WorldWideScience

Sample records for molecular dynamics dissipation

  1. Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.

    Science.gov (United States)

    van den Broek, Karina; Kuhn, Hubert; Zielesny, Achim

    2018-05-21

    Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated "all-in-one" simulation systems.

  2. Dissipation enhanced vibrational sensing in an olfactory molecular switch

    International Nuclear Information System (INIS)

    Chęcińska, Agata; Heaney, Libby; Pollock, Felix A.; Nazir, Ahsan

    2015-01-01

    Motivated by a proposed olfactory mechanism based on a vibrationally activated molecular switch, we study electron transport within a donor-acceptor pair that is coupled to a vibrational mode and embedded in a surrounding environment. We derive a polaron master equation with which we study the dynamics of both the electronic and vibrational degrees of freedom beyond previously employed semiclassical (Marcus-Jortner) rate analyses. We show (i) that in the absence of explicit dissipation of the vibrational mode, the semiclassical approach is generally unable to capture the dynamics predicted by our master equation due to both its assumption of one-way (exponential) electron transfer from donor to acceptor and its neglect of the spectral details of the environment; (ii) that by additionally allowing strong dissipation to act on the odorant vibrational mode, we can recover exponential electron transfer, though typically at a rate that differs from that given by the Marcus-Jortner expression; (iii) that the ability of the molecular switch to discriminate between the presence and absence of the odorant, and its sensitivity to the odorant vibrational frequency, is enhanced significantly in this strong dissipation regime, when compared to the case without mode dissipation; and (iv) that details of the environment absent from previous Marcus-Jortner analyses can also dramatically alter the sensitivity of the molecular switch, in particular, allowing its frequency resolution to be improved. Our results thus demonstrate the constructive role dissipation can play in facilitating sensitive and selective operation in molecular switch devices, as well as the inadequacy of semiclassical rate equations in analysing such behaviour over a wide range of parameters

  3. Deterministic constant-temperature dynamics for dissipative quantum systems

    International Nuclear Information System (INIS)

    Sergi, Alessandro

    2007-01-01

    A novel method is introduced in order to treat the dissipative dynamics of quantum systems interacting with a bath of classical degrees of freedom. The method is based upon an extension of the Nose-Hoover chain (constant temperature) dynamics to quantum-classical systems. Both adiabatic and nonadiabatic numerical calculations on the relaxation dynamics of the spin-boson model show that the quantum-classical Nose-Hoover chain dynamics represents the thermal noise of the bath in an accurate and simple way. Numerical comparisons, both with the constant-energy calculation and with the quantum-classical Brownian motion treatment of the bath, show that the quantum-classical Nose-Hoover chain dynamics can be used to introduce dissipation in the evolution of a quantum subsystem even with just one degree of freedom for the bath. The algorithm can be computationally advantageous in modelling, within computer simulation, the dynamics of a quantum subsystem interacting with complex molecular environments. (fast track communication)

  4. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    Energy Technology Data Exchange (ETDEWEB)

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)

    2014-12-14

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

  5. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    International Nuclear Information System (INIS)

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

    2014-01-01

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics

  6. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

    International Nuclear Information System (INIS)

    Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

    2011-01-01

    Highlights: → Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. → Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. → We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. → With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

  7. Dynamics of quasi-stable dissipative systems

    CERN Document Server

    Chueshov, Igor

    2015-01-01

    This book is  devoted to background material and recently developed mathematical methods in the study of infinite-dimensional dissipative systems. The theory of such systems is motivated by the long-term goal to establish rigorous mathematical models for turbulent and chaotic phenomena. The aim here is to offer general methods and abstract results pertaining to fundamental dynamical systems properties related to dissipative long-time behavior. The book systematically presents, develops and uses the quasi-stability method while substantially extending it by including for consideration new classes of models and PDE systems arising in Continuum Mechanics. The book can be used as a textbook in dissipative dynamics at the graduate level.   Igor Chueshov is a Professor of Mathematics at Karazin Kharkov National University in Kharkov, Ukraine.

  8. Dissipative quantum dynamics and nonlinear sigma-model

    International Nuclear Information System (INIS)

    Tarasov, V.E.

    1992-01-01

    Sedov variational principle which is the generalization of the least action principle for the dissipative and irreversible processes and the classical dissipative mechanics in the phase space is considered. Quantum dynamics for the dissipative and irreversible processes is constructed. As an example of the dissipative quantum theory the nonlinear two-dimensional sigma-model is considered. The conformal anomaly of the energy momentum tensor trace for closed bosonic string on the affine-metric manifold is investigated. The two-loop metric beta-function for nonlinear dissipative sigma-model was calculated. The results are compared with the ultraviolet two-loop conterterms for affine-metric sigma model. 71 refs

  9. Micellar polymerization: Computer simulations by dissipative particle dynamics.

    Science.gov (United States)

    Shupanov, Ruslan; Chertovich, Alexander; Kos, Pavel

    2018-07-15

    Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular-weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  10. Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

    Science.gov (United States)

    Ghaani, Mohammad Reza; English, Niall J

    2018-03-21

    Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

  11. Influence of Dissipative Particle Dynamics parameters and wall models on planar micro-channel flows

    Science.gov (United States)

    Wang, Yuyi; She, Jiangwei; Zhou, Zhe-Wei; microflow Group Team

    2017-11-01

    Dissipative Particle Dynamics (DPD) is a very effective approach in simulating mesoscale hydrodynamics. The influence of solid boundaries and DPD parameters are typically very strong in DPD simulations. The present work studies a micro-channel Poisseuille flow. Taking the neutron scattering experiment and molecular dynamics simulation result as bench mark, the DPD results of density distribution and velocity profile are systematically studied. The influence of different levels of coarse-graining, the number densities of wall and fluid, conservative force coefficients, random and dissipative force coefficients, different wall model and reflective boundary conditions are discussed. Some mechanisms behind such influences are discussed and the artifacts in the simulation are identified with the bench mark. Chinese natural science foundation (A020405).

  12. Effect of dissipation on dynamical fusion thresholds

    International Nuclear Information System (INIS)

    Sierk, A.J.

    1986-01-01

    The existence of dynamical thresholds to fusion in heavy nuclei (A greater than or equal to 200) due to the nature of the potential-energy surface is shown. These thresholds exist even in the absence of dissipative forces, due to the coupling between the various collective deformation degrees of freedom. Using a macroscopic model of nuclear shape dynamics, It is shown how three different suggested dissipation mechanisms increase by varying amounts the excitation energy over the one-dimensional barrier required to cause compound-nucleus formation. The recently introduced surface-plus-window dissipation may give a reasonable representation of experimental data on fusion thresholds, in addition to properly describing fission-fragment kinetic energies and isoscalar giant multipole widths. Scaling of threshold results to asymmetric systems is discussed. 48 refs., 10 figs

  13. 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.

  14. New derivation of relativistic dissipative fluid dynamics

    International Nuclear Information System (INIS)

    Jaiswal, Amaresh; Bhalerao, Rajeev S.; Pal, Subrata

    2012-01-01

    Relativistic dissipative hydrodynamics has been quite successful in explaining the spectra and azimuthal anisotropy of particles produced in heavy-ion collisions at the RHIC and recently at the LHC. The first-order dissipative fluid dynamics or the relativistic Navier-Stokes (NS) theory involves parabolic differential equations and suffers from a causality and instability. The second-order or Israel-Stewart (IS) theory with its hyperbolic equations restores causality but may not guarantee stability. The correct formulation of relativistic viscous fluid dynamics is far from settled and is under intense investigation

  15. Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

    Czech Academy of Sciences Publication Activity Database

    Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

    2015-01-01

    Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

  16. On multi-dissipative dynamic systems

    DEFF Research Database (Denmark)

    Thygesen, Uffe Høgsbro

    1999-01-01

    We consider deterministic dynamic systems with state space representations which are dissipative in the sense of Willems (1972) with respect to several supply rates. This property is of interest in robustness analysis and in multi-objective control. We give conditions under which the convex cone...

  17. New results from dissipative diabatic dynamics and nuclear elastoplasticity

    International Nuclear Information System (INIS)

    Noerenberg, W.; Technische Hochschule Darmstadt

    1986-10-01

    I present new results about dissipative diabatic dynamics and nuclear elastoplasticity, in particular on a self-consistent diabatic formulation, on first numerical calculations of dissipative diabatic dynamics in two collective degrees of freedom, on quasi-elastic recoil in central nucleus-nucleus collisions, on the diabatic hindrance of fusion reactions and on the diabatic emission of nucleons in central nucleus-nucleus collisions. (orig./HSI)

  18. Stable schemes for dissipative particle dynamics with conserved energy

    Energy Technology Data Exchange (ETDEWEB)

    Stoltz, Gabriel, E-mail: stoltz@cermics.enpc.fr

    2017-07-01

    This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal conduction) to effective single-variable dynamics, and to approximate the solution of these dynamics with one step of a Metropolis–Hastings algorithm. This ensures by construction that no negative internal energies are encountered during the simulation, and hence allows to increase the admissible timesteps to integrate the dynamics, even for systems with small heat capacities. Stability is only limited by the Hamiltonian part of the dynamics, which suggests resorting to multiple timestep strategies where the stochastic part is integrated less frequently than the Hamiltonian one.

