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Sample records for relaxation molecular dynamics

  1. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

  2. Excitation dynamics and relaxation in a molecular heterodimer

    International Nuclear Information System (INIS)

    Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

    2012-01-01

    Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

  3. Molecular dynamics study on the relaxation properties of bilayered ...

    Indian Academy of Sciences (India)

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  4. Dynamics of relaxation to a stationary state for interacting molecular motors

    Science.gov (United States)

    Gomes, Luiza V. F.; Kolomeisky, Anatoly B.

    2018-01-01

    Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscle contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed.

  5. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2017-07-01

    Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.

  6. Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

    Science.gov (United States)

    Fuson, Michael M.

    2017-01-01

    Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

  7. Relaxation Dynamics of Nanoparticle-Tethered Polymer Chains

    KAUST Repository

    Kim, Sung A

    2015-09-08

    © 2015 American Chemical Society. Relaxation dynamics of nanoparticle-tethered cis-1,4-polyisoprene (PI) are investigated using dielectric spectroscopy and rheometry. A model system composed of polymer chains densely grafted to spherical SiO2 nanoparticles to form self-suspended suspensions facilitates detailed studies of slow global chain and fast segmental mode dynamics under surface and geometrical confinement-from experiments performed in bulk materials. We report that unentangled polymer molecules tethered to nanoparticles relax far more slowly than their tethered entangled counterparts. Specifically, at fixed grafting density we find, counterintuitively, that increasing the tethered polymer molecular weight up to values close to the entanglement molecular weight speeds up chain relaxation dynamics. Decreasing the polymer grafting density for a fixed molecular weight has the opposite effect: it dramatically slows down chain relaxation, increases interchain coupling, and leads to a transition in rheological response from simple fluid behavior to viscoelastic fluid behavior for tethered PI chains that are unentangled by conventional measures. Increasing the measurement temperature produces an even stronger elastic response and speeds up molecular relaxation at a rate that decreases with grafting density and molecular weight. These observations are discussed in terms of chain confinement driven by crowding between particles and by the existence of an entropic attractive force produced by the space-filling constraint on individual chains in a self-suspended material. Our results indicate that the entropic force between densely grafted polymer molecules couples motions of individual chains in an analogous manner to reversible cross-links in associating polymers.

  8. Generalized extended Navier-Stokes theory: Multiscale spin relaxation in molecular fluids

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt

    2013-01-01

    This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia...

  9. Relaxation dynamics following transition of solvated electrons

    International Nuclear Information System (INIS)

    Barnett, R.B.; Landman, U.; Nitzan, A.

    1989-01-01

    Relaxation dynamics following an electronic transition of an excess solvated electron in clusters and in bulk water is studied using an adiabatic simulation method. In this method the solvent evolves classically and the electron is constrained to a specified state. The coupling between the solvent and the excess electron is evaluated via the quantum expectation value of the electron--water molecule interaction potential. The relaxation following excitation (or deexcitation) is characterized by two time scales: (i) a very fast (/similar to/20--30 fs) one associated with molecular rotations in the first solvation shell about the electron, and (ii) a slower stage (/similar to/200 fs), which is of the order of the longitudinal dielectric relaxation time. The fast relaxation stage exhibits an isotope effect. The spectroscopical consequences of the relaxation dynamics are discussed

  10. A study of internal energy relaxation in shocks using molecular dynamics based models

    International Nuclear Information System (INIS)

    Li, Zheng; Parsons, Neal; Levin, Deborah A.

    2015-01-01

    Recent potential energy surfaces (PESs) for the N 2 + N and N 2 + N 2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N 2 + N 2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N 2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available

  11. Generalized extended Navier-Stokes theory: multiscale spin relaxation in molecular fluids.

    Science.gov (United States)

    Hansen, J S

    2013-09-01

    This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia per unit mass. In the regime of large moment of inertia the fast relaxation is wave-vector independent and dominated by the coupling between spin and the fluid streaming velocity, whereas for small inertia the relaxation is slow and spin diffusion plays a significant role. The fast wave-vector-independent relaxation is also observed for highly packed systems. The transverse and longitudinal spin modes have, to a good approximation, identical relaxation, indicating that the longitudinal and transverse spin viscosities have same value. The relaxation is also shown to be isomorphic invariant. Finally, the effect of the coupling in the zero frequency and wave-vector limit is quantified by a characteristic length scale; if the system dimension is comparable to this length the coupling must be included into the fluid dynamical description. It is found that the length scale is independent of moment of inertia but dependent on the state point.

  12. Charge Relaxation Dynamics of an Electrolytic Nanocapacitor

    Science.gov (United States)

    2015-01-01

    Understanding ion relaxation dynamics in overlapping electric double layers (EDLs) is critical for the development of efficient nanotechnology-based electrochemical energy storage, electrochemomechanical energy conversion, and bioelectrochemical sensing devices as well as the controlled synthesis of nanostructured materials. Here, a lattice Boltzmann (LB) method is employed to simulate an electrolytic nanocapacitor subjected to a step potential at t = 0 for various degrees of EDL overlap, solvent viscosities, ratios of cation-to-anion diffusivity, and electrode separations. The use of a novel continuously varying and Galilean-invariant molecular-speed-dependent relaxation time (MSDRT) with the LB equation recovers a correct microscopic description of the molecular-collision phenomena and enhances the stability of the LB algorithm. Results for large EDL overlaps indicated oscillatory behavior for the ionic current density, in contrast to monotonic relaxation to equilibrium for low EDL overlaps. Further, at low solvent viscosities and large EDL overlaps, anomalous plasmalike spatial oscillations of the electric field were observed that appeared to be purely an effect of nanoscale confinement. Employing MSDRT in our simulations enabled modeling of the fundamental physics of the transient charge relaxation dynamics in electrochemical systems operating away from equilibrium wherein Nernst–Einstein relation is known to be violated. PMID:25678941

  13. TURBULENCE DECAY AND CLOUD CORE RELAXATION IN MOLECULAR CLOUDS

    International Nuclear Information System (INIS)

    Gao, Yang; Law, Chung K.; Xu, Haitao

    2015-01-01

    The turbulent motion within molecular clouds is a key factor controlling star formation. Turbulence supports molecular cloud cores from evolving to gravitational collapse and hence sets a lower bound on the size of molecular cloud cores in which star formation can occur. On the other hand, without a continuous external energy source maintaining the turbulence, such as in molecular clouds, the turbulence decays with an energy dissipation time comparable to the dynamic timescale of clouds, which could change the size limits obtained from Jean's criterion by assuming constant turbulence intensities. Here we adopt scaling relations of physical variables in decaying turbulence to analyze its specific effects on the formation of stars. We find that the decay of turbulence provides an additional approach for Jeans' criterion to be achieved, after which gravitational infall governs the motion of the cloud core. This epoch of turbulence decay is defined as cloud core relaxation. The existence of cloud core relaxation provides a more complete understanding of the effect of the competition between turbulence and gravity on the dynamics of molecular cloud cores and star formation

  14. Resonances in field-cycling NMR on molecular crystals. (reversible) Spin dynamics or (irreversible) relaxation?; Resonanzen in Field-Cycling-NMR an Molekuelkristallen. (reversible) Spindynamik oder (irreversible) Relaxation?

    Energy Technology Data Exchange (ETDEWEB)

    Tacke, Christian

    2015-07-01

    Multi spin systems with spin 1/2 nuclei and dipolar coupled quadrupolar nuclei can show so called ''quadrupolar dips''. There are two main reasons for this behavior: polarization transfer and relaxation. They look quite alike and without additional research cannot be differentiated easily in most cases. These two phenomena have quite different physical and theoretical backgrounds. For no or very slow dynamics, polarization transfer will take place, which is energy conserving inside the spin system. This effect can entirely be described using quantum mechanics on the spin system. Detailed knowledge about the crystallography is needed, because this affects the relevant hamiltonians directly. For systems with fast enough dynamics, relaxation takes over, and the energy flows from the spin system to the lattice; thus a more complex theoretical description is needed. This description has to include a dynamic model, usually in the form of a spectral density function. Both models should include detailed modelling of the complete spin system. A software library was developed to be able to model complex spin systems. It allows to simulate polarization transfer or relaxation effects. NMR measurements were performed on the protonic conductor K{sub 3}H(SO{sub 4}){sub 2}. A single crystal shows sharp quadrupolar dips at room temperature. Dynamics could be excluded using relaxation measurements and literature values. Thus, a polarization transfer analysis was used to describe those dips with good agreement. As a second system, imidazolium based molecular crystals were analyzed. The quadrupolar dips were expected to be caused by polarization transfer; this was carefully analyzed and found not to be true. A relaxation based analysis shows good agreement with the measured data in the high temperature area. It leverages a two step spectral density function, which indicates two distinct dynamic processes happening in this system.

  15. Stretched exponential relaxation in molecular and electronic glasses

    International Nuclear Information System (INIS)

    Phillips, J.C.

    1996-01-01

    is often better than the quoted experimental accuracies ∼5%. The extrinsic cases are identified by explicit structural signatures which are discussed at length. The discussion also includes recent molecular dynamical simulations for metallic glasses, spin glasses, quasicrystals and polymers which have achieved the intermediate relaxed Kohlrausch state and which have obtained values of β in excellent agreement with the prediction of the microscopic theory. (author)

  16. Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

    Science.gov (United States)

    Fačkovec, B; Vanden-Eijnden, E; Wales, D J

    2015-07-28

    A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

  17. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  18. Modern problems of relaxation gas dynamics

    International Nuclear Information System (INIS)

    Losev, S.A.; Osipov, A.I.

    1985-01-01

    Some of the dynamical characteristics of relaxation processes are studied. Unfortunately, many dynamical characteristics of relaxation processes, necessary for the solution of important scientific and applied problems, are not known. These problems require further development of experimental methods of the study of nonequilibrium gas. It is known, that gas systems are shifted from the equilibrium by different methods: by acoustic and shock wav es, by means of gas expansion in nozzles and jets, by powerful radiations (laser, first of all), by electric discharges, in burning and combustion devices, etc. Non-equilibrium gas is produced in installations of continuum, impulse and periodic regime. Molecular beams, shock tubes (especially with nozzles), flow and jet installations, aerodynamical tubes, plasmatrons, vessels with a gas, influenced by the strong radiation, burners and combustion devices, where the study of non-euilibrium gas is helpful to solve the problems of the determination of kinetic equations and constants of physico-chemical kinetics

  19. Selective excitation, relaxation, and energy channeling in molecular systems

    International Nuclear Information System (INIS)

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

  20. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3{NIT(C6H4OPh)}]: A μ+ spin relaxation study

    Science.gov (United States)

    Arosio, Paolo; Corti, Maurizio; Mariani, Manuel; Orsini, Francesco; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

    2015-05-01

    The spin dynamics of the molecular magnetic chain [Dy(hfac)3{NIT(C6H4OPh)}] were investigated by means of the Muon Spin Relaxation (μ+SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac)3{NIT(C6H4OPh)}] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ+SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λinterm(T), associated with the intermediate relaxing component. The experimental λinterm(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ0 exp(Δ/kBT), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

  1. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ+ spin relaxation study

    International Nuclear Information System (INIS)

    Arosio, Paolo; Orsini, Francesco; Corti, Maurizio; Mariani, Manuel; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

    2015-01-01

    The spin dynamics of the molecular magnetic chain [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] were investigated by means of the Muon Spin Relaxation (μ + SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ + SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ interm (T), associated with the intermediate relaxing component. The experimental λ interm (T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ 0 exp(Δ/k B T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state

  2. Non-exponential dynamic relaxation in strongly nonequilibrium nonideal plasmas

    International Nuclear Information System (INIS)

    Morozov, I V; Norman, G E

    2003-01-01

    Relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics method for nonideal two-component non-degenerate plasmas. Three limiting examples of initial states of strongly nonequilibrium plasma are considered: zero electron velocities, zero ion velocities and zero velocities of both electrons and ions. The initial non-exponential stage, its duration τ nB and subsequent exponential stages of the relaxation process are studied for a wide range of the nonideality parameter and the ion mass

  3. Stretched exponential relaxation in molecular and electronic glasses

    Science.gov (United States)

    Phillips, J. C.

    1996-09-01

    der Waals supercooled liquids and glasses, orientational glasses, water, fused salts, and heme proteins. In the intrinsic cases the theory of 0034-4885/59/9/003/img5 is often accurate to 2%, which is often better than the quoted experimental accuracies 0034-4885/59/9/003/img12. The extrinsic cases are identified by explicit structural signatures which are discussed at length. The discussion also includes recent molecular dynamical simulations for metallic glasses, spin glasses, quasicrystals and polymers which have achieved the intermediate relaxed Kohlrausch state and which have obtained values of 0034-4885/59/9/003/img2 in excellent agreement with the prediction of the microscopic theory.

  4. Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

    Science.gov (United States)

    Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

    2018-05-01

    We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of

  5. Investigation of effective impact parameters in electron-ion temperature relaxation via Particle-Particle Coulombic molecular dynamics

    Science.gov (United States)

    Zhao, Yinjian

    2017-09-01

    Aiming at a high simulation accuracy, a Particle-Particle (PP) Coulombic molecular dynamics model is implemented to study the electron-ion temperature relaxation. In this model, the Coulomb's law is directly applied in a bounded system with two cutoffs at both short and long length scales. By increasing the range between the two cutoffs, it is found that the relaxation rate deviates from the BPS theory and approaches the LS theory and the GMS theory. Also, the effective minimum and maximum impact parameters (bmin* and bmax*) are obtained. For the simulated plasma condition, bmin* is about 6.352 times smaller than the Landau length (bC), and bmax* is about 2 times larger than the Debye length (λD), where bC and λD are used in the LS theory. Surprisingly, the effective relaxation time obtained from the PP model is very close to the LS theory and the GMS theory, even though the effective Coulomb logarithm is two times greater than the one used in the LS theory. Besides, this work shows that the PP model (commonly known as computationally expensive) is becoming practicable via GPU parallel computing techniques.

  6. Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations.

    Science.gov (United States)

    Qvist, Johan; Mattea, Carlos; Sunde, Erik P; Halle, Bertil

    2012-05-28

    Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ∼48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R) D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.

  7. Capturing molecular multimode relaxation processes in excitable gases based on decomposition of acoustic relaxation spectra

    Science.gov (United States)

    Zhu, Ming; Liu, Tingting; Wang, Shu; Zhang, Kesheng

    2017-08-01

    Existing two-frequency reconstructive methods can only capture primary (single) molecular relaxation processes in excitable gases. In this paper, we present a reconstructive method based on the novel decomposition of frequency-dependent acoustic relaxation spectra to capture the entire molecular multimode relaxation process. This decomposition of acoustic relaxation spectra is developed from the frequency-dependent effective specific heat, indicating that a multi-relaxation process is the sum of the interior single-relaxation processes. Based on this decomposition, we can reconstruct the entire multi-relaxation process by capturing the relaxation times and relaxation strengths of N interior single-relaxation processes, using the measurements of acoustic absorption and sound speed at 2N frequencies. Experimental data for the gas mixtures CO2-N2 and CO2-O2 validate our decomposition and reconstruction approach.

  8. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ{sup +} spin relaxation study

    Energy Technology Data Exchange (ETDEWEB)

    Arosio, Paolo, E-mail: paolo.arosio@guest.unimi.it; Orsini, Francesco [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Corti, Maurizio [Department of Physics, Università degli Studi di Pavia and INSTM, Pavia (Italy); Mariani, Manuel [Department of Physics and Astronomy, Università degli Studi di Bologna, Bologna (Italy); Bogani, Lapo [Physikalisches Institut, Universität Stuttgart, Stuttgart (Germany); Caneschi, Andrea [INSTM and Department of Chemistry, University of Florence, Firenze (Italy); Lago, Jorge [Departamento de Quimica Inorganica, Universidad del Pais Vasco, Bilbao (Spain); Lascialfari, Alessandro [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Centro S3, Istituto Nanoscienze - CNR, Modena (Italy)

    2015-05-07

    The spin dynamics of the molecular magnetic chain [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] were investigated by means of the Muon Spin Relaxation (μ{sup +}SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ{sup +}SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ{sub interm}(T), associated with the intermediate relaxing component. The experimental λ{sub interm}(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ{sub 0} exp(Δ/k{sub B}T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

  9. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  10. The effect of the Magnus force on skyrmion relaxation dynamics

    OpenAIRE

    Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

    2018-01-01

    We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between Magnus force, repulsive skyrmion-skyrmion interaction and thermal noise yields different regimes during non-equilibrium relaxation. In the noise-dominated regime the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slo...

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

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

    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 motion 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.

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

    International Nuclear Information System (INIS)

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin

    2015-01-01

    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 motion 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

  13. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  14. Effect of the Magnus force on skyrmion relaxation dynamics

    Science.gov (United States)

    Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

    2018-01-01

    We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between the Magnus force, the repulsive skyrmion-skyrmion interaction, and the thermal noise yields different regimes during nonequilibrium relaxation. In the noise-dominated regime, the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slow decaying correlations. These two regimes are characterized by different values of the aging exponent. In general, the Magnus force accelerates the approach to the steady state.

  15. Simulations of vibrational relaxation in dense molecular fluids

    International Nuclear Information System (INIS)

    Holian, B.L.

    1985-07-01

    In the understanding of high-temperatre and -pressure chemistry in explosives, first step is the study of the transfer of energy from translational degrees of freedom into internal vibrations of the molecules. We present new methods using nonequilibrium molecular dynamics (NEMD) for measuring vibrational relaxation in a diatomic fluid, where we expect a classical treatment of many-body collisions to be relevant because of the high densities (2 to 3 times compressed compared to the normal fluid) and high temperatures (2000 to 4000 K) involved behind detonation waves. NEMD techniques are discussed, including their limitations, and qualitative results presented

  16. Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

    International Nuclear Information System (INIS)

    Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

    2009-01-01

    Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.

  17. From beta-relaxation to alpha-decay: Atomistic picture from molecular dynamics simulations for glass-forming Ni0.5Zr0.5 melt

    Energy Technology Data Exchange (ETDEWEB)

    Teichler, Helmar [Inst. Materialphysik, Univ Goettingen (Germany)

    2013-07-01

    In glass-forming melts the decay of structural fluctuation shows the well known transition from beta-relaxation (von-Schweidler law with exponent b) to alpha-decay (KWW law with exponent beta). Here we present results from molecular dynamics simulations for a metallic glass forming Ni0.5Zr0.5 model aimed at giving an understanding of this transition on the atomistic scale. At the considered temperature below mode coupling Tc, the dynamics of the system can be interpreted by residence of the particles in their neighbour cages and escape from the cages as rare processes. Our analysis yields that the fraction of residing particles is characterized by a hierarchical law in time, with von-Schweidler b explicitly related to the exponent of this law. In the alpha-decay regime the stretching exponent reflects, in addition, floating of the cages due to strain effects of escaped particles. Accordingly, the change from beta-relaxation to alpha-decay indicates the transition from low to large fraction of escaped particles.

  18. Exploring the dynamics about the glass transition by muon spin relaxation and muon spin rotation

    International Nuclear Information System (INIS)

    Bermejo, F J; Bustinduy, I; Cox, S F J; Lord, J S; Cabrillo, C; Gonzalez, M A

    2006-01-01

    The capability of muon spin rotation and muon spin relaxation to explore dynamics in the vicinity of the glass transition is illustrated by results pertaining to three materials exhibiting two different glass-forming abilities. Measurements under transverse magnetic fields enable us to monitor the dynamics of muonium-labelled closed-shell molecules within the microsecond range. The results display the onset of stochastic molecular motions taking place upon crossing from below the glass-transition temperature. In turn, the molecular dynamics of radicals formed by addition of atomic muonium to unsaturated organic molecules can also be explored up to far shorter times by means of relaxation measurements under longitudinal fields. The technique is then shown to be capable of singling out stochastic reorientational motions from others, which usually are strongly coupled to them and usually dominate the material response when measured using higher-frequency probes such as neutron and light scattering

  19. Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

    Energy Technology Data Exchange (ETDEWEB)

    Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)

    2017-06-01

    Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

    The spin dynamics in the helical chain Co(hfac) 2 NITPhOMe has been investigated by 1 H NMR and μSR relaxation. In the temperature range 15< T<60 K, the results are consistent with the relaxation of the homogeneous magnetization. For T≤15 K, NMR and μSR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived

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

    Science.gov (United States)

    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 15relaxation of the homogeneous magnetization. For T⩽15 K, NMR and μSR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

  2. Second-order Monte Carlo wave-function approach to the relaxation effects on ringing revivals in a molecular system interacting with a strongly squeezed coherent field

    International Nuclear Information System (INIS)

    Nakano, Masayoshi; Kishi, Ryohei; Nitta, Tomoshige; Yamaguchi, Kizashi

    2004-01-01

    We investigate the relaxation effects on the quantum dynamics in a two-state molecular system interacting with a single-mode strongly amplitude-squeezed coherent field using the second-order Monte Carlo wave-function method. The molecular population inversion (collapse-revival behavior of Rabi oscillations) is known to show the echoes after each revival, which are referred to as ringing revivals, in the case of strongly squeezed coherent fields with oscillatory photon-number distributions due to the phase-space interference effect. Two types of relaxation effects, i.e., cavity relaxation (the dissipation of an internal single mode to outer mode) and molecular coherent (phase) relaxation caused by nuclear vibrations on ringing revivals are investigated from the viewpoint of the quantum-phase dynamics using the quasiprobability (Q function) distribution of a single-mode field and the off-diagonal molecular density matrix ρ elec1,2 (t). It turns out that the molecular phase relaxation attenuates both the entire revival-collapse behavior and the increase in ρ elec1,2 (t) during the quiescent region, whereas a very slight cavity relaxation particularly suppresses the echoes in ringing revivals more significantly than the first revival but hardly changes a primary variation in envelope of ρ elec1,2 (t) in the nonrelaxation case

  3. Corroborative evidences of TV γ -scaling of the α-relaxation originating from the primitive relaxation/JG β relaxation

    Science.gov (United States)

    Ngai, K. L.; Paluch, M.

    2017-12-01

    Successful thermodynamic scaling of the structural alpha-relaxation time or transport coefficients of glass-forming liquids determined at various temperatures T and pressures P means the data conform to a single function of the product variable TVgamma, where V is the specific volume and gamma is a material specific constant. In the past two decades we have witnessed successful TVgamma-scaling in many molecular, polymeric, and even metallic glass-formers, and gamma is related to the slope of the repulsive part of the intermolecular potential. The advances made indicate TVgamma-scaling is an important aspect of the dynamic and thermodynamic properties of glass-formers. In this paper we show the origin of TVgamma-scaling is not from the structural alpha-relaxation time. Instead it comes from its precursor, the Johari-Goldstein beta-relaxation or the primitive relaxation of the Coupling Model and their relaxation times or tau_0 respectively. It is remarkable that all relaxation times are functions of TVgamma with the same gama, as well as the fractional exponent of the Kohlrausch correlation function of the structural alpha-relaxation. We arrive at this conclusion convincingly based on corroborative evidences from a number of experiments and molecular dynamics simulations performed on a wide variety of glass-formers and in conjunction with consistency with the predictions of the Coupling Model.

  4. Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

    Directory of Open Access Journals (Sweden)

    Wolfgang Schreiner

    2012-01-01

    Full Text Available Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt has reached a stationary shape, the simulation has not yet converged.

  5. Relaxation dynamics and thermophysical properties of vegetable oils using time-domain reflectometry.

    Science.gov (United States)

    Sonkamble, Anil A; Sonsale, Rahul P; Kanshette, Mahesh S; Kabara, Komal B; Wananje, Kunal H; Kumbharkhane, Ashok C; Sarode, Arvind V

    2017-04-01

    Dielectric relaxation studies of vegetable oils are important for insights into their hydrogen bonding and intermolecular dynamics. The dielectric relaxation and thermo physical properties of triglycerides present in some vegetable oils have been measured over the frequency range of 10 MHz to 7 GHz in the temperature region 25 to 10 °C using a time-domain reflectometry approach. The frequency and temperature dependence of dielectric constants and dielectric loss factors were determined for coconut, peanut, soya bean, sunflower, palm, and olive oils. The dielectric permittivity spectra for each of the studied vegetable oils are explained using the Debye model with their complex dielectric permittivity analyzed using the Havriliak-Negami equation. The dielectric parameters static permittivity (ε 0 ), high-frequency limiting static permittivity (ε ∞ ), average relaxation time (τ 0 ), and thermodynamic parameters such as free energy (∆F τ ), enthalpy (∆H τ ), and entropy of activation (∆S τ ) were also measured. Calculation and analysis of these thermodynamic parameters agrees with the determined dielectric parameters, giving insights into the temperature dependence of the molecular dynamics of these systems.

  6. NMR investigations of molecular dynamics

    Science.gov (United States)

    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.

  7. Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou, E-mail: eatonch@gmail.com

    2014-10-01

    Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast β-relaxation is followed by a much slower α-relaxation. There is a little change in the structural properties in the β-relaxation region, while major configuration rearrangements occurred in the α-relaxation range and the crystallization process was completed at the end of α-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.

  8. Novel spin dynamics in ferrimagnetic molecular chains from {sup 1}H NMR and {mu}SR spin-lattice relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Micotti, E. E-mail: micotti@fisicavolta.unipv.it; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L

    2004-05-01

    The spin dynamics in the helical chain Co(hfac){sub 2}NITPhOMe has been investigated by {sup 1}H NMR and {mu}SR relaxation. In the temperature range 15relaxation of the homogeneous magnetization. For T{<=}15 K, NMR and {mu}SR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

  9. Extended Lagrangian Excited State Molecular Dynamics.

    Science.gov (United States)

    Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

    2018-02-13

    An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

  10. Slow molecular dynamics in the β relaxation of semicrystalline polymers studied by pure exchange 13C solid state NMR

    International Nuclear Information System (INIS)

    Azevedo, Eduardo R. de; Becker-Guedes, Fabio; Bonagamba, Tito J.; Schmidt-Rohr, Klaus; Iowa State University, Ames, IA

    2001-01-01

    The dynamics in the amorphous regions of semicrystalline polymers exert important influences on mechanical properties, but have been notoriously difficult to characterize. Two new solid-state NMR techniques, PUREX (pure exchange) and CODEX (center band-only detection of exchange) NMR, make it possible to analyze the molecular motions near the glass transition in the amorphous regions of semicrystalline polymers. This is achieved by selectively suppressing the otherwise dominant signals of the static segments in the crystallites. We have applied both NMR techniques to study the slow motions near the glass transition in semicrystalline polymers (β relaxation) and in fully amorphous samples for reference. The studied polymers were isotactic poly(1-butene) (iPB1) (form I), syndiotactic and atactic polypropylenes (sPP, and aPP, respectively), as well as polyisobutylene (PIB). We have analyzed the geometry and time scale of the slow molecular motion for all samples and determined the apparent activation energies. (author)

  11. Crystallization Behavior and Relaxation Dynamics of Supercooled S‑Ketoprofen and the Racemic Mixture along an Isochrone

    DEFF Research Database (Denmark)

    Adrjanowicz, Karolina; Kaminski, Kamil; Paluch, Marian

    2015-01-01

    In this paper, we study crystallization behavior and molecular dynamics in the supercooled liquid state of the pharmaceutically important compound ketoprofen at various thermodynamic conditions. Dielectric relaxation for a racemic mixture was investigated in a wide range of temperatures and press...

  12. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    International Nuclear Information System (INIS)

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  13. Study of local conformation and molecular movements of homo-polypeptides in aqueous solutions by using magnetic resonance and relaxation

    International Nuclear Information System (INIS)

    Perly, Bruno

    1980-01-01

    The objective of this research thesis is to study local conformations and mobilities of some typical homo-polypeptides by using techniques of magnetic resonance. By using these techniques, it is possible to make highly local observations of molecular elements which allows very efficient analysis of structural and dynamic properties of several biologically important compounds to be performed, and the study of their interactions. After a presentation of the general properties of the studied polypeptides, of magnetic resonance and of magnetic relaxation, the author presents some elements of macromolecular dynamics and movement models. Then, he reports the study of local conformations and structural transitions, applications of spin marking to the dynamic study of polypeptides, a dynamic study of the polypeptide skeleton under the form of statistic balls, the study of local movements of side chains by using nuclear relaxation, the study of the coupling of movements of main and side chains, and of the nuclear relaxation induced by a radical spin marker

  14. Hydrodynamic relaxations in dissipative particle dynamics

    Science.gov (United States)

    Hansen, J. S.; Greenfield, Michael L.; Dyre, Jeppe C.

    2018-01-01

    This paper studies the dynamics of relaxation phenomena in the standard dissipative particle dynamics (DPD) model [R. D. Groot and P. B. Warren, J. Chem. Phys. 107, 4423 (1997)]. Using fluctuating hydrodynamics as the framework of the investigation, we focus on the collective transverse and longitudinal dynamics. It is shown that classical hydrodynamic theory predicts the transverse dynamics at relatively low temperatures very well when compared to simulation data; however, the theory predictions are, on the same length scale, less accurate for higher temperatures. The agreement with hydrodynamics depends on the definition of the viscosity, and here we find that the transverse dynamics are independent of the dissipative and random shear force contributions to the stress. For high temperatures, the spectrum for the longitudinal dynamics is dominated by the Brillouin peak for large length scales and the relaxation is therefore governed by sound wave propagation and is athermal. This contrasts the results at lower temperatures and small length scale, where the thermal process is clearly present in the spectra. The DPD model, at least qualitatively, re-captures the underlying hydrodynamical mechanisms, and quantitative agreement is excellent at intermediate temperatures for the transverse dynamics.

  15. Relaxation dynamics in quantum dissipative systems: The microscopic effect of intramolecular vibrational energy redistribution

    Energy Technology Data Exchange (ETDEWEB)

    Uranga-Piña, L. [Facultad de Física, Universidad de la Habana, San Lázaro y L, Vedado, 10400 Havana (Cuba); Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany); Tremblay, J. C., E-mail: jean.c.tremblay@gmail.com [Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany)

    2014-08-21

    We investigate the effect of inter-mode coupling on the vibrational relaxation dynamics of molecules in weak dissipative environments. The simulations are performed within the reduced density matrix formalism in the Markovian regime, assuming a Lindblad form for the system-bath interaction. The prototypical two-dimensional model system representing two CO molecules approaching a Cu(100) surface is adapted from an ab initio potential, while the diatom-diatom vibrational coupling strength is systematically varied. In the weak system-bath coupling limit and at low temperatures, only first order non-adiabatic uni-modal coupling terms contribute to surface-mediated vibrational relaxation. Since dissipative dynamics is non-unitary, the choice of representation will affect the evolution of the reduced density matrix. Two alternative representations for computing the relaxation rates and the associated operators are thus compared: the fully coupled spectral basis, and a factorizable ansatz. The former is well-established and serves as a benchmark for the solution of Liouville-von Neumann equation. In the latter, a contracted grid basis of potential-optimized discrete variable representation is tailored to incorporate most of the inter-mode coupling, while the Lindblad operators are represented as tensor products of one-dimensional operators, for consistency. This procedure results in a marked reduction of the grid size and in a much more advantageous scaling of the computational cost with respect to the increase of the dimensionality of the system. The factorizable method is found to provide an accurate description of the dissipative quantum dynamics of the model system, specifically of the time evolution of the state populations and of the probability density distribution of the molecular wave packet. The influence of intra-molecular vibrational energy redistribution appears to be properly taken into account by the new model on the whole range of coupling strengths. It

  16. Structural relaxation dynamics and annealing effects of sodium silicate glass.

    Science.gov (United States)

    Naji, Mohamed; Piazza, Francesco; Guimbretière, Guillaume; Canizarès, Aurélien; Vaills, Yann

    2013-05-09

    Here we report high-precision measurements of structural relaxation dynamics in the glass transition range at the intermediate and short length scale for a strong sodium silicate glass during long annealing times. We evidence for the first time the heterogeneous dynamics at the intermediate range order by probing the acoustic longitudinal frequency in the GHz region by Brillouin light scattering spectroscopy. Or, from in-situ Raman measurements, we show that relaxation is indeed homogeneous at the interatomic length scale. Our results show that the dynamics at the intermediate range order contains two distinct relaxation time scales, a fast and a slow component, differing by about a 10-fold factor below Tg and approaching to one another past the glass transition. The slow relaxation time agrees with the shear relaxation time, proving that Si-O bond breaking constitutes the primary control of structural relaxation at the intermediate range order.

  17. Self-motion and the α-relaxation in glass-forming polymers. Molecular dynamic simulation and quasielastic neutron scattering results in polyisoprene

    International Nuclear Information System (INIS)

    Colmenero, Juan; Arbe, Arantxa; Alvarez, Fernando; Monkenbusch, Michael; Richter, Dieter; Farago, Bela; Frick, Bernhard

    2003-01-01

    The momentum transfer dependence of the self-motion of main chain hydrogens in the α-relaxation regime of a glass forming polymer, polyisoprene, has been thoroughly investigated by a combined effort involving fully atomistic molecular dynamic simulations and quasielastic neutron scattering measurements. In this way, we have established the existence of a crossover from a Gaussian regime of sublinear diffusion to a strongly non-Gaussian regime at short distances. We show that an anomalous jump diffusion model with a distribution of jump lengths gives rise to such a crossover. This model leads to a time-dependent non-Gaussian parameter exhibiting all features revealed so far from various simulations of different glass forming systems

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

    Science.gov (United States)

    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

  19. Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

    Science.gov (United States)

    Lehmann, Kevin K.

    2003-03-01

    Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

  20. Molecular Dynamics of Water in Wood Studied by Fast Field Cycling Nuclear Magnetic Resonance Relaxometry

    Directory of Open Access Journals (Sweden)

    Xinyu Li

    2016-01-01

    Full Text Available Water plays a very important role in wood and wood products. The molecular motion of water in wood is susceptible to thermal activation. Thermal energy makes water molecules more active and weakens the force between water and wood; therefore, the water molecules dynamic properties are greatly influenced. Molecular dynamics study is important for wood drying; this paper therefore focuses on water molecular dynamics in wood through fast field cycling nuclear magnetic resonance relaxometry techniques. The results show that the spin-lattice relaxation rate decreases with the Larmor frequency. Nuclear magnetic resonance dispersion profiles at different temperatures could separate the relaxation contribution of water in bigger pores and smaller pores. The T1 distribution from wide to narrow at 10 MHz Larmor frequency reflects the shrinkage of pore size with the higher temperature. The dependence of spin-lattice relaxation rate on correlation time for water molecular motion based on BPP (proposed by Bloembergen, Purcell, and Pound theory shows that water correlation time increases with higher temperature, and its activation energy, calculated using the Arrhenius transformation equation, is 9.06±0.53 kJ/mol.

  1. Dynamic signature of molecular association in methanol

    International Nuclear Information System (INIS)

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

    2016-01-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  2. Ultrafast dissociation: An unexpected tool for probing molecular dynamics

    International Nuclear Information System (INIS)

    Morin, Paul; Miron, Catalin

    2012-01-01

    Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

  3. Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA.

    Science.gov (United States)

    Chu, Xiang-Qiang; Mamontov, Eugene; O'Neill, Hugh; Zhang, Qiu

    2013-03-21

    The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.

  4. Dynamical relaxation in 2HDM models

    Science.gov (United States)

    Lalak, Zygmunt; Markiewicz, Adam

    2018-03-01

    Dynamical relaxation provides an interesting solution to the hierarchy problem in face of the missing signatures of any new physics in recent experiments. Through a dynamical process taking place in the inflationary phase of the Universe it manages to achieve a small electroweak scale without introducing new states observable in current experiments. Appropriate approximation makes it possible to derive an explicit formula for the final vevs in the double-scanning scenario extended to a model with two Higgs doublets (2HDM). Analysis of the relaxation in the 2HDM confirms that in a general case it is impossible to keep vevs of both scalars small, unless fine-tuning is present or additional symmetries are cast upon the Lagrangian. Within the slightly constrained variant of the 2HDM, where odd powers of the fields’ expectation values are not present (which can be easily enforced by requiring that the doublets have different gauge transformations or by imposing a global symmetry) it is shown that the difference between the vevs of two scalars tends to be proportional to the cutoff. The analysis of the relaxation in 2HDM indicates that in a general case the relaxation would be stopped by the first doublet that gains a vev, with the other one remaining vevless with a mass of the order of the cutoff. This happens to conform with the inert doublet model.

  5. Non-monotonic behaviour in relaxation dynamics of image restoration

    International Nuclear Information System (INIS)

    Ozeki, Tomoko; Okada, Masato

    2003-01-01

    We have investigated the relaxation dynamics of image restoration through a Bayesian approach. The relaxation dynamics is much faster at zero temperature than at the Nishimori temperature where the pixel-wise error rate is minimized in equilibrium. At low temperature, we observed non-monotonic development of the overlap. We suggest that the optimal performance is realized through premature termination in the relaxation processes in the case of the infinite-range model. We also performed Markov chain Monte Carlo simulations to clarify the underlying mechanism of non-trivial behaviour at low temperature by checking the local field distributions of each pixel

  6. Relaxation dynamics of multilayer triangular Husimi cacti

    Science.gov (United States)

    Galiceanu, Mircea; Jurjiu, Aurel

    2016-09-01

    We focus on the relaxation dynamics of multilayer polymer structures having, as underlying topology, the Husimi cactus. The relaxation dynamics of the multilayer structures is investigated in the framework of generalized Gaussian structures model using both Rouse and Zimm approaches. In the Rouse type-approach, we determine analytically the complete eigenvalues spectrum and based on it we calculate the mechanical relaxation moduli (storage and loss modulus) and the average monomer displacement. First, we monitor these physical quantities for structures with a fixed generation number and we increase the number of layers, such that the linear topology will smoothly come into play. Second, we keep constant the size of the structures, varying simultaneously two parameters: the generation number of the main layer, G, and the number of layers, c. This fact allows us to study in detail the crossover from a pure Husimi cactus behavior to a predominately linear chain behavior. The most interesting situation is found when the two limiting topologies cancel each other. For this case, we encounter in the intermediate frequency/time domain regions of constant slope for different values of the parameter set (G, c) and we show that the number of layers follows an exponential-law of G. In the Zimm-type approach, which includes the hydrodynamic interactions, the quantities that describe the mechanical relaxation dynamics do not show scaling behavior as in the Rouse model, except the limiting case, namely, a very high number of layers and low generation number.

  7. Hydration water dynamics in biopolymers from NMR relaxation in the rotating frame.

    Science.gov (United States)

    Blicharska, Barbara; Peemoeller, Hartwig; Witek, Magdalena

    2010-12-01

    Assuming dipole-dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10(-5)s, for which the dispersion region of spin-lattice relaxation rates in the rotating frame R(1)(ρ)=1/T(1)(ρ) appears over a range of easily accessible B(1) values. Measurements of T(1)(ρ) at constant temperature and different B(1) values then give the "dispersion profiles" for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R(1)=1/T(1). The T(1)(ρ) dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme). Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Ultrafast relaxation dynamics of electrons in Au clusters capped with dodecanethiol molecules

    International Nuclear Information System (INIS)

    Hamanaka, Y.; Fukagawa, K.; Tai, Y.; Murakami, J.; Nakamura, A.

    2006-01-01

    We have investigated electron relaxation dynamics of size-selected Au clusters capped by dodecanethiol molecules in the cluster sizes of 28-142 atoms using femtosecond pump-probe spectroscopy. Absorption spectra of 28-71-atom clusters show discrete peaks due to the optical transitions between quantized states, while an absorption band due to the surface plasmon is observed in 142-atom clusters. In the differential absorption spectra measured by the pump-probe experiments, a large redshift of 140 meV lasting over 10 ps and absorption bleaching decaying within 2 ps are observed at the absorption peaks of 28-atom clusters. The redshift is ascribed to a charge transfer between Au clusters and dodecanethiol molecules adsorbed on the cluster surface, and the bleaching is due to blocking of the optical transitions between the ground state and the occupied electronic states due to the Pauli's-exclusion principle. Such behavior is in contrast to the 142-atom clusters, where the cooling of hot electrons generated by photo-excitation determines the relaxation dynamics. These results indicate molecular properties of the 28-atom Au cluster-dodecanethiol system

  9. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  10. Spin dynamics of Mn12-acetate in the thermally activated tunneling regime: ac susceptibility and magnetization relaxation

    Science.gov (United States)

    Pohjola, Teemu; Schoeller, Herbert

    2000-12-01

    In this work, we study the spin dynamics of Mn12-acetate molecules in the regime of thermally assisted tunneling. In particular, we describe the system in the presence of a strong transverse magnetic field. Similar to recent experiments, the relaxation time/rate is found to display a series of resonances; their Lorentzian shape is found to stem from the tunneling. The dynamic susceptibility χ(ω) is calculated starting from the microscopic Hamiltonian and the resonant structure manifests itself also in χ(ω). Similar to recent results reported on another molecular magnet, Fe8, we find oscillations of the relaxation rate as a function of the transverse magnetic field when the field is directed along a hard axis of the molecules. This phenomenon is attributed to the interference of the geometrical or Berry phase. We propose susceptibility experiments to be carried out for strong transverse magnetic fields to study these oscillations and for a better resolution of the sharp satellite peaks in the relaxation rates.

  11. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

    Science.gov (United States)

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

    2013-11-07

    Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

  12. Dynamics of helicity transport and Taylor relaxation

    International Nuclear Information System (INIS)

    Diamond, P.H.; Malkov, M.

