accounting for logistical structure-dynamics interrelations, equations can be formulated to describe the bimodal growth curves of very different plants. The reproduction of the S-bended growth curves verifies that the relaxation modes with a broad structure-controlled distribution freeze successively until finally growth is fully blocked thus bringing about "continuous solidification".

Investigation of the spatial structure and developmental dynamics of near-Earth plasma perturbations under the action of powerful HF radio waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belov, A. S., E-mail: alexis-belov@yandex.ru

2015-10-15

Results of numerical simulations of the near-Earth plasma perturbations induced by powerful HF radio waves from the SURA heating facility are presented. The simulations were performed using a modified version of the SAMI2 ionospheric model for the input parameters corresponding to the series of in-situ SURA–DEMETER experiments. The spatial structure and developmental dynamics of large-scale plasma temperature and density perturbations have been investigated. The characteristic formation and relaxation times of the induced large-scale plasma perturbations at the altitudes of the Earth’s outer ionosphere have been determined.

Ultrafast carrier dynamics in a GaN/Al 0.18Ga0.82N superlattice

NASA Astrophysics Data System (ADS)

Mahler, Felix; Tomm, Jens W.; Reimann, Klaus; Woerner, Michael; Elsaesser, Thomas; Flytzanis, Christos; Hoffmann, Veit; Weyers, Markus

2018-04-01

Relaxation processes of photoexcited carriers in a GaN /Al0.18Ga0.82N superlattice are studied in femtosecond spectrally resolved reflectivity measurements at ambient temperature. The transient reflectivity reveals electron trapping into defect states close to the conduction-band minimum with a 150-200 fs time constant, followed by few-picosecond carrier cooling. A second slower trapping process into a different manifold of defect states is observed on a time scale of approximately 10 ps. Our results establish the prominent role of structural defects and disorder for ultrafast carrier dynamics in nitride semiconductor structures.

Dynamic Structural Changes of SiO₂ Supported Pt-Ni Bimetallic Catalysts over Redox Treatments Revealed by NMR and EPR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Suochang; Walter, Eric D.; Zhao, Zhenchao

2015-08-18

SiO 2 supported Pt-Ni bimetallic catalysts with different nickel loadings were prepared and their structural changes after redox treatments were studied by XRD, NMR, and EPR. It is found that the paramagnetic Ni species are mainly located on the surface of silica lattice. The relaxation of detected 29Si nuclei in our samples is mainly governed by a spin-diffusion mechanism. The paramagnetic effects are reflected in the spin-lattice relaxation of Q 4 species, with the oxidized samples presenting faster relaxation rates than the corresponding reduced ones. Meanwhile the Q 3 species, which are in close contact with the paramagnetic nickel ions,more » are “spectrally invisible”. In reducing atmosphere Ni gradually diffuses into Pt NPs to form PtNi alloys. While under oxidization treatment, the alloyed Ni atoms migrate outward from the core of Pt NPs and are oxidized. The main EPR spectrum results from reduced nickel species, and the reduced samples show stronger EPR signal than the corresponding oxidized ones. However, in the reduced samples, the superparamagnetic or ferromagnetic metallic Ni particles were inside the PtNi NPs, making their influence on the 29Si relaxation in the SiO 2 support weaker than the oxidized samples.« less

Dielectric Relaxation of the Ionic Liquid 1-Ethyl-3-methylimidazolium Ethyl Sulfate: Microwave and Far-IR Properties.

PubMed

Dhumal, Nilesh R; Kiefer, Johannes; Turton, David; Wynne, Klaas; Kim, Hyung J

2017-05-11

Dielectric relaxation of the ionic liquid, 1-ethyl-3-methylimidazolium ethyl sulfate (EMI + ETS - ), is studied using molecular dynamics (MD) simulations. The collective dynamics of polarization arising from cations and anions are examined. Characteristics of the rovibrational and translational components of polarization dynamics are analyzed to understand their respective roles in the microwave and terahertz regions of dielectric relaxation. The MD results are compared with the experimental low-frequency spectrum of EMI + ETS - , obtained via ultrafast optical Kerr effect (OKE) measurements.

Topographies and dynamics on multidimensional potential energy surfaces

NASA Astrophysics Data System (ADS)

Ball, Keith Douglas

The stochastic master equation is a valuable tool for elucidating potential energy surface (PES) details that govern structural relaxation in clusters, bulk systems, and protein folding. This work develops a comprehensive framework for studying non-equilibrium relaxation dynamics using the master equation. Since our master equations depend upon accurate partition function models for use in Rice-Ramsperger-Kassel-Marcus (RRK(M) transition state theory, this work introduces several such models employing various harmonic and anharmonic approximations and compares their predicted equilibrium population distributions with those determined from molecular dynamics. This comparison is performed for the fully-delineated surfaces (KCl)5 and Ar9 to evaluate model performance for potential surfaces with long- and short-range interactions, respectively. For each system, several models perform better than a simple harmonic approximation. While no model gives acceptable results for all minima, and optimal modeling strategies differ for (KCl)5 and Ar9, a particular one-parameter model gives the best agreement with simulation for both systems. We then construct master equations from these models and compare their isothermal relaxation predictions for (KCl)5 and Ar9 with molecular dynamics simulations. This is the first comprehensive test of the kinetic performance of partition function models of its kind. Our results show that accurate modeling of transition-state partition functions is more important for (KCl)5 than for Ar9 in reproducing simulation results, due to a marked stiffening anharmonicity in the transition-state normal modes of (KCl)5. For both systems, several models yield qualitative agreement with simulation over a large temperature range. To examine the robustness of the master equation when applied to larger systems, for which full topographical descriptions would be either impossible or infeasible, we compute relaxation predictions for Ar11 using a master equation constructed from data representing the full PES, and compare these predictions to those of reduced master equations based on statistical samples of the full PES. We introduce a sampling method which generates random, Boltzmann-weighted, energetically 'downhill' sequences. The study reveals that, at moderate temperatures, the slowest relaxation timescale converges as the number of sequences in a sample grows to ~1000. Furthermore, the asymptotic timescale is comparable to the full-PES value.

Deformation of DNA molecules by hydrodynamic focusing

NASA Astrophysics Data System (ADS)

Wong, Pak Kin; Lee, Yi-Kuen; Ho, Chih-Ming

2003-12-01

The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil stretch transition was observed when the Deborah number (De) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.

"Structure and dynamics in complex chemical systems: Gaining new insights through recent advances in time-resolved spectroscopies.” ACS Division of Physical Chemistry Symposium presented at the Fall National ACS Meeting in Boston, MA, August 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Daniel

8-Session Symposium on STRUCTURE AND DYNAMICS IN COMPLEX CHEMICAL SYSTEMS: GAINING NEW INSIGHTS THROUGH RECENT ADVANCES IN TIME-RESOLVED SPECTROSCOPIES. The intricacy of most chemical, biochemical, and material processes and their applications are underscored by the complex nature of the environments in which they occur. Substantial challenges for building a global understanding of a heterogeneous system include (1) identifying unique signatures associated with specific structural motifs within the heterogeneous distribution, and (2) resolving the significance of each of multiple time scales involved in both small- and large-scale nuclear reorganization. This symposium focuses on the progress in our understanding of dynamics inmore » complex systems driven by recent innovations in time-resolved spectroscopies and theoretical developments. Such advancement is critical for driving discovery at the molecular level facilitating new applications. Broad areas of interest include: Structural relaxation and the impact of structure on dynamics in liquids, interfaces, biochemical systems, materials, and other heterogeneous environments.« less

Cooling rate and stress relaxation in silica melts and glasses via microsecond molecular dyanmics

DOE PAGES

Lane, J. Matthew D.

2015-07-22

We have conducted extremely long molecular dynamics simulations of glasses to microsecond times, which close the gap between experimental and atomistic simulation time scales by two to three orders of magnitude. The static, thermal, and structural properties of silica glass are reported for glass cooling rates down to 5×10 9 K/s and viscoelastic response in silica melts and glasses are studied over nine decades of time. We finally present results from relaxation of hydrostatic compressive stress in silica and show that time-temperature superposition holds in these systems for temperatures from 3500 to 1000 K.

A quantum relaxation-time approximation for finite fermion systems

NASA Astrophysics Data System (ADS)

Reinhard, P.-G.; Suraud, E.

2015-03-01

We propose a relaxation time approximation for the description of the dynamics of strongly excited fermion systems. Our approach is based on time-dependent density functional theory at the level of the local density approximation. This mean-field picture is augmented by collisional correlations handled in relaxation time approximation which is inspired from the corresponding semi-classical picture. The method involves the estimate of microscopic relaxation rates/times which is presently taken from the well established semi-classical experience. The relaxation time approximation implies evaluation of the instantaneous equilibrium state towards which the dynamical state is progressively driven at the pace of the microscopic relaxation time. As test case, we consider Na clusters of various sizes excited either by a swift ion projectile or by a short and intense laser pulse, driven in various dynamical regimes ranging from linear to strongly non-linear reactions. We observe a strong effect of dissipation on sensitive observables such as net ionization and angular distributions of emitted electrons. The effect is especially large for moderate excitations where typical relaxation/dissipation time scales efficiently compete with ionization for dissipating the available excitation energy. Technical details on the actual procedure to implement a working recipe of such a quantum relaxation approximation are given in appendices for completeness.

Multidimensional dynamic piezoresponse measurements. Unraveling local relaxation behavior in relaxor-ferroelectrics via big data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasudevan, Rama K.; Zhang, Shujun; Okatan, Mahmut Baris

Compositional and charge disorder in ferroelectric relaxors lies at the heart of the unusual properties of these systems, such as aging and non-ergodicity, polarization rotations, and a host of temperature and field-driven phase transitions. However, much information about the field-dynamics of the polarization in the prototypical ferroelectric relaxor (1-x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO 3 (PMN-xPT) remains unprobed at the mesoscopic level. We use a piezoresponse force microscopy-based dynamic multimodal relaxation spectroscopy technique, enabling the study of ferroelectric switching and polarization relaxation at mesoscopic length scales, and carry out measurements on a PMN-0.28PT sample with minimal polishing. Results indicate that beyond amore » threshold DC bias the average relaxation increases as the system attempts to relax to the previous state. Phenomenological fitting reveals the presence of mesoscale heterogeneity in relaxation amplitudes and clearly suggests the presence of two distinct amplitudes. Independent component analysis reveals the presence of a disorder component of the relaxation, which is found to be strongly anti-correlated with the maximum piezoresponse at that location, suggesting smaller disorder effects where the polarization reversal is large and vice versa. The disorder in the relaxation amplitudes is postulated to arise from rhombohedral and field-induced tetragonal phase in the crystal, with each phase associated with its own relaxation amplitude. As a result, these studies highlight the crucial importance of the mixture of ferroelectric phases in the compositions in proximity of the morphotropic phase boundary in governing the local response and further highlight the ability of PFM voltage and time spectroscopies, in conjunction with big-data multivariate analyses, to locally map disorder and correlate it with parameters governing the dynamic behavior.« less

Multidimensional dynamic piezoresponse measurements. Unraveling local relaxation behavior in relaxor-ferroelectrics via big data

DOE PAGES

Vasudevan, Rama K.; Zhang, Shujun; Okatan, Mahmut Baris; ...

2015-08-19

Compositional and charge disorder in ferroelectric relaxors lies at the heart of the unusual properties of these systems, such as aging and non-ergodicity, polarization rotations, and a host of temperature and field-driven phase transitions. However, much information about the field-dynamics of the polarization in the prototypical ferroelectric relaxor (1-x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO 3 (PMN-xPT) remains unprobed at the mesoscopic level. We use a piezoresponse force microscopy-based dynamic multimodal relaxation spectroscopy technique, enabling the study of ferroelectric switching and polarization relaxation at mesoscopic length scales, and carry out measurements on a PMN-0.28PT sample with minimal polishing. Results indicate that beyond amore » threshold DC bias the average relaxation increases as the system attempts to relax to the previous state. Phenomenological fitting reveals the presence of mesoscale heterogeneity in relaxation amplitudes and clearly suggests the presence of two distinct amplitudes. Independent component analysis reveals the presence of a disorder component of the relaxation, which is found to be strongly anti-correlated with the maximum piezoresponse at that location, suggesting smaller disorder effects where the polarization reversal is large and vice versa. The disorder in the relaxation amplitudes is postulated to arise from rhombohedral and field-induced tetragonal phase in the crystal, with each phase associated with its own relaxation amplitude. As a result, these studies highlight the crucial importance of the mixture of ferroelectric phases in the compositions in proximity of the morphotropic phase boundary in governing the local response and further highlight the ability of PFM voltage and time spectroscopies, in conjunction with big-data multivariate analyses, to locally map disorder and correlate it with parameters governing the dynamic behavior.« less

Hard-sphere-like dynamics in highly concentrated alpha-crystallin suspensions

DOE PAGES

Vodnala, Preeti; Karunaratne, Nuwan; Lurio, Laurence; ...