  19. Dynamic response function and large-amplitude dissipative collective motion

    International Nuclear Information System (INIS)

    Wu Xizhen; Zhuo Yizhong; Li Zhuxia; Sakata, Fumihiko.

    1993-05-01

    Aiming at exploring microscopic dynamics responsible for the dissipative large-amplitude collective motion, the dynamic response and correlation functions are introduced within the general theory of nuclear coupled-master equations. The theory is based on the microscopic theory of nuclear collective dynamics which has been developed within the time-dependent Hartree-Fock (TDHF) theory for disclosing complex structure of the TDHF-manifold. A systematic numerical method for calculating the dynamic response and correlation functions is proposed. By performing numerical calculation for a simple model Hamiltonian, it is pointed out that the dynamic response function gives an important information in understanding the large-amplitude dissipative collective motion which is described by an ensemble of trajectories within the TDHF-manifold. (author)

  20. Dynamical properties of dissipative XYZ Heisenberg lattices

    Science.gov (United States)

    Rota, R.; Minganti, F.; Biella, A.; Ciuti, C.

    2018-04-01

    We study dynamical properties of dissipative XYZ Heisenberg lattices where anisotropic spin-spin coupling competes with local incoherent spin flip processes. In particular, we explore a region of the parameter space where dissipative magnetic phase transitions for the steady state have been recently predicted by mean-field theories and exact numerical methods. We investigate the asymptotic decay rate towards the steady state both in 1D (up to the thermodynamical limit) and in finite-size 2D lattices, showing that critical dynamics does not occur in 1D, but it can emerge in 2D. We also analyze the behavior of individual homodyne quantum trajectories, which reveal the nature of the transition.

  1. Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

    Science.gov (United States)

    English, Niall J; Clarke, Elaine T

    2013-09-07

    Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

  2. Relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium

    Science.gov (United States)

    Green, Jason R.; Costa, Anthony B.; Grzybowski, Bartosz A.; Szleifer, Igal

    2013-01-01

    Connections between microscopic dynamical observables and macroscopic nonequilibrium (NE) properties have been pursued in statistical physics since Boltzmann, Gibbs, and Maxwell. The simulations we describe here establish a relationship between the Kolmogorov–Sinai entropy and the energy dissipated as heat from a NE system to its environment. First, we show that the Kolmogorov–Sinai or dynamical entropy can be separated into system and bath components and that the entropy of the system characterizes the dynamics of energy dissipation. Second, we find that the average change in the system dynamical entropy is linearly related to the average change in the energy dissipated to the bath. The constant energy and time scales of the bath fix the dynamical relationship between these two quantities. These results provide a link between microscopic dynamical variables and the macroscopic energetics of NE processes. PMID:24065832

  3. Viscosity measurement techniques in Dissipative Particle Dynamics

    Science.gov (United States)

    Boromand, Arman; Jamali, Safa; Maia, Joao M.

    2015-11-01

    In this study two main groups of viscosity measurement techniques are used to measure the viscosity of a simple fluid using Dissipative Particle Dynamics, DPD. In the first method, a microscopic definition of the pressure tensor is used in equilibrium and out of equilibrium to measure the zero-shear viscosity and shear viscosity, respectively. In the second method, a periodic Poiseuille flow and start-up transient shear flow is used and the shear viscosity is obtained from the velocity profiles by a numerical fitting procedure. Using the standard Lees-Edward boundary condition for DPD will result in incorrect velocity profiles at high values of the dissipative parameter. Although this issue was partially addressed in Chatterjee (2007), in this work we present further modifications (Lagrangian approach) to the original LE boundary condition (Eulerian approach) that will fix the deviation from the desired shear rate at high values of the dissipative parameter and decrease the noise to signal ratios in stress measurement while increases the accessible low shear rate window. Also, the thermostat effect of the dissipative and random forces is coupled to the dynamic response of the system and affects the transport properties like the viscosity and diffusion coefficient. We investigated thoroughly the dependency of viscosity measured by both Eulerian and Lagrangian methodologies, as well as numerical fitting procedures and found that all the methods are in quantitative agreement.

  4. 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

  5. CECAM Workshop: Dissipative Particle Dynamics: Addressing Deficiencies and Establishing NewFrontiers

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin

    2009-01-01

    Roč. 35, č. 9 (2009), s. 766-769 ISSN 0892-7022. [CECAM Worskhop on the Dissipative Particle Dynamic Method (DPD). Lausanne, 16.07.2008-18.07.2008] Institutional research plan: CEZ:AV0Z40720504 Keywords : mesoscale * simulation * dissipative particle dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.028, year: 2009

  6. 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...

  7. Attractors of dissipative structure in three dissipative fluids

    International Nuclear Information System (INIS)

    Kondoh, Yoshiomi

    1993-10-01

    A general theory with use of auto-correlations for distributions is presented to derive that realization of coherent structures in general dissipative dynamic systems is equivalent to that of self-organized states with the minimum dissipation rate for instantaneously contained energy. Attractors of dissipative structure are shown to be given by eigenfunctions for dissipative dynamic operators of the dynamic system and to constitute the self-organized and self-similar decay phase. Three typical examples applied to incompressible viscous fluids, to incompressible viscous and resistive magnetohydrodynamic (MHD) fluids and to compressible resistive MHD plasmas are presented to lead to attractors in the three dissipative fluids and to describe a common physical picture of self-organization and bifurcation of the dissipative structure. (author)

  8. Analytical description of critical dynamics for two-dimensional dissipative nonlinear maps

    International Nuclear Information System (INIS)

    Méndez-Bermúdez, J.A.; Oliveira, Juliano A. de; Leonel, Edson D.

    2016-01-01

    The critical dynamics near the transition from unlimited to limited action diffusion for two families of well known dissipative nonlinear maps, namely the dissipative standard and dissipative discontinuous maps, is characterized by the use of an analytical approach. The approach is applied to explicitly obtain the average squared action as a function of the (discrete) time and the parameters controlling nonlinearity and dissipation. This allows to obtain a set of critical exponents so far obtained numerically in the literature. The theoretical predictions are verified by extensive numerical simulations. We conclude that all possible dynamical cases, independently on the map parameter values and initial conditions, collapse into the universal exponential decay of the properly normalized average squared action as a function of a normalized time. The formalism developed here can be extended to many other different types of mappings therefore making the methodology generic and robust. - Highlights: • We analytically approach scaling properties of a family of two-dimensional dissipative nonlinear maps. • We derive universal scaling functions that were obtained before only approximately. • We predict the unexpected condition where diffusion and dissipation compensate each other exactly. • We find a new universal scaling function that embraces all possible dissipative behaviors.

  9. Dynamics of charged viscous dissipative cylindrical collapse with full causal approach

    Energy Technology Data Exchange (ETDEWEB)

    Shah, S.M.; Abbas, G. [The Islamia University of Bahawalpur, Department of Mathematics, Bahawalpur (Pakistan)

    2017-11-15

    The aim of this paper is to investigate the dynamical aspects of a charged viscous cylindrical source by using the Misner approach. To this end, we have considered the more general charged dissipative fluid enclosed by the cylindrical symmetric spacetime. The dissipative nature of the source is due to the presence of dissipative variables in the stress-energy tensor. The dynamical equations resulting from such charged cylindrical dissipative source have been coupled with the causal transport equations for heat flux, shear and bulk viscosity, in the context of the Israel-Steward theory. In this case, we have the considered Israel-Steward transportation equations without excluding the thermodynamics viscous/heat coupling coefficients. The results are compared with the previous works in which such coefficients were excluded and viscosity variables do not satisfy the casual transportation equations. (orig.)

  10. Restrictions in Model Reduction for Polymer Chain Models in Dissipative Particle Dynamics

    KAUST Repository

    Moreno Chaparro, Nicolas

    2014-06-06

    We model high molecular weight homopolymers in semidilute concentration via Dissipative Particle Dynamics (DPD). We show that in model reduction methodologies for polymers it is not enough to preserve system properties (i.e., density ρ, pressure p, temperature T, radial distribution function g(r)) but preserving also the characteristic shape and length scale of the polymer chain model is necessary. In this work we apply a DPD-model-reduction methodology for linear polymers recently proposed; and demonstrate why the applicability of this methodology is limited upto certain maximum polymer length, and not suitable for solvent coarse graining.