    2003-01-01

    A simple model of the dynamics of Taylor relaxation is derived using symmetry principles alone. No statistical closure approximations are invoked or detailed plasma model properties assumed. Notably, the model predicts several classes of nondiffusive helicity transport phenomena, including traveling nonlinear waves and superdiffusive turbulent pulses. A universal expression for the scaling of the effective magnetic Reynolds number of a system undergoing Taylor relaxation is derived. Some basic properties of intermittency in helicity transport are examined

  13. Nonadiabatic excited-state molecular dynamics: On-the-fly limiting of essential excited states

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Tammie [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Naumov, Artem [Skolkovo Institute of Science and Technology, Moscow 143026 (Russian Federation); Fernandez-Alberti, Sebastian [Universidad Nacional de Quilmes, Roque Saenz Pea 352, B1876BXD Bernal (Argentina); Tretiak, Sergei, E-mail: serg@lanl.gov [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2016-12-20

    The simulation of nonadiabatic dynamics in extended molecular systems involving hundreds of atoms and large densities of states is particularly challenging. Nonadiabatic coupling terms (NACTs) represent a significant numerical bottleneck in surface hopping approaches. Rather than using unreliable NACT cutting schemes, here we develop “on-the-fly” state limiting methods to eliminate states that are no longer essential for the non-radiative relaxation dynamics as a trajectory proceeds. We propose a state number criteria and an energy-based state limit. The latter is more physically relevant by requiring a user-imposed energy threshold. For this purpose, we introduce a local kinetic energy gauge by summing contributions from atoms within the spatial localization of the electronic wavefunction to define the energy available for upward hops. The proposed state limiting schemes are implemented within the nonadiabatic excited-state molecular dynamics framework to simulate photoinduced relaxation in poly-phenylene vinylene (PPV) and branched poly-phenylene ethynylene (PPE) oligomers for benchmark evaluation.

  14. Space and time dynamical heterogeneity in glassy relaxation. The role of democratic clusters

    International Nuclear Information System (INIS)

    Appignanesi, G A; Rodriguez Fris, J A

    2009-01-01

    In this work we review recent computational advances in the understanding of the relaxation dynamics of supercooled glass-forming liquids. In such a supercooled regime these systems experience a striking dynamical slowing down which can be rationalized in terms of the picture of dynamical heterogeneities, wherein the dynamics can vary by orders of magnitude from one region of the sample to another and where the sizes and timescales of such slowly relaxing regions are expected to increase considerably as the temperature is decreased. We shall focus on the relaxation events at a microscopic level and describe the finding of the collective motions of particles responsible for the dynamical heterogeneities. In so doing, we shall demonstrate that the dynamics in different regions of the system is not only heterogeneous in space but also in time. In particular, we shall be interested in the events relevant to the long-time structural relaxation or α relaxation. In this regard, we shall focus on the discovery of cooperatively relaxing units involving the collective motion of relatively compact clusters of particles, called 'democratic clusters' or d-clusters. These events have been shown to trigger transitions between metabasins of the potential energy landscape (collections of similar configurations or structures) and to consist of the main steps in the α relaxation. Such events emerge in systems quite different in nature such as simple model glass formers and supercooled amorphous water. Additionally, another relevant issue in this context consists in the determination of a link between structure and dynamics. In this context, we describe the relationship between the d-cluster events and the constraints that the local structure poses on the relaxation dynamics, thus revealing their role in reformulating structural constraints. (topical review)

  15. Incorporation of quantum statistical features in molecular dynamics

    International Nuclear Information System (INIS)

    Ohnishi, Akira; Randrup, J.

    1995-01-01

    We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)

  16. Dynamics of the α-relaxation in glass-forming polymers. Study by neutron scattering and relaxation techniques

    Science.gov (United States)

    Colmenero, J.

    1993-12-01

    The dynamics of the α-relaxation in three different polymeric systems, poly(vinyl methyl ether) (PVME), poly(vinyl chloride) (PVC) and poly(bisphenol A, 2-hydroxypropylether) (PH) has been studied by means of relaxation techniques and quasielastic neutron scattering (backscattering spectrometers IN10 and IN13 at the ILL-Grenoble). By using these techniques we have covered a wide time scale ranging from mesoscopic to macroscopic times (10 -10 -10 1 s). For analyzing the experimental data we have developed a phenomenological procedure in the frequency domain based on the Havriliak-Negami relaxation function, which in fact implies a Kohlrausch-Williams-Watts relaxation function in the time domain. The results obtained indicate that the dynamics of the α-relaxation in a wide time scale shows a clear non-Debye behaviour. The shape of the relaxation functions is found to be similar for the different techniques used and independent of temperature and momentum transfer ( Q). Moreover, the characteristic relaxation times deduced from the fitting of the experimental data can also be described using only one Vogel-Fulcher functional form. Besides we found that the Q-dependence of the relaxation times obtained by QENS is given by a power law, τ( Q) ∞ Q- n ( n>2), n being dependent on the system, and that the Q-behaviour and the non-Debye behaviour are directly correlated. In the case of PVC, time of flight (TOF) neutron scattering experiments confirm these results in a shorter time scale (2×10 -11 -2× 10 -12 s). Moreover, TOF results also suggest the possibility of interpreting the “fast process” usually detected in glass-forming systems as a Debye-like short regime of the α-relaxation.

  17. Universal divergenceless scaling between structural relaxation and caged dynamics in glass-forming systems.

    Science.gov (United States)

    Ottochian, A; De Michele, C; Leporini, D

    2009-12-14

    On approaching the glass transition, the microscopic kinetic unit spends increasing time rattling in the cage of the first neighbors, whereas its average escape time, the structural relaxation time tau(alpha), increases from a few picoseconds up to thousands of seconds. A thorough study of the correlation between tau(alpha) and the rattling amplitude, expressed by the Debye-Waller factor, was carried out. Molecular-dynamics simulations of both a model polymer system and a binary mixture were performed by varying the temperature, the density rho, the potential and the polymer length to consider the structural relaxation as well as both the rotational and the translation diffusion. The present simulations, together with MD studies on other glassformers, evidence the scaling between the structural relaxation and the caged dynamics. An analytic model of the master curve is developed in terms of two characteristic length scales a(2) (1/2) and sigma(a(2) ) (1/2), pertaining to the distance to be covered by the kinetic unit to reach a transition state. The model does not imply tau(alpha) divergences. The comparison with the experiments supports the numerical evidence over a range of relaxation times as wide as about eighteen orders of magnitude. A comparison with other scaling and correlation procedures is presented. In particular, the density scaling of the length scales a(2) (1/2), sigma(a(2) ) (1/2) proportional to rho(-1/3) is shown to be not supported by the present simulations. The study suggests that the equilibrium and the moderately supercooled states of the glassformers possess key information on the huge slowing-down of their relaxation close to the glass transition. The latter, according to the present simulations, exhibits features consistent with the Lindemann melting criterion and the free-volume model.

  18. The effect of host relaxation and dynamics on guest molecule dynamics in H2/tetrahydrofuranhydrate.

    Science.gov (United States)

    Peterson, Vanessa K; Shoko, Elvis; Kearley, Gordon J

    2011-01-01

    We use ab initio molecular dynamics simulations to obtain classically the effects of H2O cage motions on the potential-energy surface (PES) of encapsulated H2 in the H2/tetrahydrofuran-hydrate system. The significant differences between the PES for the H2 in rigid and flexible cages that we find will influence calculation of the quantum dynamics of the H2. Part of these differences arises from the relaxation of the H2O cage around the classical H2, with a second part arising from the coupling of both translational and rotational motions of H2 with the H20 cage. We find that isotopic substitution of 2H for 1H of the H2O cage affects the coupling, which has implications for experiments that require the use of 2H2O, including inelastic neutron scattering that uses 2H2O cages in order to focus on the H2 guest dynamics. Overall, this work emphasizes the importance of taking into account cage dynamics in any approach used to understand the dynamics of H2 guests in porous framework materials.

  19. Relaxation Dynamics of Nanoparticle-Tethered Polymer Chains

    KAUST Repository

    Kim, Sung A; Mangal, Rahul; Archer, Lynden A.

    2015-01-01

    © 2015 American Chemical Society. Relaxation dynamics of nanoparticle-tethered cis-1,4-polyisoprene (PI) are investigated using dielectric spectroscopy and rheometry. A model system composed of polymer chains densely grafted to spherical SiO2

  20. Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

    International Nuclear Information System (INIS)

    Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2014-01-01

    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 for 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

  1. A simple measurement method of molecular relaxation in a gas by reconstructing acoustic velocity dispersion

    Science.gov (United States)

    Zhu, Ming; Liu, Tingting; Zhang, Xiangqun; Li, Caiyun

    2018-01-01

    Recently, a decomposition method of acoustic relaxation absorption spectra was used to capture the entire molecular multimode relaxation process of gas. In this method, the acoustic attenuation and phase velocity were measured jointly based on the relaxation absorption spectra. However, fast and accurate measurements of the acoustic attenuation remain challenging. In this paper, we present a method of capturing the molecular relaxation process by only measuring acoustic velocity, without the necessity of obtaining acoustic absorption. The method is based on the fact that the frequency-dependent velocity dispersion of a multi-relaxation process in a gas is the serial connection of the dispersions of interior single-relaxation processes. Thus, one can capture the relaxation times and relaxation strengths of N decomposed single-relaxation dispersions to reconstruct the entire multi-relaxation dispersion using the measurements of acoustic velocity at 2N  +  1 frequencies. The reconstructed dispersion spectra are in good agreement with experimental data for various gases and mixtures. The simulations also demonstrate the robustness of our reconstructive method.

  2. Dynamics of relaxed inflation

    Science.gov (United States)

    Tangarife, Walter; Tobioka, Kohsaku; Ubaldi, Lorenzo; Volansky, Tomer

    2018-02-01

    The cosmological relaxation of the electroweak scale has been proposed as a mechanism to address the hierarchy problem of the Standard Model. A field, the relaxion, rolls down its potential and, in doing so, scans the squared mass parameter of the Higgs, relaxing it to a parametrically small value. In this work, we promote the relaxion to an inflaton. We couple it to Abelian gauge bosons, thereby introducing the necessary dissipation mechanism which slows down the field in the last stages. We describe a novel reheating mechanism, which relies on the gauge-boson production leading to strong electro-magnetic fields, and proceeds via the vacuum production of electron-positron pairs through the Schwinger effect. We refer to this mechanism as Schwinger reheating. We discuss the cosmological dynamics of the model and the phenomenological constraints from CMB and other experiments. We find that a cutoff close to the Planck scale may be achieved. In its minimal form, the model does not generate sufficient curvature perturbations and additional ingredients, such as a curvaton field, are needed.

  3. Nonequilibrium thermodynamics and information theory: basic concepts and relaxing dynamics

    International Nuclear Information System (INIS)

    Altaner, Bernhard

    2017-01-01

    Thermodynamics is based on the notions of energy and entropy. While energy is the elementary quantity governing physical dynamics, entropy is the fundamental concept in information theory. In this work, starting from first principles, we give a detailed didactic account on the relations between energy and entropy and thus physics and information theory. We show that thermodynamic process inequalities, like the second law, are equivalent to the requirement that an effective description for physical dynamics is strongly relaxing. From the perspective of information theory, strongly relaxing dynamics govern the irreversible convergence of a statistical ensemble towards the maximally non-commital probability distribution that is compatible with thermodynamic equilibrium parameters. In particular, Markov processes that converge to a thermodynamic equilibrium state are strongly relaxing. Our framework generalizes previous results to arbitrary open and driven systems, yielding novel thermodynamic bounds for idealized and real processes. (paper)

  4. Dynamics and relaxation in confined medium. Application to 129Xe magnetic relaxation in Vycor

    International Nuclear Information System (INIS)

    Pasquier, Virginie

    1995-01-01

    Porous media morphology and topology drive the exploration of pore space by fluid. So, analysis of transport process, associated with relaxation mechanism, allows indirect study of pore geometry. The purpose of this work is to understand better the relation between geometry and transport. This study involves two parts: a modelization and prediction step is followed by an experimental application of magnetic relaxation. Numerical simulations and analytical models allow to quantify the influence on the solid interface of the dynamical behavior of confined gas in disordered porous media (granular structure and porous network) or in common geometry (cylindrical and lamellar interfaces). The formalism of diffusion propagator is a powerful tool to quantify the influence of the pore geometry on the diffusion of confined gas. The propagator holds all dynamical information on the system; it also predicts the temporal evolution of the autocorrelation functions of the Hamiltonian describing local coupling. In an intermediate time scale, magnetic relaxation shows complex diffusional regime: the autocorrelation functions decrease in a power law with a exponent smaller than d/2 (where d is the Euclidian dimension of the system). This behavior is analogous to dynamic in low-dimensional space, but here arises from surface correlations of the porous media. The long-time behavior of the autocorrelation functions retrieves the asymptotic decrease t -d/2 . Moreover, atypical behavior is observed for the Knudsen diffusion between infinite planes. It turns out that 129 Xe NMR is a appropriate technique to characterize organization and diffusion of gas confined in Vycor. Systematic studies of temperature and pressure effect on the 129 Xe chemical shift allow to specify the Xe/solid interaction. The analysis of the relaxation measurements, thanks to the numerical development, confirms conclusions arising from the study of diffusion propagator. (author) [fr

  5. Segmental dynamics in polymer melts by relaxation techniques and quasielastic neutron scattering

    Science.gov (United States)

    Colmenero, J.

    1993-01-01

    The dynamics of the segmental α-relaxation in three different polymeric systems, poly(vinyl methy ether) (PVME), poly(vinyl chloride) (PVC) and poly(bisphenol A, 2-hydroxypropylether) (PH) has been studied by means of relaxation techniques and quasielastic neutron scattering (backscattering spectrometers IN10 and IN13 at the ILL-Grenoble). By using these techniques we have covered a wide timescale ranging from mesoscopic to macroscopic times (10-10-101s). For analyzing the experimental data we have developed a phenomenological procedure in the frequency domain based on the Havriliak-Negami relaxation function which in fact implies a Kohlrausch-Williams-Watts relaxation function in the time domain. The results obtained indicate that the dynamics of the α-relaxation in a wide timescale shows a clear non-Debye behaviour. The shape of the relaxation function is found to be similar for the different techniques used and independent of temperature and momentum transfer (Q). Moreover the characteristic relaxation times deduced from the fitting of the experimental data can also be described using only one Vogel-Fulcher functional form. Besides we found that the Q-dependence of the relaxation times obtained by QENS is given by a power law, τ(Q) propto Q-n (n > 2) n being dependent on the system, and that the Q-behaviour and the non-Debye behaviour are directly correlated. We discuss this correlation taking into account several data of the dynamics of the α-relaxation previously reported in the literature. We also outline a possible scenario for explaining this empirical correlation.

  6. Thermal relaxation of molecular oxygen in collisions with nitrogen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Andrienko, Daniil A., E-mail: daniila@umich.edu; Boyd, Iain D. [Department of Aerospace Engineering, University of Michigan, 1320 Beal Ave., Ann Arbor, Michigan 48108 (United States)

    2016-07-07

    Investigation of O{sub 2}–N collisions is performed by means of the quasi-classical trajectory method on the two lowest ab initio potential energy surfaces at temperatures relevant to hypersonic flows. A complete set of bound–bound and bound–free transition rates is obtained for each precollisional rovibrational state. Special attention is paid to the vibrational and rotational relaxations of oxygen as a result of chemically non-reactive interaction with nitrogen atoms. The vibrational relaxation of oxygen partially occurs via the formation of an intermediate NO{sub 2} complex. The efficient energy randomization results in rapid vibrational relaxation at low temperatures, compared to other molecular systems with a purely repulsive potential. The vibrational relaxation time, computed by means of master equation studies, is nearly an order of magnitude lower than the relaxation time in N{sub 2}–O collisions. The rotational nonequilibrium starts to play a significant effect at translational temperatures above 8000 K. The present work provides convenient relations for the vibrational and rotational relaxation times as well as for the quasi-steady dissociation rate coefficient and thus fills a gap in data due to a lack of experimental measurements for this system.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr; Meier, Christoph [Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse (France); Falvo, Cyril [Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay (France)

    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 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.

  8. Nonlinear Relaxation in Population Dynamics

    Science.gov (United States)

    Cirone, Markus A.; de Pasquale, Ferdinando; Spagnolo, Bernardo

    We analyze the nonlinear relaxation of a complex ecosystem composed of many interacting species. The ecological system is described by generalized Lotka-Volterra equations with a multiplicative noise. The transient dynamics is studied in the framework of the mean field theory and with random interaction between the species. We focus on the statistical properties of the asymptotic behaviour of the time integral of the ith population and on the distribution of the population and of the local field.

  9. Vibrational relaxation dynamics of SD molecules in As2S3: Observation of an anomalous isotope effect

    International Nuclear Information System (INIS)

    Engholm, J.R.; Happek, U.; Rella, C.W.

    1995-01-01

    It is generally assumed that the vibrational relaxation of molecular impurities in crystals and glasses mainly depends on the order of the decay process, with lower order processes leading to more rapid relaxation (a behavior that is known under the term open-quotes gap-lawclose quotes). Here we present measurements that contradict this assumption. Using high intensity psec pulses of the Stanford FEL we measured the relaxation rate of the SD vibrational stretch mode (at a frequency of 1800 cm) by applying a pump-probe technique. We find relaxation rates on the order of 2x10 9 sec -1 , which are a factor of 2 lower than those found for the isotope molecule SH (at a frequency of about 2500 cm - 1 ) in the same host 1 . We recall that the relaxation of the SD vibrational stretch mode is controlled by a lower order process as compared to the SH molecule, which is due to the smaller number of host vibrational quanta to match the energy of the stretch mode; a fact we have confirmed experimentally by temperature dependent relaxation measurements. Thus our remits are in marked contrast to the so-called open-quotes Gap-Lawclose quotes and emphasize the importance of the molecule - host coupling in the relaxation dynamics

  10. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.

    Science.gov (United States)

    Gnanasekaran, Ramachandran; Xu, Yao; Leitner, David M

    2010-12-23

    Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.

  11. Modeling cytoskeletal flow over adhesion sites: competition between stochastic bond dynamics and intracellular relaxation

    International Nuclear Information System (INIS)

    Sabass, Benedikt; Schwarz, Ulrich S

    2010-01-01

    In migrating cells, retrograde flow of the actin cytoskeleton is related to traction at adhesion sites located at the base of the lamellipodium. The coupling between the moving cytoskeleton and the stationary adhesions is mediated by the continuous association and dissociation of molecular bonds. We introduce a simple model for the competition between the stochastic dynamics of elastic bonds at the moving interface and relaxation within the moving actin cytoskeleton represented by an internal viscous friction coefficient. Using exact stochastic simulations and an analytical mean field theory, we show that the stochastic bond dynamics lead to biphasic friction laws as observed experimentally. At low internal dissipation, stochastic bond dynamics lead to a regime of irregular stick-and-slip motion. High internal dissipation effectively suppresses cooperative effects among bonds and hence stabilizes the adhesion.

  12. Electron spin relaxation in cryptochrome-based magnetoreception

    DEFF Research Database (Denmark)

    Kattnig, Daniel R; Solov'yov, Ilia A; Hore, P J

    2016-01-01

    The magnetic compass sense of migratory birds is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the retina. An important requirement of this hypothesis is that electron spin relaxation is slow enough for the Earth's magnetic field to have...... this question for a structurally characterized model cryptochrome expected to share many properties with the putative avian receptor protein. To this end we combine all-atom molecular dynamics simulations, Bloch-Redfield relaxation theory and spin dynamics calculations to assess the effects of spin relaxation...... on the performance of the protein as a compass sensor. Both flavin-tryptophan and flavin-Z˙ radical pairs are studied (Z˙ is a radical with no hyperfine interactions). Relaxation is considered to arise from modulation of hyperfine interactions by librational motions of the radicals and fluctuations in certain...

  13. Tracking ultrafast relaxation dynamics of furan by femtosecond photoelectron imaging

    International Nuclear Information System (INIS)

    Liu, Yuzhu; Knopp, Gregor; Qin, Chaochao; Gerber, Thomas

    2015-01-01

    Graphical abstract: - Highlights: • Relaxation dynamics of furan are tracked by femtosecond photoelectron imaging. • The mechanism for ultrafast formation of α-carbene and β-carbene is proposed. • Ultrafast internal conversion from S 2 to S 1 is observed. • The transient characteristics of the fragment ions are obtained. • Single-color multi-photon ionization dynamics at 800 nm are also studied. - Abstract: Ultrafast internal conversion dynamics of furan has been studied by femtosecond photoelectron imaging (PEI) coupled with photofragmentation (PF) spectroscopy. Photoelectron imaging of single-color multi-photon ionization and two-color pump–probe ionization are obtained and analyzed. Photoelectron bands are assigned to the related states. The time evolution of the photoelectron signal by pump–probe ionization can be well described by a biexponential decay: two rapid relaxation pathways with time constants of ∼15 fs and 85 (±11) fs. The rapid relaxation is ascribed to the ultrafast internal conversion (IC) from the S 2 state to the vibrationally hot S 1 state. The second relaxation process is attributed to the redistributions and depopulation of secondarily populated high vibronic S 1 state and the formation of α-carbene and β-carbene by H immigration. Additionally, the transient characteristics of the fragment ions are also measured and discussed as a complementary understanding

  14. Relaxation towards phase-locked dynamics in long Josephson junctions

    DEFF Research Database (Denmark)

    Salerno, M.; Grønbech-Jensen, Niels; Samuelsen, Mogens Rugholm

    1995-01-01

    We study the relaxation phenomenon towards phase-locked dynamics in long Josephson junctions. In particular the dependence of the relaxation frequency for the equal time of flight solution on the junction parameters is derived. The analysis is based on a phase-locked map and is compared with direct...... numerical experiments performed both on the map and on the perturbed sine-Gordon equation. As an interesting result we find that very close to a bifurcation the relaxation frequency is exactly equal to the half of the step frequency, i.e., the frequency characterizing the period-one solution....

  15. Microscopic dynamics and relaxation processes in liquid hydrogen fluoride

    International Nuclear Information System (INIS)

    Angelini, R.; Giura, P.; Monaco, G.; Sette, F.; Fioretto, D.; Ruocco, G.

    2004-01-01

    Inelastic x-ray scattering and Brillouin light scattering measurements of the dynamic structure factor of liquid hydrogen fluoride have been performed in the temperature range T=214-283 K. The data, analyzed using a viscoelastic model with a two time-scale memory function, show a positive dispersion of the sound velocity c(Q) between the low frequency value c 0 (Q) and the high frequency value c ∞α (Q). This finding confirms the existence of a structural (α) relaxation directly related to the dynamical organization of the hydrogen bonds network of the system. The activation energy E a of the process has been extracted by the analysis of the temperature behavior of the relaxation time τ α (T) that follows an Arrhenius law. The obtained value for E a , when compared with that observed in another hydrogen bond liquid as water, suggests that the main parameter governing the α-relaxation process is the number of hydrogen bonds per molecule

  16. Nuclear spin-lattice relaxation in carbon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Panich, A.M., E-mail: pan@bgu.ac.i [Department of Physics, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105 (Israel); Sergeev, N.A. [Institute of Physics, University of Szczecin, 70-451 Szczecin (Poland)

    2010-04-15

    Interpretation of nuclear spin-lattice relaxation data in the carbon nanostructures is usually based on the analysis of fluctuations of dipole-dipole interactions of nuclear spins and anisotropic electron-nuclear interactions responsible for chemical shielding, which are caused by molecular dynamics. However, many nanocarbon systems such as fullerene and nanotube derivatives, nanodiamonds and carbon onions reveal noticeable amount of paramagnetic defects with unpaired electrons originating from dangling bonds. The interaction between nuclear and electron spins strongly influences the nuclear spin-lattice relaxation, but usually is not taken into account, thus the relaxation data are not correctly interpreted. Here we report on the temperature dependent NMR spectra and spin-lattice relaxation measurements of intercalated fullerenes C{sub 60}(MF{sub 6}){sub 2} (M=As and Sb), where nuclear relaxation is caused by both molecular rotation and interaction between nuclei and unpaired electron spins. We present a detailed theoretical analysis of the spin-lattice relaxation data taking into account both these contributions. Good agreement between the experimental data and calculations is obtained. The developed approach would be useful in interpreting the NMR relaxation data in different nanostructures and their intercalation compounds.

  17. Hotspot relaxation dynamics in a current-carrying superconductor

    Science.gov (United States)

    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.

  18. Molecular order and T1-relaxation, cross-relaxation in nitroxide spin labels

    Science.gov (United States)

    Marsh, Derek

    2018-05-01

    Interpretation of saturation-recovery EPR experiments on nitroxide spin labels whose angular rotation is restricted by the orienting potential of the environment (e.g., membranes) currently concentrates on the influence of rotational rates and not of molecular order. Here, I consider the dependence on molecular ordering of contributions to the rates of electron spin-lattice relaxation and cross relaxation from modulation of N-hyperfine and Zeeman anisotropies. These are determined by the averages and , where θ is the angle between the nitroxide z-axis and the static magnetic field, which in turn depends on the angles that these two directions make with the director of uniaxial ordering. For saturation-recovery EPR at 9 GHz, the recovery rate constant is predicted to decrease with increasing order for the magnetic field oriented parallel to the director, and to increase slightly for the perpendicular field orientation. The latter situation corresponds to the usual experimental protocol and is consistent with the dependence on chain-labelling position in lipid bilayer membranes. An altered dependence on order parameter is predicted for saturation-recovery EPR at high field (94 GHz) that is not entirely consistent with observation. Comparisons with experiment are complicated by contributions from slow-motional components, and an unexplained background recovery rate that most probably is independent of order parameter. In general, this analysis supports the interpretation that recovery rates are determined principally by rotational diffusion rates, but experiments at other spectral positions/field orientations could increase the sensitivity to order parameter.

  19. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure

    International Nuclear Information System (INIS)

    Powers, R.; Jones, C.R.; Gorenstein, D.G.

    1990-01-01

    Assignment of the 1H and 31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and 1H-31P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. JH3'-P coupling constants for each of the phosphates of the decamer were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4'-C3'-O3'-P torsional angles were obtained. Comparison of the 31P chemical shifts and JH3'-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for 31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 31P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix

  20. A comparative study of ibuprofen and ketoprofen glass-forming liquids by molecular dynamics simulations

    Science.gov (United States)

    Ottou Abe, M. T.; Correia, N. T.; Ndjaka, J. M. B.; Affouard, F.

    2015-10-01

    In this paper, structural and dynamical properties of ibuprofen and ketoprofen glass-forming liquids have been investigated by means of molecular dynamics simulations. Molecular mobility of both materials is analyzed with respect to the different inter-molecular linear/cyclic hydrogen bonding associations. For ibuprofen, the dominant organization is found to be composed of small hydrogen bonding aggregates corresponding to cyclic dimers through the carboxyl group. For ketoprofen, the propensity of cyclic dimers is significantly reduced by the formation of hydrogen bonds with the ketone oxygen of the molecule altering the hydrogen bond (HB) associating structures that can be formed and thus molecular dynamics. The issue of the presence/absence of the peculiar low frequency Debye-type process in dielectric relaxation spectroscopy (DRS) data in these materials is addressed. Results obtained from simulations confirm that the Debye process originates from the internal cis-trans conversion of the —COOH carboxyl group. It is shown that the specific intermolecular HB structures associated to a given profen control the main dynamical features of this conversion, in particular its separation from the α-process, which make it detectable or not from DRS. For ibuprofen, the possible role of the —CCCO torsion motion, more "local" than the —COOH motion since it is less influenced by the intermolecular HBs, is suggested in the microscopic origin of the quite intense secondary γ-relaxation process detected from DRS.

  1. Molecular-dynamics simulations of thin polyisoprene films confined between amorphous silica substrates

    International Nuclear Information System (INIS)

    Guseva, D. V.; Komarov, P. V.; Lyulin, Alexey V.

    2014-01-01

    Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 g g is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed

  2. Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

    Science.gov (United States)

    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.

  3. Hierarchical relaxation dynamics in a tilted two-band Bose-Hubbard model

    Science.gov (United States)

    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.

  4. Revealing the Link between Structural Relaxation and Dynamic Heterogeneity in Glass-Forming Liquids.

    Science.gov (United States)

    Wang, Lijin; Xu, Ning; Wang, W H; Guan, Pengfei

    2018-03-23

    Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the abrupt slowdown of structural relaxation. However, it still remains elusive whether there is an underlying link between structural relaxation and dynamic heterogeneity. Here, we unravel the link by introducing a characteristic time scale hiding behind an identical dynamic heterogeneity for various model glass-forming liquids. We find that the time scale corresponds to the kinetic fragility of liquids. Moreover, it leads to scaling collapse of both the structural relaxation time and dynamic heterogeneity for all liquids studied, together with a characteristic temperature associated with the same dynamic heterogeneity. Our findings imply that studying the glass transition from the viewpoint of dynamic heterogeneity is more informative than expected.

  5. Revealing the Link between Structural Relaxation and Dynamic Heterogeneity in Glass-Forming Liquids

    Science.gov (United States)

    Wang, Lijin; Xu, Ning; Wang, W. H.; Guan, Pengfei

    2018-03-01

    Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the abrupt slowdown of structural relaxation. However, it still remains elusive whether there is an underlying link between structural relaxation and dynamic heterogeneity. Here, we unravel the link by introducing a characteristic time scale hiding behind an identical dynamic heterogeneity for various model glass-forming liquids. We find that the time scale corresponds to the kinetic fragility of liquids. Moreover, it leads to scaling collapse of both the structural relaxation time and dynamic heterogeneity for all liquids studied, together with a characteristic temperature associated with the same dynamic heterogeneity. Our findings imply that studying the glass transition from the viewpoint of dynamic heterogeneity is more informative than expected.

  6. Tracking ultrafast relaxation dynamics of furan by femtosecond photoelectron imaging

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yuzhu, E-mail: yuzhu.liu@gmail.com [School of Physics and Optoelectronic Engineering, Nanjing University of Information Science and Technology, Nanjing 210044 (China); Knopp, Gregor [Paul Scherrer Institute, Villigen 5232 (Switzerland); Qin, Chaochao [Department of Physics, Henan Normal University, Xinxiang 453007 (China); Gerber, Thomas [Paul Scherrer Institute, Villigen 5232 (Switzerland)

    2015-01-13

    Graphical abstract: - Highlights: • Relaxation dynamics of furan are tracked by femtosecond photoelectron imaging. • The mechanism for ultrafast formation of α-carbene and β-carbene is proposed. • Ultrafast internal conversion from S{sub 2} to S{sub 1} is observed. • The transient characteristics of the fragment ions are obtained. • Single-color multi-photon ionization dynamics at 800 nm are also studied. - Abstract: Ultrafast internal conversion dynamics of furan has been studied by femtosecond photoelectron imaging (PEI) coupled with photofragmentation (PF) spectroscopy. Photoelectron imaging of single-color multi-photon ionization and two-color pump–probe ionization are obtained and analyzed. Photoelectron bands are assigned to the related states. The time evolution of the photoelectron signal by pump–probe ionization can be well described by a biexponential decay: two rapid relaxation pathways with time constants of ∼15 fs and 85 (±11) fs. The rapid relaxation is ascribed to the ultrafast internal conversion (IC) from the S{sub 2} state to the vibrationally hot S{sub 1} state. The second relaxation process is attributed to the redistributions and depopulation of secondarily populated high vibronic S{sub 1} state and the formation of α-carbene and β-carbene by H immigration. Additionally, the transient characteristics of the fragment ions are also measured and discussed as a complementary understanding.

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

    Science.gov (United States)

    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.

  8. Free volume and relaxation dynamics of polymeric systems

    International Nuclear Information System (INIS)

    Bartos, J.; Kristiak, J.

    1999-01-01

    In this contribution use of positron annihilation spectroscopy (PALS) for the study of free volume and relaxation dynamics of some polymeric systems (1,4-polybutadiene, cis-1,4-polyisoprene, polyisobutylene, trans-1,4-polychloropropene, atactic polypropylene and 1,2-polybutadiene) is discussed

  9. Stability investigations of relaxing molecular gas flows. Results and perspectives

    Science.gov (United States)

    Grigor'ev, Yurii N.; Ershov, Igor V.

    2017-10-01

    This article presents results of systematic investigations of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The effect can be a new way for control stability and laminar turbulent transition in aerodynamic flows. The consideration of suppression of inviscid acoustic waves in 2D shear flows is presented. Nonlinear evolution of large-scale vortices and Kelvin — Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both classical linear and nonlinear energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of this article is to show the new dissipative effect, which can be used for flow control and laminarization.

  10. Nonequilibrium thermodynamics and information theory: basic concepts and relaxing dynamics

    Science.gov (United States)

    Altaner, Bernhard

    2017-11-01

    Thermodynamics is based on the notions of energy and entropy. While energy is the elementary quantity governing physical dynamics, entropy is the fundamental concept in information theory. In this work, starting from first principles, we give a detailed didactic account on the relations between energy and entropy and thus physics and information theory. We show that thermodynamic process inequalities, like the second law, are equivalent to the requirement that an effective description for physical dynamics is strongly relaxing. From the perspective of information theory, strongly relaxing dynamics govern the irreversible convergence of a statistical ensemble towards the maximally non-commital probability distribution that is compatible with thermodynamic equilibrium parameters. In particular, Markov processes that converge to a thermodynamic equilibrium state are strongly relaxing. Our framework generalizes previous results to arbitrary open and driven systems, yielding novel thermodynamic bounds for idealized and real processes. , which features invited work from the best early-career researchers working within the scope of J. Phys. A. This project is part of the Journal of Physics series’ 50th anniversary celebrations in 2017. Bernhard Altaner was selected by the Editorial Board of J. Phys. A as an Emerging Talent.

  11. Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

    International Nuclear Information System (INIS)

    Bernado, Pau; Fernandes, Miguel X.; Jacobs, Doris M.; Fiebig, Klaus; Garcia de la Torre, Jose; Pons, Miquel

    2004-01-01

    Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1

  12. Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bernado, Pau [Institut de Biologie Structurale, Jean Pierre Ebel (France); Fernandes, Miguel X. [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Jacobs, Doris M. [Johann Wolfgang Goethe-Universitaet Frankfurt, Institut fuer Organische Chemie und Chemische Biologie (Germany); Fiebig, Klaus [Affinium Pharmaceuticals (Canada); Garcia de la Torre, Jose [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Pons, Miquel [Laboratori de RMN de Biomolecules, Parc Cientific de Barcelona (Spain)], E-mail: mpons@ub.edu

    2004-05-15

    Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1.

  13. Dielectric dispersion, relaxation dynamics and thermodynamic studies of Beta-Alanine in aqueous solutions using picoseconds time domain reflectometry

    Science.gov (United States)

    Vinoth, K.; Ganesh, T.; Senthilkumar, P.; Sylvester, M. Maria; Karunakaran, D. J. S. Anand; Hudge, Praveen; Kumbharkhane, A. C.

    2017-09-01

    The aqueous solution of beta-alanine characterised and studied by their dispersive dielectric properties and relaxation process in the frequency domain of 10×106 Hz to 30×109 Hz with varying concentration in mole fractions and temperatures. The molecular interaction and dielectric parameters are discussed in terms of counter-ion concentration theory. The static permittivity (ε0), high frequency dielectric permittivity (ε∞) and excess dielectric parameters are accomplished by frequency depended physical properties and relaxation time (τ). Molecular orientation, ordering and correlation factors are reported as confirmation of intermolecular interactions. Ionic conductivity and thermo dynamical properties are concluded with the behaviour of the mixture constituents. Solute-solvent, solute-solute interaction, structure making and breaking abilities of the solute in aqueous medium are interpreted. Fourier Transform Infrared (FTIR) spectra of beta- alanine single crystal and liquid state have been studied. The 13C Nuclear Magnetic Resonance (NMR) spectral studies give the signature for resonating frequencies and chemical shifts of beta-alanine.

  14. Electron spin relaxation can enhance the performance of a cryptochrome-based magnetic compass sensor

    DEFF Research Database (Denmark)

    Kattnig, Daniel R; Sowa, Jakub K; Solov'yov, Ilia A

    2016-01-01

    thaliana cryptochrome 1 were obtained from molecular dynamics (MD) simulations and used to calculate the spin relaxation caused by modulation of the exchange and dipolar interactions. We find that intermediate spin relaxation rates afford substantial enhancements in the sensitivity of the reaction yields....... Here we argue that certain spin relaxation mechanisms can enhance its performance. We focus on the flavin-tryptophan radical pair in cryptochrome, currently the only candidate magnetoreceptor molecule. Correlation functions for fluctuations in the distance between the two radicals in Arabidopsis...... to an Earth-strength magnetic field. Supported by calculations using toy radical pair models, we argue that these enhancements could be consistent with the molecular dynamics and magnetic interactions in avian cryptochromes....

  15. Quantifying protein dynamics in the ps–ns time regime by NMR relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, Griselda; LeMaster, David M., E-mail: david.lemaster@health.ny.gov [University at Albany - SUNY, Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health (United States)

    2016-11-15

    Both {sup 15}N chemical shift anisotropy (CSA) and sufficiently rapid exchange linebroadening transitions exhibit relaxation contributions that are proportional to the square of the magnetic field. Deconvoluting these contributions is further complicated by residue-dependent variations in protein amide {sup 15}N CSA values which have proven difficult to accurately measure. Exploiting recently reported improvements for the implementation of T{sub 1} and T{sub 1ρ} experiments, field strength-dependent studies have been carried out on the B3 domain of protein G (GB3) as well as on the immunophilin FKBP12 and a H87V variant of that protein in which the major conformational exchange linebroadening transition is suppressed. By applying a zero frequency spectral density rescaling analysis to the relaxation data collected at magnetic fields from 500 to 900 MHz {sup 1}H, differential residue-specific {sup 15}N CSA values have been obtained for GB3 which correlate with those derived from solid state and liquid crystalline NMR measurements to a level similar to the correlation among those previously reported studies. Application of this analysis protocol to FKBP12 demonstrated an efficient quantitation of both weak exchange linebroadening contributions and differential residue-specific {sup 15}N CSA values. Experimental access to such differential residue-specific {sup 15}N CSA values should significantly facilitate more accurate comparisons with molecular dynamics simulations of protein motion that occurs within the timeframe of global molecular tumbling.

  16. Stress relaxation in viscous soft spheres.

    Science.gov (United States)

    Boschan, Julia; Vasudevan, Siddarth A; Boukany, Pouyan E; Somfai, Ellák; Tighe, Brian P

    2017-10-04

    We report the results of molecular dynamics simulations of stress relaxation tests in athermal viscous soft sphere packings close to their unjamming transition. By systematically and simultaneously varying both the amplitude of the applied strain step and the pressure of the initial condition, we access both linear and nonlinear response regimes and control the distance to jamming. Stress relaxation in viscoelastic solids is characterized by a relaxation time τ* that separates short time scales, where viscous loss is substantial, from long time scales, where elastic storage dominates and the response is essentially quasistatic. We identify two distinct plateaus in the strain dependence of the relaxation time, one each in the linear and nonlinear regimes. The height of both plateaus scales as an inverse power law with the distance to jamming. By probing the time evolution of particle velocities during relaxation, we further identify a correlation between mechanical relaxation in the bulk and the degree of non-affinity in the particle velocities on the micro scale.

  17. Adiabatic fast passage application in solid state NMR study of cross relaxation and molecular dynamics in heteronuclear systems.

    Science.gov (United States)

    Baranowski, M; Woźniak-Braszak, A; Jurga, K

    2016-01-01

    The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2MHz and 28.411MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins (1)H are polarized in the magnetic field B0 while fluorine spins (19)F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Density dependence of relaxation dynamics in glass formers, and ...

    Indian Academy of Sciences (India)

    Anshul D S Parmar

    formers, we study the variation of relaxation dynamics with density, rather than temperature, as a control ... stronger behaviour, the use of scaled variables involving temperature and ... of the temperature dependence of B as written defines.

  19. AC relaxation in the iron(8) molecular magnet

    Science.gov (United States)

    Rose, Geordie

    2000-11-01

    We investigate the low energy magnetic relaxation characteristics of the ``iron eight'' (Fe8) molecular magnet. Each molecule in this material contains a cluster of eight Fe 3+ ions surrounded by organic ligands. The molecules arrange themselves into a regular lattice with triclinic symmetry. At sufficiently low energies, the electronic spins of the Fe3+ ions lock together into a ``quantum rotator'' with spin S = 10. We derive a low energy effective Hamiltonian for this system, valid for temperatures less than Tc ~ 360 mK , where Tc is the temperature at which the Fe8 system crosses over into a ``quantum regime'' where relaxation characteristics become temperature independent. We show that in this regime the dominant environmental coupling is to the environmental spin bath in the molecule. We show how to explicitly calculate these couplings, given crystallographic information about the molecule, and do this for Fe8. We use this information to calculate the linewidth, topological decoherence and orthogonality blocking parameters. All of these quantities are shown to exhibit an isotope effect. We demonstrate that orthogonality blocking in Fe8 is significant and suppresses coherent tunneling. We then use our low energy effective Hamiltonian to calculate the single-molecule relaxation rate in the presence of an external magnetic field with both AC and DC components by solving the Landau-Zener problem in the presence of a nuclear spin bath. Both sawtooth and sinusoidal AC fields are analyzed. This single-molecule relaxation rate is then used as input into a master equation in order to take into account the many-molecule nature of the full system. Our results are then compared to quantum regime relaxation experiments performed on the Fe8 system.