2018-02-02

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

Hard-sphere-like dynamics in highly concentrated alpha-crystallin suspensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vodnala, Preeti; Karunaratne, Nuwan; Lurio, Laurence

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

Gain and refractive index dynamics in p-doped InAs quantum dash semiconductor optical amplifiers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Komolibus, Katarzyna; Tyndall National Institute, University College Cork, Cork T12 R5CP; Piwonski, Tomasz, E-mail: tomasz.piwonski@tyndall.ie

The ultrafast carrier dynamics in a p-doped dash-in-a-well structure at 1.5 μm is experimentally investigated. An analysis of the timescales related to carrier relaxation and escape processes as well as the “dynamical” linewidth enhancement factor is presented and compared with results obtained from similar un-doped materials. Intentional p-doping of the active region results in an enhancement of the intermediate timescale of the gain dynamics associated with phonon-assisted electron capture and a reduction of the α-factor due to increased differential gain.

Hard-sphere-like dynamics in highly concentrated alpha-crystallin suspensions

NASA Astrophysics Data System (ADS)

Vodnala, Preeti; Karunaratne, Nuwan; Lurio, Laurence; Thurston, George M.; Vega, Michael; Gaillard, Elizabeth; Narayanan, Suresh; Sandy, Alec; Zhang, Qingteng; Dufresne, Eric M.; Foffi, Giuseppe; Grybos, Pawel; Kmon, Piotr; Maj, Piotr; Szczygiel, Robert

2018-02-01

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f (q ,τ ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

Thermal emergence of laser-induced spin dynamics for a Ni4 cluster

NASA Astrophysics Data System (ADS)

Sold, S.; Lefkidis, G.; Kamble, B.; Berakdar, J.; Hübner, W.

2018-05-01

We investigate the thermodynamic behavior of laser-induced spin dynamics of a perfect and a distorted Ni4 square in combination with an external thermal bath, by using the Lindblad-superoperator formalism. The energies of the planar molecules are determined with highly correlated ab initio quantum-chemistry calculations. When the distorted structure couples to the thermal bath a unique spin dynamics, i.e., a spin flip, emerges, due to the interplay of optically and thermally induced electronic transitions. The charge and spin relaxation times in dependence on the coupling strength and the bath temperature are determined and compared.

Hierarchical relaxation dynamics in a tilted two-band Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Cosme, Jayson G.

2018-04-01

We numerically examine slow and hierarchical relaxation dynamics of interacting bosons described by a tilted two-band Bose-Hubbard model. The system is found to exhibit signatures of quantum chaos within the spectrum and the validity of the eigenstate thermalization hypothesis for relevant physical observables is demonstrated for certain parameter regimes. Using the truncated Wigner representation in the semiclassical limit of the system, dynamics of relevant observables reveal hierarchical relaxation and the appearance of prethermalized states is studied from the perspective of statistics of the underlying mean-field trajectories. The observed prethermalization scenario can be attributed to different stages of glassy dynamics in the mode-time configuration space due to dynamical phase transition between ergodic and nonergodic trajectories.

Relaxation dynamics of dysprosium(III) single molecule magnets.

PubMed

Guo, Yun-Nan; Xu, Gong-Feng; Guo, Yang; Tang, Jinkui

2011-10-21

Over the past decade, lanthanide compounds have become of increasing interest in the field of Single Molecule Magnets (SMMs) due to the large inherent anisotropy of the metal ions. Heavy lanthanide metal systems, in particular those containing the dysprosium(III) ion, have been extensively employed to direct the formation of a series of SMMs. Although remarkable progress is being made regarding the synthesis and characterization of lanthanide-based SMMs, the understanding and control of the relaxation dynamics of strongly anisotropic systems represents a formidable challenge, since the dynamic behaviour of lanthanide-based SMMs is significantly more complex than that of transition metal systems. This perspective paper describes illustrative examples of pure dysprosium(III)-based SMMs, published during the past three years, showing new and fascinating phenomena in terms of magnetic relaxation, aiming at shedding light on the features relevant to modulating relaxation dynamics of polynuclear lanthanide SMMs. This journal is © The Royal Society of Chemistry 2011

Dynamical predictive power of the generalized Gibbs ensemble revealed in a second quench.

PubMed

Zhang, J M; Cui, F C; Hu, Jiangping

2012-04-01

We show that a quenched and relaxed completely integrable system is hardly distinguishable from the corresponding generalized Gibbs ensemble in a dynamical sense. To be specific, the response of the quenched and relaxed system to a second quench can be accurately reproduced by using the generalized Gibbs ensemble as a substitute. Remarkably, as demonstrated with the transverse Ising model and the hard-core bosons in one dimension, not only the steady values but even the transient, relaxation dynamics of the physical variables can be accurately reproduced by using the generalized Gibbs ensemble as a pseudoinitial state. This result is an important complement to the previously established result that a quenched and relaxed system is hardly distinguishable from the generalized Gibbs ensemble in a static sense. The relevance of the generalized Gibbs ensemble in the nonequilibrium dynamics of completely integrable systems is then greatly strengthened.

Relaxation dynamics of ultracold bosons in a double-well potential: Thermalization and prethermalization in a nearly integrable model

NASA Astrophysics Data System (ADS)

Cosme, Jayson G.

2015-09-01

We numerically investigate the relaxation dynamics in an isolated quantum system of interacting bosons trapped in a double-well potential after an integrability breaking quench. Using the statistics of the spectrum, we identify the postquench Hamiltonian as nonchaotic and close to integrability over a wide range of interaction parameters. We demonstrate that the system exhibits thermalization in the context of the eigenstate thermalization hypothesis (ETH). We also explore the possibility of an initial state to delocalize with respect to the eigenstates of the postquench Hamiltonian even for energies away from the middle of the spectrum. We observe distinct regimes of equilibration process depending on the initial energy. For low energies, the system rapidly relaxes in a single step to a thermal state. As the energy increases towards the middle of the spectrum, the relaxation dynamics exhibits prethermalization and the lifetime of the metastable states grows. Time evolution of the occupation numbers and the von Neumann entropy in the mode-partitioned system underpins the analyses of the relaxation dynamics.

Carrier thermalization dynamics in single zincblende and wurtzite InP Nanowires.

PubMed

Wang, Yuda; Jackson, Howard E; Smith, Leigh M; Burgess, Tim; Paiman, Suriati; Gao, Qiang; Tan, Hark Hoe; Jagadish, Chennupati

2014-12-10

Using transient Rayleigh scattering (TRS) measurements, we obtain photoexcited carrier thermalization dynamics for both zincblende (ZB) and wurtzite (WZ) InP single nanowires (NW) with picosecond resolution. A phenomenological fitting model based on direct band-to-band transition theory is developed to extract the electron-hole-plasma density and temperature as a function of time from TRS measurements of single nanowires, which have complex valence band structures. We find that the thermalization dynamics of hot carriers depends strongly on material (GaAs NW vs InP NW) and less strongly on crystal structure (ZB vs WZ). The thermalization dynamics of ZB and WZ InP NWs are similar. But a comparison of the thermalization dynamics in ZB and WZ InP NWs with ZB GaAs NWs reveals more than an order of magnitude slower relaxation for the InP NWs. We interpret these results as reflecting their distinctive phonon band structures that lead to different hot phonon effects. Knowledge of hot carrier thermalization dynamics is an essential component for effective incorporation of nanowire materials into electronic devices.

Dielectric relaxation dynamics and AC conductivity scaling of metal-organic framework (MOF-5) based polymer electrolyte nanocomposites incorporated with ionic liquid

NASA Astrophysics Data System (ADS)

Dutta, Rituraj; Kumar, A.

2017-10-01

Dielectric relaxation dynamics and AC conductivity scaling of a metal-organic framework (MOF-5) based poly (vinylidene fluoride-co-hexafluoropropylene) (PVdf-HFP) incorporated with 1-Butyl-3-methylimidazolium hexafluorophosphate have been studied over a frequency range of 40 Hz-5 MHz and in the temperature range of 300 K-380 K. High values of dielectric permittivity (~{{\\varepsilon }\\prime} ) having strong dispersion are obtained at low frequency because of interfacial polarization. The real part of the dielectric modulus spectra (M‧) shows no prominent peak, whereas the imaginary part (M″) shows certain peaks, with a reduction in relaxation time (τ) that can be attributed to a non-Debye relaxation mechanism. The spectra also depict both concentration- and temperature-independent scaling behavior. The power law dependent variation of AC conductivity follows the jump relaxation model and reveals activated ion hopping over diffusion barriers. The value of the frequency exponent is observed to decrease with increasing concentration of ionic liquid, indicating the forward hopping of ions in the relaxation process. The AC conductivity scaling curves at different temperatures also depict the temperature-independent relaxation dynamics.

Structure and dynamics of mica-confined films of [C10C1Pyrr][NTf2] ionic liquid

NASA Astrophysics Data System (ADS)

Freitas, Adilson Alves de; Shimizu, Karina; Smith, Alexander M.; Perkin, Susan; Canongia Lopes, José Nuno

2018-05-01

The structure of the ionic liquid 1-decyl-1-methylpyrrolidinium bis[(trifluoromethane)sulfonyl]imide, [C10C1Pyrr][NTf2], has been probed using Molecular Dynamics (MD) simulations. The simulations endeavour to model the behaviour of the ionic liquid in bulk isotropic conditions and also at interfaces and in confinement. The MD results have been confronted and validated with scattering and surface force experiments reported in the literature. The calculated structure factors, distribution functions, and density profiles were able to provide molecular and mechanistic insights into the properties of these long chain ionic liquids under different conditions, in particular those that lead to the formation of multi-layered ionic liquid films in confinement. Other properties inaccessible to experiment such as in-plane structures and relaxation rates within the films have also been analysed. Overall the work contributes structural and dynamic information relevant to many applications of ionic liquids with long alkyl chains, ranging from nanoparticle synthesis to lubrication.

Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent.

PubMed

Mamontov, E; O'Neill, H

2017-01-01

We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. We have utilized quasielastic neutron scattering. A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics and relaxation of charge carriers in poly(methylmethacrylate)-lithium salt based polymer electrolytes plasticized with ethylene carbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pal, P.; Ghosh, A., E-mail: sspag@iacs.res.in

2016-07-28

In this paper, we have studied the dynamics and relaxation of charge carriers in poly(methylmethacrylate)-lithium salt based polymer electrolytes plasticized with ethylene carbonate. Structural and thermal properties have been examined using X-ray diffraction and differential scanning calorimetry, respectively. We have analyzed the complex conductivity spectra by using power law model coupled with the contribution of electrode polarization at low frequencies and high temperatures. The temperature dependence of the ionic conductivity and crossover frequency exhibits Vogel-Tammann-Fulcher type behavior indicating a strong coupling between the ionic and the polymer chain segmental motions. The scaling of the ac conductivity indicates that relaxation dynamicsmore » of charge carriers follows a common mechanism for all temperatures and ethylene carbonate concentrations. The analysis of the ac conductivity also shows the existence of a nearly constant loss in these polymer electrolytes at low temperatures and high frequencies. The fraction of free anions and ion pairs in polymer electrolyte have been obtained from the analysis of Fourier transform infrared spectra. It is observed that these quantities influence the behavior of the composition dependence of the ionic conductivity.« less

Theory of Aging, Rejuvenation, and the Nonequilibrium Steady State in Deformed Polymer Glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Kang

The nonlinear Langevin equation theory of segmental relaxation, elasticity, and mechanical response of polymer glasses is extended to describe the coupled effects of physical aging, mechanical rejuvenation, and thermal history. The key structural variable is the amplitude of density fluctuations, and segmental dynamics proceeds via stress-modified activated barrier hopping on a dynamic free-energy profile. Mechanically generated disorder rejuvenation is quantified by a dissipative work argument and increases the amplitude of density fluctuations, thereby speeding up relaxation beyond that induced by the landscape tilting mechanism. The theory makes testable predictions for the time evolution and nonequilibrium steady state of the alphamore » relaxation time, density fluctuation amplitude, elastic modulus, and other properties. Model calculations reveal a rich dependence of these quantities on preaging time, applied stress, and temperature that reflects the highly nonlinear competition between physical aging and mechanical disordering. Thermal history is erased in the long-time limit, although the nonequilibrium steady state is not the literal fully rejuvenated freshly quenched glass. The present work provides the conceptual foundation for a quantitative treatment of the nonlinear mechanical response of polymer glasses under a variety of deformation protocols.« less

Applying the relaxation model of interfacial heat transfer to calculate the liquid outflow with supercritical initial parameters

NASA Astrophysics Data System (ADS)

Alekseev, M. V.; Vozhakov, I. S.; Lezhnin, S. I.; Pribaturin, N. A.