  11. Restrictions in Model Reduction for Polymer Chain Models in Dissipative Particle Dynamics

    KAUST Repository

    Moreno Chaparro, Nicolas; Nunes, Suzana Pereira; Calo, Victor M.

    2014-01-01

    We model high molecular weight homopolymers in semidilute concentration via Dissipative Particle Dynamics (DPD). We show that in model reduction methodologies for polymers it is not enough to preserve system properties (i.e., density ρ, pressure p, temperature T, radial distribution function g(r)) but preserving also the characteristic shape and length scale of the polymer chain model is necessary. In this work we apply a DPD-model-reduction methodology for linear polymers recently proposed; and demonstrate why the applicability of this methodology is limited upto certain maximum polymer length, and not suitable for solvent coarse graining.

  12. 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

  13. Quantum dynamics in nanoscale magnets in dissipative environments

    NARCIS (Netherlands)

    Miyashita, S; Saito, K; Kobayashi, H.; de Raedt, H.A.

    2000-01-01

    In discrete energy structure of nanoscale magnets, nonadiabatic transitions at avoided level crossings lead to fundamental processes of dynamics of magnetizations. The thermal environment causes dissipative effects on these processes. In this paper we review the features of the nonadiabatic

  14. Microscopic description of dissipative dynamics of a level-crossing transition

    Energy Technology Data Exchange (ETDEWEB)

    Scala, M.; Militello, B.; Messina, A. [Dipartimento di Fisica dell' Universita di Palermo, Via Archirafi 36, I-90123 Palermo (Italy); Vitanov, N. V. [Department of Physics, Sofia University, 5 James Bourchier Boulevard, BG-1164 Sofia (Bulgaria)

    2011-08-15

    We analyze the effect of a dissipative bosonic environment on the Landau-Zener-Stueckelberg-Majorana (LZSM) level crossing model by using a microscopic approach to derive the relevant master equation. For an environment at zero temperature and weak dissipation, our microscopic approach confirms the independence of the survival probability on the decay rate that has been predicted earlier by the simple phenomenological LZSM model. For strong decay the microscopic approach predicts a notable increase of the survival probability, which signals dynamical decoupling of the initial state. Unlike the phenomenological model, our approach makes it possible to study the dependence of the system dynamics on the temperature of the environment. In the limit of very high temperature we find that the dynamics is characterized by a very strong dynamical decoupling of the initial state--the temperature-induced quantum Zeno effect.

  15. Towards better integrators for dissipative particle dynamics simulations

    DEFF Research Database (Denmark)

    Besold, Gerhard; Vattulainen, Ilpo Tapio; Karttunen, Mikko

    2000-01-01

    Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the com...

  16. Correlated Photon Dynamics in Dissipative Rydberg Media

    Science.gov (United States)

    Zeuthen, Emil; Gullans, Michael J.; Maghrebi, Mohammad F.; Gorshkov, Alexey V.

    2017-07-01

    Rydberg blockade physics in optically dense atomic media under the conditions of electromagnetically induced transparency (EIT) leads to strong dissipative interactions between single photons. We introduce a new approach to analyzing this challenging many-body problem in the limit of a large optical depth per blockade radius. In our approach, we separate the single-polariton EIT physics from Rydberg-Rydberg interactions in a serialized manner while using a hard-sphere model for the latter, thus capturing the dualistic particle-wave nature of light as it manifests itself in dissipative Rydberg-EIT media. Using this approach, we analyze the saturation behavior of the transmission through one-dimensional Rydberg-EIT media in the regime of nonperturbative dissipative interactions relevant to current experiments. Our model is able to capture the many-body dynamics of bright, coherent pulses through these strongly interacting media. We compare our model with available experimental data in this regime and find good agreement. We also analyze a scheme for generating regular trains of single photons from continuous-wave input and derive its scaling behavior in the presence of imperfect single-photon EIT.

  17. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hong Min [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kondaraju, Sasidhar [Department of Mechanical Science, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 751013 (India); Lee, Jung Shin [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Suh, Youngho; Lee, Joonho H. [Samsung Electronics, Mechatronics R& D Center, Hwaseong-si, Gyeonggi-do 445-330 (Korea, Republic of); Lee, Joon Sang, E-mail: joonlee@yonsei.ac.kr [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2017-07-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  18. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    International Nuclear Information System (INIS)

    Yoon, Hong Min; Kondaraju, Sasidhar; Lee, Jung Shin; Suh, Youngho; Lee, Joonho H.; Lee, Joon Sang

    2017-01-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  19. Universal shape characteristics for the mesoscopic star-shaped polymer via dissipative particle dynamics simulations

    Science.gov (United States)

    Kalyuzhnyi, O.; Ilnytskyi, J. M.; Holovatch, Yu; von Ferber, C.

    2018-05-01

    In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different heterogeneous star polymers with the same molecular weight. We analyse the gyration radius and asphericity at the poor, good and θ-solvent regimes. Detailed explanation based on interplay between enthalpic and entropic contributions to the free energy and analyses on of the asphericity of individual branches are provided to explain the increase of the apsphericity in θ-solvent regime.

  20. Smoothed dissipative particle dynamics with angular momentum conservation

    Energy Technology Data Exchange (ETDEWEB)

    Müller, Kathrin, E-mail: k.mueller@fz-juelich.de; Fedosov, Dmitry A., E-mail: d.fedosov@fz-juelich.de; Gompper, Gerhard, E-mail: g.gompper@fz-juelich.de

    2015-01-15

    Smoothed dissipative particle dynamics (SDPD) combines two popular mesoscopic techniques, the smoothed particle hydrodynamics and dissipative particle dynamics (DPD) methods, and can be considered as an improved dissipative particle dynamics approach. Despite several advantages of the SDPD method over the conventional DPD model, the original formulation of SDPD by Español and Revenga (2003) [9], lacks angular momentum conservation, leading to unphysical results for problems where the conservation of angular momentum is essential. To overcome this limitation, we extend the SDPD method by introducing a particle spin variable such that local and global angular momentum conservation is restored. The new SDPD formulation (SDPD+a) is directly derived from the Navier–Stokes equation for fluids with spin, while thermal fluctuations are incorporated similarly to the DPD method. We test the new SDPD method and demonstrate that it properly reproduces fluid transport coefficients. Also, SDPD with angular momentum conservation is validated using two problems: (i) the Taylor–Couette flow with two immiscible fluids and (ii) a tank-treading vesicle in shear flow with a viscosity contrast between inner and outer fluids. For both problems, the new SDPD method leads to simulation predictions in agreement with the corresponding analytical theories, while the original SDPD method fails to capture properly physical characteristics of the systems due to violation of angular momentum conservation. In conclusion, the extended SDPD method with angular momentum conservation provides a new approach to tackle fluid problems such as multiphase flows and vesicle/cell suspensions, where the conservation of angular momentum is essential.

  1. Dynamically controlled energy dissipation for fast magnetic vortex switching

    Science.gov (United States)

    Badea, R.; Berezovsky, J.

    2017-09-01

    Manipulation of vortex states in magnetic media provides new routes towards information storage and processing technology. The typical slow relaxation times (˜100 ns) of magnetic vortex dynamics may present an obstacle to the realization of these applications. Here, we investigate how a vortex state in a ferromagnetic microdisk can be manipulated in a way that translates the vortex core while enhancing energy dissipation to rapidly damp the vortex dynamics. We use time-resolved differential magneto-optical Kerr effect microscopy to measure the motion of the vortex core in response to applied magnetic fields. We first map out how the vortex core becomes sequentially trapped by pinning sites as it translates across the disk. After applying a fast magnetic field step to translate the vortex from one pinning site to another, we observe long-lived dynamics of the vortex as it settles to the new equilibrium. We then demonstrate how the addition of a short (<10 ns) magnetic field pulse can induce additional energy dissipation, strongly damping the long-lived dynamics. A model of the vortex dynamics using the Thiele equation of motion explains the mechanism behind this effect.

  2. Quench dynamics of a disordered array of dissipative coupled cavities.

    Science.gov (United States)

    Creatore, C; Fazio, R; Keeling, J; Türeci, H E

    2014-09-08

    We investigate the mean-field dynamics of a system of interacting photons in an array of coupled cavities in the presence of dissipation and disorder. We follow the evolution of an initially prepared Fock state, and show how the interplay between dissipation and disorder affects the coherence properties of the cavity emission, and show that these properties can be used as signatures of the many-body phase of the whole array.