  20. Stability and suppression of turbulence in relaxing molecular gas flows

    CERN Document Server

    Grigoryev, Yurii N

    2017-01-01

    This book presents an in-depth systematic investigation of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The work describes the theoretical foundations of a new way to control stability and laminar turbulent transitions in aerodynamic flows. It develops hydrodynamic models for describing thermal nonequilibrium gas flows which allow the consideration of suppression of inviscid acoustic waves in 2D shear flows. Then, nonlinear evolution of large-scale vortices and Kelvin-Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both linear and nonlinear classical energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of the book is to show the new dissipative effect, which can be used for flo...

  1. Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Paavilainen, S.; Rog, T.; Vattulainen, I.

    2011-01-01

    We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

  2. Vibrational relaxation of a triatomic molecular impurity: D2O in vitreous As2S3

    International Nuclear Information System (INIS)

    Rella, C.W.; Schwettman, H.A.; Engholm, J.R.

    1995-01-01

    Measurements of the relaxation of the D 2 O stretch mode in vitreous As 2 S 3 are presented. Because the bending mode of the molecule offers an intra-molecular decay channel for the stretch mode, the decay scheme of the D 2 O molecule is more complex than that of diatomic molecules. The asymmetric stretch mode of D 2 O has a frequency of 2680 cm -1 . To study the relaxation of this mode we applied a pump-probe technique, using intense psec; pulses of the Stanford Free Electron Laser. Due to the small cross-section of the vibrational mode, successful efforts were made to improve the signal to noise ratio by using a laser stabilization system and a tightly focused beam to increase the intensity, by averaging the signal with a kHz repetition rate and by using samples with an optimized D 2 O concentration. A rapid relaxation rate on the order of 5 x 10 9 sec -1 at low temperature is found that increases with temperature. Recalling that the bending mode of the D 2 O molecule has a frequency of 1170 cm -1 , one would expect a decay in a third order process, involving two quanta of the bending mode plus a vibrational host quanta with a frequency of 340 cm -1 , which coincides with a fundamental frequency of the pyramidal building blocks of the glassy As 2 S 3 host. Instead, we find from the temperature dependence of the relaxation rate that the D 2 O stretching mode relaxes in a higher order process. This indicates that the relaxation dynamics of small molecules is more complex than generally assumed

  3. Slow logarithmic relaxation in models with hierarchically constrained dynamics

    OpenAIRE

    Brey, J. J.; Prados, A.

    2000-01-01

    A general kind of models with hierarchically constrained dynamics is shown to exhibit logarithmic anomalous relaxation, similarly to a variety of complex strongly interacting materials. The logarithmic behavior describes most of the decay of the response function.

  4. Chirped-pulse manipulated carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs

    International Nuclear Information System (INIS)

    Lee, Chao-Kuei; Lin, Yuan-Yao; Lin, Sung-Hui; Lin, Gong-Ru; Pan, Ci-Ling

    2014-01-01

    Chirped pulse controlled carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs are investigated by degenerate pump-probe technique. Varying the chirped condition of excited pulse from negative to positive increases the carrier relaxation time so as to modify the dispersion and reshape current pulse in time domain. The spectral dependence of carrier dynamics is analytically derived and explained by Shockley-Read Hall model. This observation enables the new feasibility of controlling carrier dynamics in ultrafast optical devices via the chirped pulse excitations

  5. Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

    Science.gov (United States)

    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.

  6. Relaxation Dynamics of a Granular Pile on a Vertically Vibrating Plate

    Science.gov (United States)

    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.

  7. Vibrational and Rotational Energy Relaxation in Liquids

    DEFF Research Database (Denmark)

    Petersen, Jakob

    Vibrational and rotational energy relaxation in liquids are studied by means of computer simulations. As a precursor for studying vibrational energy relaxation of a solute molecule subsequent to the formation of a chemical bond, the validity of the classical Bersohn-Zewail model for describing......, the vibrational energy relaxation of I2 subsequent to photodissociation and recombination in CCl4 is studied using classical Molecular Dynamics simulations. The vibrational relaxation times and the time-dependent I-I pair distribution function are compared to new experimental results, and a qualitative agreement...... is found in both cases. Furthermore, the rotational energy relaxation of H2O in liquid water is studied via simulations and a power-and-work analysis. The mechanism of the energy transfer from the rotationally excited H2O molecule to its water neighbors is elucidated, i.e. the energy-accepting degrees...

  8. On the field-induced switching of molecular organization in a biaxial nematic cell and its relaxation

    Science.gov (United States)

    Ricci, Matteo; Berardi, Roberto; Zannoni, Claudio

    2015-08-01

    We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls.

  9. Three-stage classical molecular dynamics model for simulation of heavy-ion fusion

    Directory of Open Access Journals (Sweden)

    Godre Subodh S.

    2015-01-01

    Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.

  10. Effect of high pressure on the relaxation dynamics of glass-forming liquids

    Energy Technology Data Exchange (ETDEWEB)

    Paluch, M; Grzybowska, K; Grzybowski, A [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland)

    2007-05-23

    A glass is usually formed by cooling a liquid at a rate sufficient to avoid crystallization. In the vicinity of the glass transition the structural relaxation time increases with lowering temperature in a non-Arrhenius fashion and the structural relaxation function reveals a non-Debye behaviour. However, liquid can be also vitrified by keeping it at a constant temperature and increasing the pressure. This pressure-induced transition to the glassy state is also accompanied by dramatic changes in the relaxation dynamics. Herein we discuss the behaviour of the structural relaxation times of glass-forming liquids and polymer melts under high pressure.

  11. Effect of high pressure on the relaxation dynamics of glass-forming liquids

    International Nuclear Information System (INIS)

    Paluch, M; Grzybowska, K; Grzybowski, A

    2007-01-01

    A glass is usually formed by cooling a liquid at a rate sufficient to avoid crystallization. In the vicinity of the glass transition the structural relaxation time increases with lowering temperature in a non-Arrhenius fashion and the structural relaxation function reveals a non-Debye behaviour. However, liquid can be also vitrified by keeping it at a constant temperature and increasing the pressure. This pressure-induced transition to the glassy state is also accompanied by dramatic changes in the relaxation dynamics. Herein we discuss the behaviour of the structural relaxation times of glass-forming liquids and polymer melts under high pressure

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

    International Nuclear Information System (INIS)

    Bieri, Michael; D’Auvergne, Edward J.; Gooley, Paul R.

    2011-01-01

    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.

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

    Science.gov (United States)

    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.

  14. Non-equilibrium relaxation and near-arrest dynamics in colloidal suspensions

    International Nuclear Information System (INIS)

    Medina-Noyola, M; RamIrez-Gonzalez, Pedro

    2009-01-01

    In this work we propose a theory to describe the irreversible diffusive relaxation of the local concentration of a colloidal dispersion that proceeds toward its stable thermodynamic equilibrium state, but which may in the process be trapped in metastable or dynamically arrested states. The central assumption of this theory is that the irreversible relaxation of the macroscopically observed mean value n-bar(r,t) of the local concentration of colloidal particles is described by a diffusion equation involving a local mobility b*(r,t) that depends not only on the mean value n-bar(r,t) but also on the covariance σ(r,r';t)≡δn(r,t)δn(r',t)-bar of the fluctuations δn(r,t)≡n(r,t)-n-bar(r,t). This diffusion equation must hence be solved simultaneously with the relaxation equation for the covariance σ(r,r';t), and here we also derive the corresponding relaxation equation. The dependence of the local mobility b*(r,t) on the mean value and the covariance is determined by a self-consistent set of equations involving now the spatially and temporally non-local time-dependent correlation functions, which in a uniform system in equilibrium reduces to the self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics. The resulting general theory considers the possibility that these relaxation processes occur under the influence of external fields, such as gravitational forces acting in the process of sedimentation. In this paper, however, we describe a simpler application, in which the system remains spatially uniform during the irreversible relaxation process, and discuss the general features of the glass transition scenario predicted by this non-equilibrium theory.

  15. Mechanical Spectroscopy: Some Applications On Structural Changes And Relaxation Dynamics In Soft Matter

    Directory of Open Access Journals (Sweden)

    Wu Xuebang

    2015-09-01

    Full Text Available The general trend in soft matter is to study systems of increasing complexity covering a wide range in time and frequency. Mechanical spectroscopy is a powerful tool for understanding the structure and relaxation dynamics of these materials over a large temperature range and frequency scale. In this work, we collect a few recent applications using low-frequency mechanical spectroscopy for elucidating the structural changes and relaxation dynamics in soft matter, largely based on the author’s group. We illustrate the potential of mechanical spectroscopy with three kinds of soft materials: colloids, polymers and granular systems. Examples include structural changes in colloids, segmental relaxations in amorphous polymers, and resonant dissipation of grain chains in three-dimensional media. The present work shows that mechanical spectroscopy has been applied as a necessary and complementary tool to study the dynamics of such complex systems.

  16. String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

    Science.gov (United States)

    Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

    2018-03-01

    Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.

  17. Anomalous relaxation in binary mixtures: a dynamic facilitation picture

    International Nuclear Information System (INIS)

    Moreno, A J; Colmenero, J

    2007-01-01

    Recent computational investigations of polymeric and non-polymeric binary mixtures have reported anomalous relaxation features when both components exhibit very different mobilities. Anomalous relaxation is characterized by sublinear power-law behaviour for mean-squared displacements, logarithmic decay in dynamic correlators, and a striking concave-to-convex crossover in the latter by tuning the relevant control parameter, in analogy with predictions of the mode-coupling theory for state points close to higher-order transitions. We present Monte Carlo simulations on a coarse-grained model for relaxation in binary mixtures. The liquid structure is substituted by a three-dimensional array of cells. A spin variable is assigned to each cell, representing unexcited and excited local states of a mobility field. Changes in local mobility (spin flip) are permitted according to kinetic constraints determined by the mobilities of the neighbouring cells. We introduce two types of cell ('fast' and 'slow') with very different rates for spin flip. This coarse-grained model qualitatively reproduces the mentioned anomalous relaxation features observed for real binary mixtures

  18. Relaxation dynamics of a quantum emitter resonantly coupled to a metal nanoparticle

    DEFF Research Database (Denmark)

    Nerkararyan, K. V.; Bozhevolnyi, S. I.

    2014-01-01

    consequence of this relaxation process is that the emission, being largely determined by the MNP, comes out with a substantial delay. A large number of system parameters in our analytical description opens new possibilities for controlling quantum emitter dynamics. (C) 2014 Optical Society of America......The presence of a metal nanoparticle (MNP) near a quantum dipole emitter, when a localized surface plasmon mode is excited via the resonant coupling with an excited quantum dipole, dramatically changes the relaxation dynamics: an exponential decay changes to step-like behavior. The main physical...

  19. Investigation of impurity defects in α-iron by molecular dynamics method

    International Nuclear Information System (INIS)

    Kevorkyan, Yu.R.

    1986-01-01

    Investigation of the configuration of impurity defects in α-iron by the molecular dynamics method is presented. The Jhonson model potential has been used to calculate the interaction of matrix atoms. The impurity-matrix atom interaction is described by the same form of the potential shifted along the axis of interatomic distances for a definite value. The correspondence between the shift value and change in the radius of the impurity defect is established on the basis of calculation of the relaxation volume. Possible configurations of the impurity - interstitial matrix atom complexes are obtained for the given model of the impurity defect, dimensional boundaries of possible transitions between different configurations are determined. Formation and bound energies, relaxation volumes of impurity defects are calculated

  20. Dynamical renormalization group approach to relaxation in quantum field theory

    International Nuclear Information System (INIS)

    Boyanovsky, D.; Vega, H.J. de

    2003-01-01

    The real time evolution and relaxation of expectation values of quantum fields and of quantum states are computed as initial value problems by implementing the dynamical renormalization group (DRG). Linear response is invoked to set up the renormalized initial value problem to study the dynamics of the expectation value of quantum fields. The perturbative solution of the equations of motion for the field expectation values of quantum fields as well as the evolution of quantum states features secular terms, namely terms that grow in time and invalidate the perturbative expansion for late times. The DRG provides a consistent framework to resum these secular terms and yields a uniform asymptotic expansion at long times. Several relevant cases are studied in detail, including those of threshold infrared divergences which appear in gauge theories at finite temperature and lead to anomalous relaxation. In these cases the DRG is shown to provide a resummation akin to Bloch-Nordsieck but directly in real time and that goes beyond the scope of Bloch-Nordsieck and Dyson resummations. The nature of the resummation program is discussed in several examples. The DRG provides a framework that is consistent, systematic, and easy to implement to study the non-equilibrium relaxational dynamics directly in real time that does not rely on the concept of quasiparticle widths

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    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.

  3. Effect of holographic grating period on its relaxation in a molecular glassy film

    International Nuclear Information System (INIS)

    Ozols, A; Augustovs, P; Kokars, V; Traskovskis, K; Saharov, D

    2013-01-01

    Holographic grating (HG) relaxation has been experimentally studied in 5,5,5-triphenylpentyl 4-((4-(bis(5,5,5-triphenylpentyl)amino) phenyl) diazenyl) benzoate molecular glassy film for HG periods (Λ) of 0.50, 2.0 and 8.6 μm. A strong effect of HG period on its relaxation is found manifesting itself differently in the volume and on the surface. The volume part of HG is fairly stable during 40 days if Λ > 0.50μm whereas the surface part of HG (most probably, surface relief grating) exhibits relaxational self-enhancement which is maximal at Λ = 8.6μm. It is proposed that thermostimulated directional mass transfer in the process of relaxation can be responsible for this relaxational self-enhancement. Weak HG recording and relatively fast HG decay takes place at Λ=0.50 μm. Therefore, effective chromophore photoorientation domain of about 0.2 μm is supposed

  4. Dynamic relaxation method in analysis of reinforced concrete bent elements

    Directory of Open Access Journals (Sweden)

    Anna Szcześniak

    2015-12-01

    Full Text Available The paper presents a method for the analysis of nonlinear behaviour of reinforced concrete bent elements subjected to short-term static load. The considerations in the range of modelling of deformation processes of reinforced concrete element were carried out. The method of structure effort analysis was developed using the finite difference method. The Dynamic Relaxation Method, which — after introduction of critical damping — allows for description of the static behaviour of a structural element, was used to solve the system of nonlinear equilibrium equations. In order to increase the method effectiveness in the range of the post-critical analysis, the Arc Length Parameter on the equilibrium path was introduced into the computational procedure.[b]Keywords[/b]: reinforced concrete elements, physical nonlinearity, geometrical nonlinearity, dynamic relaxation method, arc-length method

  5. Relaxation and transport properties of liquid n-triacontane

    International Nuclear Information System (INIS)

    Kondratyuk, N D; Lankin, A V; Norman, G E; Stegailov, V V

    2015-01-01

    Molecular modelling is used to calculate transport properties and to study relaxation of liquid n-triacontane (C 30 H 62 ). The problem is important in connection with the behavior of liquid isolators in a pre-breakdown state. Two all-atom models and a united-atom model are used. Shear viscosity is calculated using the Green-Kubo formula. The force fields are compared with each other using the following criteria: the required time for one molecular dynamics step, the compliance of the main physical and transport properties with experimental values. The problem of the system equilibration is considered. The united-atom potential is used to model the n-triacontane liquid with an initial directional orientation. The time of relaxation to the disordered state, when all molecules orientations are randomized, are obtained. The influence of the molecules orientations on the shear viscosity value and the shear viscosity relaxation are treated. (paper)

  6. Comparison of single-ion molecular dynamics in common solvents

    Science.gov (United States)

    Muralidharan, A.; Pratt, L. R.; Chaudhari, M. I.; Rempe, S. B.

    2018-06-01

    Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γ (t ), observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γ (t ). But the corresponding analysis of the solventberg Li+(H2O)4 does conform to the standard picture set by all the PF6- results.

  7. Spin dynamics at level crossing in molecular AF rings probed by NMR

    International Nuclear Information System (INIS)

    Lascialfari, A.; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J.

    2004-01-01

    The low-temperature spin dynamics in molecular rings with a finite number (N≤10) of magnetic ions was studied by means of 1 H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T 1 (B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8

  8. Multidimensional dynamic piezoresponse measurements. Unraveling local relaxation behavior in relaxor-ferroelectrics via big data

    International Nuclear Information System (INIS)

    Vasudevan, Rama K.; Zhang, Shujun; Okatan, Mahmut Baris; Jesse, Stephen; Kalinin, Sergei V.; Bassiri-Gharb, Nazanin

    2015-01-01

    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 1/3 Nb 2/3 )O 3-x PbTiO 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 a 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

  9. Complex dynamics of memristive circuits: Analytical results and universal slow relaxation

    Science.gov (United States)

    Caravelli, F.; Traversa, F. L.; Di Ventra, M.

    2017-02-01

    Networks with memristive elements (resistors with memory) are being explored for a variety of applications ranging from unconventional computing to models of the brain. However, analytical results that highlight the role of the graph connectivity on the memory dynamics are still few, thus limiting our understanding of these important dynamical systems. In this paper, we derive an exact matrix equation of motion that takes into account all the network constraints of a purely memristive circuit, and we employ it to derive analytical results regarding its relaxation properties. We are able to describe the memory evolution in terms of orthogonal projection operators onto the subspace of fundamental loop space of the underlying circuit. This orthogonal projection explicitly reveals the coupling between the spatial and temporal sectors of the memristive circuits and compactly describes the circuit topology. For the case of disordered graphs, we are able to explain the emergence of a power-law relaxation as a superposition of exponential relaxation times with a broad range of scales using random matrices. This power law is also universal, namely independent of the topology of the underlying graph but dependent only on the density of loops. In the case of circuits subject to alternating voltage instead, we are able to obtain an approximate solution of the dynamics, which is tested against a specific network topology. These results suggest a much richer dynamics of memristive networks than previously considered.

  10. Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

    International Nuclear Information System (INIS)

    Wang, J.; Gutierre, M.S.

    2010-01-01

    This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

  11. Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model.

    Science.gov (United States)

    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.

  12. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  13. Relaxation processes and glass transition of confined polymer melts: A molecular dynamics simulation of 1,4-polybutadiene between graphite walls.

    Science.gov (United States)

    Solar, M; Binder, K; Paul, W

    2017-05-28

    Molecular dynamics simulations of a chemically realistic model for 1,4-polybutadiene in a thin film geometry confined by two graphite walls are presented. Previous work on melts in the bulk has shown that the model faithfully reproduces static and dynamic properties of the real material over a wide temperature range. The present work studies how these properties change due to nano-confinement. The focus is on orientational correlations observable in nuclear magnetic resonance experiments and on the local intermediate incoherent neutron scattering function, F s (q z , z, t), for distances z from the graphite walls in the range of a few nanometers. Temperatures from about 2T g down to about 1.15T g , where T g is the glass transition temperature in the bulk, are studied. It is shown that weakly attractive forces between the wall atoms and the monomers suffice to effectively bind a polymer coil that is near the wall. For a wide regime of temperatures, the Arrhenius-like adsorption/desorption kinetics of the monomers is the slowest process, while very close to T g the Vogel-Fulcher-Tammann-like α-relaxation takes over. The α-process is modified only for z≤1.2 nm due to the density changes near the walls, less than expected from studies of coarse-grained (bead-spring-type) models. The weakness of the surface effects on the glass transition in this case is attributed to the interplay of density changes near the wall with the torsional potential. A brief discussion of pertinent experiments is given.

  14. Modeling shockwave deformation via molecular dynamics

    International Nuclear Information System (INIS)

    Holian, B.L.

    1987-01-01

    Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too

  15. Substrate binding and catalytic mechanism in phospholipase C from Bacillus cereus. a molecular mechanics and molecular dynamics study

    DEFF Research Database (Denmark)

    da Graça Thrige, D; Buur, J R; Jørgensen, Flemming Steen

    1997-01-01

    cereus including a docked substrate molecule was subjected to a stepwise molecular mechanics energy minimization. Second, the location of the nucleophilic water molecule in the active site of the fully relaxed enzyme-substrate complex was determined by evaluation of nonbonded interaction energies between...... water molecule was verified during a 100 ps molecular dynamics simulation. During the simulation the substrate undergoes a conformational change, but retains its localization in the active site. The contacts between the enzyme, the substrate, and the nucleophilic water molecule display some fluctuations...... the strong electrostatic interactions in the active site realistically during energy minimization, delocalization of the charges from the three zinc ions was considered. Therefore, quantum mechanics calculations on the zinc ions and the zinc-coordinating residues were carried out prior to the molecular...

  16. Dynamical relaxation of the CP phases in next-to-minimal supersymmetry

    International Nuclear Information System (INIS)

    Demir, D.A.

    1999-11-01

    After promoting the phases of the soft masses to dynamical fields corresponding to Goldstone bosons of spontaneously broken global symmetries in the supersymmetry breaking sector, the next-to-minimal supersymmetric model is found to solve the μ problem and the strong CP problem simultaneously with an invisible axion. The domain wall problem persists in the form of axionic domain formation. Relaxation dynamics of the physical CP-violating phases is determined only by the short-distance physics and their relaxation values are not necessarily close to the CP-conserving points. Consequently, the solution of tile supersymmetric CP problem may require heavy enough superpartners and nonminimal flavor structures, where the latter may be also relevant for avoiding the formation of axionic domain walls. (author)

  17. A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides

    NARCIS (Netherlands)

    Feenstra, K Anton; Peter, Christine; Scheek, Ruud M; van Gunsteren, Wilfred F; Mark, Alan E

    Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The

  18. Electron-nuclear corellations for photoinduced dynamics in molecular dimers

    Science.gov (United States)

    Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

    2003-03-01

    Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

  19. On the Use of Molecular Weight Cutoff Cassettes to Measure Dynamic Relaxivity of Novel Gadolinium Contrast Agents: Example Using Hyaluronic Acid Polymer Complexes in Phosphate-Buffered Saline

    Directory of Open Access Journals (Sweden)

    Nima Kasraie

    2011-01-01

    Full Text Available The aims of this study were to determine whether standard extracellular contrast agents of Gd(III ions in combination with a polymeric entity susceptible to hydrolytic degradation over a finite period of time, such as Hyaluronic Acid (HA, have sufficient vascular residence time to obtain comparable vascular imaging to current conventional compounds and to obtain sufficient data to show proof of concept that HA with Gd-DTPA ligands could be useful as vascular imaging agents. We assessed the dynamic relaxivity of the HA bound DTPA compounds using a custom-made phantom, as well as relaxation rates at 10.72 MHz with concentrations ranging between 0.09 and 7.96 mM in phosphate-buffered saline. Linear dependences of static longitudinal relaxation rate (R1 on concentration were found for most measured samples, and the HA samples continued to produce high signal strength after 24 hours after injection into a dialysis cassette at 3T, showing superior dynamic relaxivity values compared to conventional contrast media such as Gd-DTPA-BMA.

  20. On the relation between quasi-static and dynamic stress induced reversible structural relaxation of amorphous alloys

    International Nuclear Information System (INIS)

    Krueger, P.; Stucky, T.; Boewe, M.; Neuhaeuser, H.

    1993-01-01

    Quasi-static stress relaxation and dynamic internal friction measurements of stress induced reversible structural relaxation were performed on the amorphous alloy Fe 40 Ni 40 B 20 . The kinetics can be well described by a stretched exponential Kohlrausch-Williams-Watts quasi-static relaxation. The thermally activated part of the internal friction shows an Arrhenius temperature behaviour for a fixed vibration frequency and an inverse power frequency behaviour for a fixed temperature. The activation energies calculated from the Arrhenius equation and from the frequency shift method are significantly different. In order to explain this discrepancy the relation between the quasi-static and the dynamic descriptions of the reversible relaxation is reexamined. In particular it is shown that these two activation energies are connected by the Kohlrausch exponent of the quasi-static relaxation. (orig.)

  1. Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions

    Directory of Open Access Journals (Sweden)

    Morker Mitul R.

    2015-01-01

    Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.

  2. Spin dynamics at level crossing in molecular AF rings probed by NMR

    Energy Technology Data Exchange (ETDEWEB)

    Lascialfari, A. E-mail: lascialfari@fisicavolta.unipv.it; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J

    2004-05-01

    The low-temperature spin dynamics in molecular rings with a finite number (N{<=}10) of magnetic ions was studied by means of {sup 1}H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T{sub 1}(B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8.

  3. Inhomogeneous Relaxation of a Molecular Layer on an Insulator due to Compressive Stress

    Science.gov (United States)

    Bocquet, F.; Nony, L.; Mannsfeld, S. C. B.; Oison, V.; Pawlak, R.; Porte, L.; Loppacher, Ch.

    2012-05-01

    We discuss the inhomogeneous stress relaxation of a monolayer of hexahydroxytriphenylene (HHTP) which adopts the rare line-on-line (LOL) coincidence on KCl(001) and forms moiré patterns. The fact that the hexagonal HHTP layer is uniaxially compressed along the LOL makes this system an ideal candidate to discuss the influence of inhomogeneous stress relaxation. Our work is a combination of noncontact atomic force microscopy experiments, density functional theory and potential energy calculations, and a thorough interpretation by means of the Frenkel-Kontorova model. We show that the assumption of a homogeneous molecular layer is not valid for this organic-inorganic heteroepitaxial system since the best calculated energy configuration correlates with the experimental data only if inhomogeneous relaxations of the layer are taken into account.

  4. Comparative classical and 'ab initio' molecular dynamics study of molten and glassy germanium dioxide

    International Nuclear Information System (INIS)

    Hawlitzky, M; Horbach, J; Binder, K; Ispas, S; Krack, M

    2008-01-01

    A molecular dynamics (MD) study of the static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modeled by the classical pair potential proposed by Oeffner and Elliott (OE) (1998 Phys. Rev. B 58 14791). We compare our results to experiments and previous simulations. In addition, an 'ab initio' method, the so-called Car-Parrinello molecular dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO 2 , the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO 2 , for high temperatures the dynamics of molten GeO 2 is compatible with a description in terms of mode coupling theory

  5. Molecular theory of mass transfer kinetics and dynamics at gas-water interface

    International Nuclear Information System (INIS)

    Morita, Akihiro; Garrett, Bruce C

    2008-01-01

    The mass transfer mechanism across gas-water interface is studied with molecular dynamics (MD) simulation. The MD results provide a robust and qualitatively consistent picture to previous studies about microscopic aspects of mass transfer, including interface structure, free energy profiles for the uptake, scattering dynamics and energy relaxation of impinging molecules. These MD results are quantitatively compared with experimental uptake measurements, and we find that the apparent inconsistency between MD and experiment could be partly resolved by precise decomposition of the observed kinetics into elemental steps. Remaining issues and future perspectives toward constructing a comprehensive multi-scale description of interfacial mass transfer are summarized.

  6. Investigation of the spectroscopy and relaxation dynamics of benzaldehyde using molecular orbital calculations and laser ionization time-of-flight mass spectroscopy

    Science.gov (United States)

    da Silva, Maria Cristina Rodrigues

    1998-11-01

    Molecular orbital methods and laser ionization mass spectrometry measurements are used to investigate the spectroscopy and relaxation dynamics of benzaldehyde following excitation to its S2(/pi/pi/sp/*) state. Energies, equilibrium geometries and vibrational frequencies of ground and low-lying excited states of benzaldehyde neutral and cation determined by ab initio calculations provide a theoretical description of the electronic spectroscopy of benzaldehyde and of the changes occurring on excitation and ionization. The S2(/pi/pi/sp/*)[/gets]S0 excitation spectrum of jet-cooled benzaldehyde acquired using two-color laser ionization mass spectrometry techniques is interpreted with the aid of these calculations. The spectrum is dominated by the origin band and by transitions involving some of the ring modes consistent with the results of the molecular orbital calculations that indicate that the major geometric changes on excitation to S2 are located in the aromatic ring. Ten fundamental vibrations of the S2(/pi/pi/sp/*) state are assigned. The dissociation dynamics of benzaldehyde into benzene and carbon monoxide following excitation to its S2(/pi/pi/sp/*) state are investigated under jet- cooled conditions by two-color laser ionization mass spectrometry using a pump-probe technique. This experimental arrangement allows monitoring the benzaldehyde reactant and the benzene product ion signals as a function of the time delay between the excitation and ionization steps. A kinetic model is proposed to explain the observed biexponential decay of the benzaldehyde signal and the single exponential growth of the benzene product signal in terms of a sequential decay of two excited states of benzaldehyde, one of which leads to formation of benzene molecules in its lowest triplet state. Reactant disappearance and product appearance rates are determined for a number of vibronic transitions of the S2 state. They are found to increase with excitation energy without any indication

  7. Solution conformation and dynamics of a tetrasaccharide related to the LewisX antigen deduced by NMR relaxation measurements

    International Nuclear Information System (INIS)

    Poveda, Ana; Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus

    1997-01-01

    1 H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-α-N-acetyl-galactosaminyl-β-galactopyranosyl-(1 → 4)[3-O-α-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, 13 C-NMR relaxation data have also been recorded at both fields. The 1 H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The 13 C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the 1 H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS 2 . Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data

  8. Flux ropes and 3D dynamics in the relaxation scaling experiment

    International Nuclear Information System (INIS)

    Intrator, T P; Feng, Y; Weber, T E; Swan, H O; Sun, X; Dorf, L; Sears, J A

    2013-01-01

    Flux ropes form basic building blocks for magnetic dynamics in many plasmas, are macroscopic analogues of magnetic field lines, and are irreducibly three dimensional (3D). We have used the relaxation scaling experiment (RSX) to study flux ropes, and have found many new features involving 3D dynamics, kink instability driven reconnection, nonlinearly stable but kinking flux ropes, and large flows. (paper)

  9. Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations.

    Science.gov (United States)

    Solomentsev, Gleb; Diehl, Carl; Akke, Mikael

    2018-03-06

    FKBP12 (FK506 binding protein 12 kDa) is an important drug target. Nuclear magnetic resonance (NMR) order parameters, describing amplitudes of motion on the pico- to nanosecond time scale, can provide estimates of changes in conformational entropy upon ligand binding. Here we report backbone and methyl-axis order parameters of the apo and FK506-bound forms of FKBP12, based on 15 N and 2 H NMR relaxation. Binding of FK506 to FKBP12 results in localized changes in order parameters, notably for the backbone of residues E54 and I56 and the side chains of I56, I90, and I91, all positioned in the binding site. The order parameters increase slightly upon FK506 binding, indicating an unfavorable entropic contribution to binding of TΔ S = -18 ± 2 kJ/mol at 293 K. Molecular dynamics simulations indicate a change in conformational entropy, associated with all dihedral angles, of TΔ S = -26 ± 9 kJ/mol. Both these values are significant compared to the total entropy of binding determined by isothermal titration calorimetry and referenced to a reactant concentration of 1 mM ( TΔ S = -29 ± 1 kJ/mol). Our results reveal subtle differences in the response to ligand binding compared to that of the previously studied rapamycin-FKBP12 complex, despite the high degree of structural homology between the two complexes and their nearly identical ligand-FKBP12 interactions. These results highlight the delicate dependence of protein dynamics on drug interactions, which goes beyond the view provided by static structures, and reinforce the notion that protein conformational entropy can make important contributions to the free energy of ligand binding.

  10. Relaxation of the magnetization in magnetic molecules

    Science.gov (United States)

    Carretta, S.; Bianchi, A.; Liviotti, E.; Santini, P.; Amoretti, G.

    2006-04-01

    Several mechanisms characterize the relaxation dynamics in magnetic molecules. We investigate two of them, spin-lattice coupling and incoherent quantum tunneling. The effect of the phonon heat bath is studied by analyzing the exponential time decay of the autocorrelation of the magnetization. We show that in ferromagnetic (Cu6) and antiferromagnetic (Fe6) molecular rings this decay is characterized by a single characteristic time. At very low temperature, relaxation through incoherent quantum tunneling may occur in nanomagnets such as Fe8 or Ni4. The mixing between levels with different values of the total spin (S mixing) greatly influences this mechanism. In particular, we demonstrate that a fourth-order anisotropy term O44, required to interpret experimental electron paramagnetic resonance and relaxation data in Ni4, naturally arises when S mixing is considered in calculations.

  11. Dielectric and mechanical relaxation in isooctylcyanobiphenyl (8*OCB)

    Energy Technology Data Exchange (ETDEWEB)

    Pawlus, S; Mierzwa, M; Paluch, M; Rzoska, S J [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Roland, C M, E-mail: michal.mierzwa@us.edu.p [Chemistry Division, Naval Research Laboratory, Code 6120, Washington, DC 20375-5342 (United States)

    2010-06-16

    The dynamics of isooctylcyanobiphenyl (8*OCB) was characterized using dielectric and mechanical spectroscopies. This isomer of the liquid crystalline octylcyanobiphenyl (8OCB) vitrifies during cooling or on application of pressure, exhibiting the typical features of glass-forming liquids: non-Debye relaxation function, non-Arrhenius temperature dependence of the relaxation times, {tau}{sub {alpha}}, a dynamic crossover at T {approx} 1.6T{sub g}. This crossover is evidenced by changes in the behavior of both the peak shape and the temperature dependence of {tau}{sub {alpha}}. The primary relaxation time at the crossover, 2 ns at ambient pressure, is the smallest value reported to date for any molecular liquid or polymer. Interestingly, at all temperatures below this crossover, {tau}{sub {alpha}}and the dc conductivity remain coupled (i.e., conform to the Debye-Stokes-Einstein relation). Two secondary relaxations are observed in the glassy state, one of which is identified as the Johari-Goldstein process. Unlike the case for 8OCB, no liquid crystalline phase could be attained for 8*OCB, demonstrating that relatively small differences in chemical structure can effect substantial changes in the intermolecular potential.

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

    Science.gov (United States)

    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.

  13. Numerical modeling of bubble dynamics in viscoelastic media with relaxation

    Science.gov (United States)

    Warnez, M. T.; Johnsen, E.

    2015-06-01

    Cavitation occurs in a variety of non-Newtonian fluids and viscoelastic materials. The large-amplitude volumetric oscillations of cavitation bubbles give rise to high temperatures and pressures at collapse, as well as induce large and rapid deformation of the surroundings. In this work, we develop a comprehensive numerical framework for spherical bubble dynamics in isotropic media obeying a wide range of viscoelastic constitutive relationships. Our numerical approach solves the compressible Keller-Miksis equation with full thermal effects (inside and outside the bubble) when coupled to a highly generalized constitutive relationship (which allows Newtonian, Kelvin-Voigt, Zener, linear Maxwell, upper-convected Maxwell, Jeffreys, Oldroyd-B, Giesekus, and Phan-Thien-Tanner models). For the latter two models, partial differential equations (PDEs) must be solved in the surrounding medium; for the remaining models, we show that the PDEs can be reduced to ordinary differential equations. To solve the general constitutive PDEs, we present a Chebyshev spectral collocation method, which is robust even for violent collapse. Combining this numerical approach with theoretical analysis, we simulate bubble dynamics in various viscoelastic media to determine the impact of relaxation time, a constitutive parameter, on the associated physics. Relaxation time is found to increase bubble growth and permit rebounds driven purely by residual stresses in the surroundings. Different regimes of oscillations occur depending on the relaxation time.

  14. Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: longitudinal relaxation dispersion for a dipole-coupled spin-1/2 pair.

    Science.gov (United States)

    Chang, Zhiwei; Halle, Bertil

    2013-10-14

    In complex biological or colloidal samples, magnetic relaxation dispersion (MRD) experiments using the field-cycling technique can characterize molecular motions on time scales ranging from nanoseconds to microseconds, provided that a rigorous theory of nuclear spin relaxation is available. In gels, cross-linked proteins, and biological tissues, where an immobilized macromolecular component coexists with a mobile solvent phase, nuclear spins residing in solvent (or cosolvent) species relax predominantly via exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings. The physical or chemical exchange processes that dominate the MRD typically occur on a time scale of microseconds or longer, where the conventional perturbation theory of spin relaxation breaks down. There is thus a need for a more general relaxation theory. Such a theory, based on the stochastic Liouville equation (SLE) for the EMOR mechanism, is available for a single quadrupolar spin I = 1. Here, we present the corresponding theory for a dipole-coupled spin-1/2 pair. To our knowledge, this is the first treatment of dipolar MRD outside the motional-narrowing regime. Based on an analytical solution of the spatial part of the SLE, we show how the integral longitudinal relaxation rate can be computed efficiently. Both like and unlike spins, with selective or non-selective excitation, are treated. For the experimentally important dilute regime, where only a small fraction of the spin pairs are immobilized, we obtain simple analytical expressions for the auto-relaxation and cross-relaxation rates which generalize the well-known Solomon equations. These generalized results will be useful in biophysical studies, e.g., of intermittent protein dynamics. In addition, they represent a first step towards a rigorous theory of water (1)H relaxation in biological tissues, which is a prerequisite for unravelling the molecular basis of soft

  15. Molecular dynamics calculations of defect energetics in β-SiC

    International Nuclear Information System (INIS)

    Huang, H.; El-Azab, A.; Ghoniem, N.

    1993-01-01

    The Molecular Dynamics (MD) method is used to calculate defect energetics in β-silicon carbide. Many-body interaction effects in this covalent material are accounted for by using a hybrid of two-body and three-body potentials. Calculated bulk properties of β-SiC based on this potential are in agreement with experimental data to within 17%. A micro-crystal is constructed to represent the computational cell and external forces are applied to the micro-crystal so that it behaves as a part of an infinite medium. The potential energy for the unperturbed computational cell is first calculated. The cell is then set at a defect configuration and relaxed, and the potential energy of the relaxed cell is calculated. The difference between the potential energy of the unperturbed cell and that of the defect-containing cell is used to calculate the formation and binding energies of point defects, defect clusters and helium-vacancy clusters in SiC

  16. A concurrent multiscale micromorphic molecular dynamics

    International Nuclear Information System (INIS)

    Li, Shaofan; Tong, Qi

    2015-01-01

    In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

  17. Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions

    International Nuclear Information System (INIS)

    Sonoda, Milton T; Dolores Elola, M; Skaf, Munir S

    2016-01-01

    The static dielectric permittivity and dielectric relaxation properties of fructose aqueous solutions of different concentrations ranging from 1.0 to 4.0 mol l −1 are investigated by means of molecular dynamics simulations. The contributions from intra- and interspecies molecular correlations were computed individually for both the static and frequency-dependent dielectric properties, and the results were compared with the available experimental data. Simulation results in the time- and frequency-domains were analyzed and indicate that the presence of fructose has little effect on the position of the fast, high-frequency (>500 cm −1 ) components of the dielectric response spectrum. The low-frequency (<0.1 cm −1 ) components, however, are markedly influenced by sugar concentration. Our analysis indicates that fructose–fructose and fructose–water interactions strongly affect the rotational-diffusion regime of molecular motions in the solutions. Increasing fructose concentration not only enhances sugar–sugar and sugar-water low frequency contributions to the dielectric loss spectrum but also slows down the reorientational dynamics of water molecules. These results are consistent with previous computer simulations carried out for other disaccharide aqueous solutions. (paper)

  18. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  19. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    International Nuclear Information System (INIS)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver

    2015-01-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom

  20. Molecular packing, hydrogen bonding, and fast dynamics in lysozyme/trehalose/glycerol and trehalose/glycerol glasses at low hydration

    OpenAIRE

    Lerbret, Adrien; Affouard, Frédéric

    2017-01-01

    Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\\sim$ \\AA ) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme...

  1. Relaxation oscillations and transport barrier dynamics in tokamak edge plasmas

    International Nuclear Information System (INIS)

    Benkadda, Sadruddin; Beyer, Peter; Fuhr-Chaudier, Guillaume; Garbet, Xavier; Ghendrih, Philippe; Sarazin, Yanick

    2004-01-01

    Oscillations of turbulent transport of particles and energy in magnetically confined plasmas can be easily observed in simulations of a variety of turbulence models. These oscillations typically involve a mechanism of energy exchange between fluctuations and a poloidal shear flow. This kind of ''predator-prey'' mechanism is found to be not relevant for transport barrier relaxations. In RBM simulations of resistive ballooning turbulence with transport barrier, relaxation oscillations of the latter are observed even in the case of frozen poloidal shear flow. These relaxations are due to a transitory growth of a mode localized at the barrier center. A one-dimensional model for the evolution of such a mode in the presence of a shear flow describes a transitory growth of an initial perturbation. Oscillations in the case of a finite steady-state shear flow are possible due to the coupling of the mode to the dynamics of the pressure profile. (author)

  2. Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

    International Nuclear Information System (INIS)

    Elkins, Madeline H.; Williams, Holly L.; Neumark, Daniel M.

    2015-01-01

    The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism

  3. Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

    Science.gov (United States)

    Elkins, Madeline H.; Williams, Holly L.; Neumark, Daniel M.

    2015-06-01

    The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism.

  4. Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, Madeline H.; Williams, Holly L. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Neumark, Daniel M. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-06-21

    The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism.