2017-09-01

A comparative numerical simulation of the supercritical fluid outflow on the thermodynamic equilibrium and non-equilibrium relaxation models of phase transition for different times of relaxation has been performed. The model for the fixed relaxation time based on the experimentally determined radius of liquid droplets was compared with the model of dynamically changing relaxation time, calculated by the formula (7) and depending on local parameters. It is shown that the relaxation time varies significantly depending on the thermodynamic conditions of the two-phase medium in the course of outflowing. The application of the proposed model with dynamic relaxation time leads to qualitatively correct results. The model can be used for both vaporization and condensation processes. It is shown that the model can be improved on the basis of processing experimental data on the distribution of the droplet sizes formed during the breaking up of the liquid jet.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adichtchev, S. V.; Malinovsky, V. K.; Surovtsev, N. V., E-mail: lab21@iae.nsk.su

Low-frequency (down to 30 GHz) inelastic light scattering is studied in a multicomponent glass ZBLAN (ZrF{sub 4}-BaF{sub 2}-LaF{sub 3}-AlF{sub 3}-NaF) in a wide temperature range. The contributions of the THz vibrational spectrum (boson peak) and of the fast relaxation are extracted and analyzed. It is shown that the fast relaxation spectrum is described by a distribution of relaxation times leading to a power-law ν{sup α} dependence in the frequency range 30–300 GHz. Temperature dependence of α(T) is well described by the Gilroy-Phillips model, while the integrated intensity of the fast relaxation increases significantly with the temperature. This feature distinguishes themore » fast relaxation in ZBLAN from the case of most single-component glasses. Thermodynamic and kinetic fragility indexes are significantly different for the ZBLAN glass. The correlations between the boson peak intensity, elastic moduli, and fragility index, found earlier for single-component glasses, are fulfilled for the thermodynamic fragility index of ZBLAN. In contrast, the correlation between the fast relaxation intensity at T{sub g} and the fragility holds better for the kinetic fragility index of ZBLAN. We propose that thermodynamic and kinetic fragilities reflect different aspects of glassy dynamics in the case of glass formers with the complex chemical composition and structure topology: the former correlates with the elastic properties and the boson peak, the latter with the relaxation.« less

Average-atom treatment of relaxation time in x-ray Thomson scattering from warm dense matter.

PubMed

Johnson, W R; Nilsen, J

2016-03-01

The influence of finite relaxation times on Thomson scattering from warm dense plasmas is examined within the framework of the average-atom approximation. Presently most calculations use the collision-free Lindhard dielectric function to evaluate the free-electron contribution to the Thomson cross section. In this work, we use the Mermin dielectric function, which includes relaxation time explicitly. The relaxation time is evaluated by treating the average atom as an impurity in a uniform electron gas and depends critically on the transport cross section. The calculated relaxation rates agree well with values inferred from the Ziman formula for the static conductivity and also with rates inferred from a fit to the frequency-dependent conductivity. Transport cross sections determined by the phase-shift analysis in the average-atom potential are compared with those evaluated in the commonly used Born approximation. The Born approximation converges to the exact cross sections at high energies; however, differences that occur at low energies lead to corresponding differences in relaxation rates. The relative importance of including relaxation time when modeling x-ray Thomson scattering spectra is examined by comparing calculations of the free-electron dynamic structure function for Thomson scattering using Lindhard and Mermin dielectric functions. Applications are given to warm dense Be plasmas, with temperatures ranging from 2 to 32 eV and densities ranging from 2 to 64 g/cc.

Average-atom treatment of relaxation time in x-ray Thomson scattering from warm dense matter

DOE PAGES

Johnson, W. R.; Nilsen, J.

2016-03-14

Here, the influence of finite relaxation times on Thomson scattering from warm dense plasmas is examined within the framework of the average-atom approximation. Presently most calculations use the collision-free Lindhard dielectric function to evaluate the free-electron contribution to the Thomson cross section. In this work, we use the Mermin dielectric function, which includes relaxation time explicitly. The relaxation time is evaluated by treating the average atom as an impurity in a uniform electron gas and depends critically on the transport cross section. The calculated relaxation rates agree well with values inferred from the Ziman formula for the static conductivity andmore » also with rates inferred from a fit to the frequency-dependent conductivity. Transport cross sections determined by the phase-shift analysis in the average-atom potential are compared with those evaluated in the commonly used Born approximation. The Born approximation converges to the exact cross sections at high energies; however, differences that occur at low energies lead to corresponding differences in relaxation rates. The relative importance of including relaxation time when modeling x-ray Thomson scattering spectra is examined by comparing calculations of the free-electron dynamic structure function for Thomson scattering using Lindhard and Mermin dielectric functions. Applications are given to warm dense Be plasmas, with temperatures ranging from 2 to 32 eV and densities ranging from 2 to 64 g/cc.« less

Relaxation Dynamics of a Granular Pile on a Vertically Vibrating Plate

NASA Astrophysics Data System (ADS)

Tsuji, Daisuke; Otsuki, Michio; Katsuragi, Hiroaki

2018-03-01

Nonlinear relaxation dynamics of a vertically vibrated granular pile is experimentally studied. In the experiment, the flux and slope on the relaxing pile are measured by using a high-speed laser profiler. The relation of these quantities can be modeled by the nonlinear transport law assuming the uniform vibrofluidization of an entire pile. The fitting parameter in this model is only the relaxation efficiency, which characterizes the energy conversion rate from vertical vibration into horizontal transport. We demonstrate that this value is a constant independent of experimental conditions. The actual relaxation is successfully reproduced by the continuity equation with the proposed model. Finally, its specific applicability toward an astrophysical phenomenon is shown.

Static and Dynamic Magnetic Response in Ferrofluids

DTIC Science & Technology

2007-10-30

much below (dodecane) the carrier fluid freezing temperatures providing interesting regimes to study the relaxation mechanisms associated with the...blocking temperature was just above (hexane) and much below (dodecane) the carrier fluid freezing temperatures providing interesting regimes to study...focused mainly on the following tasks: 1. Chemical synthesis of iron oxide and soft ferrite nanoparticles using co- precipitation, structural and

Dielectric relaxation studies of binary mixture of β-picoline and methanol using time domain reflectometry at different temperatures

NASA Astrophysics Data System (ADS)

Trivedi, C. M.; Rana, V. A.; Hudge, P. G.; Kumbharkhane, A. C.

2016-08-01

Complex permittivity spectra of binary mixtures of varying concentrations of β-picoline and Methanol (MeOH) have been obtained using time domain reflectometry (TDR) technique over frequency range 10 MHz to 25 GHz at 283.15, 288.15, 293.15 and 298.15 K temperatures. The dielectric relaxation parameters namely static permittivity (ɛ0), high frequency limit permittivity (ɛ∞1) and the relaxation time (τ) were determined by fitting complex permittivity data to the single Debye/Cole-Davidson model. Complex nonlinear least square (CNLS) fitting procedure was carried out using LEVMW software. The excess permittivity (ɛ0E) and the excess inverse relaxation time (1/τ)E which contain information regarding molecular structure and interaction between polar-polar liquids were also determined. From the experimental data, parameters such as effective Kirkwood correlation factor (geff), Bruggeman factor (fB) and some thermo dynamical parameters have been calculated. Excess parameters were fitted to the Redlich-Kister polynomial equation. The values of static permittivity and relaxation time increase nonlinearly with increase in the mol-fraction of MeOH at all temperatures. The values of excess static permittivity (ɛ0E) and the excess inverse relaxation time (1/τ)E are negative for the studied β-picoline — MeOH system at all temperatures.

Spin relaxation dynamics of holes in intrinsic GaAs quantum wells studied by transient circular dichromatic absorption spectroscopy at room temperature.

PubMed

Fang, Shaoyin; Zhu, Ruidan; Lai, Tianshu

2017-03-21

Spin relaxation dynamics of holes in intrinsic GaAs quantum wells is studied using time-resolved circular dichromatic absorption spectroscopy at room temperature. It is found that ultrafast dynamics is dominated by the cooperative contributions of band filling and many-body effects. The relative contribution of the two effects is opposite in strength for electrons and holes. As a result, transient circular dichromatic differential transmission (TCD-DT) with co- and cross-circularly polarized pump and probe presents different strength at several picosecond delay time. Ultrafast spin relaxation dynamics of excited holes is sensitively reflected in TCD-DT with cross-circularly polarized pump and probe. A model, including coherent artifact, thermalization of nonthermal carriers and the cooperative contribution of band filling and many-body effects, is developed, and used to fit TCD-DT with cross-circularly polarized pump and probe. Spin relaxation time of holes is achieved as a function of excited hole density for the first time at room temperature, and increases with hole density, which disagrees with a theoretical prediction based on EY spin relaxation mechanism, implying that EY mechanism may be not dominant hole spin relaxation mechanism at room temperature, but DP mechanism is dominant possibly.

Ultrafast excited-state dynamics of RNA and DNA C tracts

NASA Astrophysics Data System (ADS)

Cohen, Boiko; Larson, Matthew H.; Kohler, Bern

2008-06-01

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC) 18 were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC) 18 at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ˜100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.

Oscillators and relaxation phenomena in Pleistocene climate theory

PubMed Central

Crucifix, Michel

2012-01-01

Ice sheets appeared in the northern hemisphere around 3 Ma (million years) ago and glacial–interglacial cycles have paced Earth's climate since then. Superimposed on these long glacial cycles comes an intricate pattern of millennial and sub-millennial variability, including Dansgaard–Oeschger and Heinrich events. There are numerous theories about these oscillations. Here, we review a number of them in order to draw a parallel between climatic concepts and dynamical system concepts, including, in particular, the relaxation oscillator, excitability, slow–fast dynamics and homoclinic orbits. Namely, almost all theories of ice ages reviewed here feature a phenomenon of synchronization between internal climate dynamics and astronomical forcing. However, these theories differ in their bifurcation structure and this has an effect on the way the ice age phenomenon could grow 3 Ma ago. All theories on rapid events reviewed here rely on the concept of a limit cycle excited by changes in the surface freshwater balance of the ocean. The article also reviews basic effects of stochastic fluctuations on these models, including the phenomenon of phase dispersion, shortening of the limit cycle and stochastic resonance. It concludes with a more personal statement about the potential for inference with simple stochastic dynamical systems in palaeoclimate science. PMID:22291227

Optimized "detectors" for dynamics analysis in solid-state NMR

NASA Astrophysics Data System (ADS)

Smith, Albert A.; Ernst, Matthias; Meier, Beat H.

2018-01-01

Relaxation in nuclear magnetic resonance (NMR) results from stochastic motions that modulate anisotropic NMR interactions. Therefore, measurement of relaxation-rate constants can be used to characterize molecular-dynamic processes. The motion is often characterized by Markov processes using an auto-correlation function, which is assumed to be a sum of multiple decaying exponentials. We have recently shown that such a model can lead to severe misrepresentation of the real motion, when the real correlation function is more complex than the model. Furthermore, multiple distributions of motion may yield the same set of dynamics data. Therefore, we introduce optimized dynamics "detectors" to characterize motions which are linear combinations of relaxation-rate constants. A detector estimates the average or total amplitude of motion for a range of motional correlation times. The information obtained through the detectors is less specific than information obtained using an explicit model, but this is necessary because the information contained in the relaxation data is ambiguous, if one does not know the correct motional model. On the other hand, if one has a molecular dynamics trajectory, one may calculate the corresponding detector responses, allowing direct comparison to experimental NMR dynamics analysis. We describe how to construct a set of optimized detectors for a given set of relaxation measurements. We then investigate the properties of detectors for a number of different data sets, thus gaining an insight into the actual information content of the NMR data. Finally, we show an example analysis of ubiquitin dynamics data using detectors, using the DIFRATE software.

Exploring the relationship between nanoscale dynamics and macroscopic rheology in natural polymer gums

DOE PAGES

Grein-Iankovski, Aline; Riegel-Vidotti, Izabel C.; Simas-Tosin, Fernanda F.; ...