  3. Patterns and Interfaces in Dissipative Dynamics

    CERN Document Server

    Pismen, L.M

    2006-01-01

    Spontaneous pattern formation in nonlinear dissipative systems far from equilibrium is a paradigmatic case of emergent behaviour associated with complex systems. It is encountered in a great variety of settings, both in nature and technology, and has numerous applications ranging from nonlinear optics through solid and fluid mechanics, physical chemistry and chemical engineering to biology. Nature creates its variety of forms through spontaneous pattern formation and self-assembly, and this strategy is likely to be imitated by future biomorphic technologies. This book is a first-hand account by one of the leading players in this field, which gives in-depth descriptions of analytical methods elucidating the complex evolution of nonlinear dissipative systems, and brings the reader to the forefront of current research. The introductory chapter on the theory of dynamical systems is written with a view to applications of its powerful methods to spatial and spatio-temporal patterns. It is followed by two chapters t...

  4. Dissipation and energy balance in electronic dynamics of Na clusters

    Science.gov (United States)

    Vincendon, Marc; Suraud, Eric; Reinhard, Paul-Gerhard

    2017-06-01

    We investigate the impact of dissipation on the energy balance in the electron dynamics of metal clusters excited by strong electro-magnetic pulses. The dynamics is described theoretically by Time-Dependent Density-Functional Theory (TDDFT) at the level of Local Density Approximation (LDA) augmented by a self interaction correction term and a quantum collision term in Relaxation-Time Approximation (RTA). We evaluate the separate contributions to the total excitation energy, namely energy exported by electron emission, potential energy due to changing charge state, intrinsic kinetic and potential energy, and collective flow energy. The balance of these energies is studied as function of the laser parameters (frequency, intensity, pulse length) and as function of system size and charge. We also look at collisions with a highly charged ion and here at the dependence on the impact parameter (close versus distant collisions). Dissipation turns out to be small where direct electron emission prevails namely for laser frequencies above any ionization threshold and for slow electron extraction in distant collisions. Dissipation is large for fast collisions and at low laser frequencies, particularly at resonances. Contribution to the Topical Issue "Dynamics of Systems at the Nanoscale", edited by Andrey Solov'yov and Andrei Korol.

  5. Real-time dynamics of dissipative quantum systems

    International Nuclear Information System (INIS)

    Chow, K.S.

    1988-01-01

    The first part of this thesis motivates a real time approach to the dynamics of dissipative quantum systems. We review previous imaginary time methods for calculating escape rates and discuss their applications to the analysis of data in macroscopic quantum tunneling experiments. In tunneling experiments on heavily damped Superconducting Quantum Interference Devices, the instanton method gave results that compare reasonably well with data. In tunneling experiments on weakly damped Current Biased Josephson Junctions, two problems arise. First, the classical limit of the instanton result disagrees with the classical rate of thermal activation. Second, the instanton method cannot predict the microwave enhancement of escape rates. In the third chapter, we discuss our real time approach to the dynamics of dissipative systems in terms of a kinetic equation for the reduced density matrix. We demonstrate some known equilibrium properties of dissipative systems through the kinetic equation and derived the bath induced widths and energy shifts. In the low damping limit, the kinetic equation reduces to a much simpler master equation. The classical limit of the master equation is completely equivalent to the Fokker-Planck equation that describes thermal activation. In the fourth chapter, we apply the master equation to the problem of tunneling and resonance enhancement of tunneling in weakly damped current biased Josephson junctions. In the classical regime, microwaves of the appropriate frequency induce resonances between many neighboring levels and an asymmetrical resonance peak is measured. We can calibrate the junction parameters by fitting the stationary solution of the master equation to the classical resonance data. In the quantum regime, the stationary solution of the master equation, predicts well-resolved resonance peaks which agree very well with the observed data

  6. Noise Induced Dissipation in Discrete-Time Classical and Quantum Dynamical Systems

    OpenAIRE

    Wolowski, Lech

    2004-01-01

    We introduce a new characteristics of chaoticity of classical and quantum dynamical systems by defining the notion of the dissipation time which enables us to test how the system responds to the noise and in particular to measure the speed at which an initially closed, conservative system converges to the equilibrium when subjected to noisy (stochastic) perturbations. We prove fast dissipation result for classical Anosov systems and ...

  7. Non-equilibrium dynamics of open systems and fluctuation-dissipation theorems

    Czech Academy of Sciences Publication Activity Database

    Špička, Václav; Velický, B.; Kalvová, Anděla

    2017-01-01

    Roč. 65, 6-8 (2017), s. 1-23, č. článku 1700032. ISSN 0015-8208 Institutional support: RVO:68378271 Keywords : non-equilibrium * fluctuation-dissipation theorems * non-equilibrium Greens function * transient and steady state magnetic current * molecular bridge Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics ( physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 2.434, year: 2016

  8. On the molecular dynamics in the hurricane interactions with its environment

    Science.gov (United States)

    Meyer, Gabriel; Vitiello, Giuseppe

    2018-06-01

    By resorting to the Burgers model for hurricanes, we study the molecular motion involved in the hurricane dynamics. We show that the Lagrangian canonical formalism requires the inclusion of the environment degrees of freedom. This also allows the description of the motion of charged particles. In view of the role played by moist convection, cumulus and cloud water droplets in the hurricane dynamics, we discuss on the basis of symmetry considerations the role played by the molecular electrical dipoles and the formation of topologically non-trivial structures. The mechanism of energy storage and dissipation, the non-stationary time dependent Ginzburg-Landau equation and the vortex equation are studied. Finally, we discuss the fractal self-similarity properties of hurricanes.

  9. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2014-08-17

    Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  10. Dynamics of the conservative and dissipative spin-orbit problem

    CERN Document Server

    Celletti, A; Lega, E

    2006-01-01

    We investigate the dynamics of the spin--orbit coupling under different settings. First we consider the conservative problem, and then we add a dissipative torque as provided by MacDonald's or Darwin's models. By means of frequency analysis and of the computation of the maximum Lyapunov indicator we explore the different dynamical behaviors associated to the main resonances. In particular we focus on the 1:1 and 3:2 resonances in which the Moon and Mercury are actually trapped.

  11. Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

    2015-06-09

    The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

  12. Dynamics of dissipative systems and computational physics

    International Nuclear Information System (INIS)

    Adam, Gh.; Scutaru, H.; Ixaru, L.; Adam, S.; Rizea, M.; Stefanescu, E.; Mihalache, D.; Mazilu, D.; Crasovan, L.

    2002-01-01

    During the first year of research activity in the frame of this project there have been investigated two main topics: I. Dynamics of systems of fermions in complex dissipative media; II. Solitons with topologic charge in dissipative systems. An essential problem of the quantum information systems is the controllability and observability of the quantum states, generally described by Lindblad's master equation with phenomenological coefficients. In its usual form, this equation describes a decay of the mean-values, but not necessarily the expected decaying transitions. The basic and very difficult problem of a dissipative quantum theory is to project the evolution of the total system (the system of interest + the environment) on the space of the system of interest. In this case, one obtains a quantum master equation where the system evolution is described by two terms: 1) a Hamiltonian term for the processes with energy conservation, and 2) a non-Hamiltonian term with coefficients depending on the dissipative coupling. That means that a master equation is based on some approximations enabling the replacement of the operators of the dissipative environment with average value coefficients. It is often assumed that the evolution operators of the dissipative system define a semigroup, not a group as in the case of an isolated system. In this framework, Lindblad obtained a quantum master equation in agreement with all the quantum-mechanical principles. However, the Lindblad master equation was unable to secure a correct description of the decaying states. To do that, one has to take into account the transition operators between the system eigenstates with appropriate coefficients. Within this investigation, we have obtained an equation obeying to this requirement, giving the ρ(t) time derivative in terms of creation-annihilation operators of the single-particle states |i>, and λ ij , representing the dissipative coefficients, the microscopic expressions of which are

  13. Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

    International Nuclear Information System (INIS)

    Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

    2010-01-01

    Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

  14. Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

    Energy Technology Data Exchange (ETDEWEB)

    Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

    2010-08-15

    Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

  15. Measurement fidelity in the presence of coherent dynamics or dissipation

    Science.gov (United States)

    You, Jian-Qiang; Ashhab, S.; Nori, Franco

    2011-03-01

    We analyze the problem of a charge qubit probed by a quantum point contact when the measurement is concurrent with Hamiltonian-induced coherent dynamics or dissipation. This additional dynamics changes the state of the qubit before the measurement is completed. As a result, the measurement fidelity is reduced. We calculate the reduction in measurement fidelity in these cases. References: S. Ashhab, J. Q. You, and F. Nori, New J. Phys. 11, 083017 (2009); Phys. Scr. T137, 014005 (2009).

  16. Causal dissipation for the relativistic dynamics of ideal gases.

    Science.gov (United States)

    Freistühler, Heinrich; Temple, Blake

    2017-05-01

    We derive a general class of relativistic dissipation tensors by requiring that, combined with the relativistic Euler equations, they form a second-order system of partial differential equations which is symmetric hyperbolic in a second-order sense when written in the natural Godunov variables that make the Euler equations symmetric hyperbolic in the first-order sense. We show that this class contains a unique element representing a causal formulation of relativistic dissipative fluid dynamics which (i) is equivalent to the classical descriptions by Eckart and Landau to first order in the coefficients of viscosity and heat conduction and (ii) has its signal speeds bounded sharply by the speed of light. Based on these properties, we propose this system as a natural candidate for the relativistic counterpart of the classical Navier-Stokes equations.