  5. Solution conformation and dynamics of a tetrasaccharide related to the Lewis{sup X} antigen deduced by NMR relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Poveda, Ana [Universidad Autonoma de Madrid, Servicio Interdepartamental de Investigacion (Spain); Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus [Instituto de Quimica Organica, CSIC, Grupo de Carbohidratos (Spain)

    1997-07-15

    {sup 1}H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-{alpha}-N-acetyl-galactosaminyl-{beta}-galactopyranosyl-(1{sup {yields}}4)[3-O-{alpha}-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, {sup 13}C-NMR relaxation data have also been recorded at both fields. The {sup 1}H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The{sup 13}C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the{sup 1}H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS{sup 2}. Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data.

  6. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    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.

  7. The classical and quantum dynamics of molecular spins on graphene

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

  8. Thermal parameter identification for non-Fourier heat transfer from molecular dynamics

    Science.gov (United States)

    Singh, Amit; Tadmor, Ellad B.

    2015-10-01

    Fourier's law leads to a diffusive model of heat transfer in which a thermal signal propagates infinitely fast and the only material parameter is the thermal conductivity. In micro- and nano-scale systems, non-Fourier effects involving coupled diffusion and wavelike propagation of heat can become important. An extension of Fourier's law to account for such effects leads to a Jeffreys-type model for heat transfer with two relaxation times. We propose a new Thermal Parameter Identification (TPI) method for obtaining the Jeffreys-type thermal parameters from molecular dynamics simulations. The TPI method makes use of a nonlinear regression-based approach for obtaining the coefficients in analytical expressions for cosine and sine-weighted averages of temperature and heat flux over the length of the system. The method is applied to argon nanobeams over a range of temperature and system sizes. The results for thermal conductivity are found to be in good agreement with standard Green-Kubo and direct method calculations. The TPI method is more efficient for systems with high diffusivity and has the advantage, that unlike the direct method, it is free from the influence of thermostats. In addition, the method provides the thermal relaxation times for argon. Using the determined parameters, the Jeffreys-type model is able to reproduce the molecular dynamics results for a short-duration heat pulse where wavelike propagation of heat is observed thereby confirming the existence of second sound in argon. An implementation of the TPI method in MATLAB is available as part of the online supplementary material.

  9. Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements.

    Science.gov (United States)

    Yasaka, Yoshiro; Klein, Michael L; Nakahara, Masaru; Matubayasi, Nobuyuki

    2012-02-21

    The rotational dynamics of benzene and water in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride are studied using molecular dynamics (MD) simulation and NMR T(1) measurements. MD trajectories based on an effective potential are used to calculate the (2)H NMR relaxation time, T(1) via Fourier transform of the relevant rotational time correlation function, C(2R)(t). To compensate for the lack of polarization in the standard fixed-charge modeling of the IL, an effective ionic charge, which is smaller than the elementary charge is employed. The simulation results are in closest agreement with NMR experiments with respect to the temperature and Larmor frequency dependencies of T(1) when an effective charge of ±0.5e is used for the anion and the cation, respectively. The computed C(2R)(t) of both solutes shows a bi-modal nature, comprised of an initial non-diffusive ps relaxation plus a long-time ns tail extending to the diffusive regime. Due to the latter component, the solute dynamics is not under the motional narrowing condition with respect to the prevalent Larmor frequency. It is shown that the diffusive tail of the C(2R)(t) is most important to understand frequency and temperature dependencies of T(1) in ILs. On the other hand, the effect of the initial ps relaxation is an increase of T(1) by a constant factor. This is equivalent to an "effective" reduction of the quadrupolar coupling constant (QCC). Thus, in the NMR T(1) analysis, the rotational time correlation function can be modeled analytically in the form of aexp (-t/τ) (Lipari-Szabo model), where the constant a, the Lipari-Szabo factor, contains the integrated contribution of the short-time relaxation and τ represents the relaxation time of the exponential (diffusive) tail. The Debye model is a special case of the Lipari-Szabo model with a = 1, and turns out to be inappropriate to represent benzene and water dynamics in ILs since a is as small as 0.1. The use of the Debye model would result in

  10. Dynamical X-ray scattering from the relaxed structures

    International Nuclear Information System (INIS)

    Benediktovitch, A.; Feranchuk, I.; Ulyanenkov, A.

    2009-01-01

    High-resolution X-ray diffraction is now widely used analytical tool for investigation of nano scale multilayered structures in semiconductor and optical technologies. The HRXRD method delivers unique information on the crystallographic lattice of the samples, concentration of solid solutions, lattice mismatches, layer thicknesses, defect distribution, and relaxation degree of the epitaxial layers. The evaluation of the experimental results, however, requires a robust and precise theory due to complex dynamical scattering of X-rays from near perfect crystallographic structure of the samples. Usually, the Takagi-Taupin approach [1] or the recurrent matrix methods [2] are used for the simulation of the X-ray diffraction profiles from the epitaxial multilayered structures. The use of these theories, however, becomes essentially difficult, when the lateral lattice mismatches are present in multilayers, for example, in the case of partially or fully relaxed epitaxially grown samples. In the present work, the general solution of this problem is found analytically. The angular divergence of the incident beam is also considered and the algorithm for the diffracted profile mapping in the reciprocal space is developed. The experimental reciprocal space mapping of typical AlGaN/GaN/AlN samples with partially relaxed layers is compared to the simulated maps, which describe well the location and character of the diffraction spots caused by different layers. (author)

  11. Full quantum treatment of charge dynamics in amorphous molecular semiconductors

    Science.gov (United States)

    de Vries, Xander; Friederich, Pascal; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.

    2018-02-01

    We present a treatment of charge dynamics in amorphous molecular semiconductors that accounts for the coupling of charges to all intramolecular phonon modes in a fully quantum mechanical way. Based on ab initio calculations, we derive charge transfer rates that improve on the widely used semiclassical Marcus rate and obtain benchmark results for the mobility and energetic relaxation of electrons and holes in three semiconductors commonly applied in organic light-emitting diodes. Surprisingly, we find very similar results when using the simple Miller-Abrahams rate. We conclude that extracting the disorder strength from temperature-dependent charge transport studies is very possible but extracting the reorganization energy is not.

  12. Dynamics of a model of two delay-coupled relaxation oscillators

    Science.gov (United States)

    Ruelas, R. E.; Rand, R. H.

    2010-08-01

    This paper investigates the dynamics of a new model of two coupled relaxation oscillators. The model replaces the usual DDE (differential-delay equation) formulation with a discrete-time approach with jumps. Existence, bifurcation and stability of in-phase periodic motions is studied. Simple periodic motions, which involve exactly two jumps per period, are found to have large plateaus in parameter space. These plateaus are separated by regions of complicated dynamics, reminiscent of the Devil's Staircase. Stability of motions in the in-phase manifold are contrasted with stability of motions in the full phase space.

  13. Impacts of Base-Case and Post-Contingency Constraint Relaxations on Static and Dynamic Operational Security

    Science.gov (United States)

    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

  14. Carrier relaxation dynamics in InAs/InGaAlAs quantum dashes

    KAUST Repository

    Ryasnyanskiy, A.I.; Biaggio, I.; Djie, Hery Susanto; Ooi, Boon S.; Tan, C.L.

    2011-01-01

    We characterize size-dependent carrier relaxation dynamics of partial laser structures containing quantum dashes by time-resolved degenerate four wave mixing between 1.2 and 1.6 ?m. © 2010 Elsevier B.V. All rights reserved.

  15. Carrier relaxation dynamics in InAs/InGaAlAs quantum dashes

    KAUST Repository

    Ryasnyanskiy, A.I.

    2011-03-01

    We characterize size-dependent carrier relaxation dynamics of partial laser structures containing quantum dashes by time-resolved degenerate four wave mixing between 1.2 and 1.6 ?m. © 2010 Elsevier B.V. All rights reserved.

  16. Quantum dynamics of nuclear spins and spin relaxation in organic semiconductors

    Science.gov (United States)

    Mkhitaryan, V. V.; Dobrovitski, V. V.

    2017-06-01

    We investigate the role of the nuclear-spin quantum dynamics in hyperfine-induced spin relaxation of hopping carriers in organic semiconductors. The fast-hopping regime, when the carrier spin does not rotate much between subsequent hops, is typical for organic semiconductors possessing long spin coherence times. We consider this regime and focus on a carrier random-walk diffusion in one dimension, where the effect of the nuclear-spin dynamics is expected to be the strongest. Exact numerical simulations of spin systems with up to 25 nuclear spins are performed using the Suzuki-Trotter decomposition of the evolution operator. Larger nuclear-spin systems are modeled utilizing the spin-coherent state P -representation approach developed earlier. We find that the nuclear-spin dynamics strongly influences the carrier spin relaxation at long times. If the random walk is restricted to a small area, it leads to the quenching of carrier spin polarization at a nonzero value at long times. If the random walk is unrestricted, the carrier spin polarization acquires a long-time tail, decaying as 1 /√{t } . Based on the numerical results, we devise a simple formula describing the effect quantitatively.

  17. F19 relaxation in non-magnetic hexafluorides

    International Nuclear Information System (INIS)

    Rigny, P.

    1969-01-01

    The interesting properties of the fluorine magnetic resonance in the hexafluorides of molybdenum, tungsten and uranium, are very much due to large anisotropies of the chemical shift tensors. In the solid phases these anisotropies, the values of which are deduced from line shape studies, allow one to show that the molecules undergo hindered rotations about the metal atom. The temperature and frequency dependence of the fluorine longitudinal relaxation times shows that the relaxation is due to the molecular motion. The dynamical parameters of this motion are then deduced from the complete study of the fluorine relaxation in the rotating frame. In the liquid phases, the existence of anisotropies allows an estimation of the different contributions to the relaxation. In particular, the frequency and temperature dependence of the relaxation shows it to be dominated by the spin-rotation interaction. We have shown that the strength of this interaction can be deduced from the chemical shifts, and the angle through which the molecule rotates quasi-freely can be determined. In the hexafluorides, this angle is roughly one radian at 70 C, and with the help of this value, the friction coefficients which describe the intermolecular interactions are discussed. (author) [fr

  18. The Influence of the Relaxation Time on the Dynamic Hysteresis in Perovskite Solar Cells

    Directory of Open Access Journals (Sweden)

    Palici Alexandra

    2018-01-01

    Full Text Available We investigate the dynamic behavior of perovskite solar cells by focusing on the relaxation time τ, which corresponds to the slow de-polarization process from an initial bias pre-poled state. The dynamic electrical model (DEM is employed for simulating the J-V characteristics for different bias scan rates and pre-poling conditions. Depending on the sign of the initial polarization normal or inverted hysteresis may be induced. For fixed pre-poling conditions, the relaxation time, in relation to the bias scan rate, governs the magnitude of the dynamic hysteresis. In the limit of large τ the hysteretic effects are vanishing for the typical range of bias scan rates considered, while for very small τ the hysteresis is significant only when it is comparable with the measurement time interval.

  19. NMR and molecular dynamics of small solutes in liquid crystals

    International Nuclear Information System (INIS)

    Luyten, P.R.

    1984-01-01

    NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

  20. Molecular motion of micellar solutes: a 13C NMR relaxation study

    International Nuclear Information System (INIS)

    Stark, R.E.; Kasakevich, M.L.; Granger, J.W.

    1982-01-01

    A series of simple NMR relaxation experiments have been performed on nitrobenzene and aniline dissolved in the ionic detergents sodium dodecyl sulfate (SDS) and hexadecyltrimethylammonium bromide (CTAB). Using 13 C relaxation rates at various molecular sites, and comparing data obtained in organic media with those for micellar solutions, the viscosity at the solubilization site was estimated and a detailed picture of motional restrictions imposed by the micellar enviroment was derived. Viscosities of 8 to 17 cp indicate a rather fluid environment for solubilized nitrobenzene; both additives exhibit altered motional preferences in CTAB solutions only. As an aid in interpretation of the NMR data, quasi-elastic light scattering and other physical techniques have been used to evaluate the influence of organic solutes on micellar size and shape. The NMR methods are examined critically in terms of their general usefulness for studies of solubilization in detergent micelles. 48 references

  1. Molecular relaxation behavior and isothermal crystallization above glass transition temperature of amorphous hesperetin.

    Science.gov (United States)

    Shete, Ganesh; Khomane, Kailas S; Bansal, Arvind Kumar

    2014-01-01

    The purpose of this paper was to investigate the relaxation behavior of amorphous hesperetin (HRN), using dielectric spectroscopy, and assessment of its crystallization kinetics above glass transition temperature (Tg ). Amorphous HRN exhibited both local (β-) and global (α-) relaxations. β-Relaxation was observed below Tg , whereas α-relaxation prominently emerged above Tg . β-Relaxation was found to be of Johari-Goldstein type and was correlated with α-process by coupling model. Secondly, isothermal crystallization experiments were performed at 363 K (Tg + 16.5 K), 373 K (Tg + 26.5 K), and 383 K (Tg + 36.5 K). The kinetics of crystallization, obtained from the normalized dielectric strength, was modeled using the Avrami model. Havriliak-Negami (HN) shape parameters, αHN and αHN .βHN , were analyzed during the course of crystallization to understand the dynamics of amorphous phase during the emergence of crystallites. HN shape parameters indicated that long range (α-like) were motions affected to a greater extent than short range (β-like) motions during isothermal crystallization studies at all temperature conditions. The variable behavior of α-like motions at different isothermal crystallization temperatures was attributed to evolving crystallites with time and increase in electrical conductivity with temperature. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

  2. Variational formulation of relaxed and multi-region relaxed magnetohydrodynamics

    Science.gov (United States)

    Dewar, R. L.; Yoshida, Z.; Bhattacharjee, A.; Hudson, S. R.

    2015-12-01

    > Ideal magnetohydrodynamics (IMHD) is strongly constrained by an infinite number of microscopic constraints expressing mass, entropy and magnetic flux conservation in each infinitesimal fluid element, the latter preventing magnetic reconnection. By contrast, in the Taylor relaxation model for formation of macroscopically self-organized plasma equilibrium states, all these constraints are relaxed save for the global magnetic fluxes and helicity. A Lagrangian variational principle is presented that leads to a new, fully dynamical, relaxed magnetohydrodynamics (RxMHD), such that all static solutions are Taylor states but also allows state with flow. By postulating that some long-lived macroscopic current sheets can act as barriers to relaxation, separating the plasma into multiple relaxation regions, a further generalization, multi-region relaxed magnetohydrodynamics (MRxMHD) is developed.

  3. Simple molecular mechanism of heat transfer: Debye relaxation versus power-law

    International Nuclear Information System (INIS)

    Gall, M.; Kutner, R.

    2005-01-01

    We study a simple molecular model (at coarse-grain level) as a basis of irreversible heat transfer through a diathermic partition. The partition separates into two adjacent parts a box containing ideal point particles that communicate only though this partition. We provide the basic mechanism of energy transfer between the left- and right-hand side gas samples by assuming equipartition of kinetic energy of all outgoing particles colliding with the partition at a given time. We analyse and compare two essentially different cases (A) the reference one, where we assume that the border walls of the box and the diathermic partitions can randomize the direction of motion of rebounding particles, and (B) the case where we assume the mirror collisions of particles with the border walls and the partition. In both cases the rebounding of the particles from border walls is elastic. The above introduced assumptions allow us to numerically simulate and analytically consider, for example, the relaxation of temperatures of both gas samples and the entropy of the system. However, in both cases the long-time relaxation is essentially different since in case (A) it is an exponential one, while in case (B) it seems to be a power-law relaxation. The obtained results well agree in case (A) with the predictions of the phenomenological, linear theory of irreversible theory had to be developed which assumes time-dependence of heat conductivity; it describes the relaxation of the system far from equilibrium. The explanation of the results obtained in this case is, nevertheless, an intriguing problem. (author)

  4. Dynamics of solutions and fluid mixtures by NMR

    International Nuclear Information System (INIS)

    Delpuech, J.J.

    1994-01-01

    After a short introduction to NMR spectroscopy, with a special emphasis on dynamical aspects, an overview on two fundamental aspects of molecular dynamics, NMR relaxation and its relationship with molecular reorientation, and magnetization transfer phenomena induced by molecular rate processes (dynamic NMR) is presented, followed by specific mechanisms of relaxation encountered in paramagnetic systems or with quadrupolar nuclei. Application fields are then reviewed: solvent exchange on metal ions with a variable pressure NMR approach, applications of field gradients in NMR, aggregation phenomena and micro-heterogeneity in surfactant solutions, polymers and biopolymers in the liquid state, liquid-like molecules in rigid matrices and in soft matter (swollen polymers and gels, fluids in and on inorganic materials, food)

  5. Linear rheology and structure of molecular bottlebrushes with short side chains

    International Nuclear Information System (INIS)

    López-Barrón, Carlos R.; Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

    2015-01-01

    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 w /M 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 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, 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 SC ). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N SC values. The apparent flow activation energies are a decreasing function of N SC , and their values explain the differences in zero-shear viscosity measured at different temperatures

  6. Communication: Slow relaxation, spatial mobility gradients, and vitrification in confined films

    International Nuclear Information System (INIS)

    Mirigian, Stephen; Schweizer, Kenneth S.

    2014-01-01

    Two decades of experimental research indicate that spatial confinement of glass-forming molecular and polymeric liquids results in major changes of their slow dynamics beginning at large confinement distances. A fundamental understanding remains elusive given the generic complexity of activated relaxation in supercooled liquids and the major complications of geometric confinement, interfacial effects, and spatial inhomogeneity. We construct a predictive, quantitative, force-level theory of relaxation in free-standing films for the central question of the nature of the spatial mobility gradient. The key new idea is that vapor interfaces speed up barrier hopping in two distinct, but coupled, ways by reducing near surface local caging constraints and spatially long range collective elastic distortion. Effective vitrification temperatures, dynamic length scales, and mobile layer thicknesses naturally follow. Our results provide a unified basis for central observations of dynamic and pseudo-thermodynamic measurements

  7. Communication: Slow relaxation, spatial mobility gradients, and vitrification in confined films

    Energy Technology Data Exchange (ETDEWEB)

    Mirigian, Stephen [Department of Materials Science, University of Illinois, Urbana, Illinois 61801 (United States); Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu [Department of Materials Science, University of Illinois, Urbana, Illinois 61801 (United States); Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Department of Chemistry, University of Illinois, Urbana, Illinois 61801 (United States); Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801 (United States)

    2014-10-28

    Two decades of experimental research indicate that spatial confinement of glass-forming molecular and polymeric liquids results in major changes of their slow dynamics beginning at large confinement distances. A fundamental understanding remains elusive given the generic complexity of activated relaxation in supercooled liquids and the major complications of geometric confinement, interfacial effects, and spatial inhomogeneity. We construct a predictive, quantitative, force-level theory of relaxation in free-standing films for the central question of the nature of the spatial mobility gradient. The key new idea is that vapor interfaces speed up barrier hopping in two distinct, but coupled, ways by reducing near surface local caging constraints and spatially long range collective elastic distortion. Effective vitrification temperatures, dynamic length scales, and mobile layer thicknesses naturally follow. Our results provide a unified basis for central observations of dynamic and pseudo-thermodynamic measurements.

  8. Memory effects in the relaxation of a confined granular gas

    Science.gov (United States)

    Brey, J. Javier; de Soria, M. I. García; Maynar, P.; Buzón, V.

    2014-09-01

    The accuracy of a model to describe the horizontal dynamics of a confined quasi-two-dimensional system of inelastic hard spheres is discussed by comparing its predictions for the relaxation of the temperature in a homogenous system with molecular dynamics simulation results for the original system. A reasonably good agreement is found. Next the model is used to investigate the peculiarities of the nonlinear evolution of the temperature when the parameter controlling the energy injection is instantaneously changed while the system was relaxing. This can be considered as a nonequilibrium generalization of the Kovacs effect. It is shown that, in the low-density limit, the effect can be accurately described by using a simple kinetic theory based on the first Sonine approximation for the one-particle distribution function. Some possible experimental implications are indicated.

  9. Incipient plasticity and indentation response of MgO surfaces using molecular dynamics

    Science.gov (United States)

    Tran, Anh-Son; Hong, Zheng-Han; Chen, Ming-Yuan; Fang, Te-Hua

    2018-05-01

    The mechanical characteristics of magnesium oxide (MgO) based on nanoindentation are studied using molecular dynamics (MD) simulation. The effects of indenting speed and temperature on the structural deformation and loading-unloading curve are investigated. Results show that the strained surface of the MgO expands to produce a greater relaxation of atoms in the surroundings of the indent. The dislocation propagation and pile-up for MgO occur more significantly with the increasing temperature from 300 K to 973 K. In addition, with increasing temperature, the high strained atoms with a great perturbation appearing at the groove location.

  10. Kinetic details of crystallization in supercooled liquid Pb during the isothermal relaxation

    International Nuclear Information System (INIS)

    Zhou Lili; Liu Rangsu; Tian Zean; Liu Hairong; Hou Zhaoyang; Peng Ping; Zhu Xuanmin; Liu Quanhui

    2012-01-01

    The kinetic details of crystallization in supercooled liquid Pb during the isothermal relaxation process have been investigated by molecular dynamics simulations, and the microstructure evolution analyzed by the cluster-type index method (CTIM) and the tracing method. It has been found that, the dynamic features are consistently correlated with the microstructure evolution and the crystallization characteristics in the mean square displacement (MSD) and the non-Gaussian parameter (NGP): the β relaxation regime corresponds to the minor structural rearrangement because of the “cage effect”, and the atoms attempt to escape from the “cages”; the α relaxation regime is related to a more diffusive movement of atoms, and the appearance of the second plateau in MSD and the non-zero plateau in NGP corresponds to the completion of crystallization. In addition, three distinct stages of nucleation, growth of nuclei and coarsening of crystallites in the crystallization process have been clearly revealed.

  11. Stress relaxation of bi-disperse polystyrene melts

    DEFF Research Database (Denmark)

    Hengeller, Ludovica; Huang, Qian; Dorokhin, Andriy

    2016-01-01

    We present start-up of uniaxial extension followed by stress relaxation experiments of a bi-disperse 50 % by weight blend of 95k and 545k molecular weight polystyrene. We also show, for comparison, stress relaxation measurements of the polystyrene melts with molecular weight 95k and 545k, which...... are the components of the bi-disperse melt. The measurements show three separated relaxation regimes: a fast regime, a transition regime, and a slow regime. In the fast regime, the orientation of the long chains is frozen and the stress relaxation is due to stretch relaxation of the short chains primarily....... Conversely in the slow regime, the long chains have retracted and undergo relaxation of orientation in fully relaxed short chains....

  12. Relaxation of synchronization on complex networks.

    Science.gov (United States)

    Son, Seung-Woo; Jeong, Hawoong; Hong, Hyunsuk

    2008-07-01

    We study collective synchronization in a large number of coupled oscillators on various complex networks. In particular, we focus on the relaxation dynamics of the synchronization, which is important from the viewpoint of information transfer or the dynamics of system recovery from a perturbation. We measure the relaxation time tau that is required to establish global synchronization by varying the structural properties of the networks. It is found that the relaxation time in a strong-coupling regime (K>Kc) logarithmically increases with network size N , which is attributed to the initial random phase fluctuation given by O(N-1/2) . After elimination of the initial-phase fluctuation, the relaxation time is found to be independent of the system size; this implies that the local interaction that depends on the structural connectivity is irrelevant in the relaxation dynamics of the synchronization in the strong-coupling regime. The relaxation dynamics is analytically derived in a form independent of the system size, and it exhibits good consistency with numerical simulations. As an application, we also explore the recovery dynamics of the oscillators when perturbations enter the system.

  13. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  14. Temperature and momentum transfer dependence of the dynamics of the α-relaxation in polymer melts. A quasielastic neutron scattering study

    Science.gov (United States)

    Colmenero, J.; Alegría, A.; Arbe, A.; Frick, B.

    1992-12-01

    The dynamics of the α-relaxation in three glass-forming polymeric systems, poly(vinyl methyl ether) (PVME), poly(vinyl chloride) (PVC), and poly(bisphenol A, 2-hydroxypropylether) (PH) has been studied by means of quasielastic neutron scattering and compared with the results obtained from relaxation techniques. The results indicate that the dynamics of the α-relaxation in a wide timescale shows a clear non-Debye behaviour and can be well described by means of the same spectral shape, which is found to be independent of temperature and momentum transfer ( Q). Moreover, the Havriliak-Negami characteristic times deduced from the fitting of the experimental data can also be described using only one Vogel-Fulcher functional form. This implies a self-consistent description of the dynamics of the α-relaxation obtained by very different probes. Besides, we found that the Q-dependence of the characteristic times obtained by QENS is given by a power law, τ(Q) ∝ Q - n ( n > 2), n being dependent on the system, and that the Q-behaviour and the non-Debye behaviour are directly correlated. These results have main implications about the physical mechanisms behind the dynamics of the α-relaxation.

  15. Non-linear calculation of PCRV using dynamic relaxation

    International Nuclear Information System (INIS)

    Schnellenbach, G.

    1979-01-01

    A brief review is presented of a numerical method called the dynamic relaxation method for stress analysis of the concrete in prestressed concrete pressure vessels. By this method the three-dimensional elliptic differential equations of the continuum are changed into the four-dimensional hyperbolic differential equations known as wave equations. The boundary value problem of the static system is changed into an initial and boundary value problem for which a solution exists if the physical system is defined at time t=0. The effect of non-linear stress-strain behaviour of the material as well as creep and cracking are considered

  16. Study of molecular dynamics of bornyl chloride C{sub 10}H{sub 17}Cl; Badania dynamiki molekularnej chlorku bornylu, C{sub 10}H{sub 17}Cl

    Energy Technology Data Exchange (ETDEWEB)

    Holderna-Natkaniec, K.; Wasicki, J.W. [Univ. A. Mickiewicza, Poznan (Poland); Natkaniec, I. [Lab. of Neutron Physics, Joint Inst. for Nuclear Research, Dubna (Joint Institute for Nuclear Research (JINR))

    1995-12-31

    Inelastic incoherent neutron scattering as well as NMR methods have been used for the study of molecular dynamics of bornyl chloride. The temperature dependence of spin-lattice relaxation time has been determined. The different type of molecular reorientations have been postulated in three terpene phases existed in 10-186 K temperature range. 5 refs, 3 figs.

  17. New Insight in Understanding the mechanical responses of polymer glasses using molecular dynamic simulation

    Science.gov (United States)

    Zheng, Yexin; Wang, Shi-Qing; Tsige, Mesfin

    The Kremer-Grest bead-spring model has been the standard model in molecular dynamics simulation of polymer glasses. However, due to current computational limitations in accessing relevant time scales in polymer glasses in a reasonable amount of CPU time, simulation of mechanical response of polymer glasses in molecular dynamic simulations requires a much higher quenching rate and deformation rate than used in experiments. Despite several orders of magnitude difference in time scale between simulation and experiment, previous studies have shown that simulations can produce meaningful results that can be directly compared with experimental results. In this work we show that by tuning the quenching rate and deformation rate relative to the segmental relaxation times, a reasonable mechanical response shows up in the glassy state. Specifically, we show a younger glass prepared with a faster quenching rate shows glassy responses only when the imposed deformation rate is proportionally higher. the National Science Foundation (DMR-1444859 and DMR-1609977).

  18. Collective dynamic dipole moment and orientation fluctuations, cooperative hydrogen bond relaxations, and their connections to dielectric relaxation in ionic acetamide deep eutectics: Microscopic insight from simulations

    Energy Technology Data Exchange (ETDEWEB)

    Das, Suman [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Biswas, Ranjit, E-mail: ranjit@bose.res.in, E-mail: biswaroop.mukherjee@gmail.com [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Thematic Unit for Excellence – Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Mukherjee, Biswaroop, E-mail: ranjit@bose.res.in, E-mail: biswaroop.mukherjee@gmail.com [Thematic Unit for Excellence – Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India)

    2016-08-28

    The paper reports a detailed simulation study on collective reorientational relaxation, cooperative hydrogen bond (H-bond) fluctuations, and their connections to dielectric relaxation (DR) in deep eutectic solvents made of acetamide and three uni-univalent electrolytes, lithium nitrate (LiNO{sub 3}), lithium bromide (LiBr), and lithium perchlorate (LiClO{sub 4}). Because cooperative H-bond fluctuations and ion migration complicate the straightforward interpretation of measured DR timescales in terms of molecular dipolar rotations for these conducting media which support extensive intra- and inter-species H-bonding, one needs to separate out the individual components from the overall relaxation for examining the microscopic origin of various timescales. The present study does so and finds that reorientation of ion-complexed acetamide molecules generates relaxation timescales that are in sub-nanosecond to nanosecond range. This explains in molecular terms the nanosecond timescales reported by recent giga-Hertz DR measurements. Interestingly, the simulated survival timescale for the acetamide-Li{sup +} complex has been found to be a few tens of nanosecond, suggesting such a cation-complexed species may be responsible for a similar timescale reported by mega-Hertz DR measurements of acetamide/potassium thiocyanate deep eutectics near room temperature. The issue of collective versus single particle relaxation is discussed, and jump waiting time distributions are determined. Dependence on anion-identity in each of the cases has been examined. In short, the present study demonstrates that assumption of nano-sized domain formation is not required for explaining the DR detected nanosecond and longer timescales in these media.

  19. Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

    Science.gov (United States)

    Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt

    2011-05-01

    Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ˜ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension , neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ˜ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)], 10.1063/1.3587137.

  20. Atomistic simulation of processes in Ni-base alloys with account for local relaxations

    International Nuclear Information System (INIS)

    Bursik, Jiri

    2007-01-01

    Ordering in Ni-base superalloys is the crucial process controlling the development of the characteristic two-phase microstructure and subsequently the mechanical properties. Systems containing up to six alloying elements typical of advanced Ni-based superalloys are modelled in this work using a Monte Carlo approach with phenomenological Lennard-Jones pair potentials and interactions up to the third coordination sphere. Three-dimensional crystal block is used with over 10 5 atoms. Molecular dynamics approach is used to relax local atomic positions in course of ordering processes under applied stress. The importance of taking into account both relaxation of modelled block dimensions and relaxation of local atomic positions is discussed

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

    Science.gov (United States)

    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.

  2. NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure

    International Nuclear Information System (INIS)

    Nikonowicz, E.P.; Meadows, R.P.; Gorenstein, D.G.

    1990-01-01

    Until very recently interproton distances from NOESY experiments have been derived solely from the two-spin approximation method. Unfortunately, even at short mixing times, there is a significant error in many of these distances. A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Bloch equations avoids the approximation of the two-spin method. The authors calculated the structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d-(CGCAGAATTCGCG) 2 , by an iterative refinement approach using a hybrid relaxation matrix method combined with restrained molecular dynamics calculations. Distances from the 2D NOESY spectra have been calculated from the relaxation rate matrix which has been evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix derived distances have then been used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure is then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. Although the crystal structure of the tridecamer clearly shows the extrahelical adenosine looped out way from the duplex, the NOESY distance restrained hybrid matrix/molecular dynamics structural refinement establishes that the extrahelical adenosine stacks into the duplex

  3. Dielectric relaxation study of the dynamics of monosaccharides: D-ribose and 2-deoxy-D-ribose

    Energy Technology Data Exchange (ETDEWEB)

    Kaminski, K; Kaminska, E; Wlodarczyk, P; Paluch, M; Ziolo, J [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Ngai, K L [Naval Research Laboratory, Washington, DC 20375-5320 (United States)

    2008-08-20

    The dielectric loss spectra of two closely related monosaccharides, D-ribose and 2-deoxy-D-ribose, measured at ambient and elevated pressures are presented. 2-deoxy-D-ribose and D-ribose are respectively the building blocks of the backbone chains in the nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Small differences in the structure between D-ribose and 2-deoxy-D-ribose result in changes of the glass transition temperature T{sub g}, as well as the dielectric strength and activation enthalpy of the secondary relaxations. However, the frequency dispersion of the structural {alpha}-relaxation for the same relaxation time remains practically the same. Two secondary relaxations are present in both sugars. The slower secondary relaxation shifts to lower frequencies with increasing applied pressure, but not the faster one. This pressure dependence indicates that the slower secondary relaxation is the important and 'universal' Johari-Goldstein {beta}-relaxation of both sugars according to one of the criteria set up to classify secondary relaxations. Additional confirmation of this conclusion comes from good agreement of the observed relaxation time of the slower secondary relaxation with the primitive relaxation time calculated from the coupling model. All the dynamic properties of D-ribose and 2-deoxy-D-ribose are similar to the other monosaccharides, glucose, fructose, galactose and sorbose, except for the much larger relaxation strength of the {alpha}-relaxation of the former compared to the latter. The difference may distinguish the chemical and biological functions of D-ribose and 2-deoxy-D-ribose from the other monosaccharides.

  4. Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bousige, Colin; Boţan, Alexandru; Coasne, Benoît, E-mail: coasne@mit.edu [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Ulm, Franz-Josef [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Pellenq, Roland J.-M. [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); CINaM, CNRS/Aix Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09 (France)

    2015-03-21

    We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

  5. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    International Nuclear Information System (INIS)

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-01-01

    Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement

  6. Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

    International Nuclear Information System (INIS)

    Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

    2014-01-01

    We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example

  7. Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

    International Nuclear Information System (INIS)

    Mattea, C.

    2006-01-01

    Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

  8. Dynamics of Block Copolymer Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    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 also 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.

  9. A nuclear magnetic relaxation study of hydrogen exchange and water dynamics in aqueous systems

    International Nuclear Information System (INIS)

    Lankhorst, D.

    1983-01-01

    In this thesis exchange of water protons in solutions of some weak electrolytes and polyelectrolytes is studied. Also the dynamical behaviour of water molecules in pure water is investigated. For these purposes nuclear magnetic resonance relaxation measurements, in solutions of oxygen-17 enriched water, are interpreted. The exchange rate of the water protons is derived from the contribution of 1 H- 17 O scalar coupling to the proton transverse relaxation rate. This rate is measured by the Carr-Purcell technique. (Auth.)

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

    Science.gov (United States)

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

    2013-11-07

    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.

  11. Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

    Science.gov (United States)

    Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

    2018-06-05

    The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.

  12. The impact of different phytosterols on the molecular dynamics in the hydrophobic/hydrophilic interface phosphatidylcholine- liposomes

    DEFF Research Database (Denmark)

    Hellgren, Lars; Sandelius, A.S.

    2001-01-01

    Plant sterols differ from cholesterol in having an alkyl group at Delta -24, and, in the case of stigmasterol, also a Delta -22 double bond. The effects of 10 mol% of three plant sterols (campesterol, fl-sitosterol, stigmasterol) and cholesterol on the molecular dynamics and phase behavior...... in multilamellar liposomes made from different phosphatidylcholine (PC) molecular species have been compared, utilizing the fluorescent probe Laurdan (2-dimethyl-amino-6-laurylnaphthalene). Laurdan reports the molecular mobility in the hydrophilic/hydrophobic interface of the membrane by determining the rate...... of dipolar relaxation of water molecules close to the glycerol backbone of PC. Our results showed that the Delta -24 alkyl group of plant sterols did not affect their ability to reduce molecular mobility in this region of the PC membranes. However, the plant sterols had a decreased capacity compared...

  13. Dynamics of transfer of electron excitation in a donor-acceptor system with a carbon chain and ways of its relaxation

    Directory of Open Access Journals (Sweden)

    M.M. Sevryukova

    2017-12-01

    Full Text Available The optical properties and dynamics of transport of electron excitation and the ways of its relaxation in the supramolecular D–π–A complex on the basis of merocyanines have been investigated. There have been found two components in the transfer of charge: fast and slow, which correspond to different conformational states of the carbon chain in merocyanines. It was found that the main photoluminescence of the studied molecular solutions of merocyanines by its nature is similar to the exciplex luminescence, as a manifestation of resonant and charge transfer interaction in an excited state. The lifetime in this state is about 2000 ps.

  14. Critical thickness and strain relaxation in molecular beam epitaxy-grown SrTiO3 films

    International Nuclear Information System (INIS)

    Wang, Tianqi; Ganguly, Koustav; Marshall, Patrick; Xu, Peng; Jalan, Bharat

    2013-01-01

    We report on the study of the critical thickness and the strain relaxation in epitaxial SrTiO 3 film grown on (La 0.3 Sr 0.7 )(Al 0.65 Ta 0.35 )O 3 (001) (LSAT) substrate using the hybrid molecular beam epitaxy approach. No change in the film's lattice parameter (both the in-plane and the out-of-plane) was observed up to a film thickness of 180 nm, which is in sharp contrast to the theoretical critical thickness of ∼12 nm calculated using the equilibrium theory of strain relaxation. For film thicknesses greater than 180 nm, the out-of-plane lattice parameter was found to decrease hyperbolically in an excellent agreement with the relaxation via forming misfit dislocations. Possible mechanisms are discussed by which the elastic strain energy can be accommodated prior to forming misfit dislocations leading to such anomalously large critical thickness

  15. Relaxation and physical aging in network glasses: a review.

    Science.gov (United States)

    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.

  16. Fast evaluation of protein dynamics from deficient 15N relaxation data

    KAUST Repository

    Jaremko, Łukasz

    2018-03-28

    Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S and R, can be elucidated. The generalized order parameter, S, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.

  17. Fast evaluation of protein dynamics from deficient 15N relaxation data

    KAUST Repository

    Jaremko, Łukasz; Jaremko, Mariusz; Ejchart, Andrzej; Nowakowski, Michał

    2018-01-01

    Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S and R, can be elucidated. The generalized order parameter, S, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.

  18. Effect of surface hydrophobicity on the dynamics of water at the nanoscale confinement: A molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Choudhury, Niharendu

    2013-01-01

    Highlights: • We present atomistic MD simulation of water confined between two paraffin-like plates. • Effect of plate hydrophobicity on the confined water dynamics is investigated. • Diffusivity of confined water is calculated from mean squared displacements. • Rotational dynamics of the confined water has bimodal nature of relaxation. • Monotonic dependence of translational and rotational dynamics on hydrophobicity. - Abstract: We present detailed molecular dynamics simulations of water in and around a pair of plates immersed in water to investigate the effect of degree of hydrophobicity or hydrophilicity of the plates on dynamics of water confined between the two plates. The nature of the plate has been tuned from hydrophobic to hydrophilic and vice versa by varying plate-water dispersion interaction. Analyses of the translational dynamics as performed by calculating mean squared displacements of the confined water reveal a monotonically decreasing trend of the diffusivity with increasing hydrophilicity of the plates. Orientational dynamics of the confined water also follows the same monotonic trend. Although orientational time constant almost does not change with the increase of plate-water dispersion interaction in the hydrophobic regime corresponding to the smaller plate-water attraction, it changes considerably in the hydrophilic regime corresponding to larger plate-water dispersion interactions

  19. Dynamics of merging: post-merger mixing and relaxation of an Illustris galaxy

    Science.gov (United States)

    Young, Anthony M.; Williams, Liliya L. R.; Hjorth, Jens

    2018-02-01

    During the merger of two galaxies, the resulting system undergoes violent relaxation and seeks stable equilibrium. However, the details of this evolution are not fully understood. Using Illustris simulation, we probe two physically related processes, mixing and relaxation. Though the two are driven by the same dynamics—global time-varying potential for the energy, and torques caused by asymmetries for angular momentum—we measure them differently. We define mixing as the redistribution of energy and angular momentum between particles of the two merging galaxies. We assess the degree of mixing as the difference between the shapes of their energy distributions, N(E)s, and their angular momentum distributions, N(L2)s. We find that the difference is decreasing with time, indicating mixing. To measure relaxation, we compare N(E) of the newly merged system to N(E) of a theoretical prediction for relaxed collisionless systems, DARKexp, and witness the system becoming more relaxed, in the sense that N(E) approaches DARKexp N(E). Because the dynamics driving mixing and relaxation are the same, the timescale is similar for both. We measure two sequential timescales: a rapid, 1 Gyr phase after the initial merger, during which the difference in N(E) of the two merging halos decreases by ~ 80%, followed by a slow phase, when the difference decreases by ~ 50% over ~ 8.5 Gyrs. This is a direct measurement of the relaxation timescale. Our work also draws attention to the fact that when a galaxy has reached Jeans equilibrium it may not yet have reached a fully relaxed state given by DARKexp, in that it retains information about its past history. This manifests itself most strongly in stars being centrally concentrated. We argue that it is particularly difficult for stars, and other tightly bound particles, to mix because they have less time to be influenced by the fluctuating potential, even across multiple merger events.

  20. Dynamic mesh adaptation for front evolution using discontinuous Galerkin based weighted condition number relaxation

    International Nuclear Information System (INIS)

    Greene, Patrick T.; Schofield, Samuel P.; Nourgaliev, Robert

    2017-01-01

    A new mesh smoothing method designed to cluster cells near a dynamically evolving interface is presented. The method is based on weighted condition number mesh relaxation with the weight function computed from a level set representation of the interface. The weight function is expressed as a Taylor series based discontinuous Galerkin projection, which makes the computation of the derivatives of the weight function needed during the condition number optimization process a trivial matter. For cases when a level set is not available, a fast method for generating a low-order level set from discrete cell-centered fields, such as a volume fraction or index function, is provided. Results show that the low-order level set works equally well as the actual level set for mesh smoothing. Meshes generated for a number of interface geometries are presented, including cases with multiple level sets. Lastly, dynamic cases with moving interfaces show the new method is capable of maintaining a desired resolution near the interface with an acceptable number of relaxation iterations per time step, which demonstrates the method's potential to be used as a mesh relaxer for arbitrary Lagrangian Eulerian (ALE) methods.