2016-11-02

Here, we report a study connecting the nanoscale and macroscale structure and dynamics of Acacia mearnsii gum as probed by small-angle x-ray scattering (SAXS), x-ray photon correlation spectroscopy (XPCS) and rheology. Acacia gum, in general, is a complex polysaccharide used extensively in industry. Over the analyzed concentration range (15 to 30 wt%) the A. mearnsii gum is found to have a gel-like linear rheology and to exhibit shear thinning flow behavior under steady shear. The gum exhibited a steadily increasing elastic modulus with increasing time after they were prepared and also the emergence of shear thickening events within the shearmore » thinning behavior, characteristic of associative polymers. XPCS measurements using gold nanoparticles as tracers were used to explore the microscopic dynamics within the biopolymer gels and revealed a two-step relaxation process with a partial decay at inaccessibly short times, suggesting caged motion of the nanoparticles, followed by a slow decay at later delay times. Non-diffusive motion evidenced by a compressed exponential line shape and an inverse relationship between relaxation time and wave vector characterizes the slow dynamics of A. mearnsii gum gels. Surprisingly, we have determined that the nanometer-scale mean square displacement of the nanoparticles showed a close relationship to the values predicted from the macroscopic elastic properties of the material, obtained through the rheology experiments. Our results demonstrate the potential applicability of the XPCS technique in the natural polymers field to connect their macroscale properties with their nanoscale structure and dynamics.« less

Exploring the relationship between nanoscale dynamics and macroscopic rheology in natural polymer gums

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grein-Iankovski, Aline; Riegel-Vidotti, Izabel C.; Simas-Tosin, Fernanda F.

Here, we report a study connecting the nanoscale and macroscale structure and dynamics of Acacia mearnsii gum as probed by small-angle x-ray scattering (SAXS), x-ray photon correlation spectroscopy (XPCS) and rheology. Acacia gum, in general, is a complex polysaccharide used extensively in industry. Over the analyzed concentration range (15 to 30 wt%) the A. mearnsii gum is found to have a gel-like linear rheology and to exhibit shear thinning flow behavior under steady shear. The gum exhibited a steadily increasing elastic modulus with increasing time after they were prepared and also the emergence of shear thickening events within the shearmore » thinning behavior, characteristic of associative polymers. XPCS measurements using gold nanoparticles as tracers were used to explore the microscopic dynamics within the biopolymer gels and revealed a two-step relaxation process with a partial decay at inaccessibly short times, suggesting caged motion of the nanoparticles, followed by a slow decay at later delay times. Non-diffusive motion evidenced by a compressed exponential line shape and an inverse relationship between relaxation time and wave vector characterizes the slow dynamics of A. mearnsii gum gels. Surprisingly, we have determined that the nanometer-scale mean square displacement of the nanoparticles showed a close relationship to the values predicted from the macroscopic elastic properties of the material, obtained through the rheology experiments. Our results demonstrate the potential applicability of the XPCS technique in the natural polymers field to connect their macroscale properties with their nanoscale structure and dynamics.« less

Ultrafast Solvation Dynamics and Vibrational Coherences of Halogenated Boron-Dipyrromethene Derivatives Revealed through Two-Dimensional Electronic Spectroscopy.

PubMed

Lee, Yumin; Das, Saptaparna; Malamakal, Roy M; Meloni, Stephen; Chenoweth, David M; Anna, Jessica M

2017-10-18

Boron-dipyrromethene (BODIPY) chromophores have a wide range of applications, spanning areas from biological imaging to solar energy conversion. Understanding the ultrafast dynamics of electronically excited BODIPY chromophores could lead to further advances in these areas. In this work, we characterize and compare the ultrafast dynamics of halogenated BODIPY chromophores through applying two-dimensional electronic spectroscopy (2DES). Through our studies, we demonstrate a new data analysis procedure for extracting the dynamic Stokes shift from 2DES spectra revealing an ultrafast solvent relaxation. In addition, we extract the frequency of the vibrational modes that are strongly coupled to the electronic excitation, and compare the results of structurally different BODIPY chromophores. We interpret our results with the aid of DFT calculations, finding that structural modifications lead to changes in the frequency, identity, and magnitude of Franck-Condon active vibrational modes. We attribute these changes to differences in the electron density of the electronic states of the structurally different BODIPY chromophores.

Time-resolved observation of protein allosteric communication

PubMed Central

Buchenberg, Sebastian; Sittel, Florian; Stock, Gerhard

2017-01-01

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response (≲0.1 ns), inelastic reorganization (∼100 ns), and structural relaxation (≳1μs). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed. PMID:28760989

Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Debnarova, Andrea; Techert, Simone; Schmatz, Stefan

2010-09-28

We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems,more » which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.« less

Multiple conformational states of the hammerhead ribozyme, broad time range of relaxation and topology of dynamics

PubMed Central

Menger, Marcus; Eckstein, Fritz; Porschke, Dietmar

2000-01-01

The dynamics of a hammerhead ribozyme was analyzed by measurements of fluorescence-detected temperature jump relaxation. The ribozyme was substituted at different positions by 2-aminopurine (2-AP) as fluorescence indicator; these substitutions do not inhibit catalysis. The general shape of relaxation curves reported from different positions of the ribozyme is very similar: a fast decrease of fluorescence, mainly due to physical quenching, is followed by a slower increase of fluorescence due to conformational relaxation. In most cases at least three relaxation time constants in the time range from a few microseconds to ~200 ms are required for fitting. Although the relaxation at different positions of the ribozyme is similar in general, suggesting a global type of ribozyme dynamics, a close examination reveals differences, indicating an individual local response. For example, 2-AP in a tetraloop reports mainly the local loop dynamics known from isolated loops, whereas 2-AP located at the core, e.g. at the cleavage site or its vicinity, also reports relatively large amplitudes of slower components of the ribozyme dynamics. A variant with an A→G substitution in domain II, resulting in an inactive form, leads to the appearance of a particularly slow relaxation process (τ ≈200 ms). Addition of Mg2+ ions induces a reduction of amplitudes and in most cases a general increase of time constants. Differences between the hammerhead variants are clearly demonstrated by subtraction of relaxation curves recorded under corresponding conditions. The changes induced in the relaxation response by Mg2+ are very similar to those induced by Ca2+. The relaxation data do not provide any evidence for formation of Mg2+-inner sphere complexes in hammerhead ribozymes, because a Mg2+-specific relaxation effect was not visible. However, a Mg2+-specific effect was found for a dodeca-riboadenylate substituted with 2-AP, showing that the fluorescence of 2-AP is able to indicate inner sphere complexation. Amplitudes and time constants show that the equilibrium constant of inner sphere complexation is 1.2, corresponding to 55% inner sphere state of the Mg2+ complexes; the rate constant 6.6 × 103 s–1 for inner sphere complexation is relatively low and shows the existence of some barrier(s) on the way to inner sphere complexes. PMID:11071929

Effects of Dynamical Evolution on Globular Clusters’ Internal Kinematics

NASA Astrophysics Data System (ADS)

Tiongco, Maria; Vesperini, Enrico; Varri, Anna Lisa

2018-01-01

The synergy between recent photometric, spectroscopic, and astrometric studies is revealing that globular clusters deviate from the traditional picture of dynamically simple and single stellar population systems. Complex kinematical features such as velocity anisotropy and rotation, and the existence of multiple stellar populations are some of the key observational findings. My thesis work has aimed to build a theoretical framework to interpret these new observational results and to understand their link with a globular cluster’s dynamical history.I have focused on the study of the evolution of globular clusters' internal kinematics, as driven by two-body relaxation, and the interplay between internal angular momentum and the external Galactic tidal field. With a specifically-designed, large survey of direct N-body simulations, I have explored the three-dimensional structure of the velocity space of tidally-perturbed clusters, by characterizing their degree of anisotropy and their rotational properties. These studies have proved that a cluster's kinematical properties contain a distinct imprints of the cluster’s initial structural properties, dynamical history, and tidal environment. By relaxing a number of simplifying assumptions that are traditionally imposed, I have also showed how the interplay between a cluster's internal evolution and the interaction with the host galaxy can produce complex morphological and kinematical properties, such as a counter-rotating core and a twisting of the projected isodensity contours.Building on this fundamental understanding, I have then studied the dynamics of multiple stellar populations in globular clusters, with attention to the largely unexplored role of angular momentum. I have analyzed the evolution of clusters with stellar populations characterized by different initial structural and kinematical properties to determine how long these differences are preserved, and in what cases they could still be observable in present-day systems.This body of results provides essential guidance for a meaningful interpretation of the emerging dynamical complexity of globular clusters in the era of Gaia and other upcoming large spectroscopic surveys.

Real-time decay of a highly excited charge carrier in the one-dimensional Holstein model

NASA Astrophysics Data System (ADS)

Dorfner, F.; Vidmar, L.; Brockt, C.; Jeckelmann, E.; Heidrich-Meisner, F.

2015-03-01

We study the real-time dynamics of a highly excited charge carrier coupled to quantum phonons via a Holstein-type electron-phonon coupling. This is a prototypical example for the nonequilibrium dynamics in an interacting many-body system where excess energy is transferred from electronic to phononic degrees of freedom. We use diagonalization in a limited functional space (LFS) to study the nonequilibrium dynamics on a finite one-dimensional chain. This method agrees with exact diagonalization and the time-evolving block-decimation method, in both the relaxation regime and the long-time stationary state, and among these three methods it is the most efficient and versatile one for this problem. We perform a comprehensive analysis of the time evolution by calculating the electron, phonon and electron-phonon coupling energies, and the electronic momentum distribution function. The numerical results are compared to analytical solutions for short times, for a small hopping amplitude and for a weak electron-phonon coupling. In the latter case, the relaxation dynamics obtained from the Boltzmann equation agrees very well with the LFS data. We also study the time dependence of the eigenstates of the single-site reduced density matrix, which defines the so-called optimal phonon modes. We discuss their structure in nonequilibrium and the distribution of their weights. Our analysis shows that the structure of optimal phonon modes contains very useful information for the interpretation of the numerical data.

Several routes to the glassy states in the one component soft core system: revisited by molecular dynamics.

PubMed

Habasaki, Junko; Ueda, Akira

2011-02-28

Molecular dynamics simulations have been performed to study the glass transition for the soft core system with a pair potential φ(n)(r) = ε(σ∕r)(n) of n = 12. Using the compressibility factor, PV/Nk(B)T=P̃(ρ*), its phase diagram can be represented as a function of a reduced density, ρ∗ = ρ(ε∕k(B)T)(3∕n), where ρ = Nσ(3)∕V. In the present work, NVE relaxations to the glassy or crystalline states starting from the unstable states in the phase diagram have been revisited in details and compared with other processes. Relaxation processes can be characterized by the time dependence of the dynamical compressibility factor (PV/Nk(B)T)(t) (≡g(ρ(t)*)) on the phase diagram. In some cases, g(ρ(t)*) reached a crystal branch in the phase diagram; however, metastable states are found in many cases. With connecting points for the metastable states in the phase diagram, we can define a glass branch where the dynamics of particles are almost frozen. The structures observed there have common properties characterized as glasses. Although overlaps of glass forming process and nanocrystallization process are observed in some cases, these behaviors are distinguishable to each other by the characteristics of structures. There are several routes to the glass branch and we suggest that all of them are the glass transition.

Exciton recombination dynamics in CdSe nanowires: bimolecular to three-carrier Auger kinetics.

PubMed

Robel, István; Bunker, Bruce A; Kamat, Prashant V; Kuno, Masaru

2006-07-01

Ultrafast relaxation dynamics of charge carriers in CdSe quantum wires with diameters between 6 and 8 nm are studied as a function of carrier density. At high electron-hole pair densities above 10(19) cm(-3) the dominant process for carrier cooling is the "bimolecular" Auger recombination of one-dimensional (1D) excitons. However, below this excitation level an unexpected transition from a bimolecular (exciton-exciton) to a three-carrier Auger relaxation mechanism occurs. Thus, depending on excitation intensity, electron-hole pair relaxation dynamics in the nanowires exhibit either 1D or 0D (quantum dot) character. This dual nature of the recovery kinetics defines an optimal intensity for achieving optical gain in solution-grown nanowires given the different carrier-density-dependent scaling of relaxation rates in either regime.

Characterization of LaRC-CPI semicrystalline polyimide using thermal, dynamic mechanical and dielectric relaxation techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rich, D.C.; Huo, P.P.; Liu, C.