  17. Statistical and dynamical properties of a dissipative kicked rotator

    Science.gov (United States)

    Oliveira, Diego F. M.; Leonel, Edson D.

    2014-11-01

    Some dynamical and statistical properties for a conservative as well as the dissipative problem of relativistic particles in a waveguide are considered. For the first time, two different types of dissipation namely: (i) due to viscosity and; (ii) due to inelastic collision (upon the kick) are considered individually and acting together. For the first case, and contrary to what is expected for the original Zaslavsky’s relativistic model, we show there is a critical parameter where a transition from local to global chaos occurs. On the other hand, after considering the introduction of dissipation also on the kick, the structure of the phase space changes in the sense that chaotic and periodic attractors appear. We study also the chaotic sea by using scaling arguments and we proposed an analytical argument to reinforce the validity of the scaling exponents obtained numerically. In principle such an approach can be extended to any two-dimensional map. Finally, based on the Lyapunov exponent, we show that the parameter space exhibits infinite families of self-similar shrimp-shape structures, corresponding to periodic attractors, embedded in a large region corresponding to chaotic attractors.

  18. Quantum dissipative dynamics and decoherence of dimers on helium droplets

    International Nuclear Information System (INIS)

    Schlesinger, Martin

    2011-01-01

    In this thesis, quantum dynamical simulations are performed in order to describe the vibrational motion of diatomic molecules in a highly quantum environment, so-called helium droplets. We aim to reproduce and explain experimental findings which were obtained from dimers on helium droplets. Nanometer-sized helium droplets contain several thousands of 4 He atoms. They serve as a host for embedded atoms or molecules and provide an ultracold ''refrigerator'' for them. Spectroscopy of molecules in or on these droplets reveals information on both the molecule and the helium environment. The droplets are known to be in the superfluid He II phase. Superfluidity in nanoscale systems is a steadily growing field of research. Spectra obtained from full quantum simulations for the unperturbed dimer show deviations from measurements with dimers on helium droplets. These deviations result from the influence of the helium environment on the dimer dynamics. In this work, a well-established quantum optical master equation is used in order to describe the dimer dynamics effectively. The master equation allows to describe damping fully quantum mechanically. By employing that equation in the quantum dynamical simulation, one can study the role of dissipation and decoherence in dimers on helium droplets. The effective description allows to explain experiments with Rb 2 dimers on helium droplets. Here, we identify vibrational damping and associated decoherence as the main explanation for the experimental results. The relation between decoherence and dissipation in Morse-like systems at zero temperature is studied in more detail. The dissipative model is also used to investigate experiments with K 2 dimers on helium droplets. However, by comparing numerical simulations with experimental data, one finds that further mechanisms are active. Here, a good agreement is obtained through accounting for rapid desorption of dimers. We find that decoherence occurs in the electronic manifold of the

  19. Dynamic load mitigation using dissipative elastic metamaterials with multiple Maxwell-type oscillators

    Science.gov (United States)

    Alamri, Sagr; Li, Bing; Tan, K. T.

    2018-03-01

    Dissipative elastic metamaterials have attracted increased attention in recent times. This paper presents the development of a dissipative elastic metamaterial with multiple Maxwell-type resonators for stress wave attenuation. The mechanism of the dissipation effect on the vibration characteristics is systematically investigated by mass-spring-damper models with single and dual resonators. Based on the parameter optimization, it is revealed that a broadband wave attenuation region (stopping band) can be obtained by properly utilizing interactions from resonant motions and viscoelastic effects of the Maxwell-type oscillators. The relevant numerical verifications are conducted for various cases, and excellent agreement between the numerical and theoretical frequency response functions is shown. The design of this dissipative metamaterial system is further applied for dynamic load mitigation and blast wave attenuation. Moreover, the transient response in the continuum model is designed and analyzed for more robust design. By virtue of the bandgap merging effect induced by the Maxwell-type damper, the transient blast wave can be almost completely suppressed in the low frequency range. A significantly improved performance of the proposed dissipative metamaterials for stress wave mitigation is verified in both time and frequency domains.

  20. Explicit dissipative structures

    International Nuclear Information System (INIS)

    Roessler, O.E.

    1987-01-01

    Dissipative structures consisting of a few macrovariables arise out of a sea of reversible microvariables. Unexpected residual effects of the massive underlying reversibility, on the macrolevel, cannot therefore be excluded. In the age of molecular-dynamics simulations, explicit dissipative structures like excitable systems (explicit observers) can be generated in a computer from first reversible principles. A class of classical, 1-D Hamiltonian systems of chaotic type is considered which has the asset that the trajectorial behavior in phase space can be understood geometrically. If, as nuatural, the number of particle types is much smaller than that of particles, the Gibbs symmetry must be taken into account. The permutation invariance drastically changes the behavior in phase space (quasi-periodization). The explicity observer becomes effectively reversible on a short time scale. In consequence, his ability to measure microscopic motions is suspended in a characteristic fashion. Unlike quantum mechanics whose holistic nature cannot be transcended, the present holistic (internal-interface) effects - mimicking the former to some extent - can be understood fully in principle

  1. An extended dissipative particle dynamics model

    CERN Document Server

    Cotter, C J

    2003-01-01

    The method of dissipative particle dynamics (DPD) was introduced by Hoogerbrugge & Koelman to study meso-scale material processes. The theoretical investigation of the DPD method was initiated by Espanol who used a Fokker-Planck formulation of the DPD method and applied the Mori-Zwanzig projection operator calculus to obtain the equations of hydrodynamics for DPD. A current limitation of DPD is that it requires a clear separation of scales between the resolved and unresolved processes. In this note, we suggest a simple extension of DPD that allows for inclusion of unresolved processes with exponentially decaying variance for any value of the decay rate. The main point of the extension is that it is as easy to implement as DPD in a numerical algorithm.

  2. Nonreactive spreading at high-temperature revisited for metal systems via molecular dynamics.

    Science.gov (United States)

    Benhassine, M; Saiz, E; Tomsia, A P; De Coninck, J

    2009-10-06

    The spreading for Cu and Ag droplets on top of a rigid solid surface modeling Mo is herewith considered via molecular dynamics. The dynamics of the base radius and the contact angle are recorded and fitted using the molecular-kinetic theory. A method is described to determine for liquid metals at the microscopic level the parameters appearing in this theory. These microscopic parameters are calculated directly in the simulations and compared to the fitted values. The agreement between the fitted values and the calculated ones shows that the dissipation of energy within the drop is caused primarily by the friction of liquid atoms over the substrate. This validation supports the understanding of the mechanisms controlling the spreading of liquid metals which, up to now, were based on experimental data and fitting procedures.

  3. 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.

  4. Causal dissipation and shock profiles in the relativistic fluid dynamics of pure radiation.

    Science.gov (United States)

    Freistühler, Heinrich; Temple, Blake

    2014-06-08

    CURRENT THEORIES OF DISSIPATION IN THE RELATIVISTIC REGIME SUFFER FROM ONE OF TWO DEFICITS: either their dissipation is not causal or no profiles for strong shock waves exist. This paper proposes a relativistic Navier-Stokes-Fourier-type viscosity and heat conduction tensor such that the resulting second-order system of partial differential equations for the fluid dynamics of pure radiation is symmetric hyperbolic. This system has causal dissipation as well as the property that all shock waves of arbitrary strength have smooth profiles. Entropy production is positive both on gradients near those of solutions to the dissipation-free equations and on gradients of shock profiles. This shows that the new dissipation stress tensor complies to leading order with the principles of thermodynamics. Whether higher order modifications of the ansatz are required to obtain full compatibility with the second law far from the zero-dissipation equilibrium is left to further investigations. The system has exactly three a priori free parameters χ , η , ζ , corresponding physically to heat conductivity, shear viscosity and bulk viscosity. If the bulk viscosity is zero (as is stated in the literature) and the total stress-energy tensor is trace free, the entire viscosity and heat conduction tensor is determined to within a constant factor.

  5. Considering human exposure to pesticides in food products: Importance of dissipation dynamics

    DEFF Research Database (Denmark)

    Fantke, Peter; Juraske, Ronnie; Jolliet, Olivier

    2014-01-01

    The general public is continuously concerned about effects from pesticide exposure via residues in food crops. However, impacts from pesticide exposure are mostly neglected in food product-related LCAs. Time-to-harvest and dissipation from crops mainly drive residue dynamics with dissipation...... as most uncertain aspect in characterization modeling. We analyzed measured half-lives (n=4513) with 95% falling between 0.6 and 29 days. With ~500 pesticides authorized alone in the EU for several hundred crops, however, experimental stud-ies only cover few possible pesticide-crop combinations. Therefore......, we estimated dissipation from measured data and provide reference half-lives for 333 pesticides applied at 20°C under field conditions. Our framework allows for detailed explorations of dietary choices in LCA with respect to human health impacts from pesticide exposure via crop consumption. The next...