  1. Spin dynamics of the itinerant helimagnet MnSi studied by positive muon spin relaxation

    International Nuclear Information System (INIS)

    Kadono, R.; Matsuzaki, T.; Yamazaki, T.; Kreitzman, S.R.; Brewer, J.H.

    1990-03-01

    The local magnetic fields and spin dynamics of the itinerant helimagnet MnSi(T c ≅ 29.5 K) have been studied experimentally using positive muon spin rotation/relaxation (μ + SR) methods. In the ordered phase (T c ), zero-field μSR was used to measure the hyperfine fields at the muon sites as well as the muon spin-lattice relaxation time T 1 μ . Two magnetically inequivalent interstitial μ + sites were found with hyperfine coupling constants A hf (1) = -3.94 kOe/μ B and A hf (2) = -6.94 kOe/μ B , respectively. In the paramagnetic phase (T > T c ), the muon-nuclear spin double relaxation technique was used to simultaneously but independently determine the spin-lattice relaxation time T 1 Mn of 55 Mn spins and that of positive muons (T 1 μ ) over a wide temperature range (T c 1 Mn and T 1 μ in both phases shows systematic deviations from the predictions of self-consistent renormalization (SCR) theory. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr [Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris (France); Charpentier, Thibault [CEA, IRAMIS, NIMBE, LSDRM, UMR CEA-CNRS 3685, F-91191 Gif-sur-Yvette Cedex (France)

    2015-11-21

    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 EFG 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.

  3. The dynamic relaxation method in the structural analysis of concrete pressure vessels

    International Nuclear Information System (INIS)

    Davidson, I.; Assis Bastos, M.R. de; Camargo, P.B. de.

    1977-01-01

    The dynamic relaxation method, applied to 3 dimensional concrete structures, especially pressure vessels, is demonstrated. It utilizes the finite difference method and allows the growth of cracks to be followed up to the point of vessel rupture. A FORTRAN IV program is developed, which can also be utilized, with the necessary modifications, for other structure calculations [pt

  4. Quantitative measurement of exchange dynamics in proteins via {sup 13}C relaxation dispersion of {sup 13}CHD{sub 2}-labeled samples

    Energy Technology Data Exchange (ETDEWEB)

    Rennella, Enrico; Schuetz, Anne K.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2016-06-15

    Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit {sup 13}CH{sub 3}- or {sup 13}CHD{sub 2}-labeling in otherwise highly deuterated proteins. The {sup 13}CHD{sub 2} label offers the unique advantage of providing {sup 13}C, {sup 1}H and {sup 2}H spin probes, however a disadvantage has been the lack of an experiment to record {sup 13}C Carr–Purcell–Meiboom–Gill relaxation dispersion that monitors millisecond time-scale dynamics, implicated in a wide range of biological processes. Herein we develop an experiment that eliminates artifacts that would normally result from the scalar coupling between {sup 13}C and {sup 2}H spins that has limited applications in the past. The utility of the approach is established with a number of applications, including measurement of ms dynamics of a disease mutant of a 320 kDa p97 complex.

  5. Structural relaxation of polydisperse hard spheres: comparison of the mode-coupling theory to a Langevin dynamics simulation.

    Science.gov (United States)

    Weysser, F; Puertas, A M; Fuchs, M; Voigtmann, Th

    2010-07-01

    We analyze the slow glassy structural relaxation as measured through collective and tagged-particle density correlation functions obtained from Brownian dynamics simulations for a polydisperse system of quasi-hard spheres in the framework of the mode-coupling theory (MCT) of the glass transition. Asymptotic analyses show good agreement for the collective dynamics when polydispersity effects are taken into account in a multicomponent calculation, but qualitative disagreement at small q when the system is treated as effectively monodisperse. The origin of the different small-q behavior is attributed to the interplay between interdiffusion processes and structural relaxation. Numerical solutions of the MCT equations are obtained taking properly binned partial static structure factors from the simulations as input. Accounting for a shift in the critical density, the collective density correlation functions are well described by the theory at all densities investigated in the simulations, with quantitative agreement best around the maxima of the static structure factor and worst around its minima. A parameter-free comparison of the tagged-particle dynamics however reveals large quantitative errors for small wave numbers that are connected to the well-known decoupling of self-diffusion from structural relaxation and to dynamical heterogeneities. While deviations from MCT behavior are clearly seen in the tagged-particle quantities for densities close to and on the liquid side of the MCT glass transition, no such deviations are seen in the collective dynamics.

  6. Molecular mobility of nematic E7 confined to molecular sieves with a low filling degree.

    Science.gov (United States)

    Brás, A R; Frunza, S; Guerreiro, L; Fonseca, I M; Corma, A; Frunza, L; Dionísio, M; Schönhals, A

    2010-06-14

    The nematic liquid crystalline mixture E7 was confined with similar filling degrees to molecular sieves with constant composition but different pore diameters (from 2.8 to 6.8 nm). Fourier transform infrared analysis proved that the E7 molecules interact via the cyanogroup with the pore walls of the molecular sieves. The molecular dynamics of the system was investigated by broadband dielectric spectroscopy (10(-2)-10(9) Hz) covering a wide temperature range of approximately 200 K from temperatures well above the isotropic-nematic transition down to the glass transition of bulk E7. A variety of relaxation processes is observed including two modes that are located close to the bulk behavior in its temperature dependence. For all confined samples, two relaxation processes, at frequencies lower than the processes observed for the bulk, were detected. At lower temperatures, their relaxation rates have different temperature dependencies whereas at higher temperatures, they seem to collapse into one chart. The temperature dependence of the slowest process (S-process) obeys the Vogel-Fulcher-Tammann law indicating a glassy dynamics of the E7 molecules anchored to the pore surface. The pore size dependence of both the Vogel temperature and fragility revealed a steplike transition around 4 nm pore size, which indicates a transition from a strong to a fragile behavior. The process with a relaxation rate in between the bulklike and the S-process (I-process) shows no dependence on the pore size. The agreement of the I-process with the behavior of a 5CB surface layer adsorbed on nonporous silica leads to the assignment of E7 molecules anchored at the outer surface of the microcrystals of the molecular sieves.

  7. Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

    Science.gov (United States)

    Yagasaki, Takuma; Saito, Shinji

    2009-09-15

    elucidated by introducing the "translation-free" molecular dynamics simulation. The isotropic pump-probe signal and the polarization anisotropy decay show fast transfer of the librational energy to the surrounding water molecules, followed by relaxation to the hot ground state. These theoretical methods do not require frequently used assumptions and can thus be called ab initio methods; together with multidimensional nonlinear spectroscopies, they provide powerful methods for examining the inter- and intramolecular details of water dynamics.

  8. Relaxations and fast dynamics of the plastic crystal cyclo-octanol investigated by broadband dielectric spectroscopy

    OpenAIRE

    Lunkenheimer, Peter

    1997-01-01

    Relaxations and fast dynamics of the plastic crystal cyclo-octanol investigated by broadband dielectric spectroscopy / R. Brand, P. Lunkenheimer, A. Loidl. - In: Physical review. B. 56. 1997. S. R5713-R5716

  9. Vibrational relaxation in liquids: Comparisons between gas phase and liquid phase theories

    International Nuclear Information System (INIS)

    Russell, D.J.

    1990-12-01

    The vibrational relaxation of iodine in liquid xenon was studied to understand what processes are important in determining the density dependence of the vibrational relaxation. This examination will be accomplished by taking simple models and comparing the results to both experimental outcomes and the predictions of molecular dynamics simulations. The vibration relaxation of iodine is extremely sensitive to the iodine potential. The anharmonicity of iodine causes vibrational relaxation to be much faster at the top of the iodine well compared to the vibrational relaxation at the bottom. A number of models are used in order to test the ability of the Isolated Binary Collision theory's ability to predict the density dependence of the vibrational relaxation of iodine in liquid xenon. The models tested vary from the simplest incorporating only the fact that the solvent occupies volume to models that incorporate the short range structure of the liquid in the radial distribution function. None of the models tested do a good job of predicting the actual relaxation rate for a given density. This may be due to a possible error in the choice of potentials to model the system

  10. Molecular dynamics in supercooled liquid and glassy states of antibiotics: azithromycin, clarithromycin and roxithromycin studied by dielectric spectroscopy. Advantages given by the amorphous state.

    Science.gov (United States)

    Adrjanowicz, K; Zakowiecki, D; Kaminski, K; Hawelek, L; Grzybowska, K; Tarnacka, M; Paluch, M; Cal, K

    2012-06-04

    Antibiotics are chemical compounds of extremely important medical role. Their history can be traced back more than one hundred years. Despite the passing time and significant progress made in pharmacy and medicine, treatment of many bacterial infections without antibiotics would be completely impossible. This makes them particularly unique substances and explains the unflagging popularity of antibiotics within the medical community. Herein, using dielectric spectroscopy we have studied the molecular mobility in the supercooled liquid and glassy states of three well-known antibiotic agents: azithromycin, clarithromycin and roxithromycin. Dielectric studies revealed a number of relaxation processes of different molecular origin. Besides the primary α-relaxation, observed above the respective glass transition temperatures of antibiotics, two secondary relaxations in the glassy state were identified. Interestingly, the fragility index as well as activation energies of the secondary processes turned out to be practically the same for all three compounds, indicating probably much the same molecular dynamics. Long-term stability of amorphous antibiotics at room temperature was confirmed by X-ray diffraction technique, and calorimetric studies were performed to evaluate the basic thermodynamic parameters. Finally, we have also checked the experimental solubility advantages given by the amorphous form of the examined antibiotics.

  11. Simulations of the flipping images and microparameters of molecular orientations in liquids according to the molecule string model

    International Nuclear Information System (INIS)

    Wang Li-Na; Zhao Xing-Yu; Zhang Li-Li; Huang Yi-Neng

    2012-01-01

    The relaxation dynamics of liquids is one of the fundamental problems in liquid physics, and it is also one of the key issues to understand the glass transition mechanism. It will undoubtedly provide enlightenment on understanding and calculating the relaxation dynamics if the molecular orientation flipping images and relevant microparameters of liquids are studied. In this paper, we first give five microparameters to describe the individual molecular string (MS) relaxation based on the dynamical Hamiltonian of the MS model, and then simulate the images of individual MS ensemble, and at the same time calculate the parameters of the equilibrium state. The results show that the main molecular orientation flipping image in liquids (including supercooled liquid) is similar to the random walk. In addition, two pairs of the parameters are equal, and one can be ignored compared with the other. This conclusion will effectively reduce the difficulties in calculating the individual MS relaxation based on the single-molecule orientation flipping rate of the general Glauber type, and the computer simulation time of interaction MS relaxation. Moreover, the conclusion is of reference significance for solving and simulating the multi-state MS model. (condensed matter: structural, mechanical, and thermal properties)

  12. Ultrafast Librational Relaxation of H2O in Liquid Water

    DEFF Research Database (Denmark)

    Petersen, Jakob; Møller, Klaus Braagaard; Rey, Rossend

    2013-01-01

    The ultrafast librational (hindered rotational) relaxation of a rotationally excited H2O molecule in pure liquid water is investigated by means of classical nonequilibrium molecular dynamics simulations and a power and work analysis. This analysis allows the mechanism of the energy transfer from...... the excited H2O to its water neighbors, which occurs on a sub-100 fs time scale, to be followed in molecular detail, i.e., to determine which water molecules receive the energy and in which degrees of freedom. It is found that the dominant energy flow is to the four hydrogen-bonded water partners in the first...

  13. Color molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Hatsuda, Tetsuo

    2000-01-01

    We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

  14. Dynamics of Exciton Relaxation in LH2 Antenna Probed by Multipulse Nonlinear Spectroscopy

    NARCIS (Netherlands)

    Novoderezhkin, V.I.; Cohen Stuart, T.A.; van Grondelle, R.

    2011-01-01

    We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump - dump - probe spectroscopy (Th. A. Cohen StuartM. VengrisV. I. NovoderezhkinR. J. CogdellC. N. HunterR. van Grondelle, submitted). The theory of pump - dump - probe response is evaluated using the doorway -

  15. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  16. Molecular excitation dynamics and relaxation quantum theory and spectroscopy

    CERN Document Server

    Valkunas, Leonas; Mancal, Tomas

    2013-01-01

    Meeting the need for a work that brings together quantum theory and spectroscopy to convey excitation processes to advanced students and specialists wishing to conduct research and understand the entire field rather than just single aspects.Written by an experienced author and recognized authority in the field, this text covers numerous applications and offers examples taken from different disciplines. As a result, spectroscopists, molecular physicists, physical chemists, and biophysicists will all find this a must-have for their research. Also suitable as supplementary reading in graduate

  17. Little evidence for dynamic divergences in ultraviscous molecular liquids

    DEFF Research Database (Denmark)

    Hecksher, Tina; Nielsen, Albena; Olsen, Niels Boye

    2008-01-01

    The physics of the ultraviscous liquid phase preceding glass formation continues to pose major problems that remain unsolved. It is actively debated, for instance, whether the marked increase of the relaxation time reflects an underlying phase transition to a state of infinite relaxation time....... To elucidate the empirical evidence for this intriguing scenario, some of the most accurate relaxationtime data available for any class of ultraviscous liquids-those obtained by dielectric relaxation experiments on organic liquids just above the glass transition-were compiled. Analysis of data for 42 liquids...... shows that there is no compelling evidence for the Vogel-Fulcher-Tammann (VFT) prediction that the relaxation time diverges at a finite temperature.We conclude that theories with a dynamic divergence of the VFT formlack a direct experimental basis....

  18. Improved dynamical scaling analysis using the kernel method for nonequilibrium relaxation.

    Science.gov (United States)

    Echinaka, Yuki; Ozeki, Yukiyasu

    2016-10-01

    The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results more reliable and reproducible and enables automatic and faster parameter estimation. Applying this method, the bootstrap method is introduced and a numerical discrimination for the transition type is proposed.

  19. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

  20. Spin relaxation dynamics of holes in intrinsic GaAs quantum wells studied by transient circular dichromatic absorption spectroscopy at room temperature.

    Science.gov (United States)

    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.

  1. Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

    Science.gov (United States)

    Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

    2015-01-28

    We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

  2. Isotope effect on hydrated electron relaxation dynamics studied with time-resolved liquid jet photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, Madeline H.; Williams, Holly L. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Neumark, Daniel M., E-mail: dneumark@berkeley.edu [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2016-05-14

    The excited state relaxation dynamics of the solvated electron in H{sub 2}O and D{sub 2}O are investigated using time-resolved photoelectron spectroscopy in a liquid microjet. The data show that the initial excited state decays on a time scale of 75 ± 12 fs in H{sub 2}O and 102 ± 8 fs in D{sub 2}O, followed by slower relaxation on time scales of 400 ± 70 fs and 390 ± 70 fs that are isotopically invariant within the precision of our measurements. Based on the time evolution of the transient signals, the faster and slower time constants are assigned to p → s internal conversion (IC) of the hydrated electron and relaxation on the ground electronic state, respectively. This assignment is consistent with the non-adiabatic mechanism for relaxation of the hydrated electron and yields an isotope effect of 1.4 ± 0.2 for IC of the hydrated electron.

  3. Isotope effect on hydrated electron relaxation dynamics studied with time-resolved liquid jet photoelectron spectroscopy

    Science.gov (United States)

    Elkins, Madeline H.; Williams, Holly L.; Neumark, Daniel M.

    2016-05-01

    The excited state relaxation dynamics of the solvated electron in H2O and D2O are investigated using time-resolved photoelectron spectroscopy in a liquid microjet. The data show that the initial excited state decays on a time scale of 75 ± 12 fs in H2O and 102 ± 8 fs in D2O, followed by slower relaxation on time scales of 400 ± 70 fs and 390 ± 70 fs that are isotopically invariant within the precision of our measurements. Based on the time evolution of the transient signals, the faster and slower time constants are assigned to p → s internal conversion (IC) of the hydrated electron and relaxation on the ground electronic state, respectively. This assignment is consistent with the non-adiabatic mechanism for relaxation of the hydrated electron and yields an isotope effect of 1.4 ± 0.2 for IC of the hydrated electron.

  4. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  5. Proton spin-lattice relaxation in a liquid crystal-Aerosil complex above the bulk isotropization temperature

    Energy Technology Data Exchange (ETDEWEB)

    Anoardo, E.; Grinberg, F.; Vilfan, M.; Kimmich, R

    2004-02-16

    We present a study of the molecular dynamics in an octylcyanobiphenyl (8CB)-Aerosil complex above the bulk isotropization temperature. Using proton nuclear magnetic relaxation experiments in the laboratory frame (T{sub 1}{sup -1}) and in the rotating-frame (T{sub 1{rho}}{sup -1}), we found a notable increase of the relaxation rates in the kHz frequency range as compared to the bulk 8CB liquid crystal at the same temperature. The field-cycling technique was used for the laboratory frame experiments while a conventional apparatus was used for the rotating frame method. The observed behavior is analyzed with the aid of Monte Carlo simulations on the basis of a two-phase fast-exchange model distinguishing surface-ordered and bulk phases. Two processes affecting the low frequency relaxation could be identified: reorientation mediated by translational displacements, accounting for molecular reorientations, and exchange losses of molecules from the surface to the bulk.

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

    Science.gov (United States)

    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.

  7. Extended Thermodynamics of Rarefied Polyatomic Gases: 15-Field Theory Incorporating Relaxation Processes of Molecular Rotation and Vibration

    Directory of Open Access Journals (Sweden)

    Takashi Arima

    2018-04-01

    Full Text Available After summarizing the present status of Rational Extended Thermodynamics (RET of gases, which is an endeavor to generalize the Navier–Stokes and Fourier (NSF theory of viscous heat-conducting fluids, we develop the molecular RET theory of rarefied polyatomic gases with 15 independent fields. The theory is justified, at mesoscopic level, by a generalized Boltzmann equation in which the distribution function depends on two internal variables that take into account the energy exchange among the different molecular modes of a gas, that is, translational, rotational, and vibrational modes. By adopting the generalized Bhatnagar, Gross and Krook (BGK-type collision term, we derive explicitly the closed system of field equations with the use of the Maximum Entropy Principle (MEP. The NSF theory is derived from the RET theory as a limiting case of small relaxation times via the Maxwellian iteration. The relaxation times introduced in the theory are shown to be related to the shear and bulk viscosities and heat conductivity.

  8. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Fabrizio Marinelli

    2009-08-01

    Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

  9. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

    Science.gov (United States)

    Armen, Roger S; Chen, Jianhan; Brooks, Charles L

    2009-10-13

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

  10. Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

    Science.gov (United States)

    Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

    2018-04-10

    Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of

  11. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  12. Thermally induced magnetic relaxation in square artificial spin ice

    Science.gov (United States)

    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.

  13. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-01

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  14. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  15. The elastoplastic calculation of disks with the help of dynamic relaxation

    International Nuclear Information System (INIS)

    Zerna, W.; Schnellenbach, G.; Ick, U.

    1973-12-01

    The possibilities for the computation of elasticplastic properties via dynamic relaxation are shown. From the various theories of plasticity the laws of Prandtl-Reuzs for solidifying materials were chosen for in this investigation. The calculation is carried out directly without further linearizations in a single computer run. It is possible to obtain an approximate solution via a direct process involving a fictitious elastic material law. Two disks with - according to the theory of elasticity - single stress points are used as examples. (orig.) [de

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

    Science.gov (United States)

    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.

  17. Connection between slow and fast dynamics of molecular liquids around the glass transition

    International Nuclear Information System (INIS)

    Niss, Kristine; Dalle-Ferrier, Cecile; Frick, Bernhard; Russo, Daniela; Dyre, Jeppe; Alba-Simionesco, Christiane

    2010-01-01

    The mean-square displacement (MSD) was measured by neutron scattering at various temperatures and pressures for a number of molecular glass-forming liquids. The MSD is invariant along the glass-transition line at the pressure studied, thus establishing an 'intrinsic' Lindemann criterion for any given liquid. A one-to-one connection between the MSD's temperature dependence and the liquid's fragility is found when the MSD is evaluated on a time scale of ∼4 ns, but does not hold when the MSD is evaluated at shorter times. The findings are discussed in terms of the elastic model and the role of relaxations, and the correlations between slow and fast dynamics are addressed.

  18. Electronic relaxation dynamics of a metal atom deposited on argon cluster

    International Nuclear Information System (INIS)

    Awali, Slim

    2014-01-01

    This thesis is a study on the interaction between electronically excited atomic states and a non-reactive environment. We have theoretically and experimentally studied situations where a metal atom (Ba or K) is placed in a finite size environment (argon cluster). The presence of the medium affects the electronic levels of the atom. On the other side, the excitation of the atom induces a relaxation dynamics of the electronic energy through the deformation of the cluster. The experimental part of this work focuses on two aspects: the spectroscopy and the dynamics. In both cases a first laser electronically excites the metal atom and the second ionizes the excited system. The observable is the photoelectron spectrum recorded after photoionization and possibly information on the photoion which are also produced. This pump/probe technique, with also two lasers, provide the ultrafast dynamic when the lasers pulses used are of ultrashort (60 fs). The use of nanosecond lasers leads to resonance spectroscopic measurement, unresolved temporally, which give information on the position of the energy levels of the studied system. From a theoretical point-of-view, the excited states of M-Ar n were calculated at the ab initio level, using large core pseudo-potential to limit the active electrons of the metal to valence electrons. The study of alkali metals (potassium) is especially well adapted to this method since only one electron is active. The ab-initio calculation and a Monte-Carlo simulation where coupled to optimize the geometry of the KAr n (n = 1-10) cluster when K is in the ground state of the neutral and the ion, or excited in the 4p or 5s state. Calculations were also conducted in collaboration with B. Gervais (CIMAP, Caen) on KAr n clusters having several tens of argon atoms. Absorption spectra were also calculated. From an experimental point-of-view, we were able to characterize the excited states of potassium and barium perturbed by the clusters. In both cases a

  19. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  20. Dynamics in a one-dimensional ferrogel model: relaxation, pairing, shock-wave propagation.

    Science.gov (United States)

    Goh, Segun; Menzel, Andreas M; Löwen, Hartmut

    2018-05-23

    Ferrogels are smart soft materials, consisting of a polymeric network and embedded magnetic particles. Novel phenomena, such as the variation of the overall mechanical properties by external magnetic fields, emerge consequently. However, the dynamic behavior of ferrogels remains largely unveiled. In this paper, we consider a one-dimensional chain consisting of magnetic dipoles and elastic springs between them as a simple model for ferrogels. The model is evaluated by corresponding simulations. To probe the dynamics theoretically, we investigate a continuum limit of the energy governing the system and the corresponding equation of motion. We provide general classification scenarios for the dynamics, elucidating the touching/detachment dynamics of the magnetic particles along the chain. In particular, it is verified in certain cases that the long-time relaxation corresponds to solutions of shock-wave propagation, while formations of particle pairs underlie the initial stage of the dynamics. We expect that these results will provide insight into the understanding of the dynamics of more realistic models with randomness in parameters and time-dependent magnetic fields.

  1. Exciton-relaxation dynamics in lead halides

    International Nuclear Information System (INIS)

    Iwanaga, Masanobu; Hayashi, Tetsusuke

    2003-01-01

    We survey recent comprehensive studies of exciton relaxation in the crystals of lead halides. The luminescence and electron-spin-resonance studies have revealed that excitons in lead bromide spontaneously dissociate and both electrons and holes get self-trapped individually. Similar relaxation has been also clarified in lead chloride. The electron-hole separation is ascribed to repulsive correlation via acoustic phonons. Besides, on the basis of the temperature profiles of self-trapped states, we discuss the origin of luminescence components which are mainly induced under one-photon excitation into the exciton band in lead fluoride, lead chloride, and lead bromide

  2. Relaxation dynamics and coherent energy exchange in coupled vibration-cavity polaritons (Conference Presentation)

    Science.gov (United States)

    Simpkins, Blake S.; Fears, Kenan P.; Dressick, Walter J.; Dunkelberger, Adam D.; Spann, Bryan T.; Owrutsky, Jeffrey C.

    2016-09-01

    Coherent coupling between an optical transition and confined optical mode have been investigated for electronic-state transitions, however, only very recently have vibrational transitions been considered. Here, we demonstrate both static and dynamic results for vibrational bands strongly coupled to optical cavities. We experimentally and numerically describe strong coupling between a Fabry-Pérot cavity and carbonyl stretch ( 1730 cm 1) in poly-methylmethacrylate and provide evidence that the mixed-states are immune to inhomogeneous broadening. We investigate strong and weak coupling regimes through examination of cavities loaded with varying concentrations of a urethane monomer. Rabi splittings are in excellent agreement with an analytical description using no fitting parameters. Ultrafast pump-probe measurements reveal transient absorption signals over a frequency range well-separated from the vibrational band, as well as drastically modified relaxation rates. We speculate these modified kinetics are a consequence of the energy proximity between the vibration-cavity polariton modes and excited state transitions and that polaritons offer an alternative relaxation path for vibrational excitations. Varying the polariton energies by angle-tuning yields transient results consistent with this hypothesis. Furthermore, Rabi oscillations, or quantum beats, are observed at early times and we see evidence that these coherent vibration-cavity polariton excitations impact excited state population through cavity losses. Together, these results indicate that cavity coupling may be used to influence both excitation and relaxation rates of vibrations. Opening the field of polaritonic coupling to vibrational species promises to be a rich arena amenable to a wide variety of infrared-active bonds that can be studied in steady state and dynamically.

  3. Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

    Directory of Open Access Journals (Sweden)

    Vizcaíno Sergio F

    2004-04-01

    Full Text Available Abstract Background Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. Results We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. Conclusions The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.

  4. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  5. Next generation extended Lagrangian first principles molecular dynamics.

    Science.gov (United States)

    Niklasson, Anders M N

    2017-08-07

    Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

  6. Low Parametric Sensitivity Realizations with relaxed L2-dynamic-range-scaling constraints

    OpenAIRE

    Hilaire , Thibault

    2009-01-01

    This paper presents a new dynamic-range scaling for the implementation of filters/controllers in state-space form. Relaxing the classical L2-scaling constraints by specific fixed-point considerations allows for a higher degree of freedom for the optimal L2-parametric sensitivity problem. However, overflows in the implementation are still prevented. The underlying constrained problem is converted into an unconstrained problem for which a solution can be provided. This leads to realizations whi...

  7. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  8. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  9. Study of the Molecular Dynamics of Multiarm Star Polymers with a Poly(ethyleneimine) Core and Poly(lactide) Multiarms.

    Science.gov (United States)

    Román, Frida; Colomer, Pere; Calventus, Yolanda; Hutchinson, John M

    2017-02-04

    Multiarm star polymers, denoted PEI x -PLA y and containing a hyperbranched poly(ethyleneimine) (PEI) core of different molecular weights x and poly(lactide) (PLA) arms with y ratio of lactide repeat units to N links were used in this work. Samples were preconditioned to remove the moisture content and then characterized by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and dielectric relaxation spectroscopy (DRS). The glass transition temperature, T g , is between 48 and 50 °C for all the PEI x -PLA y samples. The dielectric curves show four dipolar relaxations: γ, β, α, and α' in order of increasing temperature. The temperatures at which these relaxations appear, together with their dependence on the frequency, allows relaxation maps to be drawn, from which the activation energies of the sub- T g γ- and β-relaxations and the Vogel-Fulcher-Tammann parameters of the α-relaxation glass transition are obtained. The dependence of the characteristic features of these relaxations on the molecular weight of the PEI core and on the ratio of lactide repeat units to N links permits the assignation of molecular motions to each relaxation. The γ-relaxation is associated with local motions of the -OH groups of the poly(lactide) chains, the β-relaxation with motions of the main chain of poly(lactide), the α-relaxation with global motions of the complete assembly of PEI core and PLA arms, and the α'-relaxation is related to the normal mode relaxation due to fluctuations of the end-to-end vector in the PLA arms, without excluding the possibility that it could be a Maxwell-Wagner-Sillars type ionic peak because the material may have nano-regions of different conductivity.

  10. Study of the Molecular Dynamics of Multiarm Star Polymers with a Poly(ethyleneimine Core and Poly(lactide Multiarms

    Directory of Open Access Journals (Sweden)

    Frida Román

    2017-02-01

    Full Text Available Multiarm star polymers, denoted PEIx-PLAy and containing a hyperbranched poly(ethyleneimine (PEI core of different molecular weights x and poly(lactide (PLA arms with y ratio of lactide repeat units to N links were used in this work. Samples were preconditioned to remove the moisture content and then characterized by thermogravimetric analysis (TGA, differential scanning calorimetry (DSC and dielectric relaxation spectroscopy (DRS. The glass transition temperature, Tg, is between 48 and 50 °C for all the PEIx-PLAy samples. The dielectric curves show four dipolar relaxations: γ, β, α, and α′ in order of increasing temperature. The temperatures at which these relaxations appear, together with their dependence on the frequency, allows relaxation maps to be drawn, from which the activation energies of the sub-Tg γ- and β-relaxations and the Vogel–Fulcher–Tammann parameters of the α-relaxation glass transition are obtained. The dependence of the characteristic features of these relaxations on the molecular weight of the PEI core and on the ratio of lactide repeat units to N links permits the assignation of molecular motions to each relaxation. The γ-relaxation is associated with local motions of the –OH groups of the poly(lactide chains, the β-relaxation with motions of the main chain of poly(lactide, the α-relaxation with global motions of the complete assembly of PEI core and PLA arms, and the α′-relaxation is related to the normal mode relaxation due to fluctuations of the end-to-end vector in the PLA arms, without excluding the possibility that it could be a Maxwell–Wagner–Sillars type ionic peak because the material may have nano-regions of different conductivity.

  11. Selective optical switching of interface-coupled relaxation dynamics in carbon nanotube-Si heterojunctions

    KAUST Repository

    Ponzoni, Stefano

    2014-10-16

    By properly tuning the photon energy of a femtosecond laser pump, we disentangle, in carbon nanotube-Si (CNT/Si) heterojunctions, the fast relaxation dynamics occurring in CNT from the slow repopulation dynamics due to hole charge transfer at the junction. In this way we are able to track the transfer of the photogenerated holes from the Si depletion layer to the CNT layer, under the action of the built-in heterojunction potential. This also clarifies that CNT play an active role in the junction and do not act only as channels for charge collection and transport.

  12. Selective optical switching of interface-coupled relaxation dynamics in carbon nanotube-Si heterojunctions

    KAUST Repository

    Ponzoni, Stefano; Galimberti, Gianluca; Sangaletti, L.; Castrucci, Paola; Del Gobbo, Silvano; Morbidoni, Maurizio; Scarselli, Manuela A.; Pagliara, Stefania

    2014-01-01

    By properly tuning the photon energy of a femtosecond laser pump, we disentangle, in carbon nanotube-Si (CNT/Si) heterojunctions, the fast relaxation dynamics occurring in CNT from the slow repopulation dynamics due to hole charge transfer at the junction. In this way we are able to track the transfer of the photogenerated holes from the Si depletion layer to the CNT layer, under the action of the built-in heterojunction potential. This also clarifies that CNT play an active role in the junction and do not act only as channels for charge collection and transport.

  13. Structural relaxation in the dynamics of glycerol: a joint visible, UV and x-ray inelastic scattering study

    International Nuclear Information System (INIS)

    Giugni, A; Cunsolo, A

    2006-01-01

    We describe an experimental study of the dynamic structure factor of liquid glycerol performed by complementary inelastic techniques such as Brillouin visible, ultraviolet and x-ray scattering. The spectra have been collected as a function of both temperature and momentum transfer. The relevant hypersonic parameters are evaluated from the spectral lineshape analysis modelling the data with a simple hydrodynamic profile. The study of their frequency dependence allows us to observe the occurrence of an active structural relaxation and to measure the related timescale. We also find signatures of further relaxation processes occurring below the accessible frequency window. As a result, the dynamic window traditionally probed in spectroscopic experiments is greatly extended and partially bridges the gap between MHz and THz techniques

  14. Mechanisms of relaxation and spin decoherence in nanomagnets

    Science.gov (United States)

    van Tol, Johan

    Relaxation in spin systems is of great interest with respect to various possible applications like quantum information processing and storage, spintronics, and dynamic nuclear polarization (DNP). The implementation of high frequencies and fields is crucial in the study of systems with large zero-field splitting or large interactions, as for example molecular magnets and low dimensional magnetic materials. Here we will focus on the implementation of pulsed Electron Paramagnetic Resonance (ERP) at multiple frequencies of 10, 95, 120, 240, and 336 GHz, and the relaxation and decoherence processes as a function of magnetic field and temperature. Firstly, at higher frequencies the direct single-phonon spin-lattice relaxation (SLR) is considerably enhanced, and will more often than not be the dominant relaxation mechanism at low temperatures, and can be much faster than at lower fields and frequencies. In principle the measurement of the SLR rates as a function of the frequency provides a means to map the phonon density of states. Secondly, the high electron spin polarization at high fields has a strong influence on the spin fluctuations in relatively concentrated spin systems, and the contribution of the electron-electron dipolar interactions to the coherence rate can be partially quenched at low temperatures. This not only allows the study of relatively concentrated spin systems by pulsed EPR (as for example magnetic nanoparticles and molecular magnets), it enables the separation of the contribution of the fluctuations of the electron spin system from other decoherence mechanisms. Besides choice of temperature and field, several strategies in sample design, pulse sequences, or clock transitions can be employed to extend the coherence time in nanomagnets. A review will be given of the decoherence mechanisms with an attempt at a quantitative comparison of experimental rates with theory.

  15. Exploring Nuclear Photorelaxation of Pyranine in Aqueous Solution: an Integrated Ab-Initio Molecular Dynamics and Time Resolved Vibrational Analysis Approach.

    Science.gov (United States)

    Chiariello, Maria Gabriella; Rega, Nadia

    2018-03-22

    Advances in time-resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time-dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab initio molecular dynamics within an hybrid quantum mechanical/molecular mechanics framework and a time-resolved vibrational analysis based on the Wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm -1 . We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely, those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm -1 and the deformation at 280 cm -1 , are photoactivated by the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favoring the preparatory step for the photoreactivity.

  16. Crossover from Rouse dynamics to the α-relaxation in poly(vinyl ...

    Indian Academy of Sciences (India)

    directly at the structure factor peak [1–3], is subject to the same universalities as ... Recently, molecular dynamics simulations [11] as well as mode coupling theory ..... appears to relate to the internal dynamics within the Gaussian blobs.

  17. Rouse mode analysis of chain relaxation in polymer nanocomposites.

    Science.gov (United States)

    Kalathi, Jagannathan T; Kumar, Sanat K; Rubinstein, Michael; Grest, Gary S

    2015-05-28

    Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer-solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Thus, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.

  18. Dielectric relaxation spectra of liquid crystals in relation to molecular structure

    International Nuclear Information System (INIS)

    Wrobel, S.

    1986-07-01

    The dielectric spectra obtained for some members of two homologous series, i.e. for di-alkoxyazoxybenzenes and penthyl-alkoxythiobenzoates, are discussed qualitatively on the basis of the Nordio-Rigatti-Segre diffusion model. It is additionally assumed that the molecular reorientations take place about the principal axes of the inertia tensor. The distribution of correlation times, which is strongly temperature dependent in the vicinity of the clearing point, is interpreted as being caused by fluctuations of the principal axes frame which are due to conformation changes inside the end chains. The Bauer equation is used to describe both principal molecular reorientations, i.e. the reorientations about the long and short axis, observed in liquid crystalline structure by means of dielectric relaxation methods. The energies and entropies of activation have been computed for both principal reorientations. The differences between the high frequency limit of the dielectric permittivity and the refractive index squared of liquid crystals are explained in terms of two librational motions of the molecules observed by other experimental techniques, viz. far infra-red, Raman and inelastic neutron scattering spectroscopies, and found in this work on the basis of dielectrically measured energy barriers. It has been shown qualitatively that intramolecular libratory motions greatly effect the high frequency dielectric spectrum. Finally, molecular motions in liquid crystals are divided into two types: coherent and incoherent. 127 refs., 56 figs., 17 tabs. (author)

  19. Translational and rotational diffusion of dilute solid amorphous spherical nanocolloids by molecular dynamics simulation

    Science.gov (United States)

    Heyes, D. M.; Nuevo, M. J.; Morales, J. J.

    Following on from our previous study (Heyes, D. M., Nuevo, M. J, and Morales, J. J., 1996, Molec. Phys., 88, 1503), molecular dynamics simulations have been carried out of translational and rotational diffusion of atomistically rough near-spherical solid Lennard-Jones (LJ) clusters immersed in a Weeks-Chandler-Andersen liquid solvent. A single cluster consisting of up to about 100LJ particles as part of an 8000 atom fluid system was considered in each case. The translational and rotational diffusion coefficients decrease with increasing cluster size and solvent density (roughly in proportion to the molar volume of the solvent). The simulations reveal that for clusters in excess of about 30LJ atoms there is a clear separation of timescales between angular velocity and orientation relaxation which adhere well to the small-step diffusion model encapsulated in Hubbard's relationship. For 100 atom clusters both the StokesEinstein (translation) and Stokes-Einstein-Debye (rotation) equations apply approximately. The small departures from these reference solutions indicate that the translational relaxation experiences a local viscosity in excess of the bulk value (typically by ~ 30%), whereas rotational relaxation experiences a smaller viscosity than the bulk (typically by ~ 30%) reasonably in accord with the Gierer-Wirtz model. Both of these observations are consistent with an observed layering of the liquid molecules next to the cluster observed in our previous study.

  20. Molecular, dynamic, and structural origin of inhomogeneous magnetization transfer in lipid membranes.

    Science.gov (United States)

    Swanson, Scott D; Malyarenko, Dariya I; Fabiilli, Mario L; Welsh, Robert C; Nielsen, Jon-Fredrik; Srinivasan, Ashok

    2017-03-01

    To elucidate the dynamic, structural, and molecular properties that create inhomogeneous magnetization transfer (ihMT) contrast. Amphiphilic lipids, lamellar phospholipids with cholesterol, and bovine spinal cord (BSC) specimens were examined along with nonlipid systems. Magnetization transfer (MT), enhanced MT (eMT, obtained with double-sided radiofrequency saturation), ihMT (MT - eMT), and dipolar relaxation, T 1D , were measured at 2.0 and 11.7 T. The amplitude of ihMT ratio (ihMTR) is positively correlated with T 1D values. Both ihMTR and T 1D increase with increasing temperature in BSC white matter and in phospholipids and decrease with temperature in other lipids. Changes in ihMTR with temperature arise primarily from alterations in MT rather than eMT. Spectral width of MT, eMT, and ihMT increases with increasing carbon chain length. Concerted motions of phospholipids in white matter decrease proton spin diffusion leading to increased proton T 1D times and increased ihMT amplitudes, consistent with decoupling of Zeeman and dipolar spin reservoirs. Molecular specificity and dynamic sensitivity of ihMT contrast make it a suitable candidate for probing myelin membrane disorders. Magn Reson Med 77:1318-1328, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  1. Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

    Energy Technology Data Exchange (ETDEWEB)

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

  2. Molecular rotation-vibration dynamics of low-symmetric hydrate crystal in the terahertz region.

    Science.gov (United States)

    Fu, Xiaojian; Wu, Hongya; Xi, Xiaoqing; Zhou, Ji

    2014-01-16

    The rotational and vibrational dynamics of molecules in copper sulfate pentahydrate crystal are investigated with terahertz dielectric spectra. It is shown that the relaxation-like dielectric dispersion in the low frequency region is related to the reorientation of water molecules under the driving of terahertz electric field, whereas the resonant dispersion can be ascribed to lattice vibration. It is also found that, due to the hydrogen-bond effect, the vibrational mode at about 1.83 THz along [-111] direction softens with decreasing temperature, that is, the crystal expands in this direction when cooled. On the contrary, the mode hardens in the direction perpendicular to [-111] during the cooling process. This contributes to the further understanding of the molecular structure and bonding features of hydrate crystals.

  3. Ion peening and stress relaxation induced by low-energy atom bombardment of covalent solids

    International Nuclear Information System (INIS)

    Koster, Monika; Urbassek, Herbert M.

    2001-01-01

    Using molecular-dynamics simulation, we study the buildup and relaxation of stress induced by low-energy (≤150 eV) atom bombardment of a target material. The effect is brought out most clearly by using an initially compressed specimen. As target material, we employ Si, based on the Tersoff potential. By varying the bond strength in the potential, we can specifically study its effect on damage production and stress changes. We find that in general, stress is relaxed by the atom bombardment; only for low bombarding energies and strong bonds, atom bombardment increases stress. We rationalize this behavior by considering the role of energized atoms and of recoil-implanted target atoms

  4. Applicability of mode-coupling theory to polyisobutylene: a molecular dynamics simulation study.

    Science.gov (United States)

    Khairy, Y; Alvarez, F; Arbe, A; Colmenero, J

    2013-10-01

    The applicability of Mode Coupling Theory (MCT) to the glass-forming polymer polyisobutylene (PIB) has been explored by using fully atomistic molecular dynamics simulations. MCT predictions for the so-called asymptotic regime have been successfully tested on the dynamic structure factor and the self-correlation function of PIB main-chain carbons calculated from the simulated cell. The factorization theorem and the time-temperature superposition principle are satisfied. A consistent fitting procedure of the simulation data to the MCT asymptotic power-laws predicted for the α-relaxation regime has delivered the dynamic exponents of the theory-in particular, the exponent parameter λ-the critical non-ergodicity parameters, and the critical temperature T(c). The obtained values of λ and T(c) agree, within the uncertainties involved in both studies, with those deduced from depolarized light scattering experiments [A. Kisliuk et al., J. Polym. Sci. Part B: Polym. Phys. 38, 2785 (2000)]. Both, λ and T(c)/T(g) values found for PIB are unusually large with respect to those commonly obtained in low molecular weight systems. Moreover, the high T(c)/T(g) value is compatible with a certain correlation of this parameter with the fragility in Angell's classification. Conversely, the value of λ is close to that reported for real polymers, simulated "realistic" polymers and simple polymer models with intramolecular barriers. In the framework of the MCT, such finding should be the signature of two different mechanisms for the glass-transition in real polymers: intermolecular packing and intramolecular barriers combined with chain connectivity.