1993-12-31

The thermal, dynamic mechanical, and dielectric properties of the semicrystalline thermoplastic polyimide LaRC-CPI were studied. Using differential scanning calorimetry to measure heats of fusion and WAXS to measure crystallinity, the heat of fusion of perfect crystalline LaRC-CPI was determined to be 92 {+-} 2 J/g. DMA and dielectric measurements were performed on three LaRC-CPI films (as received, annealed, and amorphous). Crystallinity was found to reinforce the rubbery state resulting in a higher modulus and broader distribution of relaxation times. Broader relaxation for the crystalline LaRC-CPI was also observed in the dielectric tests. Processing strain and the thermal history were foundmore » to have a significant impact in both dynamic mechanical and dielectric relaxation measurements.« less

Unravelling the mechanisms of vibrational relaxation in solution† †All experimental data are archived in the University of Bristol's Research Data Storage Facility (DOI: 10.5523/bris.2vk036f35m5aq2dnlb79c0wcsh). ‡ ‡Electronic supplementary information (ESI) available: Further discussion of spectral lineshapes, concentration dependence of transient absorption data, theoretical calculations, IR-pump IR-probe spectra, transient absorption spectra including animation of spectra. See DOI: 10.1039/c6sc05234g Click here for additional data file. Click here for additional data file.

PubMed Central

Grubb, Michael P.; Coulter, Philip M.; Marroux, Hugo J. B.

2017-01-01

We present a systematic study of the mode-specific vibrational relaxation of NO2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO2 fragments produced from the 340 nm photolysis of N2O4 → NO2(X) + NO2(A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO2 bending and stretching modes, even at energies as high as 7000 cm–1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20–1100 ps. NO2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution. PMID:28451375

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

PubMed

Traaseth, Nathaniel J; Chao, Fa-An; Masterson, Larry R; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi

2012-06-01

NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R(1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) R(2) experiments are commonly used to characterize μs to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R(1ρ) and transverse R(2ρ)) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (k(ex)∼10(4)-10(5) s(-1)). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R(1ρ) and R(2ρ) relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R(1ρ) and R(2ρ) that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R(1ρ) experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent. Copyright © 2012 Elsevier Inc. All rights reserved.

Semiclassical dynamics of spin density waves

NASA Astrophysics Data System (ADS)

Chern, Gia-Wei; Barros, Kipton; Wang, Zhentao; Suwa, Hidemaro; Batista, Cristian D.

2018-01-01

We present a theoretical framework for equilibrium and nonequilibrium dynamical simulation of quantum states with spin-density-wave (SDW) order. Within a semiclassical adiabatic approximation that retains electron degrees of freedom, we demonstrate that the SDW order parameter obeys a generalized Landau-Lifshitz equation. With the aid of an enhanced kernel polynomial method, our linear-scaling quantum Landau-Lifshitz dynamics (QLLD) method enables dynamical SDW simulations with N ≃105 lattice sites. Our real-space formulation can be used to compute dynamical responses, such as the dynamical structure factor, of complex and even inhomogeneous SDW configurations at zero or finite temperatures. Applying the QLLD to study the relaxation of a noncoplanar topological SDW under the excitation of a short pulse, we further demonstrate the crucial role of spatial correlations and fluctuations in the SDW dynamics.

Slowing dynamics in supercooled liquids and other soft materials

NASA Astrophysics Data System (ADS)

Yardimci, Hasan

The slow structural dynamics displayed by supercooled liquids and the transition to an out-of-equilibrium glass state that they engender are among the most challenging issues in condensed matter physics. This thesis reports experimental studies designed to elucidate central aspects of these slow dynamics and the nature of the glass state. The subjects of these studies include glass forming molecular liquids and other soft materials that have been advanced as model glassy systems such as clay suspensions and block copolymer micelle solutions. The main experimental techniques employed in these investigations have been dielectric susceptibility and neutron scattering. In the first half of this thesis, we report frequency-dependent dielectric susceptibility measurements characterizing the evolution in the dynamical properties, or aging, of two supercooled liquids, sorbitol and xylitol, quenched below their calorimetric glass transition temperatures, Tg. In addition to the alpha relaxation that tracks the structural dynamics, the susceptibilities of both liquids possess a secondary Johari-Goldstein relaxation at higher frequencies. Following a quench below Tg, the susceptibility slowly approaches equilibrium behavior. For both liquids features of the Johari-Goldstein relaxation display a dependence on the time since the quench, or aging time, that is very similar to the age dependence of the alpha peak. Implications of these findings for aging in glasses and the nature of Johari-Goldstein relaxation are discussed. Further investigation of the aging in sorbitol reveals that it displays memory strikingly similar to that of a variety of glassy materials, particularly spin glasses. During a temporary stop in cooling, the susceptibility changes with time due to aging. The memory is revealed upon reheating as the susceptibility retraces these changes. To investigate the out-of-equilibrium state of the liquid as it displays this memory, we have employed a set of intricate thermal histories by interrupting the heating stage of the cycle and characterizing the subsequent aging. At temperatures above that of the original cooling stop, the liquid enters a state on heating with an effective age that is proportional to the duration of the stop, while at lower temperatures no effective age can be assigned and subtler behavior emerges. These results, which reveal differences with memory displayed by spin glasses, are discussed in the context of the liquid's energy landscape. In the second half of the thesis, we report neutron scattering measurements and dielectric studies on a set of disordered soft materials. (Abstract shortened by UMI.)

Extreme-volatility dynamics in crude oil markets

NASA Astrophysics Data System (ADS)

Jiang, Xiong-Fei; Zheng, Bo; Qiu, Tian; Ren, Fei

2017-02-01

Based on concepts and methods from statistical physics, we investigate extreme-volatility dynamics in the crude oil markets, using the high-frequency data from 2006 to 2010 and the daily data from 1986 to 2016. The dynamic relaxation of extreme volatilities is described by a power law, whose exponents usually depend on the magnitude of extreme volatilities. In particular, the relaxation before and after extreme volatilities is time-reversal symmetric at the high-frequency time scale, but time-reversal asymmetric at the daily time scale. This time-reversal asymmetry is mainly induced by exogenous events. However, the dynamic relaxation after exogenous events exhibits the same characteristics as that after endogenous events. An interacting herding model both with and without exogenous driving forces could qualitatively describe the extreme-volatility dynamics.

The effect of structural properties on rheological behaviour of starches in binary dimethyl sulfoxide-water solutions.

PubMed

Ptaszek, Anna; Ptaszek, Paweł; Dziubiński, Marek; Grzesik, N Mirosław; Liszka-Skoczylas, Marta

2017-01-01

This research study analysed the rheological properties of potato amylose and potato amylopectin in binary solutions of the following water and dimethyl sulfoxide concentrations: 90% DMSO (1), 80% DMSO (2) and 50% DMSO (3), with preparation methodology involving the dissolution at the temperature of 98°C. The studies of dynamic light scattering on the biopolymer coils and the determination of main relaxation times of the solutions were carried out. For the amylose solutions, the fast relaxation phenomena are predominant. The results of the quality tests of the hysteresis loop showed, that the amylose solutions in the solvents (1) and (2) are rheologically stable and shear-thickened. The amylose solutions in solvents (3) reveal oscillatory alterations of viscosity in the time. Amylopectin solutions are characterized by 80% share of slow relaxation phenomena, very low diffusion coefficients and hydrodynamic radii in the range of 2000 nm. The amylopectin solutions are rheologically unstable.

Quasiparticle dynamics across the full Brillouin zone of Bi 2Sr 2CaCu 2O 8+δ traced with ultrafast time and angle-resolved photoemission spectroscopy

DOE PAGES

Dakovski, Georgi L.; Durakiewicz, Tomasz; Zhu, Jian-Xin; ...

2015-10-12

A hallmark in the cuprate family of high-temperature superconductors is the nodal-antinodal dichotomy. In this regard, angle-resolved photoemission spectroscopy (ARPES) has proven especially powerful, providing band structure information directly in energy-momentum space. Time-resolved ARPES (trARPES) holds great promise of adding ultrafast temporal information, in an attempt to identify different interaction channels in the time domain. Previous studies of the cuprates using trARPES were handicapped by the low probing energy which significantly limits the accessible momentum space. Using 20.15eV, 12 fs pulses we show for the first time the evolution of quasiparticles in the antinodal region of Bi 2Sr 2CaCu 2Omore » 8+δ and demonstrate that nonmonotonic relaxation dynamics dominates above a certain fluence threshold. The dynamics is heavily influenced by transient modification of the electron-phonon interaction and phase space restrictions, in severe contrast to the monotonic relaxation in the nodal and off-nodal regions.« less

Theory of activated glassy dynamics in randomly pinned fluids.

PubMed

Phan, Anh D; Schweizer, Kenneth S

2018-02-07

We generalize the force-level, microscopic, Nonlinear Langevin Equation (NLE) theory and its elastically collective generalization [elastically collective nonlinear Langevin equation (ECNLE) theory] of activated dynamics in bulk spherical particle liquids to address the influence of random particle pinning on structural relaxation. The simplest neutral confinement model is analyzed for hard spheres where there is no change of the equilibrium pair structure upon particle pinning. As the pinned fraction grows, cage scale dynamical constraints are intensified in a manner that increases with density. This results in the mobile particles becoming more transiently localized, with increases of the jump distance, cage scale barrier, and NLE theory mean hopping time; subtle changes of the dynamic shear modulus are predicted. The results are contrasted with recent simulations. Similarities in relaxation behavior are identified in the dynamic precursor regime, including a roughly exponential, or weakly supra-exponential, growth of the alpha time with pinning fraction and a reduction of dynamic fragility. However, the increase of the alpha time with pinning predicted by the local NLE theory is too small and severely so at very high volume fractions. The strong deviations are argued to be due to the longer range collective elasticity aspect of the problem which is expected to be modified by random pinning in a complex manner. A qualitative physical scenario is offered for how the three distinct aspects that quantify the elastic barrier may change with pinning. ECNLE theory calculations of the alpha time are then presented based on the simplest effective-medium-like treatment for how random pinning modifies the elastic barrier. The results appear to be consistent with most, but not all, trends seen in recent simulations. Key open problems are discussed with regard to both theory and simulation.

Theory of activated glassy dynamics in randomly pinned fluids

NASA Astrophysics Data System (ADS)

Phan, Anh D.; Schweizer, Kenneth S.

2018-02-01

We generalize the force-level, microscopic, Nonlinear Langevin Equation (NLE) theory and its elastically collective generalization [elastically collective nonlinear Langevin equation (ECNLE) theory] of activated dynamics in bulk spherical particle liquids to address the influence of random particle pinning on structural relaxation. The simplest neutral confinement model is analyzed for hard spheres where there is no change of the equilibrium pair structure upon particle pinning. As the pinned fraction grows, cage scale dynamical constraints are intensified in a manner that increases with density. This results in the mobile particles becoming more transiently localized, with increases of the jump distance, cage scale barrier, and NLE theory mean hopping time; subtle changes of the dynamic shear modulus are predicted. The results are contrasted with recent simulations. Similarities in relaxation behavior are identified in the dynamic precursor regime, including a roughly exponential, or weakly supra-exponential, growth of the alpha time with pinning fraction and a reduction of dynamic fragility. However, the increase of the alpha time with pinning predicted by the local NLE theory is too small and severely so at very high volume fractions. The strong deviations are argued to be due to the longer range collective elasticity aspect of the problem which is expected to be modified by random pinning in a complex manner. A qualitative physical scenario is offered for how the three distinct aspects that quantify the elastic barrier may change with pinning. ECNLE theory calculations of the alpha time are then presented based on the simplest effective-medium-like treatment for how random pinning modifies the elastic barrier. The results appear to be consistent with most, but not all, trends seen in recent simulations. Key open problems are discussed with regard to both theory and simulation.

Slowdown of Interhelical Motions Induces a Glass Transition in RNA

PubMed Central

Frank, Aaron T.; Zhang, Qi; Al-Hashimi, Hashim M.; Andricioaei, Ioan

2015-01-01

RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit—the transactivation response RNA element—we present evidence from molecular dynamics simulations, supported by nuclear magnetic resonance relaxation experiments, for a dynamical transition near 230 K. This glass transition arises from the freezing out of collective interhelical motional modes. The motions, resolved with site-specificity, are dynamically heterogeneous and exhibit non-Arrhenius relaxation. The microscopic origin of the glass transition is a low-dimensional, slow manifold consisting largely of the Euler angles describing interhelical reorientation. Principal component analysis over a range of temperatures covering the glass transition shows that the abrupt slowdown of motion finds its explanation in a localization transition that traps probability density into several disconnected conformational pools over the low-dimensional energy landscape. Upon temperature increase, the probability density pools then flood a larger basin, akin to a lakes-to-sea transition. Simulations on transactivation response RNA are also used to backcalculate inelastic neutron scattering data that match previous inelastic neutron scattering measurements on larger and more complex RNA structures and which, upon normalization, give temperature-dependent fluctuation profiles that overlap onto a glass transition curve that is quasi-universal over a range of systems and techniques. PMID:26083927

Simulating the multicellular homeostasis with a cell-based discrete receptor dynamics model: The non-mutational origin of cancer and aging.