  6. 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

  7. Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

    In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

  8. Optimal control of quantum dissipative dynamics: Analytic solution for cooling the three-level Λ system

    International Nuclear Information System (INIS)

    Sklarz, Shlomo E.; Tannor, David J.; Khaneja, Navin

    2004-01-01

    We study the problem of optimal control of dissipative quantum dynamics. Although under most circumstances dissipation leads to an increase in entropy (or a decrease in purity) of the system, there is an important class of problems for which dissipation with external control can decrease the entropy (or increase the purity) of the system. An important example is laser cooling. In such systems, there is an interplay of the Hamiltonian part of the dynamics, which is controllable, and the dissipative part of the dynamics, which is uncontrollable. The strategy is to control the Hamiltonian portion of the evolution in such a way that the dissipation causes the purity of the system to increase rather than decrease. The goal of this paper is to find the strategy that leads to maximal purity at the final time. Under the assumption that Hamiltonian control is complete and arbitrarily fast, we provide a general framework by which to calculate optimal cooling strategies. These assumptions lead to a great simplification, in which the control problem can be reformulated in terms of the spectrum of eigenvalues of ρ, rather than ρ itself. By combining this formulation with the Hamilton-Jacobi-Bellman theorem we are able to obtain an equation for the globally optimal cooling strategy in terms of the spectrum of the density matrix. For the three-level Λ system, we provide a complete analytic solution for the optimal cooling strategy. For this system it is found that the optimal strategy does not exploit system coherences and is a 'greedy' strategy, in which the purity is increased maximally at each instant

  9. Exact solution for a non-Markovian dissipative quantum dynamics.

    Science.gov (United States)

    Ferialdi, Luca; Bassi, Angelo

    2012-04-27

    We provide the exact analytic solution of the stochastic Schrödinger equation describing a harmonic oscillator interacting with a non-Markovian and dissipative environment. This result represents an arrival point in the study of non-Markovian dynamics via stochastic differential equations. It is also one of the few exactly solvable models for infinite-dimensional systems. We compute the Green's function; in the case of a free particle and with an exponentially correlated noise, we discuss the evolution of Gaussian wave functions.

  10. Non-dissipative energy capture of confined liquid in nanopores

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Baoxing; Chen, Xi [Columbia Nanomechanics Research Center, Department of Earth and Environmental Engineering, Columbia University, New York, New York 10027 (United States); Lu, Weiyi; Zhao, Cang [Department of Structural Engineering, University of California–San Diego, La Jolla, California 92093-0085 (United States); Qiao, Yu, E-mail: yqiao@ucsd.edu [Department of Structural Engineering, University of California–San Diego, La Jolla, California 92093-0085 (United States); Program of Materials Science and Engineering, University of California–San Diego, La Jolla, CA 92093 (United States)

    2014-05-19

    In the past, energy absorption of protection/damping materials is mainly based on energy dissipation, which causes a fundamental conflict between the requirements of safety/comfort and efficiency. In the current study, a nanofluidic “energy capture” system is reported, which is based on nanoporous materials and nonwetting liquid. Both molecular dynamics simulations and experiments show that as the liquid overcomes the capillary effect and infiltrates into the nanopores, the mechanical energy of a stress wave could be temporarily stored by the confined liquid phase and isolated from the wave energy transmission path. Such a system can work under a relatively low pressure for mitigating high-pressure stress waves, not necessarily involved in any energy dissipation processes.

  11. Non-dissipative energy capture of confined liquid in nanopores

    International Nuclear Information System (INIS)

    Xu, Baoxing; Chen, Xi; Lu, Weiyi; Zhao, Cang; Qiao, Yu

    2014-01-01

    In the past, energy absorption of protection/damping materials is mainly based on energy dissipation, which causes a fundamental conflict between the requirements of safety/comfort and efficiency. In the current study, a nanofluidic “energy capture” system is reported, which is based on nanoporous materials and nonwetting liquid. Both molecular dynamics simulations and experiments show that as the liquid overcomes the capillary effect and infiltrates into the nanopores, the mechanical energy of a stress wave could be temporarily stored by the confined liquid phase and isolated from the wave energy transmission path. Such a system can work under a relatively low pressure for mitigating high-pressure stress waves, not necessarily involved in any energy dissipation processes.

  12. Nonequilibrium chiral fluid dynamics including dissipation and noise

    International Nuclear Information System (INIS)

    Nahrgang, Marlene; Herold, Christoph; Bleicher, Marcus; Leupold, Stefan

    2011-01-01

    We present a consistent theoretical approach for the study of nonequilibrium effects in chiral fluid dynamics within the framework of the linear σ model with constituent quarks. Treating the quarks as an equilibrated heat bath, we use the influence functional formalism to obtain a Langevin equation for the σ field. This allows us to calculate the explicit form of the damping coefficient and the noise correlators. For a self-consistent derivation of both the dynamics of the σ field and the quark fluid, we have to employ the 2PI (two-particle irreducible) effective action formalism. The energy dissipation from the field to the fluid is treated in the exact formalism of the 2PI effective action where a conserved energy-momentum tensor can be constructed. We derive its form and comment on approximations generating additional terms in the energy-momentum balance of the entire system.

  13. Real-time full-field characterization of transient dissipative soliton dynamics in a mode-locked laser

    Science.gov (United States)

    Ryczkowski, P.; Närhi, M.; Billet, C.; Merolla, J.-M.; Genty, G.; Dudley, J. M.

    2018-04-01

    Dissipative solitons are remarkably localized states of a physical system that arise from the dynamical balance between nonlinearity, dispersion and environmental energy exchange. They are the most universal form of soliton that can exist, and are seen in far-from-equilibrium systems in many fields, including chemistry, biology and physics. There has been particular interest in studying their properties in mode-locked lasers, but experiments have been limited by the inability to track the dynamical soliton evolution in real time. Here, we use simultaneous dispersive Fourier transform and time-lens measurements to completely characterize the spectral and temporal evolution of ultrashort dissipative solitons as their dynamics pass through a transient unstable regime with complex break-up and collisions before stabilization. Further insight is obtained from reconstruction of the soliton amplitude and phase and calculation of the corresponding complex-valued eigenvalue spectrum. These findings show how real-time measurements provide new insights into ultrafast transient dynamics in optics.

  14. Dissipation dynamics of terbuthylazine in soil during the maize growing season.

    Science.gov (United States)

    Stipičević, Sanja; Mendaš, Gordana; Dvoršćak, Marija; Fingler, Sanja; Galzina, Natalija; Barić, Klara

    2017-12-20

    Ever since terbuthylazine (TBA) replaced atrazine in herbicide crop treatment, its much greater persistence has raised considerable environmental concern. The aim of our field experiment was to establish the dissipation dynamics of TBA and its degradation product desethylterbuthylazine (DET) in soil over five months of maize growth. We applied TBA as part of pre-emergent treatment in the regular and double-the-regular amounts. Soil samples were collected periodically at the following depths: 0-10 cm, 10-20 cm, 20-30 cm, and 30-50 cm. For TBA and DET soil residue analysis we used microwave-assisted extraction with methanol, followed by HPLC-UV/DAD. Regardless of the application rate, more than 80 % of the applied TBA dissipated from the first 50 cm of soil in the two months after herbicide application and 120 mm of rainfall. Three months later (at maize harvest), less than 4 % of total TBA remained in the soil, mostly in the top 20 cm rich with organic carbon on which TBA is likelier to adsorb. The loss of TBA from soil coincided with the rise in DET, especially the top soil layers, during the periods of low rainfall and highest soil temperatures. This points to biodegradation as the main route of TBA dissipation in humic soils. The applied amount had no significant effect on TBA dissipation in the top (humic) layers, but in the layers with less than 1 % of organic carbon, it was higher when the doublethe- regular dose was applied.

  15. Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Gerhard, E-mail: jungge@uni-mainz.de; Schmid, Friederike, E-mail: friederike.schmid@uni-mainz.de [Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, D-55099 Mainz (Germany)

    2016-05-28

    Exact values for bulk and shear viscosity are important to characterize a fluid, and they are a necessary input for a continuum description. Here we present two novel methods to compute bulk viscosities by non-equilibrium molecular dynamics simulations of steady-state systems with periodic boundary conditions — one based on frequent particle displacements and one based on the application of external bulk forces with an inhomogeneous force profile. In equilibrium simulations, viscosities can be determined from the stress tensor fluctuations via Green-Kubo relations; however, the correct incorporation of random and dissipative forces is not obvious. We discuss different expressions proposed in the literature and test them at the example of a dissipative particle dynamics fluid.