  5. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  6. Restricted lithium ion dynamics in PEO-based block copolymer electrolytes measured by high-field nuclear magnetic resonance relaxation

    Science.gov (United States)

    Huynh, Tan Vu; Messinger, Robert J.; Sarou-Kanian, Vincent; Fayon, Franck; Bouchet, Renaud; Deschamps, Michaël

    2017-10-01

    The intrinsic ionic conductivity of polyethylene oxide (PEO)-based block copolymer electrolytes is often assumed to be identical to the conductivity of the PEO homopolymer. Here, we use high-field 7Li nuclear magnetic resonance (NMR) relaxation and pulsed-field-gradient (PFG) NMR diffusion measurements to probe lithium ion dynamics over nanosecond and millisecond time scales in PEO and polystyrene (PS)-b-PEO-b-PS electrolytes containing the lithium salt LiTFSI. Variable-temperature longitudinal (T1) and transverse (T2) 7Li NMR relaxation rates were acquired at three magnetic field strengths and quantitatively analyzed for the first time at such fields, enabling us to distinguish two characteristic time scales that describe fluctuations of the 7Li nuclear electric quadrupolar interaction. Fast lithium motions [up to O (ns)] are essentially identical between the two polymer electrolytes, including sub-nanosecond vibrations and local fluctuations of the coordination polyhedra between lithium and nearby oxygen atoms. However, lithium dynamics over longer time scales [O (10 ns) and greater] are slower in the block copolymer compared to the homopolymer, as manifested experimentally by their different transverse 7Li NMR relaxation rates. Restricted dynamics and altered thermodynamic behavior of PEO chains anchored near PS domains likely explain these results.

  7. Water interactions with varying molecular states of bovine casein: 2H NMR relaxation studies

    International Nuclear Information System (INIS)

    Kumosinski, T.F.; Pessen, H.; Prestrelski, S.J.; Farrell, H.M. Jr.

    1987-01-01

    The caseins occur in milk as spherical colloidal complexes of protein and salts with an average diameter of 1200 A, the casein micelles. Removal of Ca2+ is thought to result in their dissociation into smaller protein complexes stabilized by hydrophobic interactions and called submicelles. Whether these submicelles actually occur within the micelles as discrete particles interconnected by calcium phosphate salt bridges has been the subject of much controversy. A variety of physical measurements have shown that casein micelles contain an inordinately high amount of trapped water (2 to 7 g H 2 O/g protein). With this in mind it was of interest to determine if NMR relaxation measurements could detect the presence of this trapped water within the micelles, and to evaluate whether it is a continuum with picosecond correlation times or is associated in part with discrete submicellar structures with nanosecond motions. For this purpose the variations in 2 H NMR longitudinal and transverse relaxation rates of water with protein concentration were determined for bovine casein at various temperatures, under both submicellar and micellar conditions. D 2 O was used instead of H 2 O to eliminate cross-relaxation effects. From the protein concentration dependence of the relaxation rates, the second virial coefficient of the protein was obtained by nonlinear regression analysis. Using either an isotropic tumbling or an intermediate asymmetry model, degrees of hydration, v, and correlation times, tau c, were calculated for the caseins; from the latter parameter the Stokes radius, r, was obtained. Next, estimates of molecular weights were obtained from r and the partial specific volume. Values were in the range of those published from other methodologies for the submicelles

  8. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

  9. Dielectric studies of molecular motions in glassy and liquid nicotine

    Energy Technology Data Exchange (ETDEWEB)

    Kaminski, K [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Paluch, M [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Ziolo, J [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Ngai, K L [Naval Research Laboratory, Washington DC 20375-5320 (United States)

    2006-06-21

    The dielectric permittivity and loss spectra of glassy and liquid states of nicotine have been measured over the frequency range 10{sup -2}-10{sup 9} Hz. The relaxation spectra are similar to common small molecular glass-forming substances, showing the structural {alpha}-relaxation and its precursor, the Johari-Goldstein {beta}-relaxation. The {alpha}-relaxation is well described by the Fourier transform of the Kohlrausch-Williams-Watts stretched exponential function with an approximately constant stretch exponent that is equal to 0.70 as the glass transition temperature is approached. The dielectric {alpha}-relaxation time measured over 11 orders of magnitude cannot be described by a single Vogel-Fulcher-Tamman-Hesse equation. The most probable Johari-Goldstein {beta}-relaxation time determined from the dielectric spectra is in good agreement with the primitive relaxation time of the coupling model calculated from parameters of the structural {alpha}-relaxation. The shape of the dielectric spectra of nicotine is compared with that of other glass-formers having about the same stretch exponent, and they are shown to be nearly isomorphic. The results indicate that the molecular dynamics of nicotine conform to the general pattern found in other glass-formers, and the presence of the universal Johari-Goldstein secondary relaxation, which plays a role in the crystallization of amorphous pharmaceuticals.

  10. Numerical method of lines for the relaxational dynamics of nematic liquid crystals.

    Science.gov (United States)

    Bhattacharjee, A K; Menon, Gautam I; Adhikari, R

    2008-08-01

    We propose an efficient numerical scheme, based on the method of lines, for solving the Landau-de Gennes equations describing the relaxational dynamics of nematic liquid crystals. Our method is computationally easy to implement, balancing requirements of efficiency and accuracy. We benchmark our method through the study of the following problems: the isotropic-nematic interface, growth of nematic droplets in the isotropic phase, and the kinetics of coarsening following a quench into the nematic phase. Our results, obtained through solutions of the full coarse-grained equations of motion with no approximations, provide a stringent test of the de Gennes ansatz for the isotropic-nematic interface, illustrate the anisotropic character of droplets in the nucleation regime, and validate dynamical scaling in the coarsening regime.

  11. Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: longitudinal relaxation dispersion for spin I = 1.

    Science.gov (United States)

    Nilsson, Tomas; Halle, Bertil

    2012-08-07

    The frequency dependence of the longitudinal relaxation rate, known as the magnetic relaxation dispersion (MRD), can provide a frequency-resolved characterization of molecular motions in complex biological and colloidal systems on time scales ranging from 1 ns to 100 μs. The conformational dynamics of immobilized proteins and other biopolymers can thus be probed in vitro or in vivo by exploiting internal water molecules or labile hydrogens that exchange with a dominant bulk water pool. Numerous water (1)H and (2)H MRD studies of such systems have been reported, but the widely different theoretical models currently used to analyze the MRD data have resulted in divergent views of the underlying molecular motions. We have argued that the essential mechanism responsible for the main dispersion is the exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings when internal water molecules or labile hydrogens escape from orientationally confining macromolecular sites. In the EMOR model, the exchange process is thus not just a means of mixing spin populations but it is also the direct cause of spin relaxation. Although the EMOR theory has been used in several studies to analyze water (2)H MRD data from immobilized biopolymers, the fully developed theory has not been described. Here, we present a comprehensive account of a generalized version of the EMOR theory for spin I = 1 nuclides like (2)H. As compared to a previously described version of the EMOR theory, the present version incorporates three generalizations that are all essential in applications to experimental data: (i) a biaxial (residual) electric field gradient tensor, (ii) direct and indirect effects of internal motions, and (iii) multiple sites with different exchange rates. In addition, we describe and assess different approximations to the exact EMOR theory that are useful in various regimes. In particular, we consider the experimentally

  12. Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

    International Nuclear Information System (INIS)

    Perez, Danny

    2012-01-01

    We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

  13. Molecular dynamics of amorphous pharmaceutical fenofibrate studied by broadband dielectric spectroscopy

    Directory of Open Access Journals (Sweden)

    U. Sailaja

    2016-06-01

    Full Text Available Fenofibrate is mainly used to reduce cholesterol level in patients at risk of cardiovascular disease. Thermal transition study with the help of differential scanning calorimetry (DSC shows that the aforesaid active pharmaceutical ingredient (API is a good glass former. Based on our DSC study, the molecular dynamics of this API has been carried out by broadband dielectric spectroscopy (BDS covering wide temperature and frequency ranges. Dielectric measurements of amorphous fenofibrate were performed after its vitrification by fast cooling from a few degrees above the melting point (Tm=354.11 K to deep glassy state. The sample does not show any crystallization tendency during cooling and reaches the glassy state. The temperature dependence of the structural relaxation has been fitted by single Vogel–Fulcher–Tamman (VFT equation. From VFT fit, glass transition temperature (Tg was estimated as 250.56 K and fragility (m was determined as 94.02. This drug is classified as a fragile glass former. Deviations of experimental data from Kohlrausch–Williams–Watts (KWW fits on high-frequency flank of α-peak indicate the presence of an excess wing in fenofibrate. Based on Ngai׳s coupling model, we identified the excess wing as true Johari–Goldstein (JG process. Below the glass transition temperature one can clearly see a secondary relaxation (γ with an activation energy of 32.67 kJ/mol.

  14. Molecular dynamics simulations of self-diffusion near a symmetrical tilt grain boundary in UO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Vincent-Aublant, E.; Delaye, J.M. [CEA-Marcoule, DEN/DTCD/SECM, B.P. 17171, 30207 Bagnols sur Ceze cedex (France); Van Brutzel, L. [CEA-Saclay, DEN-DANS/DPC/SCP/LM2T, 91191 Gif-sur-Yvette (France)

    2008-07-01

    Molecular dynamics (MD) simulations have been used to study the influence of symmetrical tilt grain boundaries (GBs) in stoichiometric UO{sub 2} on uranium and oxygen self-diffusions. The study was performed on a large range of temperature varying from 300 K to 2100 K. First, the effect of the temperature on the structure and the formation energies of 6 relaxed tilt GBs was investigated. The {sigma}5 and {sigma}41 GBs geometries were chosen to study the diffusion. O and U diffusion coefficients have been calculated and compared to those obtained in a perfect stoichiometric UO{sub 2} as well as in over and under-stoichiometric matrices. (authors)

  15. Backbone dynamics of the human CC-chemokine eotaxin

    Energy Technology Data Exchange (ETDEWEB)

    Ye Jiqing; Mayer, Kristen L.; Stone, Martin J. [Indiana University, Department of Chemistry (United States)

    1999-10-15

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. {sup 15}N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. {sup 15}N longitudinal (R{sub 1}) and transverse (R{sub 2}) auto relaxation rates, heteronuclear {sup 1}H-{sup 15}N steady-state NOEs, and transverse cross-relaxation rates ({eta}{sub xy}) were obtained at 30 deg. C for all resolved backbone secondary amide groups using {sup 1} H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time ({tau}{sub m}) is 5.09{+-}0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (D{sub parallel}/D{sub perpendicular}) is 0.81{+-}0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two {beta}-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization.

  16. Atomic motions in the αβ-region of glass-forming polymers: molecular versus mode coupling theory approach

    International Nuclear Information System (INIS)

    Colmenero, Juan; Narros, Arturo; Alvarez, Fernando; Arbe, Arantxa; Moreno, Angel J

    2007-01-01

    We present fully atomistic molecular dynamics simulation results on a main-chain polymer, 1,4-polybutadiene, in the merging region of the α- and β-relaxations. A real-space analysis reveals the occurrence of localized motions ('β-like') in addition to the diffusive structural relaxation. A molecular approach provides a direct connection between the local conformational changes reflected in the atomic motions and the secondary relaxations in this polymer. Such local processes occur just in the time window where the β-process of the mode coupling theory is expected. We show that the application of this theory is still possible and yields an unusually large value of the exponent parameter. This result might originate from the competition between two mechanisms for dynamic arrest: intermolecular packing and intramolecular barriers for local conformational changes ('β-like')

  17. Role of Thickness Confinement on Relaxations of the Fast Component in a Miscible A/B Blend

    Energy Technology Data Exchange (ETDEWEB)

    Green, Peter [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sharma, Ravi P. [University of Michigan; Dong, Ban Xuan [University of Michigan

    2018-01-18

    Spatial compositional heterogeneity strongly influences the dynamics of the A and B components of bulk miscible blends. Its effects are especially apparent in mixtures, such as poly(vinyl methyl ether) (PVME)/polystyrene (PS), where there exist significant disparities between the component glass transition temperatures (Tgs) and relaxation times. The relaxation processes characterized by distinct temperature dependencies and relaxation rates manifest different local compositional environments for temperatures above and below the glass transition temperature of the miscible blend. This same behavior is shown to exist in miscible PS/PVME films as thin as 100 nm. Moreover, in thin films, the characteristic segmental relaxation times t of the PVME component of miscible PVME/PS blends confined between aluminum (Al) substrates decrease with increasing molecular weight M of the PS component. These relaxation rates are film thickness dependent, in films up to a few hundred nanometers in thickness. This is in remarkable contrast to homopolymer films, where thickness confinement effects are apparent only on length scales on the order of nanometers. These surprisingly large length scales and M dependence are associated with the preferential interfacial enrichment - wetting layer formation - of the PVME component at the external Al interfaces, which alters the local spatial blend composition within the interior of the film. The implications are that the dynamics of miscible thin film blends are dictated in part by component Tg differences, disparities in component relaxation rates, component-substrate interactions, and chain lengths (entropy of mixing).

  18. Semiquantum molecular dynamics simulation of thermal properties and heat transport in low-dimensional nanostructures

    Science.gov (United States)

    Savin, Alexander V.; Kosevich, Yuriy A.; Cantarero, Andres

    2012-08-01

    We present a detailed description of semiquantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the effects of phonon quantum statistics are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of thermal properties and heat transport in different low-dimensional nanostructures. We describe the determination of temperature in quantum lattice systems, to which the equipartition limit is not applied. We show that one can determine the temperature of such a system from the measured power spectrum and temperature- and relaxation-rate-independent density of vibrational (phonon) states. We simulate the specific heat and heat transport in carbon nanotubes, as well as the heat transport in molecular nanoribbons with perfect (atomically smooth) and rough (porous) edges, and in nanoribbons with strongly anharmonic periodic interatomic potentials. We show that the effects of quantum statistics of phonons are essential for the carbon nanotube in the whole temperature range T<500K, in which the values of the specific heat and thermal conductivity of the nanotube are considerably less than that obtained within the description based on classical statistics of phonons. This conclusion is also applicable to other carbon-based materials and systems with high Debye temperature like graphene, graphene nanoribbons, fullerene, diamond, diamond nanowires, etc. We show that the existence of rough edges and quantum statistics of phonons change drastically the low-temperature thermal conductivity of the nanoribbon in comparison with that of the nanoribbon with perfect edges and classical phonon dynamics and statistics. The semiquantum molecular

  19. Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes.

    Science.gov (United States)

    Hatmal, Ma'mon M; Taha, Mutasem O

    2018-04-23

    We previously combined molecular dynamics (classical or simulated annealing) with ligand-receptor contacts analysis as a means to extract valid pharmacophore model(s) from single ligand-receptor complexes. However, molecular dynamics methods are computationally expensive and time-consuming. Here we describe a novel method for extracting valid pharmacophore model(s) from a single crystallographic structure within a reasonable time scale. The new method is based on ligand-receptor contacts analysis following energy relaxation of a predetermined set of randomly deformed complexes generated from the targeted crystallographic structure. Ligand-receptor contacts maintained across many deformed/relaxed structures are assumed to be critical and used to guide pharmacophore development. This methodology was implemented to develop valid pharmacophore models for PI3K-γ, RENIN, and JAK1. The resulting pharmacophore models were validated by receiver operating characteristic (ROC) analysis against inhibitors extracted from the CHEMBL database. Additionally, we implemented pharmacophores extracted from PI3K-γ to search for new inhibitors from the National Cancer Institute list of compounds. The process culminated in new PI3K-γ/mTOR inhibitory leads of low micromolar IC 50 s.

  20. Relaxation dynamics of the conductive processes for PbNb2O6 ferroelectric ceramics in the frequency and time domain

    International Nuclear Information System (INIS)

    Gonzalez, R L; Leyet, Y; Guerrero, F; Guerra, J de Los S; Venet, M; Eiras, J A

    2007-01-01

    The relaxation dynamics of the conductive process present in PbNb 2 O 6 piezoelectric ceramics was investigated. A relaxation function in the time domain, Φ(t), was found from the frequency dependence of the dielectric modulus (imaginary component, M'') by using a relaxation function in the frequency domain, F*(ω). The best relaxation function, F*(ω), was found to be a Cole-Cole distribution function, in which relaxation characteristic parameters, such as α and τ CC , are involved. On the other hand, the relaxation function, Φ(t), obtained by the time domain method, was found to be a Kohlrausch-Williams-Watts (KWW) function type. The thermal evolution of the characteristics parameters of the KWW function (β and τ*) was analysed. The values of the activation energy (E a ), obtained in the whole investigated temperature interval, suggest the existence of a relaxation mechanism (a conductive process), which may be interpreted by an ion hopping between neighbouring sites within the crystalline lattice. The results are corroborated with the formalism of the AC conductivity

  1. Dynamics of exciton relaxation in LH2 antenna probed by multipulse nonlinear spectroscopy.

    Science.gov (United States)

    Novoderezhkin, Vladimir I; Cohen Stuart, Thomas A; van Grondelle, Rienk

    2011-04-28

    We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump-dump-probe spectroscopy (Th. A. Cohen Stuart, M. Vengris, V. I. Novoderezhkin, R. J. Cogdell, C. N. Hunter, R. van Grondelle, submitted). The theory of pump-dump-probe response is evaluated using the doorway-window approach in combination with the modified Redfield theory. We demonstrate that a simultaneous fit of linear spectra, pump-probe, and pump-dump-probe kinetics can be obtained at a quantitative level using the disordered exciton model, which is essentially the same as used to model the spectral fluctuations in single LH2 complexes (Novoderezhkin, V.; Rutkauskas, D.; van Grondelle, R. Biophys. J. 2006, 90, 2890). The present studies suggest that the observed relaxation rates are strongly dependent on the realization of the disorder. A big spread of the rates (exceeding 3 orders of magnitude) is correlated with the disorder-induced changes in delocalization length and overlap of the exciton wave functions. We conclude that the bulk kinetics reflect a superposition of many pathways corresponding to different physical limits of energy transfer, varying from sub-20 fs relaxation between delocalized and highly spatially overlapping exciton states to >20 ps jumps between states localized at the opposite sides of the ring.

  2. Current-driven dynamics in molecular-scale devices

    International Nuclear Information System (INIS)

    Seideman, Tamar

    2003-01-01

    We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

  3. Dynamical coupling of electrons and ions in Xray-induced dynamics

    International Nuclear Information System (INIS)

    Saalmann, Ulf; Camacho, Abraham; Rost, Jan-Michael

    2015-01-01

    Photo-absorption from short and intense Xray pulses by a molecule or a cluster triggers a complicated electron and ion dynamics. Whereas the excitation process concerns largely core-shell electrons, there are various subsequent relaxation channels like electronic decays and ionic Coulomb explosion. We will discuss the interplay of those processes for molecular clusters and fullerenes. (paper)

  4. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  5. Molecular dissipation phenomena of nanoscopic friction in the heterogeneous relaxation regime of a glass former.

    Science.gov (United States)

    Sills, Scott; Gray, Tomoko; Overney, René M

    2005-10-01

    Nanoscale sliding friction involving a polystyrene melt near its glass transition temperature Tg (373 K) exhibited dissipation phenomena that provide insight into the underlying molecular relaxation processes. A dissipative length scale that shows significant parallelism with the size of cooperatively rearranging regions (CRRs) could be experimentally deduced from friction-velocity isotherms, combined with dielectric loss analysis. Upon cooling to approximately 10 K above Tg, the dissipation length Xd grew from a segmental scale of approximately 3 A to 2.1 nm, following a power-law relationship with the reduced temperature Xd approximately TR-phi. The resulting phi=1.89+/-0.08 is consistent with growth predictions for the length scale of CRRs in the heterogeneous regime of fragile glass formers. Deviations from the power-law behavior closer to Tg suggest that long-range processes, e.g., the normal mode or ultraslow Fischer modes, may couple with the alpha relaxation, leading to energy dissipation in domains of tens of nanometers.

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

    Science.gov (United States)

    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.

  7. Friction tensor for a pair of Brownian particles: Spurious finite-size effects and molecular dynamics estimates

    International Nuclear Information System (INIS)

    Bocquet, L.; Hansen, J.P.; Piasecki, J.

    1997-01-01

    In this work, we show that in any finite system, the binary friction tenser for two Brownian particles cannot be directly estimated from an evaluation of the microscopic Green Kubo formula, involving the time integral of force-force autocorrelation functions. This pitfall is associated with a subtle inversion of the thermodynamic and long-time limits and leads to spurious results for the estimates of the friction matrix based on molecular dynamics simulations. Starting from a careful analysis of the coupled Langevin equations for two interacting Brownian particles, we derive a method to circumvent these effects and extract the binary friction tenser from the correlation function matrix of the instantaneous forces exerted by the bath particles on the fixed Brownian particles, and from the relaxation of the total momentum of the bath in a finite system. The general methodology is applied to the case of two hard or soft Brownian spheres in a bath of light particles. Numerical estimates of the relevant correlation functions and of the resulting self and mutual components of the matrix of friction tensors are obtained by molecular dynamics simulations for various spacings between the Brownian particles

  8. Thermodynamic scaling of molecular dynamics in supercooled liquid state of pharmaceuticals: Itraconazole and ketoconazole.

    Science.gov (United States)

    Tarnacka, M; Madejczyk, O; Adrjanowicz, K; Pionteck, J; Kaminska, E; Kamiński, K; Paluch, M

    2015-06-14

    Pressure-Volume-Temperature (PVT) measurements and broadband dielectric spectroscopy were carried out to investigate molecular dynamics and to test the validity of thermodynamic scaling of two homologous compounds of pharmaceutical activity: itraconazole and ketoconazole in the wide range of thermodynamic conditions. The pressure coefficients of the glass transition temperature (dT(g)/dp) for itraconazole and ketoconazole were determined to be equal to 183 and 228 K/GPa, respectively. However, for itraconazole, the additional transition to the nematic phase was observed and characterized by the pressure coefficient dT(n)/dp = 258 K/GPa. From PVT and dielectric data, we obtained that the liquid-nematic phase transition is governed by the relaxation time since it occurred at constant τ(α) = 10(-5) s. Furthermore, we plotted the obtained relaxation times as a function of T(-1)v(-γ), which has revealed that the validity of thermodynamic scaling with the γ exponent equals to 3.69 ± 0.04 and 3.64 ± 0.03 for itraconazole and ketoconazole, respectively. Further analysis of the scaling parameter in itraconazole revealed that it unexpectedly decreases with increasing relaxation time, which resulted in dramatic change of the shape of the thermodynamic scaling master curve. While in the case of ketoconazole, it remained the same within entire range of data (within experimental uncertainty). We suppose that in case of itraconazole, this peculiar behavior is related to the liquid crystals' properties of itraconazole molecule.

  9. Thermodynamic scaling of molecular dynamics in supercooled liquid state of pharmaceuticals: Itraconazole and ketoconazole

    Energy Technology Data Exchange (ETDEWEB)

    Tarnacka, M., E-mail: mtarnacka@us.edu.pl; Madejczyk, O.; Kamiński, K.; Paluch, M. [Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice (Poland); Silesian Center of Education and Interdisciplinary Research, University of Silesia, ul. 75 Pulku Piechoty 1A, 41-500 Chorzow (Poland); Adrjanowicz, K. [NanoBioMedical Centre, ul. Umultowska 85, 61-614 Poznan (Poland); Pionteck, J. [Leibniz Institute of Polymer Research Dresden, Hohe Strasse 6, D-01069 Dresden (Germany); Kaminska, E. [Department of Pharmacognosy and Phytochemistry, School of Pharmacy and Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, ul. Jagiellonska 4, 41-200 Sosnowiec (Poland)

    2015-06-14

    Pressure-Volume-Temperature (PVT) measurements and broadband dielectric spectroscopy were carried out to investigate molecular dynamics and to test the validity of thermodynamic scaling of two homologous compounds of pharmaceutical activity: itraconazole and ketoconazole in the wide range of thermodynamic conditions. The pressure coefficients of the glass transition temperature (dT{sub g}/dp) for itraconazole and ketoconazole were determined to be equal to 183 and 228 K/GPa, respectively. However, for itraconazole, the additional transition to the nematic phase was observed and characterized by the pressure coefficient dT{sub n}/dp = 258 K/GPa. From PVT and dielectric data, we obtained that the liquid-nematic phase transition is governed by the relaxation time since it occurred at constant τ {sub α} = 10{sup −5} s. Furthermore, we plotted the obtained relaxation times as a function of T{sup −1}v{sup −γ}, which has revealed that the validity of thermodynamic scaling with the γ exponent equals to 3.69 ± 0.04 and 3.64 ± 0.03 for itraconazole and ketoconazole, respectively. Further analysis of the scaling parameter in itraconazole revealed that it unexpectedly decreases with increasing relaxation time, which resulted in dramatic change of the shape of the thermodynamic scaling master curve. While in the case of ketoconazole, it remained the same within entire range of data (within experimental uncertainty). We suppose that in case of itraconazole, this peculiar behavior is related to the liquid crystals’ properties of itraconazole molecule.

  10. Approach to equilibrium of a quantum system and generalization of the Montroll-Shuler equation for vibrational relaxation of a molecular oscillator

    Science.gov (United States)

    Kenkre, V. M.; Chase, M.

    2017-08-01

    The approach to equilibrium of a quantum mechanical system in interaction with a bath is studied from a practical as well as a conceptual point of view. Explicit memory functions are derived for given models of bath couplings. If the system is a harmonic oscillator representing a molecule in interaction with a reservoir, the generalized master equation derived becomes an extension into the coherent domain of the well-known Montroll-Shuler equation for vibrational relaxation and unimolecular dissociation. A generalization of the Bethe-Teller result regarding energy relaxation is found for short times. The theory has obvious applications to relaxation dynamics at ultra-short times as in observations on the femtosecond time scale and to the investigation of quantum coherence at those short times. While vibrational relaxation in chemical physics is a primary target of the study, another system of interest in condensed matter physics, an electron or hole in a lattice subjected to a strong DC electric field that gives rise to well-known Wannier-Stark ladders, is naturally addressed with the theory. Specific system-bath interactions are explored to obtain explicit details of the dynamics. General phenomenological descriptions of the reservoir are considered rather than specific microscopic realizations.

  11. Rational extended thermodynamics of a rarefied polyatomic gas with molecular relaxation processes

    Science.gov (United States)

    Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

    2017-10-01

    We present a more refined version of rational extended thermodynamics of rarefied polyatomic gases in which molecular rotational and vibrational relaxation processes are treated individually. In this case, we need a triple hierarchy of the moment system and the system of balance equations is closed via the maximum entropy principle. Three different types of the production terms in the system, which are suggested by a generalized BGK-type collision term in the Boltzmann equation, are adopted. In particular, the rational extended thermodynamic theory with seven independent fields (ET7) is analyzed in detail. Finally, the dispersion relation of ultrasonic wave derived from the ET7 theory is confirmed by the experimental data for CO2, Cl2, and Br2 gases.

  12. Molecular motions of non-crystalline poly(aryl ether-ether-ketone) PEEK and influence of electron beam irradiation

    International Nuclear Information System (INIS)

    Sasuga, T.; Hagiwara, M.

    1985-01-01

    The dynamic mechanical relaxation of non-crystalline poly(aryl ether-ether-ketone) PEEK and the one irradiated with electron beam were studied. The three distinct γ, β, α' relaxation maxima were observed in unirradiated PEEK from low to high temperature. It was revealed from the study on the irradiation effects that three different molecular processes are overlapped in γ relaxation peak, i.e., molecular motion of water bound to main chain, local motion of main chain, and local mode of the aligned and/or oriented moiety. The β relaxation connected with the glass transition occurred at 150 deg C and it shifted to higher temperature by irradiation. The α' relaxation which can be attributed to rearrangement of molecular chain due to crystallization was observed in unirradiated PEEK approx. 180 deg C and its magnitude decreased with the increase in irradiation dose. This effect indicates the formation of structures inhibiting crystallization such as crosslinking and/or short branching during irradiation. A new relaxation, β', appeared in the temperature range of 40 deg to 100 deg C by irradiation and its magnitude increased with dose. This relaxation was attributed to rearrangement of molecular chain from loosened packing around chain ends, which were introduced into the non-crystalline region by chain scission under irradiation, to more rigid molecular packing. (author)

  13. Bulk viscosity of molecular fluids

    Science.gov (United States)

    Jaeger, Frederike; Matar, Omar K.; Müller, Erich A.

    2018-05-01

    The bulk viscosity of molecular models of gases and liquids is determined by molecular simulations as a combination of a dilute gas contribution, arising due to the relaxation of internal degrees of freedom, and a configurational contribution, due to the presence of intermolecular interactions. The dilute gas contribution is evaluated using experimental data for the relaxation times of vibrational and rotational degrees of freedom. The configurational part is calculated using Green-Kubo relations for the fluctuations of the pressure tensor obtained from equilibrium microcanonical molecular dynamics simulations. As a benchmark, the Lennard-Jones fluid is studied. Both atomistic and coarse-grained force fields for water, CO2, and n-decane are considered and tested for their accuracy, and where possible, compared to experimental data. The dilute gas contribution to the bulk viscosity is seen to be significant only in the cases when intramolecular relaxation times are in the μs range, and for low vibrational wave numbers (<1000 cm-1); This explains the abnormally high values of bulk viscosity reported for CO2. In all other cases studied, the dilute gas contribution is negligible and the configurational contribution dominates the overall behavior. In particular, the configurational term is responsible for the enhancement of the bulk viscosity near the critical point.

  14. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  15. First principles molecular dynamics without self-consistent field optimization

    International Nuclear Information System (INIS)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-01

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

  16. Hydration dynamics near a model protein surface

    International Nuclear Information System (INIS)

    Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

    2003-01-01

    The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces

  17. Anomalous behavior of secondary dielectric relaxation in polypropylene glycols

    Energy Technology Data Exchange (ETDEWEB)

    Grzybowska, K; Grzybowski, A; Ziolo, J; Rzoska, S J; Paluch, M [Institute of Physics, Silesian University, Uniwersytecka 4, 40-007 Katowice (Poland)

    2007-09-19

    A surprising slow down in the dielectric secondary {gamma}-relaxation with temperature increasing near the glass transition is confirmed for several polypropylene glycols. The peculiar behavior diminishes as the molecular weight grows. The minimal model (Dyre and Olsen 2003 Phys. Rev. Lett. 91 155703) is applied successfully to describe the temperature dependences of the {gamma}-relaxation times. The minimal model parameters are analyzed for different molecular weights. A molecular explanation of the {gamma}-process anomaly for polypropylene glycols is proposed on the basis of the minimal model prediction.

  18. Dynamical interactions between solute and solvent studied by nonlinear infrared spectroscopy

    International Nuclear Information System (INIS)

    Ohta, K.; Tominaga, K.

    2006-01-01

    Interactions between solute and solvent play an important role in chemical reaction dynamics and in many relaxation processes in condensed phases. Recently third-order nonlinear infrared (IR) spectroscopy has shown to be useful to investigate solute-solvent interaction and dynamics of the vibrational transition. These studies provide detailed information on the energy relaxation of the vibrationally excited state, and the time scale and the magnitude of the time correlation functions of the vibrational frequency fluctuations. In this work we have studied vibrational energy relaxation (VER) of solutions and molecular complexes by nonlinear IR spectroscopy, especially IR pump-probe method, to understand the microscopic interactions in liquids. (authors)

  19. Substituent effects on the relaxation dynamics of furan, furfural and β-furfural: a combined theoretical and experimental approach.

    Science.gov (United States)

    Oesterling, Sven; Schalk, Oliver; Geng, Ting; Thomas, Richard D; Hansson, Tony; de Vivie-Riedle, Regina

    2017-01-18

    For the series furan, furfural and β-furfural we investigated the effect of substituents and their positioning on the photoinduced relaxation dynamics in a combined theoretical and experimental approach. Using time resolved photoelectron spectroscopy with a high intensity probe pulse, we can, for the first time, follow the whole deactivation process of furan through a two photon probe signal. Using the extended 2-electron 2-orbital model [Nenov et al., J. Chem. Phys., 2011, 135, 034304] we explain the formation of one central conical intersection and predict the influence of the aldehyde group of the derivatives on its geometry. This, as well as the relaxation mechanisms from photoexcitation to the final outcome was investigated using a variety of theoretical methods. Complete active space self consistent field was used for on-the-fly calculations while complete active space perturbation theory and coupled cluster theory were used to accurately describe critical configurations. Experiment and theory show the relaxation dynamics of furfural and β-furfural to be slowed down, and together they disclose an additional deactivation pathway, which is attributed to the n O lonepair state introduced with the aldehyde group.

  20. Communication: High pressure specific heat spectroscopy reveals simple relaxation behavior of glass forming molecular liquid

    DEFF Research Database (Denmark)

    Roed, Lisa Anita; Niss, Kristine; Jakobsen, Bo

    2015-01-01

    The frequency dependent specific heat has been measured under pressure for the molecular glass forming liquid 5-polyphenyl-4-ether in the viscous regime close to the glass transition. The temperature and pressure dependences of the characteristic time scale associated with the specific heat...... is compared to the equivalent time scale from dielectric spectroscopy performed under identical conditions. It is shown that the ratio between the two time scales is independent of both temperature and pressure. This observation is non-trivial and demonstrates the existence of specially simple molecular...... liquids in which different physical relaxation processes are both as function of temperature and pressure/density governed by the same underlying “inner clock.” Furthermore, the results are discussed in terms of the recent conjecture that van der Waals liquids, like the measuredliquid, comply...

  1. Slowing hot-carrier relaxation in graphene using a magnetic field

    Science.gov (United States)

    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.

  2. Molecular dynamics and diffusion a compilation

    CERN Document Server

    Fisher, David

    2013-01-01

    The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

  3. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  4. Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study

    Science.gov (United States)

    Pressly, James; Riggleman, Robert; Winey, Karen

    The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.

  5. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  6. Calculation of the vibrational linewidth and line shape of Raman spectra using the relaxation function : I. method and application to nitrogen

    NARCIS (Netherlands)

    Kooi, M.E.; Smit, F.; Michels, J.P.J.; Schouten, J.A.

    2000-01-01

    The spectral line shape of the fundamental vibration of nitrogen is calculated from molecular dynamics simulations by determining the Fourier transform of the relaxation function. It has been applied to the fluid phase at various pressures and temperatures, and to solid d-N2. The validity of the

  7. Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

    Science.gov (United States)

    Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

    2014-04-21

    Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

  8. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  9. Structural relaxation and thermal conductivity coefficient of liquids

    International Nuclear Information System (INIS)

    Abdurasulov, A.

    1992-01-01

    Present article is devoted to structural relaxation and thermal conductivity coefficient of liquids. The thermoelastic properties of liquids were studied taking into account the contribution of translational and structural relaxation. The results of determination of dynamic coefficient of thermal conductivity of liquids taking into account the contribution of translational and structural relaxation are presented.

  10. Nonadiabatic electron wavepacket dynamics behind molecular autoionization

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-01

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  11. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  12. Rheology via nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1982-10-01

    The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

  13. First-principles molecular dynamics for metals

    International Nuclear Information System (INIS)

    Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

    1989-01-01

    A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

  14. Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

    Science.gov (United States)

    Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

    2010-06-03

    The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

  15. Interpretation of the U L3-edge EXAFS in uranium dioxide using molecular dynamics and density functional theory simulations

    International Nuclear Information System (INIS)

    Bocharov, Dmitry; Chollet, Melanie; Krack, Matthias; Bertsch, Johannes; Grolimund, Daniel; Martin, Matthias; Kuzmin, Alexei; Purans, Juris; Kotomin, Eugene

    2016-01-01

    X-ray absorption spectroscopy is employed to study the local structure of pure and Cr-doped UO 2 at 300 K. The U L 3 -edge EXAFS spectrum is interpreted within the multiplescattering (MS) theory using the results of the classical and ab initio molecular dynamics simulations, allowing us to validate the accuracy of theoretical models. The Cr K-edge XANES is simulated within the full-multiple-scattering formalism considering a substitutional model (Cr at U site). It is shown that both unrelaxed and relaxed structures, produced by ab initio density functional theory (DFT) calculations, fail to describe the experiment. (paper)

  16. Extended Smoluchowski models for interpreting relaxation phenomena in liquids

    International Nuclear Information System (INIS)

    Polimeno, A.; Frezzato, D.; Saielli, G.; Moro, G.J.; Nordio, P.L.

    1998-01-01

    Interpretation of the dynamical behaviour of single molecules or collective modes in liquids has been increasingly centered, in the last decade, on complex liquid systems, including ionic solutions, polymeric liquids, supercooled fluids and liquid crystals. This has been made necessary by the need of interpreting dynamical data obtained by advanced experiments, like optical Kerr effect, time dependent fluorescence shift experiments, two-dimensional Fourier-transform and high field electron spin resonance and scattering experiments like quasi-elastic neutron scattering. This communication is centered on the definition, treatment and application of several extended stochastic models, which have proved to be very effective tools for interpreting and rationalizing complex relaxation phenomena in liquids structures. First, applications of standard Fokker-Planck equations for the orientational relaxation of molecules in isotropic and ordered liquid phase are reviewed. In particular attention will be focused on the interpretation of neutron scattering in nematics. Next, an extended stochastic model is used to interpret time-domain resolved fluorescence emission experiments. A two-body stochastic model allows the theoretical interpretation of dynamical Stokes shift effects in fluorescence emission spectra, performed on probes in isotropic and ordered polar phases. Finally, for the case of isotropic fluids made of small rigid molecules, a very detailed model is considered, which includes as basic ingredients a Fokker-Planck description of the molecular vibrational motion and the slow diffusive motion of a persistent cage structure together with the decay processes related to the changing structure of the cage. (author)

  17. Correlation between electron-irradiation defects and applied stress in graphene: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Kida, Shogo; Yamamoto, Masaya; Kawata, Hiroaki; Hirai, Yoshihiko; Yasuda, Masaaki, E-mail: yasuda@pe.osakafu-u.ac.jp [Department of Physics and Electronics, Osaka Prefecture University, Sakai, Osaka 599-8531 (Japan); Tada, Kazuhiro [Department of Electrical and Control Systems Engineering, National Institute of Technology, Toyama College, Toyama 939-8630 (Japan)

    2015-09-15

    Molecular dynamics (MD) simulations are performed to study the correlation between electron irradiation defects and applied stress in graphene. The electron irradiation effect is introduced by the binary collision model in the MD simulation. By applying a tensile stress to graphene, the number of adatom-vacancy (AV) and Stone–Wales (SW) defects increase under electron irradiation, while the number of single-vacancy defects is not noticeably affected by the applied stress. Both the activation and formation energies of an AV defect and the activation energy of an SW defect decrease when a tensile stress is applied to graphene. Applying tensile stress also relaxes the compression stress associated with SW defect formation. These effects induced by the applied stress cause the increase in AV and SW defect formation under electron irradiation.

  18. How Dynamic Visualization Technology Can Support Molecular Reasoning

    Science.gov (United States)

    Levy, Dalit

    2013-01-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

  19. Superdomain dynamics in ferroelectric-ferroelastic films: Switching, jamming, and relaxation

    Science.gov (United States)

    Scott, J. F.; Hershkovitz, A.; Ivry, Y.; Lu, H.; Gruverman, A.; Gregg, J. M.

    2017-12-01

    Recent experimental work shows that ferroelectric switching can occur in large jumps in which ferroelastic superdomains switch together, rather than having the numerous smaller ferroelectric domains switch within them. In this sense, the superdomains play a role analogous to that of Abrikosov vortices in thin superconducting films under the Kosterlitz-Thouless framework, which control the dynamics more than individual Cooper pairs within them do. Here, we examine the dynamics of ferroelastic superdomains in ferroelastic ferroelectrics and their role in switching devices such as memories. Jamming of ferroelectric domains in thin films has revealed an unexpected time dependence of t-1/4 at long times (hours), but it is difficult to discriminate between power-law and exponential relaxation. Other aspects of this work, including spatial period doubling of domains, led to a description of ferroelastic domains as nonlinear processes in a viscoelastic medium, which produce folding and metastable kinetically limited states. This ¼ exponent is a surprising agreement with the well-known value of ¼ for coarsening dynamics in viscoelastic media. We try to establish a link between these two processes, hitherto considered unrelated, and with superdomains and domain bundles. We note also that high-Tc superconductors share many of the ferroelastic domain properties discussed here and that several new solar cell materials and metal-insulator transition systems are ferroelastic.