PubMed

Lou, Yuting; Chen, Yu

2016-09-07

The purpose of the study is to investigate the multicellular homeostasis in epithelial tissues over very large timescales. Inspired by the receptor dynamics of IBCell model proposed by Rejniak et al. an on-grid agent-based model for multicellular system is constructed. Instead of observing the multicellular architectural morphologies, the diversity of homeostatic states is quantitatively analyzed through a substantial number of simulations by measuring three new order parameters, the phenotypic population structure, the average proliferation age and the relaxation time to stable homeostasis. Nearby the interfaces of distinct homeostatic phases in 3D phase diagrams of the three order parameters, intermediate quasi-stable phases of slow dynamics that features quasi-stability with a large spectrum of relaxation timescales are found. A further exploration on the static and dynamic correlations among the three order parameters reveals that the quasi-stable phases evolve towards two terminations, tumorigenesis and degeneration, which are respectively accompanied by rejuvenation and aging. With the exclusion of the environmental impact and the mutational strategies, the results imply that cancer and aging may share the non-mutational origin in the intrinsic slow dynamics of the multicellular systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems

PubMed Central

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; del Giudice, Paolo

2015-01-01

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a ‘basin’ of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases. PMID:26463272

Anomalous quantum critical spin dynamics in YFe2Al10

NASA Astrophysics Data System (ADS)

Huang, K.; Tan, C.; Zhang, J.; Ding, Z.; MacLaughlin, D. E.; Bernal, O. O.; Ho, P.-C.; Baines, C.; Wu, L. S.; Aronson, M. C.; Shu, L.

2018-04-01

We report results of a muon spin relaxation (μ SR ) study of YFe2Al10 , a quasi-two-dimensional (2D) nearly ferromagnetic metal in which unconventional quantum critical behavior is observed. No static Fe2 + magnetism, with or without long-range order, is found down to 19 mK. The dynamic muon spin relaxation rate λ exhibits power-law divergences in temperature and magnetic field, the latter for fields that are too weak to affect the electronic spin dynamics directly. We attribute this to the proportionality of λ (ωμ,T ) to the dynamic structure factor S (ωμ,T ) , where ωμ≈105-107s-1 is the muon Zeeman frequency. These results suggest critical divergences of S (ωμ,T ) in both temperature and frequency. Power-law scaling and a 2D dissipative quantum XY model both yield forms for S (ω ,T ) that agree with neutron scattering data (ω ≈1012s-1 ). Extrapolation to μ SR frequencies agrees semiquantitatively with the observed temperature dependence of λ (ωμ,T ) , but predicts frequency independence for ωμ≪T , in extreme disagreement with experiment. We conclude that the quantum critical spin dynamics of YFe2Al10 is not well understood at low frequencies.

THE ZURICH ENVIRONMENTAL STUDY OF GALAXIES IN GROUPS ALONG THE COSMIC WEB. I. WHICH ENVIRONMENT AFFECTS GALAXY EVOLUTION?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carollo, C. Marcella; Cibinel, Anna; Lilly, Simon J.

2013-10-20

The Zurich Environmental Study (ZENS) is based on a sample of ∼1500 galaxy members of 141 groups in the mass range ∼10{sup 12.5-14.5} M{sub ☉} within the narrow redshift range 0.05 < z < 0.0585. ZENS adopts novel approaches, described here, to quantify four different galactic environments, namely: (1) the mass of the host group halo; (2) the projected halo-centric distance; (3) the rank of galaxies as central or satellites within their group halos; and (4) the filamentary large-scale structure density. No self-consistent identification of a central galaxy is found in ∼40% of <10{sup 13.5} M{sub ☉} groups, from whichmore » we estimate that ∼15% of groups at these masses are dynamically unrelaxed systems. Central galaxies in relaxed and unrelaxed groups generally have similar properties, suggesting that centrals are regulated by their mass and not by their environment. Centrals in relaxed groups have, however, ∼30% larger sizes than in unrelaxed groups, possibly due to accretion of small satellites in virialized group halos. At M > 10{sup 10} M{sub ☉}, satellite galaxies in relaxed and unrelaxed groups have similar size, color, and (specific) star formation rate distributions; at lower galaxy masses, satellites are marginally redder in relaxed relative to unrelaxed groups, suggesting quenching of star formation in low-mass satellites by physical processes active in relaxed halos. Overall, relaxed and unrelaxed groups show similar stellar mass populations, likely indicating similar stellar mass conversion efficiencies. In the enclosed ZENS catalog, we publish all environmental diagnostics as well as the galaxy structural and photometric measurements described in companion ZENS papers II and III.« less

Transient absorption microscopy studies of energy relaxation in graphene oxide thin film.

PubMed

Murphy, Sean; Huang, Libai

2013-04-10

Spatial mapping of energy relaxation in graphene oxide (GO) thin films has been imaged using transient absorption microscopy (TAM). Correlated AFM images allow us to accurately determine the thickness of the GO films. In contrast to previous studies, correlated TAM-AFM allows determination of the effect of interactions of GO with the substrate and between stacked GO layers on the relaxation dynamics. Our results show that energy relaxation in GO flakes has little dependence on the substrate, number of stacked layers, and excitation intensity. This is in direct contrast to pristine graphene, where these factors have great consequences in energy relaxation. This suggests intrinsic factors rather than extrinsic ones dominate the excited state dynamics of GO films.

Dynamical analysis of relaxation luminescence in ZnS:Er3+ thin film devices

NASA Astrophysics Data System (ADS)

Wang, Yu-Jiang; Wu, Chen-Xu; Chen, Mou-Zhi; Huang, Mei-Chun

2003-06-01

The relaxation luminescence of ZnS:Er3+ thin film devices fabricated by thermal evaporation with two boats is studied. The dynamical processes of the luminescence of Er3+ in ZnS are described in terms of a resonant energy transfer model, assuming that the probability of collision excitation of injected electrons with luminescence centers is expressed as a Gaussian function. It is found that the frequency distribution depends on the Lorentzian function by considering the emission from excited states as a damped oscillator. Taking into consideration the energy storing effect of traps, an expression is obtained to describe a profile that contains multiple relaxation luminescence peaks using the convolution theorem. Fitting of experimental results shows that the relaxation characteristics of the electroluminescence are related to the carriers captured by bulk traps as well as by interface states. The numerical calculation carried out agrees well with the dynamical characteristics of relaxation luminescence obtained by experiments.

Evolutions of lamellar structure during melting and solidification of Fe9577 nanoparticle from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wu, Yongquan; Shen, Tong; Lu, Xionggang

2013-03-01

A structural evolution during solidification and melting processes of nanoparticle Fe9577 was investigated from MD simulations. A perfect lamellar structure, consisting alternately of fcc and hcp layers, was obtained from solidification process. A structural heredity of early embryo is proposed to explain the structural preference of solidification. Defects were found inside the solid core and play the same role as surface premelting on melting. hcp was found more stable than fcc in high temperature. The difference between melting and solidification points can be deduced coming fully from the overcoming of thermodynamic energy barrier, instead of kinetic delay of structural relaxation.

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations

PubMed Central

Sagnella, Diane E.; Straub, John E.; Jackson, Timothy A.; Lim, Manho; Anfinrud, Philip A.

1999-01-01

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the δ- and ɛ-tautomers of the distal His-64. Vibrational population relaxation times of 335 ± 115 ps for the δ-tautomer and 640 ± 185 ps for the ɛ-tautomer were estimated by using the Landau–Teller model. Normal mode analysis was used to identify those protein residues that act as the primary “doorway” modes in the vibrational relaxation of the oscillator. Although the CO relaxation rates in both the ɛ- and δ-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the δ-tautomer with the distal His playing an important role in the energy relaxation mechanism. Time-resolved mid-IR absorbance measurements were performed on photolyzed carbonmonoxy hemoglobin (Hb13CO). From these measurements, a T1 time of 600 ± 150 ps was determined. The simulation and experimental estimates are compared and discussed. PMID:10588704

Correlation between temperature variations of static and dynamic properties in glass-forming liquids

DOE PAGES

Voylov, D. N.; Griffin, P. J.; Mercado, B.; ...

2016-12-29

In this detailed analysis of the static structure factor S(Q) in several glass-forming liquids we show that the temperature variations of the width of the main diffraction peak Q(T ) correlate with the fragility of these liquids. Our observation suggests a direct connection between rather subtle structural changes and sharp slowing down of structural relaxation in glass-forming liquids. We also show that this observation can be rationalized using the Adam-Gibbs approach, through a connection between temperature variations of structural correlation length, lc 2 /Q, and the size of cooperatively rearranging regions.

Structure and Dynamics of Water/Methanol Mixtures at Hydroxylated Silica Interfaces Relevant to Chromatography.

PubMed

Gupta, Prashant Kumar; Meuwly, Markus

2016-09-19

The spectroscopy and dynamics of water/methanol (MeOH) mixtures at hydroxylated silica surfaces is investigated from atomistic simulations. The particular focus is on how the structural dynamics of MeOH changes when comparing surface-bound and MeOH in the bulk. From analyzing the frequency frequency correlation functions it is found that the dynamics on the picosecond time scale differs by almost a factor of two. While the relaxation time is 2.0 ps for MeOH in the bulk solvent it is considerably slowed-down to 3.5 ps for surface-bound MeOH. Surface-adsorbed MeOH molecules reside there for several nanoseconds and their H-bonds are strongly oriented towards the surface-OH groups. These results are of particular relevance for chromatographic systems where the solvent may play a central role in their function. The present simulations suggest that surface-sensitive spectroscopic techniques should be useful in better characterizing such heterogeneous systems and provide detailed insight into solvent dynamics and structure relevant in chromatographic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hotspot relaxation dynamics in a current-carrying superconductor

NASA Astrophysics Data System (ADS)

Marsili, F.; Stevens, M. J.; Kozorezov, A.; Verma, V. B.; Lambert, Colin; Stern, J. A.; Horansky, R. D.; Dyer, S.; Duff, S.; Pappas, D. P.; Lita, A. E.; Shaw, M. D.; Mirin, R. P.; Nam, S. W.

2016-03-01

We experimentally studied the dynamics of optically excited hotspots in current-carrying WSi superconducting nanowires as a function of bias current, bath temperature, and excitation wavelength. We observed that the hotspot relaxation time depends on bias current, temperature, and wavelength. We explained this effect with a model based on quasiparticle recombination, which provides insight into the quasiparticle dynamics of superconductors.

Microscopic relaxations in a protein sustained down to 160 K in a non-glass forming organic solvent

DOE PAGES

Mamontov, Eugene; O'Neil, Hugh

2016-05-03

In this paper, we have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160 K. We have utilized quasielastic neutron scattering. A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamicalmore » transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160 K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. Finally, our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics.« less

Relaxation Assessment with Varied Structured Milieu (RELAX).

ERIC Educational Resources Information Center

Cassel, Russell N.; Cassel, Susie L.

1983-01-01

Describes Relaxation Assessment with Varied Structured Milieu (RELAX), a clinical program designed to assess the degree to which an individual is able to demonstrate self-control for overall general relaxation. The program is designed for use with the Cassel Biosensors biofeedback equipment. (JAC)

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Investigation of the Structure and Dynamics of Electrolytes in solvents Used for Primary and Secondary Li-Batteries.

DTIC Science & Technology

1985-02-01

permittivitles in the concentration range 0.05M to 0.3M, frequency range 1 to 90 GHz are Intepreted by two Debye relaxation processes, one due to the...and are co-authors of the published papers. They have not received any financial reward from the contract funds. FILMED 6-85 DTIC

Coherent spin dynamics of carriers in ferromagnetic semiconductor heterostructures with an Mn δ layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaitsev, S. V., E-mail: szaitsev@issp.ac.ru; Akimov, I. A.; Langer, L.