  16. Special role of neutron-halo nucleus on the momentum dissipation in heavy ion collisions

    International Nuclear Information System (INIS)

    Xing Yongzhong; Tianshui Normal Univ., Tianshui; Liu Jianye; Tianshui Normal Univ., Tianshui; Chinese Academy of Sciences, Lanzhou; Zuo Wei; Li Xiguo; Chinese Academy of Sciences, Lanzhou

    2005-01-01

    The special role of neutron-halo nucleus 19 B on the momentum dissipation was investigated by using isospin dependent quantum molecular dynamics. In order to compare and protrude the special role of neutron-halo-nucleus 19 B, the momentum dissipation induced by a same mass stable nucleus 19 F was investigated under the same incident channel condition. It is found that the weak bound neutron-halo structure of 19 B weakens the momentum dissipation process compared to those induced by stable nucleus 19 F in the lower energy region. However the nuclear stopping of colliding system with the neutron-halo nucleus 19 B decreases gradually with the increasing beam energy. For all of mass targets and impact parameters the neutron-halo nucleus 19 B weakens the momentum dissipation process. (authors)

  17. Storage functions for dissipative linear systems are quadratic state functions

    NARCIS (Netherlands)

    Trentelman, Harry L.; Willems, Jan C.

    1997-01-01

    This paper deals with dissipative dynamical systems. Dissipative dynamical systems can be used as models for physical phenomena in which energy exchange with their environment plays a role. In a dissipative dynamical system, the book-keeping of energy is done via the supply rate and a storage

  18. Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Saiz, Fernan [Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, London, SW7 2A7 (United Kingdom); Gamero-Castaño, Manuel, E-mail: mgameroc@uci.edu [Department of Mechanical and Aerospace Engineering, University of California, Irvine, California, 92697 (United States)

    2016-06-15

    The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.

  19. Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

    International Nuclear Information System (INIS)

    Saiz, Fernan; Gamero-Castaño, Manuel

    2016-01-01

    The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.

  20. Static and dynamic properties of smoothed dissipative particle dynamics

    Science.gov (United States)

    Alizadehrad, Davod; Fedosov, Dmitry A.

    2018-03-01

    In this paper, static and dynamic properties of the smoothed dissipative particle dynamics (SDPD) method are investigated. We study the effect of method parameters on SDPD fluid properties, such as structure, speed of sound, and transport coefficients, and show that a proper choice of parameters leads to a well-behaved and accurate fluid model. In particular, the speed of sound, the radial distribution function (RDF), shear-thinning of viscosity, the mean-squared displacement (〈R2 〉 ∝ t), and the Schmidt number (Sc ∼ O (103) - O (104)) can be controlled, such that the model exhibits a fluid-like behavior for a wide range of temperatures in simulations. Furthermore, in addition to the consideration of fluid density variations for fluid compressibility, a more challenging test of incompressibility is performed by considering the Poisson ratio and divergence of velocity field in an elongational flow. Finally, as an example of complex-fluid flow, we present the applicability and validity of the SDPD method with an appropriate choice of parameters for the simulation of cellular blood flow in irregular geometries. In conclusion, the results demonstrate that the SDPD method is able to approximate well a nearly incompressible fluid behavior, which includes hydrodynamic interactions and consistent thermal fluctuations, thereby providing, a powerful approach for simulations of complex mesoscopic systems.

  1. Consistent model reduction of polymer chains in solution in dissipative particle dynamics: Model description

    KAUST Repository

    Moreno Chaparro, Nicolas

    2015-06-30

    We introduce a framework for model reduction of polymer chain models for dissipative particle dynamics (DPD) simulations, where the properties governing the phase equilibria such as the characteristic size of the chain, compressibility, density, and temperature are preserved. The proposed methodology reduces the number of degrees of freedom required in traditional DPD representations to model equilibrium properties of systems with complex molecules (e.g., linear polymers). Based on geometrical considerations we explicitly account for the correlation between beads in fine-grained DPD models and consistently represent the effect of these correlations in a reduced model, in a practical and simple fashion via power laws and the consistent scaling of the simulation parameters. In order to satisfy the geometrical constraints in the reduced model we introduce bond-angle potentials that account for the changes in the chain free energy after the model reduction. Following this coarse-graining process we represent high molecular weight DPD chains (i.e., ≥200≥200 beads per chain) with a significant reduction in the number of particles required (i.e., ≥20≥20 times the original system). We show that our methodology has potential applications modeling systems of high molecular weight molecules at large scales, such as diblock copolymer and DNA.

  2. Coherence-enhanced phase-dependent dissipation in long SNS Josephson junctions: Revealing Andreev bound state dynamics

    Science.gov (United States)

    Dassonneville, B.; Murani, A.; Ferrier, M.; Guéron, S.; Bouchiat, H.

    2018-05-01

    One of the best known causes of dissipation in ac-driven quantum systems stems from photon absorption causing transitions between levels. Dissipation can also be caused by the retarded response to the time-dependent excitation, and in general gives insight into the system's relaxation times and mechanisms. Here we address the dissipation in a mesoscopic normal wire with superconducting contacts, that sustains a dissipationless supercurrent at zero frequency and that may therefore naively be expected to remain dissipationless at a frequency lower than the superconducting gap. We probe the high-frequency linear response of such a normal metal/superconductor (NS) ring to a time-dependent flux by coupling it to a highly sensitive multimode microwave resonator. Far from being the simple, dissipationless derivative of the supercurrent-versus-phase relation, the ring's ac susceptibility also displays a dissipative component whose phase dependence is a signature of the dynamical processes occurring within the Andreev spectrum. We show how dissipation is driven by the competition between two mechanisms. The first is the relaxation of the Andreev level distribution function, while the second corresponds to microwave-induced transitions within the spectrum. Depending on the relative strength of those contributions, dissipation can be maximal at π , a phase at which the proximity-induced minigap closes, or can be maximal near π /2 , a phase at which the dc supercurrent is maximal. We also find that the dissipative response paradoxically increases at low temperature and can even exceed the normal-state conductance. The results are successfully confronted with theoretical predictions of the Kubo linear response and time-dependent Usadel equations, derived from the Bogoliubov-de Gennes Hamiltonian describing the SNS junction. These experiments thus demonstrate the power of the ac susceptibility measurement of individual hybrid mesoscopic systems in probing in a controlled way

  3. Formation of giant molecular clouds in global spiral structures: the role of orbital dynamics and cloud-cloud collisions

    International Nuclear Information System (INIS)

    Roberts, W.W. Jr.; Stewart, G.R.

    1987-01-01

    The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes

  4. Stability and Control of Large-Scale Dynamical Systems A Vector Dissipative Systems Approach

    CERN Document Server

    Haddad, Wassim M

    2011-01-01

    Modern complex large-scale dynamical systems exist in virtually every aspect of science and engineering, and are associated with a wide variety of physical, technological, environmental, and social phenomena, including aerospace, power, communications, and network systems, to name just a few. This book develops a general stability analysis and control design framework for nonlinear large-scale interconnected dynamical systems, and presents the most complete treatment on vector Lyapunov function methods, vector dissipativity theory, and decentralized control architectures. Large-scale dynami

  5. Wetting kinetics of nanodroplets on lyophilic nanopillar-arrayed surfaces: A molecular dynamics study

    Science.gov (United States)

    Zong, Diyuan; Yang, Zhen; Duan, Yuanyuan

    2017-10-01

    Wetting kinetics of water droplets on substrates with lyophilic nanopillars was investigated using molecular dynamics simulations. Early spreading of the droplet is hindered by the nanopillars because of the penetration of the liquid which induce an extra dissipation in the droplet. Droplet spreading is mainly controlled by liquid viscosity and surface tension and not dependent on solid wettability. Propagation of the fringe film is hindered by the enhanced solid wettability because of the energy barrier introduced by the interaction between water molecules and nanopillars which increase with solid wettability.

  6. Isospin effect of coulomb interaction on momentum dissipation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Liu Jianye; Guo Wenjun; Li Xiguo; Xing Yongzhong

    2004-01-01

    The authors investigate the isospin effect of Coulomb interaction on the momentum dissipation or nuclear stopping in the intermediate energy heavy ion collisions by using the isospin-dependent quantum molecular dynamics model. The calculated results show that the Coulomb interaction induces obviously the reductions of the momentum dissipation. The authors also find that the variation amplitude of momentum dissipation induced by the Coulomb interaction depends sensitively on the form and strength of symmetry potential. However, the isospin effect of Coulomb interaction on the momentum dissipation is less than that induced by the in-medium nucleon-nucleon cross section. In this case, Coulomb interaction does not changes obviously the isospin effect of momentum dissipation induced by the in-medium two-body collision. In particular, the Coulomb interaction is preferable for standing up the isospin effect of in-medium nucleon-nucleon cross section on the momentum dissipation and reducing the isospin effect of symmetry potential on it, which is important for obtaining the feature about the sensitive dependence of momentum dissipation on the in-medium nucleon-nucleon cross section and weakly on the symmetry potential. (author)

  7. Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics using Shardlow-like Splitting Algorithms

    Czech Academy of Sciences Publication Activity Database

    Larentzos, J.P.; Brennan, J.K.; Moore, J.D.; Lísal, Martin; Mattson, w.D.