  20. Dielectric Relaxation Studies of Alkyl Methacrylate–Phenol Mixtures ...

    African Journals Online (AJOL)

    The Kirkwood correlation factor and the excess inverse relaxation time were determined and they yield information on the molecular interactions occurring in the systems. The values of the static permittivity and the relaxation time increase with an increase in the percentage of phenol in the mixtures. KEYWORDS: Dielectric ...

  1. Quantum dynamics of crystals of molecular magnets inside microwave resonators

    Energy Technology Data Exchange (ETDEWEB)

    Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A. E-mail: antonio@ubxlab.comtoni@ubxlab.com

    2004-05-01

    It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field.

  2. Quantum dynamics of crystals of molecular magnets inside microwave resonators

    International Nuclear Information System (INIS)

    Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A.

    2004-01-01

    It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field

  3. Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

    Science.gov (United States)

    Wu, Bin

    hydrogen bonding. It is found that the population of this bonding would increase and the corresponding relaxation would slow down as molecular charge increases. We perceive that through more and longer interaction between penetrating water molecules and polymeric part of dendrimer, the dynamics of latter could be enhanced.

  4. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Borg, Matthew K., E-mail: matthew.borg@strath.ac.uk [Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Lockerby, Duncan A., E-mail: duncan.lockerby@warwick.ac.uk [School of Engineering, University of Warwick, Coventry CV4 7AL (United Kingdom); Reese, Jason M., E-mail: jason.reese@ed.ac.uk [School of Engineering, University of Edinburgh, Edinburgh EH9 3JL (United Kingdom)

    2014-02-21

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C{sub 60} Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.

  5. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Borg, Matthew K.; Lockerby, Duncan A.; Reese, Jason M.

    2014-01-01

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C 60 Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors

  6. Physical adsorption and molecular dynamics

    International Nuclear Information System (INIS)

    Cohan, N.V.

    1981-01-01

    Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

  7. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.

    Science.gov (United States)

    Glowacki, David R; Orr-Ewing, Andrew J; Harvey, Jeremy N

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol(-1) localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral

  8. Impact of growth and annealing conditions on the parameters of Ge/Si(001) relaxed layers grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Yurasov, D. V., E-mail: Inquisitor@ipm.sci-nnov.ru [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation); Bobrov, A. I. [Lobachevsky State University of Nizhny Novgorod (Russian Federation); Daniltsev, V. M.; Novikov, A. V. [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation); Pavlov, D. A. [Lobachevsky State University of Nizhny Novgorod (Russian Federation); Skorokhodov, E. V.; Shaleev, M. V.; Yunin, P. A. [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation)

    2015-11-15

    Influence of the Ge layer thickness and annealing conditions on the parameters of relaxed Ge/Si(001) layers grown by molecular beam epitaxy via two-stage growth is investigated. The dependences of the threading dislocation density and surface roughness on the Ge layer thickness, annealing temperature and time, and the presence of a hydrogen atmosphere are obtained. As a result of optimization of the growth and annealing conditions, relaxed Ge/Si(001) layers which are thinner than 1 μm with a low threading dislocation density on the order of 10{sup 7} cm{sup –2} and a root mean square roughness of less than 1 nm are obtained.

  9. Holographic grating relaxation technique for soft matter science

    Energy Technology Data Exchange (ETDEWEB)

    Lesnichii, Vasilii, E-mail: vasilii.lesnichii@physchem.uni-freiburg.de [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101 (Russian Federation); Kiessling, Andy [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); Current address: Illinois Institute of Technology, 10 West 33rd Street, Chicago,IL60616 (United States); Bartsch, Eckhard [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); Veniaminov, Andrey, E-mail: veniaminov@phoi.ifmo.ru [ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101 (Russian Federation)

    2016-06-17

    The holographic grating relaxation technique also known as forced Rayleigh scattering consists basically in writing a holographic grating in the specimen of interest and monitoring its diffraction efficiency as a function of time, from which valuable information on mass or heat transfer and photoinduced transformations can be extracted. In a more detailed view, the shape of the relaxation curve and the relaxation rate as a function of the grating period were found to be affected by the architecture of diffusing species (molecular probes) that constitute the grating, as well as that of the environment they diffuse in, thus making it possible to access and study spatial heterogeneity of materials and different modes of e.g., polymer motion. Minimum displacements and spatial domains approachable by the technique are in nanometer range, well below spatial periods of holographic gratings. In the present paper, several cases of holographic relaxation in heterogeneous media and complex motions are exemplified. Nano- to micro-structures or inhomogeneities comparable in spatial scale with holographic gratings manifest themselves in relaxation experiments via non-exponential decay (stepwise or stretched), spatial-period-dependent apparent diffusion coefficient, or unusual dependence of diffusion coefficient on molecular volume of diffusing probes.

  10. Relationship between Structural and Stress Relaxation in a Block-Copolymer Melt

    International Nuclear Information System (INIS)

    Patel, Amish J.; Narayanan, Suresh; Sandy, Alec; Mochrie, Simon G. J.; Garetz, Bruce A.; Watanabe, Hiroshi; Balsara, Nitash P.

    2006-01-01

    The relationship between structural relaxation on molecular length scales and macroscopic stress relaxation was explored in a disordered block-copolymer melt. Experiments show that the structural relaxation time, measured by x-ray photon correlation spectroscopy is larger than the terminal stress relaxation time, measured by rheology, by factors as large as 100. We demonstrate that the structural relaxation data are dominated by the diffusion of intact micelles while the stress relaxation data are dominated by contributions due to disordered concentration fluctuations

  11. Thomas-Fermi molecular dynamics

    International Nuclear Information System (INIS)

    Clerouin, J.; Pollock, E.L.; Zerah, G.

    1992-01-01

    A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

  12. Molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

  13. Molecular dynamics for dense matter

    Science.gov (United States)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  14. Nonlinear generation of non-acoustic modes by low-frequency sound in a vibrationally relaxing gas

    International Nuclear Information System (INIS)

    Perelomova, A.

    2010-01-01

    Two dynamic equations referring to a weakly nonlinear and weakly dispersive flow of a gas in which molecular vibrational relaxation takes place, are derived. The first one governs an excess temperature associated with the thermal mode, and the second one describes variations in vibrational energy. Both quantities refer to non-wave types of gas motion. These variations are caused by the nonlinear transfer of acoustic energy into thermal mode and internal vibrational degrees of freedom of a relaxing gas. The final dynamic equations are instantaneous; they include a quadratic nonlinear acoustic source, reflecting the nonlinear character of interaction of low-frequency acoustic and non-acoustic motions of the fluid. All types of sound, periodic or aperiodic, may serve as an acoustic source of both phenomena. The low-frequency sound is considered in this study. Some conclusions about temporal behavior of non-acoustic modes caused by periodic and aperiodic sound are made. Under certain conditions, acoustic cooling takes place instead of heating. (author)

  15. General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation

    NARCIS (Netherlands)

    Prompers, J.J.; Brüschweiler, R.

    2002-01-01

    A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin

  16. Asymptotic representation of relaxation oscillations in lasers

    CERN Document Server

    Grigorieva, Elena V

    2017-01-01

    In this book we analyze relaxation oscillations in models of lasers with nonlinear elements controlling light dynamics. The models are based on rate equations taking into account periodic modulation of parameters, optoelectronic delayed feedback, mutual coupling between lasers, intermodal interaction and other factors. With the aim to study relaxation oscillations we present the special asymptotic method of integration for ordinary differential equations and differential-difference equations. As a result, they are reduced to discrete maps. Analyzing the maps we describe analytically such nonlinear phenomena in lasers as multistability of large-amplitude relaxation cycles, bifurcations of cycles, controlled switching of regimes, phase synchronization in an ensemble of coupled systems and others. The book can be fruitful for students and technicians in nonlinear laser dynamics and in differential equations.

  17. Regularities of intermediate adsorption complex relaxation

    International Nuclear Information System (INIS)

    Manukova, L.A.

    1982-01-01

    The experimental data, characterizing the regularities of intermediate adsorption complex relaxation in the polycrystalline Mo-N 2 system at 77 K are given. The method of molecular beam has been used in the investigation. The analytical expressions of change regularity in the relaxation process of full and specific rates - of transition from intermediate state into ''non-reversible'', of desorption into the gas phase and accumUlation of the particles in the intermediate state are obtained

  18. Influence of E-beam irradiation on dielectric relaxation of recycled polypropylene

    International Nuclear Information System (INIS)

    Fazilova, Z.; Gafurov, U.; Tolstov, A.

    2004-01-01

    Full text: The dielectric relaxation connected with molecular groups and polymer chain mobility for un-irradiated and e-beam irradiated recycled polypropylene was investigated. It was studied films of samples produced from virgin (initial) and e- beam irradiated of the polymer granules (E-beam source with 5 MeV energy). The dielectric losses were measured with temperature increasing and decreasing regime. The losses were measured with E8-4 bridge help (the frequency is 1kH). Heating velocity was 2 grad/min. The dielectric losses did not appeared in minus temperature region for the initial polypropylene samples. The measurement in temperature increasing and decreasing shows that the relaxation peak at ∼ 35 o C for un-irradiated and ∼70 o C for irradiated polymer samples connected with macromolecular segments mobility with water molecular groups participation. The main relaxation peak (higher 100 o C) shifts after e-beam irradiation is result of the cross-links formation. ) The peak connected with macromolecular segments mobility in polymer amorphous regions (β-relaxation process). In irradiated polypropylene on IR spectroscopy data oxygen molecular groups is increased. The molecular groupings form inter-molecular hydrogen bonds. The intermolecular bonds also hindered molecular groups and macromolecular mobility. The e-beam stimulated cross-links formation was confirmed by method of sol-gel analyses. The work was supported by STCU Fund (Project No 3009)

  19. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions

    International Nuclear Information System (INIS)

    Salmon, L.; Licinio, A.; Jensen, M.R.; Blackledge, M.; Ortega Roldan, J.L.; Van Nuland, N.; Lescop, E.

    2011-01-01

    We have recently presented a titration approach for the determination of residual dipolar couplings (RDCs) from experimentally inaccessible complexes. Here, we extend this approach to the measurement of 15 N spin relaxation rates and demonstrate that this can provide long-range structural, dynamic, and kinetic information about these elusive systems. (authors)

  20. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    Science.gov (United States)

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  1. Role of Orbital Dynamics in Spin Relaxation and Weak Antilocalization in Quantum Dots

    Science.gov (United States)

    Zaitsev, Oleg; Frustaglia, Diego; Richter, Klaus

    2005-01-01

    We develop a semiclassical theory for spin-dependent quantum transport to describe weak (anti)localization in quantum dots with spin-orbit coupling. This allows us to distinguish different types of spin relaxation in systems with chaotic, regular, and diffusive orbital classical dynamics. We find, in particular, that for typical Rashba spin-orbit coupling strengths, integrable ballistic systems can exhibit weak localization, while corresponding chaotic systems show weak antilocalization. We further calculate the magnetoconductance and analyze how the weak antilocalization is suppressed with decreasing quantum dot size and increasing additional in-plane magnetic field.

  2. Anomalous relaxation and self-organization in nonequilibrium processes

    International Nuclear Information System (INIS)

    Fatkullin, Ibrahim; Kladko, Konstantin; Mitkov, Igor; Bishop, A. R.

    2001-01-01

    We study thermal relaxation in ordered arrays of coupled nonlinear elements with external driving. We find that our model exhibits dynamic self-organization manifested in a universal stretched-exponential form of relaxation. We identify two types of self-organization, cooperative and anticooperative, which lead to fast and slow relaxation, respectively. We give a qualitative explanation for the behavior of the stretched exponent in different parameter ranges. We emphasize that this is a system exhibiting stretched-exponential relaxation without explicit disorder or frustration

  3. Dynamics of Nano-Chain Diffusing in Porous Media

    International Nuclear Information System (INIS)

    Chen Jiang-Xing; Zheng Qiang; Huang Chun-Yun; Xu Jiang-Rong; Ying He-Ping

    2015-01-01

    A coarse-grained model is proposed to study the dynamics of a nano-chain diffusing in porous media. The simulation utilizes a hybrid method which combines stochastic rotation dynamics with molecular dynamics. Solvent molecules are explicitly taken into account to represent the hydrodynamic interactions and random fluctuations. The conformation, relaxation, and diffusion properties of a polymer chain are investigated by changing the density degree of the obstacle matrix. It is found that the average size of the chain is a nonmonotonic function of the obstacle volume fraction ϕ. A dense environment may contribute to extending a linear chain, which can be characterized by larger exponents in the corresponding power law. The relaxation behavior of a stretched chain to a steady state shows dramatic crossover from exponent to power-law relaxation when the values of φ are increased. The dependence of the diffusion coefficient on the chain size is also studied. Various kinds of scaling properties are presented and discussed. The results can give additional insight into the density effect of porous media on polymer structure and dynamics. (paper)

  4. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the chi 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate

  5. Vibrational lifetimes of hydrogen on lead films: An ab initio molecular dynamics with electronic friction (AIMDEF) study

    Energy Technology Data Exchange (ETDEWEB)

    Saalfrank, Peter [Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam (Germany); Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Juaristi, J. I. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain); Alducin, M.; Muiño, R. Díez [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Blanco-Rey, M. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain)

    2014-12-21

    Using density functional theory and Ab Initio Molecular Dynamics with Electronic Friction (AIMDEF), we study the adsorption and dissipative vibrational dynamics of hydrogen atoms chemisorbed on free-standing lead films of increasing thickness. Lead films are known for their oscillatory behaviour of certain properties with increasing thickness, e.g., energy and electron spillout change in discontinuous manner, due to quantum size effects [G. Materzanini, P. Saalfrank, and P. J. D. Lindan, Phys. Rev. B 63, 235405 (2001)]. Here, we demonstrate that oscillatory features arise also for hydrogen when chemisorbed on lead films. Besides stationary properties of the adsorbate, we concentrate on finite vibrational lifetimes of H-surface vibrations. As shown by AIMDEF, the damping via vibration-electron hole pair coupling dominates clearly over the vibration-phonon channel, in particular for high-frequency modes. Vibrational relaxation times are a characteristic function of layer thickness due to the oscillating behaviour of the embedding surface electronic density. Implications derived from AIMDEF for frictional many-atom dynamics, and physisorbed species will also be given.

  6. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD{sub 3}CN treated with a parallel multi-state EVB model

    Energy Technology Data Exchange (ETDEWEB)

    Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational

  7. Molecular dynamics with deterministic and stochastic numerical methods

    CERN Document Server

    Leimkuhler, Ben

    2015-01-01

    This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

  8. Magnetic relaxation in analytical, coordination and bioinorganic chemistry

    International Nuclear Information System (INIS)

    Mikhajlov, O.

    1982-01-01

    Nuclear magnetic relaxation is a special type of nuclear magnetic resonance in which the rate is measured of energy transfer between the excited nuclei and their molecular medium (spin-lattice relaxation) or the whole nuclear spin system (spin-spin relaxation). Nuclear magnetic relaxation relates to nuclei with a spin of 1/2, primarily H 1 1 , and is mainly measured in water solutions. It is suitable for (1) analytical chemistry because the relaxation time rapidly reduces in the presence of paramagnetic ions, (2) the study of complex compounds, (3) the study of biochemical reactions in the presence of different metal ions. It is also suitable for testing the composition of a flowing liquid. Its disadvantage is that it requires complex and expensive equipment. (Ha)

  9. Universal Mechanism of Spin Relaxation in Solids

    Science.gov (United States)

    Chudnovsky, Eugene

    2006-03-01

    Conventional elastic theory ignores internal local twists and torques. Meantime, spin-lattice relaxation is inherently coupled with local elastic twists through conservation of the total angular momentum (spin + lattice). This coupling gives universal lower bound (free of fitting parameters) on the relaxation of the atomic or molecular spin in a solid [1] and on the relaxation of the electron spin in a quantum dot [2]. [1] E. M. Chudnovsky, D. A. Garanin, and R. Schilling, Phys. Rev. B 72, 094426 (2005). [2] C. Calero, E. M. Chudnovsky, and D. A. Garanin, Phys. Rev. Lett. 95, 166603 (2005).

  10. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  11. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  12. An NMR database for simulations of membrane dynamics.

    Science.gov (United States)

    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

  13. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  14. Transverse relaxation dispersion of the p7 membrane channel from hepatitis C virus reveals conformational breathing

    International Nuclear Information System (INIS)

    Dev, Jyoti; Brüschweiler, Sven; Ouyang, Bo; Chou, James J.

    2015-01-01

    The p7 membrane protein encoded by hepatitis C virus (HCV) assembles into a homo-hexamer that selectively conducts cations. An earlier solution NMR structure of the hexameric complex revealed a funnel-like architecture and suggests that a ring of conserved asparagines near the narrow end of the funnel are important for cation interaction. NMR based drug-binding experiments also suggest that rimantadine can allosterically inhibit ion conduction via a molecular wedge mechanism. These results suggest the presence of dilation and contraction of the funnel tip that are important for channel activity and that the action of the drug is attenuating this motion. Here, we determined the conformational dynamics and solvent accessibility of the p7 channel. The proton exchange measurements show that the cavity-lining residues are largely water accessible, consistent with the overall funnel shape of the channel. Our relaxation dispersion data show that residues Val7 and Leu8 near the asparagine ring are subject to large chemical exchange, suggesting significant intrinsic channel breathing at the tip of the funnel. Moreover, the hinge regions connecting the narrow and wide regions of the funnel show strong relaxation dispersion and these regions are the binding sites for rimantadine. Presence of rimantadine decreases the conformational dynamics near the asparagine ring and the hinge area. Our data provide direct observation of μs–ms dynamics of the p7 channel and support the molecular wedge mechanism of rimantadine inhibition of the HCV p7 channel

  15. Transverse relaxation dispersion of the p7 membrane channel from hepatitis C virus reveals conformational breathing

    Energy Technology Data Exchange (ETDEWEB)

    Dev, Jyoti; Brüschweiler, Sven [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States); Ouyang, Bo [Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology (China); Chou, James J., E-mail: james-chou@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2015-04-15

    The p7 membrane protein encoded by hepatitis C virus (HCV) assembles into a homo-hexamer that selectively conducts cations. An earlier solution NMR structure of the hexameric complex revealed a funnel-like architecture and suggests that a ring of conserved asparagines near the narrow end of the funnel are important for cation interaction. NMR based drug-binding experiments also suggest that rimantadine can allosterically inhibit ion conduction via a molecular wedge mechanism. These results suggest the presence of dilation and contraction of the funnel tip that are important for channel activity and that the action of the drug is attenuating this motion. Here, we determined the conformational dynamics and solvent accessibility of the p7 channel. The proton exchange measurements show that the cavity-lining residues are largely water accessible, consistent with the overall funnel shape of the channel. Our relaxation dispersion data show that residues Val7 and Leu8 near the asparagine ring are subject to large chemical exchange, suggesting significant intrinsic channel breathing at the tip of the funnel. Moreover, the hinge regions connecting the narrow and wide regions of the funnel show strong relaxation dispersion and these regions are the binding sites for rimantadine. Presence of rimantadine decreases the conformational dynamics near the asparagine ring and the hinge area. Our data provide direct observation of μs–ms dynamics of the p7 channel and support the molecular wedge mechanism of rimantadine inhibition of the HCV p7 channel.

  16. Composition-dependent hot carrier relaxation dynamics in cesium lead halide (CsPbX{sub 3}, X=Br and I) perovskite nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Heejae; Jung, Seok Il; Kim, Hyo Jin; Cha, Wonhee; Sim, Eunji; Kim, Dongho [Department of Chemistry, Yonsei University, Seoul (Korea, Republic of); Koh, Weon-Kyu [Device Laboratory, Samsung Advanced Institute of Technology, Suwon (Korea, Republic of); Kim, Jiwon [School of Integrated Technology and Underwood International College, Yonsei University, Incheon (Korea, Republic of)

    2017-04-03

    Cesium-based perovskite nanocrystals (NCs) have outstanding photophysical properties improving the performances of lighting devices. Fundamental studies on excitonic properties and hot-carrier dynamics in perovskite NCs further suggest that these materials show higher efficiencies compared to the bulk form of perovskites. However, the relaxation rates and pathways of hot-carriers are still being elucidated. By using ultrafast transient spectroscopy and calculating electronic band structures, we investigated the dependence of halide in Cs-based perovskite (CsPbX{sub 3} with X=Br, I, or their mixtures) NCs on the hot-carrier relaxation processes. All samples exhibit ultrafast (<0.6 ps) hot-carrier relaxation dynamics with following order: CsPbBr{sub 3} (310 fs)>CsPbBr{sub 1.5}I{sub 1.5} (380 fs)>CsPbI{sub 3} NC (580 fs). These result accounts for a reduced light emission efficiency of CsPbI{sub 3} NC compared to CsPbBr{sub 3} NC. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. A theoretical study of the relaxation of a phenyl group chemisorbed to an RDX freestanding thin film

    Energy Technology Data Exchange (ETDEWEB)

    Pereverzev, Andrey, E-mail: pereverzeva@missouri.edu; Sewell, Thomas D., E-mail: sewellt@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States)

    2016-08-07

    Energy relaxation from an excited phenyl group chemisorbed to the surface of a crystalline thin film of α-1,3,5-trinitro-1,3,5-triazacyclohexane (α-RDX) at 298 K and 1 atm is simulated using molecular dynamics. Two schemes are used to excite the phenyl group. In the first scheme, the excitation energy is added instantaneously as kinetic energy by rescaling momenta of the 11 atoms in the phenyl group. In the second scheme, the phenyl group is equilibrated at a higher temperature in the presence of static RDX geometries representative of the 298 K thin film. An analytical model based on ballistic phonon transport that requires only the harmonic part of the total Hamiltonian and includes no adjustable parameters is shown to predict, essentially quantitatively, the short-time dynamics of the kinetic energy relaxation (∼200 fs). The dynamics of the phenyl group for times longer than about 6 ps follows exponential decay and agrees qualitatively with the dynamics described by a master equation. Long-time heat propagation within the bulk of the crystal film is consistent with the heat equation.

  18. Effect of extender oils on the stress relaxation behavior of thermoplastic vulcanizates

    Directory of Open Access Journals (Sweden)

    2008-11-01

    Full Text Available The long term mechanical behavior of oil extended thermoplastic vulcanizates (TPV based on polypropylene (PP and acrylonitrile-butadiene rubber (NBR has been characterized by means of stress relaxation experiments. The morphology of TPV and the phase specific oil distribution which depend on the content and type of oil as well as on the mixing regime have been characterized by means of Atomic Force Microscopy (AFM, Dynamic Mechanical Thermal Analysis (DMTA and Differential Scanning Calorimetrie (DSC. The discussion of the stress relaxation behavior was carried out using the two-component model, which allows splitting the initial stress into two components: a thermal activated stress component and an athermal one. A master curve was created by shifting the relaxation curves vertically and horizontally towards the reference curve. The vertical shift factor bT is a function of the temperature dependence of the athermal stress components. It was found that the oil distribution strongly affects the athermal stress component which is related to the contribution of the structural changes, e.g. crystallinity of the PP phase and the average molecular weight between the crosslinks of the NBR phase. From the temperature dependence of the horizontal shift factor aT the main viscoelastic relaxation process was determined as the α-relaxation process of the crystalline PP phase. It is not dependent on the polarity and content of the oil as well as the mixing regime.

  19. Relaxation property of the fractional Brownian particle

    International Nuclear Information System (INIS)

    Wang Litan; Lung, C.W.

    1988-08-01

    Dynamic susceptibility of a diffusion system associated with the fractional Brownian motion (fBm) was examined for the fractal property of the Non-Debye relaxation process. The comparisons between fBm and other approaches were made. Anomalous diffusion and the Non-Debye relaxation processes were discussed with this approach. (author). 8 refs, 1 fig

  20. Stress Relaxation in Entangled Polymer Melts

    DEFF Research Database (Denmark)

    Hou, Ji-Xuan; Svaneborg, Carsten; Everaers, Ralf

    2010-01-01

    We present an extensive set of simulation results for the stress relaxation in equilibrium and step-strained bead-spring polymer melts. The data allow us to explore the chain dynamics and the shear relaxation modulus, G(t), into the plateau regime for chains with Z=40 entanglements...... and into the terminal relaxation regime for Z=10. Using the known (Rouse) mobility of unentangled chains and the melt entanglement length determined via the primitive path analysis of the microscopic topological state of our systems, we have performed parameter-free tests of several different tube models. We find...

  1. The calculation of the viscosity from the autocorrelation function using molecular and atomic stress tensors

    Science.gov (United States)

    Cui, S. T.

    The stress-stress correlation function and the viscosity of a united-atom model of liquid decane are studied by equilibrium molecular dynamics simulation using two different formalisms for the stress tensor: the atomic and the molecular formalisms. The atomic and molecular correlation functions show dramatic difference in short-time behaviour. The integrals of the two correlation functions, however, become identical after a short transient period whichis significantly shorter than the rotational relaxation time of the molecule. Both reach the same plateau value in a time period corresponding to this relaxation time. These results provide a convenient guide for the choice of the upper integral time limit in calculating the viscosity by the Green-Kubo formula.

  2. Dielectric Relaxation of Water: Theory and Experiment

    International Nuclear Information System (INIS)

    Adhikari, Narayan Prasad; Paudyal, Harihar; Johri, Manoj

    2010-06-01

    We have studied the hydrogen bond dynamics and methods for evaluation of probability and relaxation time for hydrogen bond network. Further, dielectric relaxation time has been calculated by using a diagonalization procedure by obtaining eigen values (inverse of relaxation time) of a master equation framed on the basis of Fokker-Planck equations. Microwave cavity spectrometer has been described to make measurements of relaxation time. Slater's perturbation equations are given for the analysis of the data. A comparison of theoretical and experimental data shows that there is a need for improvements in the theoretical model and experimental techniques to provide exact information about structural properties of water. (author)

  3. Evolution of dynamic susceptibility in molecular glass formers-a critical assessment

    International Nuclear Information System (INIS)

    Brodin, A; Gainaru, C; Porokhonskyy, V; Roessler, E A

    2007-01-01

    Dielectric, depolarized light scattering (LS) and optical Kerr effect (OKE) data are critically discussed in an attempt to achieve a common interpretation of the evolution of dynamic susceptibility in molecular glass formers at temperatures down to the glass transition T g . The so-called intermediate power-law, observed in OKE data below a certain temperature T x , is identified with the excess wing, long since known from dielectric spectroscopy, with a temperature-independent exponent. This is in contrast with several recent analyses that concluded a considerable temperature dependence of spectral shapes. We introduce a new approach to disentangle α-peak and excess wing contributions in the dielectric spectra, which allows for frequency-temperature superposition (FTS) of the α-process at all temperatures above T g . From the LS spectra we conclude, in particular, that FTS holds even at temperatures well above the melting point, i.e. in normal equilibrium liquids. Attempting to correlate the fragility and stretching, our conclusions are opposite to those made previously. Specifically, we observe that a high fragility is associated with a less stretched relaxation function

  4. Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager

    2009-01-01

    the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains...

  5. Molecular dynamics study of vacancy-like defects in a model glass : static behaviour

    Science.gov (United States)

    Delaye, J. M.; Limoge, Y.

    1993-10-01

    The possibility of defining vacancy-like defects in a Lennard-Jones glass is searched for in a systematic manner. Considering different relaxation levels of the same system, as well as different external pressures, we use a Molecular Dynamics simulation method, to study at constant volume or external pressure, the relaxation of a “piece” of glass, after the sudden removal of an atom. Three typical kinds of behaviour can be observed: the persistence of the empty volume left by the missing atom, its migration by clearly identifiable atomic jumps and the dissipation “on the spot”. A careful analysis of the probabilities of these three kinds of behaviour shows that a meaningful definition of vacancy-like defects can be given in a Lennard-Jones glass. Dans cet article, nous nous penchons de façon systématique sur la possibilité de définir des défauts de type lacunaire dans un verre de Lennard-Jones, à différents niveaux de relaxation et de pression, par une méthode de simulation numérique en dynamique moléculaire à volume ou à pression constants. Le défaut est créé en supprimant un atome et en suivant la réponse du système. Nous observons trois comportements typiques : la persistance sur place du “trou” laissé par l'atome supprimé, sa migration par des sauts atomiques clairement identifiés et enfin sa dissipation sur place. Une analyse détaillée de ces trois comportements montre qu'il est possible dans un verre de Lennard-Jones de définir des défauts de type lacunaire.

  6. Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi; Mueller, Karl T.

    2017-03-19

    Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directly involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.

  7. Molecular Mobility of an Amorphous Chiral Pharmaceutical Compound: Impact of Chirality and Chemical Purity.

    Science.gov (United States)

    Viel, Quentin; Delbreilh, Laurent; Coquerel, Gérard; Petit, Samuel; Dargent, Eric

    2017-08-17

    A dielectric relaxation spectroscopy (DRS) study was performed to investigate the molecular mobility of amorphous chiral diprophylline (DPL). For this purpose, both racemic DPL and a single enantiomer of DPL were considered. After fast cooling from the melt at very low temperature (-140 °C), progressive heating below and above the glass transition (T g ≈ 37 °C) induces two secondary relaxations (γ- and δ-) and primary relaxations (α-) for both enantiomeric compositions. After chemical purification of our samples by means of cooling recrystallization, no γ-process could be detected by DRS. Hence, it was highlighted that the molecular mobility in the glassy state is influenced by the presence of theophylline (TPH), the main impurity in DPL samples. We also proved that the dynamic behavior of a single enantiomer and the racemic mixture of the same purified compound are quasi-identical. This study demonstrates that the relative stability and the molecular mobility of chiral amorphous drugs are strongly sensitive to chemical purity.

  8. Violent Relaxation, Dynamical Instabilities and the Formation of Elliptical Galaxies

    Science.gov (United States)

    Aguilar, L. A.

    1990-11-01

    RESUMEN: El problema de la formaci6n de galaxias elfpticas por medjo de colapso gravitacional sin disipaci6n de energfa es estudiado usando un gran numero de simulaciones numericas. Se muestra que este tipo de colapsos, partiendo de condiciones iniciales frfas donde la energfa cinetica inicial representa s6lo un 5%, 0 , de a potencial inicial, produce sistemas relajados de forma triaxial muy similares a las galaxias elfpticas reales en sus formas y perfiles de densidad en proyecci6i . La forina triaxial resulta de la acci6n de una inestabilidad dinamica que aparece en sistemas 'inicos dominados por movimientos radiales, mientras que el perfil de densidad final Cs debido al llamado relajamiento violento que tiende a producir una distribuci6n en espacio fase unica. Estos dos fen6menos tienden a borrar los detalles particulares sobre las condiciones iniciales y dan lugar a una evoluci6n convergente hacia sistemas realistas, esto innecesario el uso de condiciones iniciales especiales (excepto por Ia condici6i de que estas deben ser frfas). Las condiciones iniciales frfas producen los movimientos radiales y fluctuaciones de la energfa potencial requeridos por ambos fen6menos. ABSTRACT: The problem of formation of elliptical galaxies via dissipationless collapse is studied using a large set of numerical simulations. It is shown that dissipationless collapses from cold initial conditions, where the total initial kinetic energy is less than 5% ofthe initial potential energy, lead to relaxed triaxial systems ery similar to real elliptical galaxies ii projected shape and density profiles. The triaxial shape is due to the of a dynamical instability that appears on systems dominated by radial orbits, while final density profile is due to violent relaxation that tends to produce a unique distribution iii space. These two phenomena erase memory of the initial prodtice a convergent evolution toward realistic systems, thus making unnecessary use o[special initial conditions (other

  9. Molecular Viscosity Sensors with Two Rotators for Optimizing the Fluorescence Intensity-Contrast Trade-Off.

    Science.gov (United States)

    Lee, Seung-Chul; Lee, Chang-Lyoul; Heo, Jeongyun; Jeong, Chan-Uk; Lee, Gyeong-Hui; Kim, Sehoon; Yoon, Woojin; Yun, Hoseop; Park, Sung O; Kwak, Sang Kyu; Park, Sung-Ha; Kwon, O-Pil

    2018-02-26

    A series of fluorescent molecular rotors obtained by introducing two rotational groups ("rotators"), which exhibit different rotational and electron-donating abilities, are discussed. Whereas the control molecular rotor, PH, includes a single rotator (the widely used phenyl group), the PO molecular rotors consist of two rotators (a phenyl group and an alkoxy group), which exhibit simultaneous strongly electron-donating and easy rotational abilities. Compared with the control rotor PH, PO molecular rotors exhibited one order of magnitude higher quantum yield (fluorescence intensity) and simultaneously exhibited significantly higher fluorescence contrast. These properties are directly related to the strong electron-donating ability and low energy barrier of rotation of the alkoxy group, as confirmed by dynamic fluorescence experiments and quantum chemical calculations. The PO molecular rotors exhibited two fluorescence relaxation pathways, whereas the PH molecular rotor exhibited a single fluorescence relaxation pathway. Cellular fluorescence imaging with PO molecular rotors for mapping cellular viscosity was successfully demonstrated. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Spin dynamics in a molecular ferrimagnetic ring, [Mn(hfac)2NITPh]6

    International Nuclear Information System (INIS)

    Itou, T.; Funahashi, S.; Oyamada, A.; Maegawa, S.; Fujita, K.; Amezawa, K.; Yamaguchi, R.

    2007-01-01

    We studied the spin dynamics of a ferrimagnetic ring [Mn(hfac) 2 NITPh] 6 with an S=12 ground state by means of H-NMR1 experiments under several fields. The spin-lattice relaxation rate increases monotonically with increasing temperature. This monotonous behavior is not reproduced by the calculation based on the lifetimes of eigenstates caused by the spin-phonon interaction. The relaxation rate is possibly caused by the dispersion resulting from the interaction between the clusters, which is far smaller than the interaction in the cluster but comparable to the nuclear Zeeman energy

  11. A fermionic molecular dynamics technique to model nuclear matter

    International Nuclear Information System (INIS)

    Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

    2009-01-01

    Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

  12. Dynamical photo-induced electronic properties of molecular junctions

    Science.gov (United States)

    Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

    2018-03-01

    Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

  13. Dynamical processes in atomic and molecular physics

    CERN Document Server

    Ogurtsov, Gennadi

    2012-01-01

    Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

  14. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

    This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

  15. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

  16. Automated NMR relaxation dispersion data analysis using NESSY

    Directory of Open Access Journals (Sweden)

    Gooley Paul R

    2011-10-01

    Full Text Available Abstract Background Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. Results The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. Conclusions NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.

  17. State resolved vibrational relaxation modeling for strongly nonequilibrium flows

    Science.gov (United States)

    Boyd, Iain D.; Josyula, Eswar

    2011-05-01

    Vibrational relaxation is an important physical process in hypersonic flows. Activation of the vibrational mode affects the fundamental thermodynamic properties and finite rate relaxation can reduce the degree of dissociation of a gas. Low fidelity models of vibrational activation employ a relaxation time to capture the process at a macroscopic level. High fidelity, state-resolved models have been developed for use in continuum gas dynamics simulations based on computational fluid dynamics (CFD). By comparison, such models are not as common for use with the direct simulation Monte Carlo (DSMC) method. In this study, a high fidelity, state-resolved vibrational relaxation model is developed for the DSMC technique. The model is based on the forced harmonic oscillator approach in which multi-quantum transitions may become dominant at high temperature. Results obtained for integrated rate coefficients from the DSMC model are consistent with the corresponding CFD model. Comparison of relaxation results obtained with the high-fidelity DSMC model shows significantly less excitation of upper vibrational levels in comparison to the standard, lower fidelity DSMC vibrational relaxation model. Application of the new DSMC model to a Mach 7 normal shock wave in carbon monoxide provides better agreement with experimental measurements than the standard DSMC relaxation model.

  18. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  19. Internal structures of self-organized relaxed states and self-similar decay phase

    International Nuclear Information System (INIS)

    Kondoh, Yoshiomi

    1992-03-01

    A thought analysis on relaxation due to nonlinear processes is presented to lead to a set of general thoughts applicable to general nonlinear dynamical systems for finding out internal structures of the self-organized relaxed state without using 'invariant'. Three applications of the set of general thoughts to energy relaxations in resistive MHD plasmas, incompressible viscous fluids, and incompressible viscous MHD fluids are shown to lead to the internal structures of the self-organized relaxed states. It is shown that all of the relaxed states in these three dynamical systems are followed by self-similar decay phase without significant change of the spatial structure. The well known relaxed state of ∇ x B = ±λ B is shown to be derived generally in the low β plasma limit. (author)

  20. Stresses and elastic constants of crystalline sodium, from molecular dynamics

    International Nuclear Information System (INIS)

    Schiferl, S.K.

    1985-02-01

    The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs

  1. Dielectric relaxation studies of dilute solutions of amides

    Energy Technology Data Exchange (ETDEWEB)

    Malathi, M.; Sabesan, R.; Krishnan, S

    2003-11-15

    The dielectric constants and dielectric losses of formamide, acetamide, N-methyl acetamide, acetanilide and N,N-dimethyl acetamide in dilute solutions of 1,4-dioxan/benzene have been measured at 308 K using 9.37 GHz, dielectric relaxation set up. The relaxation time for the over all rotation {tau}{sub (1)} and that for the group rotation {tau}{sub (2)} of (the molecules were determined using Higasi's method. The activation energies for the processes of dielectric relaxation and viscous flow were determined by using Eyring's rate theory. From relaxation time behaviour of amides in non-polar solvent, solute-solvent and solute-solute type of molecular association is proposed.

  2. Time, stress, and temperature-dependent deformation in nanostructured copper: Stress relaxation tests and simulations

    International Nuclear Information System (INIS)

    Yang, Xu-Sheng; Wang, Yun-Jiang; Wang, Guo-Yong; Zhai, Hui-Ru; Dai, L.H.; Zhang, Tong-Yi

    2016-01-01

    In the present work, stress relaxation tests, high-resolution transmission electron microscopy (HRTEM), and molecular dynamics (MD) simulations were conducted on coarse-grained (cg), nanograined (ng), and nanotwinned (nt) copper at temperatures of 22 °C (RT), 30 °C, 40 °C, 50 °C, and 75 °C. The comprehensive investigations provide sufficient information for the building-up of a formula to describe the time, stress, and temperature-dependent deformation and clarify the relationship among the strain rate sensitivity parameter, stress exponent, and activation volume. The typically experimental curves of logarithmic plastic strain rate versus stress exhibited a three staged relaxation process from a linear high stress relaxation region to a subsequent nonlinear stress relaxation region and finally to a linear low stress relaxation region, which only showed-up at the test temperatures higher than 22 °C, 22 °C, and 30 °C, respectively, in the tested cg-, ng-, and nt-Cu specimens. The values of stress exponent, stress-independent activation energy, and activation volume were determined from the experimental data in the two linear regions. The determined activation parameters, HRTEM images, and MD simulations consistently suggest that dislocation-mediated plastic deformation is predominant in all tested cg-, ng-, and nt-Cu specimens in the initial linear high stress relaxation region at the five relaxation temperatures, whereas in the linear low stress relaxation region, the grain boundary (GB) diffusion-associated deformation is dominant in the ng- and cg-Cu specimens, while twin boundary (TB) migration, i.e., twinning and detwinning with parallel partial dislocations, governs the time, stress, and temperature-dependent deformation in the nt-Cu specimens.

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

    Science.gov (United States)

    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.

  4. Vogel-Fulcher dependence of relaxation rates in a nematic monomer and elastomer

    Science.gov (United States)

    Shenoy, D.; Filippov, S.; Aliev, F.; Keller, P.; Thomsen, D.; Ratna, B.

    2000-12-01

    Dielectric relaxation spectroscopy is used to study the relaxation processes in a nematic monomer and the corresponding cross-linked polymer nematic liquid crystal (elastomer). In the frequency window 10 mHz to 2 GHz the monomer liquid crystal shows a single relaxation whereas the polymer exhibits three relaxation processes, two of which are quantitatively analyzed. The temperature dependence of relaxation times in both the monomer and polymer follows a Vogel-Fulcher behavior. The relaxation processes are identified with specific molecular motions and activation energies are calculated in a linear approximation for comparison with literature data.

  5. Dielectric relaxation studies in super-cooled liquid and glassy phases of anti-cancerous alkaloid: Brucine

    Science.gov (United States)

    Afzal, Aboothahir; Shahin Thayyil, M.; Sulaiman, M. K.; Kulkarni, A. R.

    2018-05-01

    Brucine has good anti-tumor effects, on both liver cancer and breast cancer. It has bioavailability of 40.83%. Since the bioavailability of the drug is low, an alternative method to increase its bioavailability and solubility is by changing the drug into glassy form. We used Differential Scanning Calorimetry (DSC) for studying the glass forming ability of the drug. Brucine was found to be a very good glass former glass transition temperature 365 K. Based on the DSC analysis we have used broadband dielectric spectroscopy (BDS) for studying the drug in the super cooled and glassy state. BDS is an effective tool to probe the molecular dynamics in the super cooled and glassy state. Molecular mobility is found to be present even in the glassy state of this active pharmaceutical ingredient (API) which is responsible for the instability. Our aim is to study the factors responsible for instability of this API in amorphous form. Cooling curves for dielectric permittivity and dielectric loss revealed the presence of structural (α) and secondary relaxations (β and γ). Temperature dependence of relaxation time is fitted by Vogel-Fulcher-Tammann equation and found the values of activation energy of the α relaxation, fragility and glass transition temperature. Paluch's anti correlation is also verified, that the width of the α-loss peak at or near the glass transition temperature Tg is strongly anticorrelated with the polarity of the molecule. The larger the dielectric relaxation strength Δɛ (Tg) of the system, the narrower is the α-loss peak (higher value of βKWW).