2016-09-15

The coherent spin dynamics of carriers in the heterostructures that contain an InGaAs/GaAs quantum well (QW) and an Mn δ layer, which are separated by a narrow GaAs spacer 2–10 nm thick, is comprehensively studied by the magnetooptical Kerr effect method at a picosecond time resolution. The exchange interaction of photoexcited electrons in QW with the ferromagnetic Mn δ layer manifests itself in magnetic-field and temperature dependences of the Larmor precession frequency of electron spins and is found to be very weak (several microelectron volts). Two nonoscillating components related to holes exist apart from an electron contribution to the Kerrmore » signal of polarization plane rotation. At the initial stage, a fast relaxation process, which corresponds to the spin relaxation of free photoexcited holes, is detected in the structures with a wide spacer. The second component is caused by the further spin dephasing of energyrelaxed holes, which are localized at strong QW potential fluctuations in the structures under study. The decay of all contributions to the Kerr signal in time increases substantially when the spacer thickness decreases, which correlates with the enhancement of nonradiative recombination in QW.« less

Spontaneous polarization and dielectric relaxation dynamics of ferroelectric liquid crystals derived from 2(S)-[2(S)-ethylhexyolxy] propionic acid and its (S, R)-diastereomer

NASA Astrophysics Data System (ADS)

Huang, Lei-Ching; Fu, Chao-Ming

2015-09-01

The spontaneous polarization and molecular dynamics of four ferroelectric liquid crystals (FLCs) with two different kinds of core rings and two types of diastereomeric structures were investigated in this study. The FLCs with a biphenyl ring core structure showed higher spontaneous polarization than the FLCs with a naphthalene ring core structure. The complex dielectric spectra exhibited the Goldstone mode in the ferroelectric (SmC*) phase for all FLCs. The complex dielectric spectra of the four FLCs can be optimally fitted by the Debye model and the Cole-Cole model. Moreover, the Goldstone mode was enhanced under low DC bias fields for the FLCs with the (S, R)- diastereomeric structure, whereas the mode was suppressed for the FLCs with the (S, S)- diastereomeric structure. A microscopic molecular dynamic model is proposed to describe the underlying mechanism of the particular enhancement of the Goldstone mode. The experimental results of dielectric spectra and spontaneous polarization are explained in the discussion of the mesomorphic properties related to the FLC molecular structure.

The Ultrasensitivity of Living Polymers

NASA Astrophysics Data System (ADS)

O'Shaughnessy, Ben; Vavylonis, Dimitrios

2003-03-01

Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: Even a small perturbation (e.g., temperature jump) nonlinearly distorts the CLD, eliminating or massively augmenting short chains. The origin is fast relaxation of mass variables (mean chain length, monomer concentration) which perturbs CLD shape variables before these can relax via slow chain growth rate fluctuations. Viscosity relaxation predictions agree with experiments on the best-studied synthetic system, α-methylstyrene.

From bismuth oxide/hydroxide precursor clusters towards stable oxides: Proton transfer reactions and structural reorganization govern the stability of [Bi18O13(OH)10]-nitrate clusters

NASA Astrophysics Data System (ADS)

Walther, M.; Zahn, D.

2018-01-01

Structural relaxation and stability of a Bi18-cluster as obtained from association of [Bi6O4(OH)4](NO3)6 precursor clusters in DMSO solution is investigated from a combination of quantum chemical calculations and μs-scale molecular dynamics simulations using empirical interaction potentials. The Bi18-cluster undergoes a OH⋯OH proton transfer reaction, followed by considerable structural relaxation. While the aggregation of the Bi18-cluster is induced by the dissociation of a single nitrate ion leading to [Bi6O4(OH)4](NO3)5+ as an activated precursor species that can bind two more Bi6-clusters, we find the [Bi18O13(OH)10](NO3)18-x+x species (explored for x = 1-6) rather inert against either nitrate dissociation, collision with Bi6-precursors or combinations thereof.

Realization of a scenario with two relaxation rates in the Hubbard Falicov-Kimball model

NASA Astrophysics Data System (ADS)

Barman, H.; Laad, M. S.; Hassan, S. R.

2018-02-01

A single transport relaxation rate governs the decay of both longitudinal and Hall currents in Landau Fermi liquids (FL). Breakdown of this fundamental feature, first observed in two-dimensional cuprates and subsequently in other three-dimensional correlated systems close to the Mott metal-insulator transition, played a pivotal role in emergence of a non-FL (NFL) paradigm in higher dimensions D (>1 ) . Motivated hereby, we explore the emergence of this "two relaxation rates" scenario in the Hubbard Falicov-Kimball model (HFKM) using the dynamical mean-field theory (DMFT). Specializing to D =3 , we find, beyond a critical Falicov-Kimball (FK) interaction, that two distinct relaxation rates governing distinct temperature (T ) dependence of the longitudinal and Hall currents naturally emerges in the NFL metal. Our results show good accord with the experiment in V2 -yO3 near the metal-to-insulator transition (MIT). We rationalize this surprising finding by an analytical analysis of the structure of charge and spin Hamiltonians in the underlying impurity problem, specifically through a bosonization method applied to the Wolff model and connecting it to the x-ray edge problem.

Arresting relaxation in Pickering Emulsions

NASA Astrophysics Data System (ADS)

Atherton, Tim; Burke, Chris

2015-03-01

Pickering emulsions consist of droplets of one fluid dispersed in a host fluid and stabilized by colloidal particles absorbed at the fluid-fluid interface. Everyday materials such as crude oil and food products like salad dressing are examples of these materials. Particles can stabilize non spherical droplet shapes in these emulsions through the following sequence: first, an isolated droplet is deformed, e.g. by an electric field, increasing the surface area above the equilibrium value; additional particles are then adsorbed to the interface reducing the surface tension. The droplet is then allowed to relax toward a sphere. If more particles were adsorbed than can be accommodated by the surface area of the spherical ground state, relaxation of the droplet is arrested at some non-spherical shape. Because the energetic cost of removing adsorbed colloids exceeds the interfacial driving force, these configurations can remain stable over long timescales. In this presentation, we present a computational study of the ordering present in anisotropic droplets produced through the mechanism of arrested relaxation and discuss the interplay between the geometry of the droplet, the dynamical process that produced it, and the structure of the defects observed.

Weak ferromagnetism and short range polar order in NaMnF3 thin films

NASA Astrophysics Data System (ADS)

KC, Amit; Borisov, Pavel; Shvartsman, Vladimir V.; Lederman, David

2017-02-01

The orthorhombically distorted perovskite NaMnF3 has been predicted to become ferroelectric if an a = c distortion of the bulk Pnma structure is imposed. In order to test this prediction, NaMnF3 thin films were grown on SrTiO3 (001) single crystal substrates via molecular beam epitaxy. The best films were smooth and single phase with four different twin domains. In-plane magnetization measurements revealed the presence of antiferromagnetic ordering with weak ferromagnetism below the Néel temperature TN = 66 K. For the dielectric studies, NaMnF3 films were grown on a 30 nm SrRuO3 (001) layer used as a bottom electrode grown via pulsed laser deposition. The complex permittivity as a function of frequency indicated a strong Debye-like relaxation contribution characterized by a distribution of relaxation times. A power-law divergence of the characteristic relaxation time revealed an order-disorder phase transition at 8 K. The slow relaxation dynamics indicated the formation of super-dipoles (superparaelectric moments) that extend over several unit cells, similar to polar nanoregions of relaxor ferroelectrics.

Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions.

PubMed

Pendrill, Robert; Engström, Olof; Volpato, Andrea; Zerbetto, Mirco; Polimeno, Antonino; Widmalm, Göran

2016-01-28

The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

Stress relaxing hyaluronic acid-collagen hydrogels promote cell spreading, fiber remodeling, and focal adhesion formation in 3D cell culture.

PubMed

Lou, Junzhe; Stowers, Ryan; Nam, Sungmin; Xia, Yan; Chaudhuri, Ovijit

2018-02-01

The physical and architectural cues of the extracellular matrix (ECM) play a critical role in regulating important cellular functions such as spreading, migration, proliferation, and differentiation. Natural ECM is a complex viscoelastic scaffold composed of various distinct components that are often organized into a fibrillar microstructure. Hydrogels are frequently used as synthetic ECMs for 3D cell culture, but are typically elastic, due to covalent crosslinking, and non-fibrillar. Recent work has revealed the importance of stress relaxation in viscoelastic hydrogels in regulating biological processes such as spreading and differentiation, but these studies all utilize synthetic ECM hydrogels that are non-fibrillar. Key mechanotransduction events, such as focal adhesion formation, have only been observed in fibrillar networks in 3D culture to date. Here we present an interpenetrating network (IPN) hydrogel system based on HA crosslinked with dynamic covalent bonds and collagen I that captures the viscoelasticity and fibrillarity of ECM in tissues. The IPN hydrogels exhibit two distinct processes in stress relaxation, one from collagen and the other from HA crosslinking dynamics. Stress relaxation in the IPN hydrogels can be tuned by modulating HA crosslinker affinity, molecular weight of the HA, or HA concentration. Faster relaxation in the IPN hydrogels promotes cell spreading, fiber remodeling, and focal adhesion (FA) formation - behaviors often inhibited in other hydrogel-based materials in 3D culture. This study presents a new, broadly adaptable materials platform for mimicking key ECM features of viscoelasticity and fibrillarity in hydrogels for 3D cell culture and sheds light on how these mechanical and structural cues regulate cell behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electron Tunneling in Lithium Ammonia Solutions Probed by Frequency-Dependent Electron-Spin Relaxation Studies

PubMed Central

Maeda, Kiminori; Lodge, Matthew T.J.; Harmer, Jeffrey; Freed, Jack H.; Edwards, Peter P.

2012-01-01

Electron transfer or quantum tunneling dynamics for excess or solvated electrons in dilute lithium-ammonia solutions have been studied by pulse electron paramagnetic resonance (EPR) spectroscopy at both X- (9.7 GHz) and W-band (94 GHz) frequencies. The electron spin-lattice (T1) and spin-spin (T2) relaxation data indicate an extremely fast transfer or quantum tunneling rate of the solvated electron in these solutions which serves to modulate the hyperfine (Fermi-contact) interaction with nitrogen nuclei in the solvation shells of ammonia molecules surrounding the localized, solvated electron. The donor and acceptor states of the solvated electron in these solutions are the initial and final electron solvation sites found before, and after, the transfer or tunneling process. To interpret and model our electron spin relaxation data from the two observation EPR frequencies requires a consideration of a multi-exponential correlation function. The electron transfer or tunneling process that we monitor through the correlation time of the nitrogen Fermi-contact interaction has a time scale of (1–10)×10−12 s over a temperature range 230–290K in our most dilute solution of lithium in ammonia. Two types of electron-solvent interaction mechanisms are proposed to account for our experimental findings. The dominant electron spin relaxation mechanism results from an electron tunneling process characterized by a variable donor-acceptor distance or range (consistent with such a rapidly fluctuating liquid structure) in which the solvent shell that ultimately accepts the transferring electron is formed from random, thermal fluctuations of the liquid structure in, and around, a natural hole or Bjerrum-like defect vacancy in the liquid. Following transfer and capture of the tunneling electron, further solvent-cage relaxation with a timescale of ca. 10−13 s results in a minor contribution to the electron spin relaxation times. This investigation illustrates the great potential of multi-frequency EPR measurements to interrogate the microscopic nature and dynamics of ultra fast electron transfer or quantum-tunneling processes in liquids. Our results also impact on the universal issue of the role of a host solvent (or host matrix, e.g. a semiconductor) in mediating long-range electron transfer processes and we discuss the implications of our results with a range of other materials and systems exhibiting the phenomenon of electron transfer. PMID:22568866

A Low Spin Manganese(IV) Nitride Single Molecule Magnet

PubMed Central

Ding, Mei; Cutsail, George E.; Aravena, Daniel; Amoza, Martín; Rouzières, Mathieu; Dechambenoit, Pierre; Losovyj, Yaroslav; Pink, Maren

2016-01-01

Structural, spectroscopic and magnetic methods have been used to characterize the tris(carbene)borate compound PhB(MesIm)3Mn≡N as a four-coordinate manganese(IV) complex with a low spin (S = 1/2) configuration. The slow relaxation of the magnetization in this complex, i.e. its single-molecule magnet (SMM) properties, is revealed under an applied dc field. Multireference quantum mechanical calculations indicate that this SMM behavior originates from an anisotropic ground doublet stabilized by spin-orbit coupling. Consistent theoretical and experiment data show that the resulting magnetization dynamics in this system is dominated by ground state quantum tunneling, while its temperature dependence is influenced by Raman relaxation. PMID:27746891

Odd–even structural sensitivity on dynamics in network-forming ionic liquids

DOE PAGES

Yang, Ke; Cai, Zhikun; Tyagi, Madhusudan; ...