  6. Green--Kubo formula for collisional relaxation

    International Nuclear Information System (INIS)

    Visscher, P.B.

    1988-01-01

    In this paper we generalize the Green--Kubo method (usually used for obtaining formulas for transport coefficients involving conserved densities) to relaxation processes occurring during collisions, such as the transfer of energy from vibrational to translational modes in a molecular fluid. We show that the relaxation rate can be calculated without evaluating time correlation functions over long times, and can in fact be written as a sum over collisions which makes the relation between the Green--Kubo method and approximate independent-collision models much clearer

  7. Molecular dynamics for fermions

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    2000-02-01

    The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

  8. Relaxation model of radiation-induced conductivity in polymers

    Science.gov (United States)

    Zhutayeva, Yu. R.; Khatipov, S. A.

    1999-05-01

    The paper suggests a relaxation model of radiation-induced conductivity (RIC) in polymers. According to the model, the transfer of charges generated in the polymer volume by ionizing radiation takes place with the participation of molecular relaxation processes. The mechanism of electron transport consists in the transfer of the charge directly between traps when they draw close to one another due to the rotation of macromolecule segments. The numerical solutions of the corresponding kinetic equations for different distribution functions Q( τ) of the times of molecular relaxation and for different functions of the probability P( τ, τ') of charge transfer in the `overlapping' regions of the diffusion spheres of the segments are analyzed. The relaxation model provides an explanation of the non-Arrhenius behavior of the RIC temperature dependence, the power dependence of RIC on the dose rate with a power index in the interval 0.5-1.0, the appearance of maxima in the curves of the RIC temporal dependence and their irreversible character in the region of large dose rates (more than 1 Gy/s). The model can be used for interpreting polymer RIC in conditions of kinetic mobility of macromolecules.

  9. Pattern recognition in molecular dynamics. [FORTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

    1977-07-01

    An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

  10. Unraveling the effect of the hydration level on the molecular mobility of nanolayered polymeric systems.

    Science.gov (United States)

    Borges, João; Caridade, Sofia G; Silva, Joana M; Mano, João F

    2015-02-01

    This work investigates the influence of the hydration level on the molecular mobility and glass transition dynamics of freestanding chitosan/alginate (CHT/ALG) nanolayered systems. Nonconventional dynamic mechanical analysis identifies two relaxation processes assigned to the α-relaxation of the two biopolymers, respectively, CHT and ALG, when immersed in water/ethanol mixtures. This phenomenon explains the shape memory properties of the multilayered systems induced by hydration, thus constituting promising smart materials that would be of paramount importance in a plethora of research fields, including in the biomedical and biotechnological fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Spin relaxation in nanowires by hyperfine coupling

    International Nuclear Information System (INIS)

    Echeverria-Arrondo, C.; Sherman, E.Ya.

    2012-01-01

    Hyperfine interactions establish limits on spin dynamics and relaxation rates in ensembles of semiconductor quantum dots. It is the confinement of electrons which determines nonzero hyperfine coupling and leads to the spin relaxation. As a result, in nanowires one would expect the vanishing of this effect due to extended electron states. However, even for relatively clean wires, disorder plays a crucial role and makes electron localization sufficient to cause spin relaxation on the time scale of the order of 10 ns. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  12. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    International Nuclear Information System (INIS)

    Mori, Yukie; Masuda, Yuichi

    2015-01-01

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

  13. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

    2015-09-08

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

  14. Slow dynamics in an azopolymer molecular layer studied by x-ray photon correlation spectroscopy

    International Nuclear Information System (INIS)

    Orsi, D.; Fluerasu, A.; Cristofolini, L.; Fontana, M.P.; Pontecorvo, E.; Caronna, C.; Zontone, F.; Madsen, A.

    2010-01-01

    We report the results of x-ray photon correlation spectroscopy (XPCS) experiments on multilayers of a photosensitive azo-polymer which can be softened by photoisomerization. Time correlation functions have been measured at different temperatures and momentum transfers (q) and under different illumination conditions (dark, UV or visible). The correlation functions are well described by the Kohlrausch-Williams-Watts (KWW) form with relaxation times that are proportional to q -1 . The characteristic relaxation times follow the same Vogel-Fulcher-Tammann law describing the bulk viscosity of this polymer. The out-of-equilibrium relaxation dynamics following a UV photoperturbation are accelerated, which is in agreement with a fluidification effect previously measured by rheology. The transient dynamics are characterized by two times correlation function, and dynamical heterogeneity is evidenced by calculating the variance χ of the degree of correlation as a function of ageing time. A clear peak in χ appears at a well defined time τ C which scales with q -1 and with the ageing time, in a similar fashion as previously reported in colloidal suspensions (O. Dauchot et al. Phys. Rev. Lett. 95 265701 (2005)). From an accurate analysis of the correlation functions we could demonstrate a temperature and light dependent cross-over from compressed KWW to simple exponential behavior.

  15. Computer simulation of confined liquid crystal dynamics

    International Nuclear Information System (INIS)

    Webster, R.E.

    2001-11-01

    Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)

  16. Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Chengzhen Sun; Bofeng Bai

    2017-01-01

    Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

  17. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  18. Microscopic insights into the NMR relaxation based protein conformational entropy meter

    Science.gov (United States)

    Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

    2013-01-01

    Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

  19. Relaxation time in confined disordered systems

    International Nuclear Information System (INIS)

    Chamati, H.; Korutcheva, E.

    2006-05-01

    The dynamic critical behavior of a quenched hypercubic sample of linear size L is considered within the 'random T c ' field theoretical model with purely relaxation dynamic (Model A). The dynamic finite size scaling behavior is established and analyzed when the system is quenched from a homogeneous phase towards its critical temperature. The obtained results are compared to those reported in the literature. (author)

  20. Multiscale equation-free algorithms for molecular dynamics

    Science.gov (United States)

    Abi Mansour, Andrew

    Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

  1. F{sup 19} relaxation in non-magnetic hexafluorides; Contribution a l'etude de la relaxation des fluors dans les hexafluorures non magnetiques

    Energy Technology Data Exchange (ETDEWEB)

    Rigny, P [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1967-12-01

    The interesting properties of the fluorine magnetic resonance in the hexafluorides of molybdenum, tungsten and uranium, are very much due to large anisotropies of the chemical shift tensors. In the solid phases these anisotropies, the values of which are deduced from line shape studies, allow one to show that the molecules undergo hindered rotations about the metal atom. The temperature and frequency dependence of the fluorine longitudinal relaxation times shows that the relaxation is due to the molecular motion. The dynamical parameters of this motion are then deduced from the complete study of the fluorine relaxation in the rotating frame. In the liquid phases, the existence of anisotropies allows an estimation of the different contributions to the relaxation. In particular, the frequency and temperature dependence of the relaxation shows it to be dominated by the spin-rotation interaction. We have shown that the strength of this interaction can be deduced from the chemical shifts, and the angle through which the molecule rotates quasi-freely can be determined. In the hexafluorides, this angle is roughly one radian at 70 C, and with the help of this value, the friction coefficients which describe the intermolecular interactions are discussed. (author) [French] Les proprietes de la resonance magnetique des fluors dans les hexafluorures de molybdene, tungstene et uranium sont influencees par l'existence de deplacements chimiques tres anisotropes. Dans les phases solides, la valeur de cette anisotropie peut etre determinee par l'analyse des formes de raies et son existence permet de montrer que les molecules sont en rotation empechee autour de leur atome central. L'etude du temps de relaxation longitudinal en fonction de la temperature et de la frequence montre que la relaxation est due aux mouvements moleculaires, aux plus hautes temperatures. Les proprietes dynamiques du mouvement sont obtenues par l'etude complete de la relaxation spin-reseau dans le referentiel

  2. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  3. Relaxation dynamics of glass transition in PMMA + SWCNT composites by temperature-modulated DSC

    Science.gov (United States)

    Pradhan, N. R.; Iannacchione, G. S.

    2010-03-01

    The experimental technique offered by temperature-modulated differential scanning calorimeter (TMDSC) used to investigate the thermal relaxation dynamics through the glass transition as a function of frequency was studied for pure PMMA and PMMA-single wall carbon nanotubes (SWCNTs) composites. A strong dependence of the temperature dependence peak in the imaginary part of complex heat capacity (Tmax) is found during the transition from the glass-like to the liquid-like region. The frequency dependence of Tmax of the imaginary part of heat capacity (Cp) is described by Arrhenius law. The activation energy obtained from the fitting shows increases while the characteristic relaxation time decreases with increasing mass fraction (phim) of SWCNTs. The dynamics of the composites during glass transition, at slow and high scan rates, are also the main focus of this experimental study. The change in enthalpy during heating and cooling is also reported as a function of scan rate and frequency of temperature modulation. The glass transition temperature (Tg) shows increases with increasing frequency of temperature modulation and phim of SWCNTs inside the polymer host. Experimental results show that Tg is higher at higher scan rates but as the frequency of temperature modulation increases, the Tg values of different scan rates coincide with each other and alter the scan rate dependence. From the imaginary part of heat capacity, it is obvious that Tmax is not the actual glass transition temperature of pure polymer but Tmax and Tg values can be superimposed when phim increases in the polymer host or when the sample undergoes a transition with a certain frequency of temperature modulation.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Pal, P.; Ghosh, A., E-mail: sspag@iacs.res.in [Department of Solid State Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India)

    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 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.

  6. Thermal Fluctuations in the Magnetic Ground State of the Molecular Cluster Mn12O12 Acetate from μSR and Proton NMR Relaxation

    International Nuclear Information System (INIS)

    Lascialfari, A.; Borsa, F.; Carretta, P.; Jang, Z.H.; Borsa, F.; Gatteschi, D.

    1998-01-01

    Measurements of the spin-lattice relaxation rate are reported for muons and protons as a function of temperature for different values of the applied magnetic field in the Mn 12 O 12 molecular cluster. Strongly field dependent maxima in the relaxation rate versus temperature are observed below 50thinspthinspK. The results are explained in terms of thermal fluctuations of the total magnetization of the cluster among the different orientations with respect to the anisotropy axis. The lifetimes of the different m components of the total spin, S T =10 , of the molecule are obtained from the experiment and shown to be consistent with the ones expected from a spin-phonon coupling mechanism. No clear evidence for macroscopic quantum tunneling was observed in the field dependence of the proton relaxation rate at low T . copyright 1998 The American Physical Society

  7. Fast relaxation transients in a kicked damped oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Urquizu, Merce [Laboratori d' Estudis Geofisics ' Eduard Fontsere' , IEC, Barcelona (Spain); Correig, Antoni M. [Departament d' Astronomical i Meteorologia, Laboratori d' Estudis Geofisics Eduard Fontsere, UB Marti Franques 1, E-08028 Barcelona (Spain) and Laboratori d' Estudis Geofisics ' Eduard Fontsere' , IEC, Barcelona (Spain)]. E-mail: ton.correig@am.ub.es

    2007-08-15

    Although nonlinear relaxation transients are very common in nature, very few studies are devoted to its characterization, mainly due to its short time duration. In this paper, we present a study about the nature of relaxation transients in a kicked damped oscillator, in which transients are generated in terms of continuous fast changes in the parameters of the system. We have found that transient dynamics can be described, rather than in terms of bifurcation dynamics, in terms of instantaneous stretching factors, which are related to the stability of fixed points of the corresponding stroboscopic maps.

  8. Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

    2015-05-01

    Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

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

    Science.gov (United States)

    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.

  10. Advances in dynamic relaxation techniques for nonlinear finite element analysis

    International Nuclear Information System (INIS)

    Sauve, R.G.; Metzger, D.R.

    1995-01-01

    Traditionally, the finite element technique has been applied to static and steady-state problems using implicit methods. When nonlinearities exist, equilibrium iterations must be performed using Newton-Raphson or quasi-Newton techniques at each load level. In the presence of complex geometry, nonlinear material behavior, and large relative sliding of material interfaces, solutions using implicit methods often become intractable. A dynamic relaxation algorithm is developed for inclusion in finite element codes. The explicit nature of the method avoids large computer memory requirements and makes possible the solution of large-scale problems. The method described approaches the steady-state solution with no overshoot, a problem which has plagued researchers in the past. The method is included in a general nonlinear finite element code. A description of the method along with a number of new applications involving geometric and material nonlinearities are presented. They include: (1) nonlinear geometric cantilever plate; (2) moment-loaded nonlinear beam; and (3) creep of nuclear fuel channel assemblies

  11. Universal properties of relaxation and diffusion in condensed matter

    International Nuclear Information System (INIS)

    Ngai K L

    2017-01-01

    By and large the research communities today are not fully aware of the remarkable universality in the dynamic properties of many-body relaxation/diffusion processes manifested in experiments and simulations on condensed matter with diverse chemical compositions and physical structures. I shall demonstrate the universality first from the dynamic processes in glass-forming systems. This is reinforced by strikingly similar properties of different processes in contrasting interacting systems all having nothing to do with glass transition. The examples given here include glass-forming systems of diverse chemical compositions and physical structures, conductivity relaxation of ionic conductors (liquid, glassy, and crystalline), translation and orientation ordered phase of rigid molecule, and polymer chain dynamics. Universality is also found in the change of dynamics when dimension is reduced to nanometer size in widely different systems. The remarkable universality indicates that many-body relaxation/diffusion is governed by fundamental physics to be unveiled. One candidate is classical chaos on which the coupling model is based, Universal properties predicted by this model are in accord with diverse experiments and simulations. (paper)

  12. 15N NMR relaxation studies of calcium-loaded parvalbumin show tight dynamics compared to those of other EF-hand proteins

    DEFF Research Database (Denmark)

    Baldellon, C; Alattia, J R; Strub, M P

    1998-01-01

    Dynamics of the rat alpha-parvalbumin calcium-loaded form have been determined by measurement of 15N nuclear relaxation using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed using spectral density functions and the Lipari-Szabo formalism. The major dynamic features...... for the rat alpha-parvalbumin calcium-loaded form are (1) the extreme rigidity of the helix-loop-helix EF-hand motifs and the linker segment connecting them, (2) the N and C termini of the protein being restricted in their mobility, (3) a conformational exchange occurring at the kink of helix D, and (4...... properties which are conserved in the EF-hand domains from different members of this superfamily: (1) a tendency toward higher mobility of NH vectors at relative position 2 in the Ca2+-binding loop, (2) a restricted mobility for the other residues in the binding loop, and (3) an overall rigidity...

  13. Inelastic neutron scattering investigation of the α-β crossover in glass-formers as a function of molecular architecture

    International Nuclear Information System (INIS)

    Levelut, C.; Faivre, A.; Pelous, J.; Durand, D.

    1999-01-01

    Complete text of publication follows. An experimental investigation of the relaxational processes related to the glass transition in several glass formers with more or less complex molecular architecture is presented. This inelastic neutron scattering study concentrates on the region around 1.1 to 1.5 T g where the two relaxation processes usually identified in most glass formers, the α and the β relaxations, are expected to merge or cross. A recent study comparing the dynamics of Sorbitol and Maltitol (two low molecular and complementary glasses) seems to show that the way on which the α and β processes merge depends on the differences in the chemical architecture of these polyols [1]. In the present work, linear diols, three-arm-star triols and crosslinked polyurethanes, synthesized from the latter are studied. This work is an extension of a previous study of the relaxational processes in cross-linked polyurethanes [2]. For such series of samples of similar chemical composition but with increasing complexity in the architecture, the influence of the molecular complexity on the type of merging between α and β processes is tested. This allows to discuss the α-β cross-over on molecular level. (author)

  14. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  15. Molecular quantum dynamics. From theory to applications

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

    2014-09-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

  16. Probing spin dynamics and quantum relaxation in Li Y0.998 Ho0.002 F4 via 19F NMR

    Science.gov (United States)

    Graf, M. J.; Lascialfari, A.; Borsa, F.; Tkachuk, A. M.; Barbara, B.

    2006-01-01

    We report measurements of F19 nuclear spin-lattice relaxation 1/T1 as a function of temperature and external magnetic field in a LiY0.998Ho0.002F4 single crystal, a single-ion magnet exhibiting interesting quantum effects. The F19 1/T1 is found to depend on the coupling with the diluted rare-earth (RE) moments, making it an effective probe of the rare-earth spin dynamics. The results for 1/T1 show a behavior similar to that observed in molecular nanomagnets, a result which we attribute to the discreteness of the energy levels in both cases. At intermediate temperatures the lifetime broadening of the crystal field split RE magnetic levels follows a T3 power law. At low temperature the field dependence of 1/T1 shows peaks in correspondence to the critical magnetic fields for energy level crossings (LC). A key result of this study is that the broadening of the levels at LC is found to become extremely small at low temperatures, about 1.7mT , a value which is comparable to the weak dipolar fields at the RE lattice positions. Thus, unlike the molecular magnets, decoherence effects are strongly suppressed, and it may be possible to measure directly the level repulsions at avoided level crossings.

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

    Science.gov (United States)

    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 %.

  18. Gd-DTPA-Dopamine-Bisphytanyl Amphiphile: Synthesis, Characterisation and Relaxation Parameters of the Nanoassemblies and Their Potential as MRI Contrast Agents.

    Science.gov (United States)

    Gupta, Abhishek; Willis, Scott A; Waddington, Lynne J; Stait-Gardner, Tim; de Campo, Liliana; Hwang, Dennis W; Kirby, Nigel; Price, William S; Moghaddam, Minoo J

    2015-09-28

    Here, a new amphiphilic magnetic resonance imaging (MRI) contrast agent, a Gd(III)-chelated diethylenetriaminepentaacetic acid conjugated to two branched alkyl chains via a dopamine spacer, Gd-DTPA-dopamine-bisphytanyl (Gd-DTPA-Dop-Phy), which is readily capable of self-assembling into liposomal nanoassemblies upon dispersion in an aqueous solution, is reported. In vitro relaxivities of the dispersions were found to be much higher than Magnevist, a commercially available contrast agent, at 0.47 T but comparable at 9.40 T. Analysis of variable temperature (17)O NMR transverse relaxation measurements revealed the water exchange of the nanoassemblies to be faster than that previously reported for paramagnetic liposomes. Molecular reorientation dynamics were probed by (1)H NMRD profiles using a classical inner and outer sphere relaxation model and a Lipari-Szabo "model-free" approach. High payloads of Gd(III) ions in the liposomal nanoassemblies made solely from the Gd-DTPA-Dop-Phy amphiphiles, in combination with slow molecular reorientation and fast water exchange makes this novel amphiphile a suitable candidate to be investigated as an advanced MRI contrast agent. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Ultraviolet relaxation dynamics of aniline, N, N-dimethylaniline and 3,5-dimethylaniline at 250 nm

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, James O. F.; Saalbach, Lisa; Crane, Stuart W. [Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Paterson, Martin J. [Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Townsend, Dave, E-mail: D.Townsend@hw.ac.uk [Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom)

    2015-03-21

    Time-resolved photoelectron imaging was used to investigate the electronic relaxation dynamics of gas-phase aniline, N, N-dimethylaniline, and 3,5-dimethylaniline following ultraviolet excitation at 250 nm. Our analysis was supported by ab initio coupled-cluster calculations evaluating excited state energies and (in aniline) the evolution of a range of excited state physical properties as a function of N–H bond extension. Due to a lack of consistency between several earlier studies undertaken in aniline, the specific aim of this present work was to gain new insight into the previously proposed non-adiabatic coupling interaction between the two lowest lying singlet excited states S{sub 1}(ππ{sup ∗}) and S{sub 2}(3s/πσ{sup ∗}). The methyl-substituted systems N, N-dimethylaniline and 3,5-dimethylaniline were included in order to obtain more detailed dynamical information about the key internal molecular coordinates that drive the S{sub 1}(ππ{sup ∗})/S{sub 2}(3s/πσ{sup ∗}) coupling mechanism. Our findings suggest that in all three systems, both electronic states are directly populated during the initial excitation, with the S{sub 2}(3s/πσ{sup ∗}) state then potentially decaying via either direct dissociation along the N–X stretching coordinate (X = H or CH{sub 3}) or internal conversion to the S{sub 1}(ππ{sup ∗}) state. In aniline and N, N-dimethylaniline, both pathways most likely compete in the depletion of S{sub 2}(3s/πσ{sup ∗}) state population. However, in 3,5-dimethylaniline, only the direct dissociation mechanism appears to be active. This is rationalized in terms of changes in the relative rates of the two decay pathways upon methylation of the aromatic ring system.

  20. Excited-state molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Pratt, S.T.

    1995-01-01

    This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

  1. Symmetry of quantum molecular dynamics

    International Nuclear Information System (INIS)

    Burenin, A.V.

    2002-01-01

    The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

  2. Molecular dynamics modeling of polymer flammability

    International Nuclear Information System (INIS)

    Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

    1992-01-01

    Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

  3. Stretched exponential relaxation and ac universality in disordered dielectrics

    DEFF Research Database (Denmark)

    Milovanov, Alexander V.; Rypdal, Kristoffer; Juul Rasmussen, Jens

    2007-01-01

    This paper is concerned with the connection between the properties of dielectric relaxation and alternating-current (ac) conduction in disordered dielectrics. The discussion is divided between the classical linear-response theory and a self-consistent dynamical modeling. The key issues are stretc......This paper is concerned with the connection between the properties of dielectric relaxation and alternating-current (ac) conduction in disordered dielectrics. The discussion is divided between the classical linear-response theory and a self-consistent dynamical modeling. The key issues...

  4. Slow relaxation in weakly open rational polygons.

    Science.gov (United States)

    Kokshenev, Valery B; Vicentini, Eduardo

    2003-07-01

    The interplay between the regular (piecewise-linear) and irregular (vertex-angle) boundary effects in nonintegrable rational polygonal billiards (of m equal sides) is discussed. Decay dynamics in polygons (of perimeter P(m) and small opening Delta) is analyzed through the late-time survival probability S(m) approximately equal t(-delta). Two distinct slow relaxation channels are established. The primary universal channel exhibits relaxation of regular sliding orbits, with delta=1. The secondary channel is given by delta>1 and becomes open when m>P(m)/Delta. It originates from vertex order-disorder dual effects and is due to relaxation of chaoticlike excitations.

  5. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  6. Relaxation along a fictitious field (RAFF and Z-spectroscopy using alternating-phase irradiation (ZAPI in permanent focal cerebral ischemia in rat.

    Directory of Open Access Journals (Sweden)

    Kimmo T Jokivarsi

    Full Text Available Cerebral ischemia alters the molecular dynamics and content of water in brain tissue, which is reflected in NMR relaxation, diffusion and magnetization transfer (MT parameters. In this study, the behavior of two new MRI contrasts, Relaxation Along a Fictitious Field (RAFF and Z-spectroscopy using Alternating-Phase Irradiation (ZAPI, were quantified together with conventional relaxation parameters (T1, T2 and T1ρ and MT ratios in acute cerebral ischemia in rat. The right middle cerebral artery was permanently occluded and quantitative MRI data was acquired sequentially for the above parameters for up to 6 hours. The following conclusions were drawn: 1 Time-dependent changes in RAFF and T1ρ relaxation are not coupled to those in MT. 2 RAFF relaxation evolves more like transverse, rather than longitudinal relaxation. 3 MT measured with ZAPI is less sensitive to ischemia than conventional MT. 4 ZAPI data suggest alterations in the T2 distribution of macromolecules in acute cerebral ischemia. It was shown that both RAFF and ZAPI provide complementary MRI information from acute ischemic brain tissue. The presented multiparametric MRI data may aid in the assessment of brain tissue status early in ischemic stroke.

  7. Friction and Surface Dynamics of Polymers on the Nanoscale by AFM

    NARCIS (Netherlands)

    Schönherr, Holger; Schónherr, Holger; Samori, Paolo; Tocha, E.; Vancso, Gyula J.

    2008-01-01

    In this article the measurement and understanding of friction forces and surface dynamics of polymers on the one hand and the importance of molecular relaxation processes and viscoelasticity in polymers for advanced micro- and nanoscale applications on the other hand are discussed. Particular

  8. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

    2015-04-21

    Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

  9. Vibronic relaxation in molecular mixed crystals : Pentacene in naphthalene and p-terphenyl

    NARCIS (Netherlands)

    Hesselink, Wim H.; Wiersma, Douwe A.

    1981-01-01

    Picosecond photon echo techniques are used to measure directly vibronic relaxation times in the first excited singlet state of pentacene in naphthalene and p-terphenyl. In regions of low (< 300 cm–1) and high (> 1000 cm–1) vibrational energy, relaxation is fast (τ <2 ps) due to direct phonon

  10. Dynamics of molecular superrotors in an external magnetic field

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Valery

    2015-08-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  11. Dynamics of polymers in elongational flow studied by the neutron spin-echo technique

    International Nuclear Information System (INIS)

    Rheinstaedter, Maikel C.; Sattler, Rainer; Haeussler, Wolfgang; Wagner, Christian

    2010-01-01

    The nanoscale fluctuation dynamics of semidilute high molecular weight polymer solutions of polyethylenoxide (PEO) in D 2 O under non-equilibrium flow conditions were studied by the neutron spin-echo technique. The sample cell was in contraction flow geometry and provided a pressure driven flow with a high elongational component that stretched the polymers most efficiently. Neutron scattering experiments in dilute polymer solutions are challenging because of the low polymer concentration and corresponding small quasi-elastic signals. A relaxation process with relaxation times of about 10 ps was observed, which shows anisotropic dynamics with applied flow.

  12. Anomalous relaxation and self-organization in non-equilibrium processes

    OpenAIRE

    Fatkullin, Ibrahim; Kladko, Konstantin; Mitkov, Igor; Bishop, A. R.

    2000-01-01

    We study thermal relaxation in ordered arrays of coupled nonlinear elements with external driving. We find, that our model exhibits dynamic self-organization manifested in a universal stretched-exponential form of relaxation. We identify two types of self-organization, cooperative and anti-cooperative, which lead to fast and slow relaxation, respectively. We give a qualitative explanation for the behavior of the stretched exponent in different parameter ranges. We emphasize that this is a sys...

  13. Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

    Directory of Open Access Journals (Sweden)

    Yonghua Wang

    Full Text Available MicroRNAs (miRNAs are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1 three important (PAZ, Mid and PIWI domains exist in Argonaute which define the global dynamics of the protein; 2 the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3 it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+ plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA. Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.

  14. Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

    Science.gov (United States)

    Wang, Yonghua; Li, Yan; Ma, Zhi; Yang, Wei; Ai, Chunzhi

    2010-07-29

    MicroRNAs (miRNAs) are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+)) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.

  15. Hydrodynamic Relaxation of an Electron Plasma to a Near-Maximum Entropy State

    International Nuclear Information System (INIS)

    Rodgers, D. J.; Servidio, S.; Matthaeus, W. H.; Mitchell, T. B.; Aziz, T.; Montgomery, D. C.

    2009-01-01

    Dynamical relaxation of a pure electron plasma in a Malmberg-Penning trap is studied, comparing experiments, numerical simulations and statistical theories of weakly dissipative two-dimensional (2D) turbulence. Simulations confirm that the dynamics are approximated well by a 2D hydrodynamic model. Statistical analysis favors a theoretical picture of relaxation to a near-maximum entropy state with constrained energy, circulation, and angular momentum. This provides evidence that 2D electron fluid relaxation in a turbulent regime is governed by principles of maximum entropy.

  16. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  17. Shear-stress fluctuations and relaxation in polymer glasses

    Science.gov (United States)

    Kriuchevskyi, I.; Wittmer, J. P.; Meyer, H.; Benzerara, O.; Baschnagel, J.

    2018-01-01

    We investigate by means of molecular dynamics simulation a coarse-grained polymer glass model focusing on (quasistatic and dynamical) shear-stress fluctuations as a function of temperature T and sampling time Δ t . The linear response is characterized using (ensemble-averaged) expectation values of the contributions (time averaged for each shear plane) to the stress-fluctuation relation μsf for the shear modulus and the shear-stress relaxation modulus G (t ) . Using 100 independent configurations, we pay attention to the respective standard deviations. While the ensemble-averaged modulus μsf(T ) decreases continuously with increasing T for all Δ t sampled, its standard deviation δ μsf(T ) is nonmonotonic with a striking peak at the glass transition. The question of whether the shear modulus is continuous or has a jump singularity at the glass transition is thus ill posed. Confirming the effective time-translational invariance of our systems, the Δ t dependence of μsf and related quantities can be understood using a weighted integral over G (t ) .

  18. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  19. Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

    2010-01-01

    We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

  20. Molecular dynamics study on threshold displacement energies in Fe-Cr alloys

    Science.gov (United States)

    Fu, Jiawei; Ding, Wenyi; Zheng, Mingjie; Mao, Xiaodong

    2018-03-01

    The threshold displacement energies (Ed) of Fe and Cr atoms in Fe-Cr alloys with Cr contents ranging from 0% to 21% have been obtained with molecular dynamics (MD) method. The values of Ed have been calculated along the three high-symmetry crystallographic directions [0 0 1], [0 1 1] and [1 1 1], a slightly 2° tilt from these directions, and a high-index crystallographic directions [1 3 5]. The results showed that [0 1 1] crystallographic direction had the highest Ed among the three high-symmetry directions in each Cr content alloy. Fe-9Cr had higher weighted average Ed than the other Cr content alloys for both Fe and Cr PKA due to its statistically high Ed along the [0 1 1] crystallographic direction up to 44.3 eV. And the statistical analysis on the primary damage configuration demonstrated that 〈1 1 0〉Fe-Fe dumbbells were the dominant defect structures after relaxation. These data can enrich the database of Ed in Fe-Cr alloys and have potential applications in guiding the optimization design of radiation-resistant RAFM steels.

  1. Active nematic gels as active relaxing solids

    Science.gov (United States)

    Turzi, Stefano S.

    2017-11-01

    I propose a continuum theory for active nematic gels, defined as fluids or suspensions of orientable rodlike objects endowed with active dynamics, that is based on symmetry arguments and compatibility with thermodynamics. The starting point is our recent theory that models (passive) nematic liquid crystals as relaxing nematic elastomers. The interplay between viscoelastic response and active dynamics of the microscopic constituents is naturally taken into account. By contrast with standard theories, activity is not introduced as an additional term of the stress tensor, but it is added as an external remodeling force that competes with the passive relaxation dynamics and drags the system out of equilibrium. In a simple one-dimensional channel geometry, we show that the interaction between nonuniform nematic order and activity results in either a spontaneous flow of particles or a self-organization into subchannels flowing in opposite directions.

  2. Transient absorption microscopy studies of energy relaxation in graphene oxide thin film.

    Science.gov (United States)

    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.

  3. Transient absorption microscopy studies of energy relaxation in graphene oxide thin film

    International Nuclear Information System (INIS)

    Murphy, Sean; Huang, Libai

    2013-01-01

    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. (paper)

  4. Computer simulation of confined liquid crystal dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Webster, R.E

    2001-11-01

    Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)

  5. Relaxation properties in classical diamagnetism

    Science.gov (United States)

    Carati, A.; Benfenati, F.; Galgani, L.

    2011-06-01

    It is an old result of Bohr that, according to classical statistical mechanics, at equilibrium a system of electrons in a static magnetic field presents no magnetization. Thus a magnetization can occur only in an out of equilibrium state, such as that produced through the Foucault currents when a magnetic field is switched on. It was suggested by Bohr that, after the establishment of such a nonequilibrium state, the system of electrons would quickly relax back to equilibrium. In the present paper, we study numerically the relaxation to equilibrium in a modified Bohr model, which is mathematically equivalent to a billiard with obstacles, immersed in a magnetic field that is adiabatically switched on. We show that it is not guaranteed that equilibrium is attained within the typical time scales of microscopic dynamics. Depending on the values of the parameters, one has a relaxation either to equilibrium or to a diamagnetic (presumably metastable) state. The analogy with the relaxation properties in the Fermi Pasta Ulam problem is also pointed out.

  6. Dynamics of molecular superrotors in an external magnetic field

    International Nuclear Information System (INIS)

    Korobenko, Aleksey; Milner, Valery

    2015-01-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

  7. The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

    Science.gov (United States)

    Chen, Jundong

    2018-03-01

    Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

  8. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  9. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  10. Logarithmic superposition of force response with rapid length changes in relaxed porcine airway smooth muscle.

    Science.gov (United States)

    Ijpma, G; Al-Jumaily, A M; Cairns, S P; Sieck, G C

    2010-12-01

    We present a systematic quantitative analysis of power-law force relaxation and investigate logarithmic superposition of force response in relaxed porcine airway smooth muscle (ASM) strips in vitro. The term logarithmic superposition describes linear superposition on a logarithmic scale, which is equivalent to multiplication on a linear scale. Additionally, we examine whether the dynamic response of contracted and relaxed muscles is dominated by cross-bridge cycling or passive dynamics. The study shows the following main findings. For relaxed ASM, the force response to length steps of varying amplitude (0.25-4% of reference length, both lengthening and shortening) are well-fitted with power-law functions over several decades of time (10⁻² to 10³ s), and the force response after consecutive length changes is more accurately fitted assuming logarithmic superposition rather than linear superposition. Furthermore, for sinusoidal length oscillations in contracted and relaxed muscles, increasing the oscillation amplitude induces greater hysteresivity and asymmetry of force-length relationships, whereas increasing the frequency dampens hysteresivity but increases asymmetry. We conclude that logarithmic superposition is an important feature of relaxed ASM, which may facilitate a more accurate prediction of force responses in the continuous dynamic environment of the respiratory system. In addition, the single power-function response to length changes shows that the dynamics of cross-bridge cycling can be ignored in relaxed muscle. The similarity in response between relaxed and contracted states implies that the investigated passive dynamics play an important role in both states and should be taken into account.

  11. AceCloud: Molecular Dynamics Simulations in the Cloud.

    Science.gov (United States)

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  12. Lattice Distortion Mediated Paramagnetic Relaxation in High-Spin High-Symmetry Molecular Magnets

    Science.gov (United States)

    Garg, Anupam

    1998-08-01

    Field-dependent maxima in the relaxation rate of the magnetic molecules Mn12-Ac and Fe8-tacn have commonly been ascribed to some resonant tunneling phenomena. We argue instead that the relaxation is purely due to phonons. The rate maxima arise because of a Jahn-Teller-like distortion caused by the coupling of phonons to degenerate Zeeman levels of the molecule at the top of the barrier. The binding energy of the distorted intermediate states lowers the barrier height and increases the relaxation rate. A nonperturbative calculation of this effect is carried out for a model system. An approximate result for the field variation near a maximum is found to agree reasonably with experiment.

  13. Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy

    International Nuclear Information System (INIS)

    Wang, Jianping; Yang, Fan; Zhao, Juan; Shi, Jipei

    2015-01-01

    In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH 3 CN, CHCl 3 , and CCl 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 of 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

  14. Dynamic slip of polydisperse linear polymers using partitioned plate

    Science.gov (United States)

    Ebrahimi, Marzieh; Konaganti, Vinod Kumar; Hatzikiriakos, Savvas G.

    2018-03-01

    The slip velocity of an industrial grade high molecular weight high-density polyethylene (HDPE) is studied in steady and dynamic shear experiments using a stress/strain controlled rotational rheometer equipped with a parallel partitioned plate geometry. Moreover, fluoroalkyl silane-based coating is used to understand the effect of surface energy on slip in steady and dynamic conditions. The multimode integral Kaye-Bernstein-Kearsley-Zapas constitutive model is applied to predict the transient shear response of the HDPE melt obtained from rotational rheometer. It is found that a dynamic slip model with a slip relaxation time is needed to adequately predict the experimental data at large shear deformations. Comparison of the results before and after coating shows that the slip velocity is largely affected by surface energy. Decreasing surface energy by coating increases slip velocity and decreases the slip relaxation time.

  15. Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myeong H., E-mail: myeong.lee@warwick.ac.uk; Troisi, Alessandro [Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL (United Kingdom)

    2016-06-07

    Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonian method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.

  16. Secondary relaxation in two engineering thermoplastics by neutron scattering and dielectric spectroscopy

    CERN Document Server

    Arrese, S; Alegria, A; Colmenero, J; Frick, B

    2002-01-01

    We present a preliminary investigation of the dynamics of glassy polycarbonate (PC) and polysulfone (PSF) by means of quasielastic neutron scattering and dielectric spectroscopy. Whereas the consideration of pure phenylene ring pi-flips is enough to explain the momentum-transfer (Q) dependence of the inelastic intensity measured for PSF, in the case of PC the Q dependence of both the coherent and the incoherent scattering functions reveal the existence in this polymer of some more complex motion of the phenylene ring. On the other hand, the similarity of the energy landscapes deduced from the different techniques points to a closely related molecular origin for all the relaxation/motions observed. (orig.)

  17. Secondary relaxation in two engineering thermoplastics by neutron scattering and dielectric spectroscopy

    International Nuclear Information System (INIS)

    Arrese-Igor, S.; Arbe, A.; Alegria, A.; Colmenero, J.; Frick, B.

    2002-01-01

    We present a preliminary investigation of the dynamics of glassy polycarbonate (PC) and polysulfone (PSF) by means of quasielastic neutron scattering and dielectric spectroscopy. Whereas the consideration of pure phenylene ring π-flips is enough to explain the momentum-transfer (Q) dependence of the inelastic intensity measured for PSF, in the case of PC the Q dependence of both the coherent and the incoherent scattering functions reveal the existence in this polymer of some more complex motion of the phenylene ring. On the other hand, the similarity of the energy landscapes deduced from the different techniques points to a closely related molecular origin for all the relaxation/motions observed. (orig.)

  18. A molecular dynamics study of energetic particle bombardment on diamond

    International Nuclear Information System (INIS)

    Li Rongbin; Dai Yongbing; Hu Xiaojun; Shen Hesheng; He Xianchang

    2003-01-01

    Molecular dynamic simulations, utilizing the Tersoff many-body potential, are used to investigate the microscopic processes of a single boron atom with an energy of 500 eV implanted into the diamond (001) 2 x 1 reconstructed surface. By calculating the variation of the mean coordination number with time, the lifetime of a thermal spike created by B bombardment is about 0.18 ps. Formation of the split-interstitial composed of projectile and lattice atom (B-C) is observed. The total potential energy of the system decreases about 0.56 eV with a stable B split-interstitial existing in diamond. Lattice relaxations in the diamond (001) 2 x 1 reconstructed surface or near surface of the simulated have been discussed, and the results show that the outermost layer atoms tend to move inward and other atoms move outward, while the interplanar distance between the outermost layer and the second layer has been shortened by 15%, compared with its starting interplanar distance. Stress distribution in the calculated diamond configuration is inhomogeneous. After boron implanted into diamond with an energy of 500 eV, there is an excess of compressively stressed atoms in the lattice, which induces the total stress being compressive

  19. Molecular theory for nuclear magnetic relaxation in protein solutions and tissue

    International Nuclear Information System (INIS)

    Kimmich, R.; Nusser, W.; Gneiting, T.

    1990-01-01

    A model theory is presented explaining a series of striking phenomena observed with nuclear magnetic relaxation in protein systems such as solutions or tissue. The frequency, concentration and temperature dependences of proton or deuteron relaxation times of protein solutions and tissue are explained. It is concluded that the translational diffusion of water molecules along the rugged surfaces of proteins and, to a minor degree, protein backbone fluctuations are crucial processes. The rate limiting factor of macromolecular tumbling is assumed to be given by the free water content in a certain analogy to the free-volume model of Cohen ad Turnbull. There are two characteristic water mass fractions indicating the saturation of the hydration shells and the onset of protein tumbling. A closed and relatively simple set of relaxation formulas is presented. The potentially fractal nature of the diffusion of water molecules on the protein surface is discussed. (author). 43 refs.; 4 figs

  20. Low-relaxation spin waves in laser-molecular-beam epitaxy grown nanosized yttrium iron garnet films

    Energy Technology Data Exchange (ETDEWEB)

    Lutsev, L. V., E-mail: l-lutsev@mail.ru; Korovin, A. M.; Bursian, V. E.; Gastev, S. V.; Fedorov, V. V.; Suturin, S. M.; Sokolov, N. S. [Ioffe Physical-Technical Institute, Russian Academy of Sciences, 194021 St. Petersburg (Russian Federation)

    2016-05-02

    Synthesis of nanosized yttrium iron garnet (Y{sub 3}Fe{sub 5}O{sub 12}, YIG) films followed by the study of ferromagnetic resonance (FMR) and spin wave propagation in these films is reported. The YIG films were grown on gadolinium gallium garnet substrates by laser molecular beam epitaxy. It has been shown that spin waves propagating in YIG deposited at 700 °C have low damping. At the frequency of 3.29 GHz, the spin-wave damping parameter is less than 3.6 × 10{sup −5}. Magnetic inhomogeneities of the YIG films give the main contribution to the FMR linewidth. The contribution of the relaxation processes to the FMR linewidth is as low as 1.2%.