2016-04-13

Understanding structural sensitivity on properties of materials is an important step toward the rational design of materials. As a compelling case of sensitive structure-property relationship, an odd-even effect refers to the alternating trend of physical or chemical properties on odd/even number of repeating structural units. In crystalline or semi-crystalline materials, such odd-even variations of macroscopic properties emerge as manifestations of differences in the periodic packing patterns of molecules. Therefore, due to the lack of long-range order, such odd-even phenomenon is not expected in liquids. Herein, we report the discovery of a remarkable odd-even effect of the dynamical properties in themore » liquid phase, which challenges the traditional periodic packing explanations. In a class of network-forming ionic liquid (NIL), using incoherent quasi-elastic neutron scattering measurements, we measured the dynamical properties including the diffusion coefficient and the rotational relaxation time. These dynamical properties showed pronounced alternating trends with increased number of methylene (–CH 2– ) groups in the backbone. Meanwhile, the structure factor S(Q) showed no long-range periodic packing of molecules, while the pair distribution function g(r) revealed subtle differences in the local molecular morphology. As a result, the observed dynamical odd-even phenomenon in liquids showed that profound dynamical changes originate from subtle local structural differences.« less

Glass transition dynamics of stacked thin polymer films

NASA Astrophysics Data System (ADS)

Fukao, Koji; Terasawa, Takehide; Oda, Yuto; Nakamura, Kenji; Tahara, Daisuke

2011-10-01

The glass transition dynamics of stacked thin films of polystyrene and poly(2-chlorostyrene) were investigated using differential scanning calorimetry and dielectric relaxation spectroscopy. The glass transition temperature Tg of as-stacked thin polystyrene films has a strong depression from that of the bulk samples. However, after annealing at high temperatures above Tg, the stacked thin films exhibit glass transition at a temperature almost equal to the Tg of the bulk system. The α-process dynamics of stacked thin films of poly(2-chlorostyrene) show a time evolution from single-thin-film-like dynamics to bulk-like dynamics during the isothermal annealing process. The relaxation rate of the α process becomes smaller with increase in the annealing time. The time scale for the evolution of the α dynamics during the annealing process is very long compared with that for the reptation dynamics. At the same time, the temperature dependence of the relaxation time for the α process changes from Arrhenius-like to Vogel-Fulcher-Tammann dependence with increase of the annealing time. The fragility index increases and the distribution of the α-relaxation times becomes smaller with increase in the annealing time for isothermal annealing. The observed change in the α process is discussed with respect to the interfacial interaction between the thin layers of stacked thin polymer films.

Interplay between Shear Loading and Structural Aging in a Physical Gelatin Gel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronsin, O.; Caroli, C.; Baumberger, T.

2009-09-25

We show that the aging of the mechanical relaxation of a gelatin gel exhibits the same scaling phenomenology as polymer and colloidal glasses. In addition, gelatin is known to exhibit logarithmic structural aging (stiffening). We find that stress accelerates this process. However, this effect is definitely irreducible to a mere age shift with respect to natural aging. We suggest that it is interpretable in terms of elastically aided elementary (coil->helix) local events whose dynamics gradually slows down as aging increases geometric frustration.

A Numerical Study of Automated Dynamic Relaxation for Nonlinear Static Tensioned Structures.

DTIC Science & Technology

1987-10-01

sytem f dscree fnit element equations, i.e., an algebraic system. The form of these equa- tions is the same for all nonlinear kinematic structures that...the first phase the solu- tion to the static, prestress configuration is sought. This phase is also referred to as form finding, shape finding, or the...does facilitate stability of the numerical solution. The system of equations, which is the focus of the solution methods presented, is formed by a

Experimental evidence for simultaneous relaxation processes in super spin glass γ-Fe2O3 nanoparticle system

NASA Astrophysics Data System (ADS)

Nikolic, V.; Perovic, M.; Kusigerski, V.; Boskovic, M.; Mrakovic, A.; Blanusa, J.; Spasojevic, V.

2015-03-01

Spherical γ-Fe2O3 nanoparticles with the narrow size distribution of (5 ± 1) nm were synthesized by the method of thermal decomposition from iron acetyl acetonate precursor. The existence of super spin-glass state at low temperatures and in low applied magnetic fields was confirmed by DC magnetization measurements on a SQUID magnetometer. The comprehensive investigation of magnetic relaxation dynamics in low-temperature region was conducted through the measurements of single-stop and multiple stop ZFC memory effects, ZFC magnetization relaxation, and AC susceptibility measurements. The experimental findings revealed the peculiar change of magnetic relaxation dynamics at T ≈ 10 K, which arose as a consequence of simultaneous existence of different relaxation processes in Fe2O3 nanoparticle system. Complementarity of the applied measurements was utilized in order to single out distinct relaxation processes as well as to elucidate complex relaxation mechanisms in the investigated interacting nanoparticle system.

Impacts of Base-Case and Post-Contingency Constraint Relaxations on Static and Dynamic Operational Security

NASA Astrophysics Data System (ADS)

Salloum, Ahmed

Constraint relaxation by definition means that certain security, operational, or financial constraints are allowed to be violated in the energy market model for a predetermined penalty price. System operators utilize this mechanism in an effort to impose a price-cap on shadow prices throughout the market. In addition, constraint relaxations can serve as corrective approximations that help in reducing the occurrence of infeasible or extreme solutions in the day-ahead markets. This work aims to capture the impact constraint relaxations have on system operational security. Moreover, this analysis also provides a better understanding of the correlation between DC market models and AC real-time systems and analyzes how relaxations in market models propagate to real-time systems. This information can be used not only to assess the criticality of constraint relaxations, but also as a basis for determining penalty prices more accurately. Constraint relaxations practice was replicated in this work using a test case and a real-life large-scale system, while capturing both energy market aspects and AC real-time system performance. System performance investigation included static and dynamic security analysis for base-case and post-contingency operating conditions. PJM peak hour loads were dynamically modeled in order to capture delayed voltage recovery and sustained depressed voltage profiles as a result of reactive power deficiency caused by constraint relaxations. Moreover, impacts of constraint relaxations on operational system security were investigated when risk based penalty prices are used. Transmission lines in the PJM system were categorized according to their risk index and each category was as-signed a different penalty price accordingly in order to avoid real-time overloads on high risk lines. This work also extends the investigation of constraint relaxations to post-contingency relaxations, where emergency limits are allowed to be relaxed in energy market models. Various scenarios were investigated to capture and compare between the impacts of base-case and post-contingency relaxations on real-time system performance, including the presence of both relaxations simultaneously. The effect of penalty prices on the number and magnitude of relaxations was investigated as well.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

From coupled elementary units to the complexity of the glass transition.

PubMed

Rehwald, Christian; Rubner, Oliver; Heuer, Andreas

2010-09-10

Supercooled liquids display fascinating properties upon cooling such as the emergence of dynamic length scales. Different models strongly vary with respect to the choice of the elementary subsystems as well as their mutual coupling. Here we show via computer simulations of a glass former that both ingredients can be identified via analysis of finite-size effects within the continuous-time random walk framework. The subsystems already contain complete information about thermodynamics and diffusivity, whereas the coupling determines structural relaxation and the emergence of dynamic length scales.

Breakdown of the Simple Arrhenius Law in the Normal Liquid State.

PubMed

Thoms, Erik; Grzybowski, Andrzej; Pawlus, Sebastian; Paluch, Marian

2018-04-05

It is common practice to discuss the temperature effect on molecular dynamics of glass formers above the melting temperature in terms of the Arrhenius law. Using dielectric spectroscopy measurements of dc conductivity and structural relaxation time on the example of the typical glass former propylene carbonate, we provide experimental evidence that this practice is not justified. Our conclusions are supported by employing thermodynamic density scaling and the occurrence of inflection points in isothermal dynamic data measured at elevated pressure. Additionally, we propose a more suitable approach to describe the dynamics both above and below the inflection point based on a modified MYEGA model.

Positron annihilation response and broadband dielectric spectroscopy: salol.

PubMed

Bartoš, J; Iskrová, M; Köhler, M; Wehn, R; Sauša, O; Lunkenheimer, P; Krištiak, J; Loidl, A

2011-09-01

A phenomenological analysis of the ortho-positronium (o-Ps) annihilation from positron annihilation lifetime spectroscopy (PALS) and the dynamics from broadband dielectric spectroscopy (BDS) are reported on a small molecular glass former of intermediate H-bonding and fragility: salol. The dielectric spectra extend over a very broad frequency range of about 2 × 10(-2)-3.5 × 10(11) Hz, providing information on the α-relaxation, the secondary relaxation giving rise to the excess wing, and the shallow high-frequency minimum in the micro- to milli-meter wave range. A number of empirical correlations between the o-Ps lifetime, τ(3)(T), and the various spectral and relaxation features have been observed. Thus, the phenomenological evaluation of the τ(3)(T) dependence of the PALS response of the amorphous sample reveals three characteristic PALS temperatures: T(g)(PALS), T(b1)(L) = 1.15T(g)(PALS) and T(b2)(L) = 1.25T(g)(PALS), which are discussed in relation to similar findings for some typical small molecular vdW- and H-bonded glass formers. A slighter change of the slope at T(b1)(L) appears to be related to the transition from excess wing to the primary α-process-dominated behavior, with the secondary process dominating in the deeply supercooled liquid state below T(b1)(L). The high-temperature plateau effect in the τ (3)(T) plot occurs at T(b2)(L) and agrees with the characteristic Stickel temperature, T(B)(ST), marking a qualitative change of the primary α process, but it does not follow the relation T(b2)(L) < T(α) [τ(3)(T(b2)) < τ(α)]. Both effects at T(b1)(L) and T(b2)(L) correlate with two crossovers in the spectral shape and related non-exponentiality parameter of the structural relaxation, β (KWW). Finally, the application of the two-order parameter (TOP) model to the structural relaxation as represented by the primary α relaxation times from BDS leads to the characteristic TOP temperature, T(m)(c), close to T(b1) from PALS. Within this model the phenomenological interpretation is offered based on changes in the probability of occurrence of solid-like and liquid-like domains to explain the dynamic as well as PALS responses. In summary, all the empirical correlations support further very close connections between the PALS response and the dielectric relaxation behavior in small molecule glass formers.

Anomalous relaxation in fractal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujiwara, S.; Yonezawa, F.

1995-03-01

For the purpose of studying some interesting properties of anomalous relaxation in fractal structures, we carry out Monte Carlo simulations of random walks on two-dimensional fractal structures (Sierpinski carpets with different cutouts and site-percolation clusters in a square lattice at the critical concentration). We find that the relaxation is of the Cole-Cole type [J. Chem. Phys. 9, 341 (1941)], which is one of the empirical laws of anomalous relaxation. Scaling properties are found in the relaxation function as well as in the particle density. We also find that, in strucures with almost the same fractal dimension, relaxation in structures withmore » dead ends is slower than that in structures without them. This paper ascertains that the essential aspects of the anomalous relaxation due to many-body effects can be explained in the framework of the one-body model.« less

Relaxation-type nonlocal inertial-number rheology for dry granular flows

NASA Astrophysics Data System (ADS)

Lee, Keng-lin; Yang, Fu-ling

2017-12-01

We propose a constitutive model to describe the nonlocality, hysteresis, and several flow features of dry granular materials. Taking the well-known inertial number I as a measure of sheared-induced local fluidization, we derive a relaxation model for I according to the evolution of microstructure during avalanche and dissipation processes. The model yields a nonmonotonic flow law for a homogeneous flow, accounting for hysteretic solid-fluid transition and intermittency in quasistatic flows. For an inhomogeneous flow, the model predicts a generalized Bagnold shear stress revealing the interplay of two microscopic nonlocal mechanisms: collisions among correlated structures and the diffusion of fluidization within the structures. In describing a uniform flow down an incline, the model reproduces the hysteretic starting and stopping heights and the Pouliquen flow rule for mean velocity. Moreover, a dimensionless parameter reflecting the nonlocal effect on the flow is discovered, which controls the transition between Bagnold and creeping flow dynamics.

The dielectric signature of glass density

NASA Astrophysics Data System (ADS)

Rams-Baron, M.; Wojnarowska, Z.; Knapik-Kowalczuk, J.; Jurkiewicz, K.; Burian, A.; Wojtyniak, M.; Pionteck, J.; Jaworska, M.; Rodríguez-Tinoco, C.; Paluch, M.

2017-09-01

At present, we are witnessing a renewed interest in the properties of densified glasses prepared by isobaric cooling of a liquid at elevated pressure. As high-pressure densification emerges as a promising approach in the development of glasses with customized features, understanding and controlling their unique properties represent a contemporary scientific and technological goal. The results presented herein indicate that the applied high-pressure preparation route leads to a glassy state with higher density (˜1%) and a reduced free volume of about 7%. We show that these subtle structural changes remarkably influence the dielectric response and spectral features of β-relaxation in etoricoxib glass. Our study, combining dynamical and structural techniques, reveal that β-relaxation in etoricoxib is extremely sensitive to the variations in molecular packing and can be used to probe the changes in glass density. Such connection is technologically relevant and may advance further progress in the field.