    2014-01-01

    Roč. 185, č. 7 (2014), s. 1987-1998 ISSN 0010-4655 Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : dissipative particle dynamics * shardlow splitting algorithm * numerical integration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.112, year: 2014

  8. Effect of immobilization of a bacterial consortium on diuron dissipation and community dynamics.

    Science.gov (United States)

    Bazot, Stéphane; Lebeau, Thierry

    2009-09-01

    This work intended to study the relationship between diuron herbicide dissipation and the population dynamics of co-cultivated Delftia acidovorans WDL34 (WDL34) and Arthrobacter sp. N4 (N4) for different cell formulations: free cells or immobilization in Ca-alginate beads of one or both strains. GFP-tagged WDL34 and N4 Gram staining allowed analyzing the cell growth and distribution of each strain in both beads and culture medium in the course of the time. Compared to the free cell co-culture of WDL34 and N4, immobilization of WDL34 in Ca-alginate beads co-cultivated with free N4 increased the dissipation rate of diuron by 53% (0.141 mg ml(-1) h(-1)). In that case, immobilization strongly modified the final equilibrium among both strains (highest total N4 to WDL34 ratio). Our results demonstrated that the inoculant formulation played a major role in the cell growth of each cultivated strain possibly increasing diuron dissipation. This optimized cell formulation may allow improving water and soil treatment.

  9. Copolymer natural latex in concrete: Dynamic evaluation through energy dissipation of polymer modified concrete

    Science.gov (United States)

    Andayani, Sih Wuri; Suratman, Rochim; Imran, Iswandi; Mardiyati

    2018-05-01

    Portland cement concrete have been used in construction due to its strength and ecomical value. But it has some limitations, such low flexural strength, low tensile strength, low chemical resistant and etc. Due to its limitations in flexural and tensile strength, Portland cement concrete more susceptible by seismic force. There are some methods for improving its limitations. Polymer addition into concrete mixture could be one of solution for improving the flexural and tensile strength, in aiming to get erthquake resistant properties. Also, the eartquake resistant could be achieved by improving energy dissipation capacity. In this research, the earthquake resistant evalution was approached from dynamic evaluation through energy dissipation capacity, after polymer addition as concrete additives. The polymers were natural latex (Indonesian naural resource) grafted with styrene and methacrylate, forming copolymer - natural latex methacrylate (KOLAM) and copolymer - natural latex styrene (KOLAS). They were added into concrete mixture resulting polymer modified concrete. The composition of polymer are 1%, 5% and 10% weight/weight of cement. The higher capacity of energy dissipation will give more capability in either absorbing or dissipating energy, and it was predicted would give better earthquake resistant.. The use of KOLAM gave better performance than KOLAS in energy dissipation capacity. It gave about 46% for addition of 1% w/w compared to Portland cement concrete. But for addition 5% w/w and 10% w/w, they gave about 7% and 5% higher energy dissipation capacity. The KOLAM addition into concrete mixture would reduce the maximum impact load with maximumabout 35% impact load reducing after 1% w/w addition. The higher concentration of KOLAM in concrete mixture, lower reducing of impact load, they were about 4% and 3% for KOLAM 5% and 10%. For KOLAS addition in any compositions, there were no positive trend either in energy dissipation capacity or impact load properties

  10. Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation.

    Science.gov (United States)

    Rahimi, Ehsan; Reimers, Jeffrey R

    2018-06-20

    The use of molecules to enact quantum cellular automata (QCA) cells has been proposed as a new way for performing electronic logic operations at sub-nm dimensions. A key question that arises concerns whether chemical or physical processes are to be exploited. The use of chemical reactions allows the state of a switch element to be latched in molecular form, making the output of a cell independent of its inputs, but costs energy to do the reaction. Alternatively, if purely electronic polarization is manipulated then no internal latching occurs, but no power is dissipated provided the fields from the inputs change slowly compared to the molecular response times. How these scenarios pan out is discussed by considering calculated properties of the 1,4-diallylbutane cation, a species often used as a paradigm for molecular electronic switching. Utilized are results from different calculation approaches that depict the ion either as a charge-localized mixed-valence compound functioning as a bistable switch, or else as an extremely polarizable molecule with a delocalized electronic structure. Practical schemes for using molecular cells in QCA and other devices emerge.

  11. Impact of generalized dissipative coefficient on warm inflationary dynamics in the light of latest Planck data

    Energy Technology Data Exchange (ETDEWEB)

    Jawad, Abdul; Rani, Shamaila [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); Hussain, Shahzad [Aspire College, Department of Mathematics, Hafizabad (Pakistan); Videla, Nelson [Pontificia Universidad Catolica de Valparaiso, Instituto de Fisica, Valparaiso (Chile)

    2017-10-15

    The warm inflation scenario in view of the modified Chaplygin gas is studied. We consider the inflationary expansion to be driven by a standard scalar field whose decay ratio Γ has a generic power-law dependence with the scalar field φ and the temperature of the thermal bath T. By assuming an exponential power-law dependence in the cosmic time for the scale factor a(t), corresponding to the intermediate inflation model, we solve the background and perturbative dynamics considering our model to evolve according to (1) weak dissipative regime and (2) strong dissipative regime. Specifically, we find explicit expressions for the dissipative coefficient, scalar potential, and the relevant inflationary observables like the scalar power spectrum, scalar spectral index, and tensor-to-scalar ratio. The free parameters characterizing our model are constrained by considering the essential condition for warm inflation, the conditions for the model evolves according to weak or strong dissipative regime, and the 2015 Planck results through the n{sub s}-r plane. (orig.)

  12. 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

  13. Dissipative particle dynamics of triblock copolymer melts: A midblock conformational study at moderate segregation

    Science.gov (United States)

    Tallury, Syamal S.; Spontak, Richard J.; Pasquinelli, Melissa A.

    2014-12-01

    As thermoplastic elastomers, triblock copolymers constitute an immensely important class of shape-memory soft materials due to their unique ability to form molecular networks stabilized by physical, rather than chemical, cross-links. The extent to which such networks develop in triblock and higher-order multiblock copolymers is sensitive to the formation of midblock bridges, which serve to connect neighboring microdomains. In addition to bridges, copolymer molecules can likewise form loops and dangling ends upon microphase separation or they can remain unsegregated. While prior theoretical and simulation studies have elucidated the midblock bridging fraction in triblock copolymer melts, most have only considered strongly segregated systems wherein dangling ends and unsegregated chains become relatively insignificant. In this study, simulations based on dissipative particle dynamics are performed to examine the self-assembly and networkability of moderately segregated triblock copolymers. Utilizing a density-based cluster-recognition algorithm, we demonstrate how the simulations can be analyzed to extract information about microdomain formation and permit explicit quantitation of the midblock bridging, looping, dangling, and unsegregated fractions for linear triblock copolymers varying in chain length, molecular composition, and segregation level. We show that midblock conformations can be sensitive to variations in chain length, molecular composition, and bead repulsion, and that a systematic investigation can be used to identify the onset of strong segregation where the presence of dangling and unsegregated fractions are minimal. In addition, because this clustering approach is robust, it can be used with any particle-based simulation method to quantify network formation of different morphologies for a wide range of triblock and higher-order multiblock copolymer systems.

  14. Dynamic shear-lag model for understanding the role of matrix in energy dissipation in fiber-reinforced composites.

    Science.gov (United States)

    Liu, Junjie; Zhu, Wenqing; Yu, Zhongliang; Wei, Xiaoding

    2018-07-01

    Lightweight and high impact performance composite design is a big challenge for scientists and engineers. Inspired from well-known biological materials, e.g., the bones, spider silk, and claws of mantis shrimp, artificial composites have been synthesized for engineering applications. Presently, the design of ballistic resistant composites mainly emphasizes the utilization of light and high-strength fibers, whereas the contribution from matrix materials receives less attention. However, recent ballistic experiments on fiber-reinforced composites challenge our common sense. The use of matrix with "low-grade" properties enhances effectively the impact performance. In this study, we establish a dynamic shear-lag model to explore the energy dissipation through viscous matrix materials in fiber-reinforced composites and the associations of energy dissipation characteristics with the properties and geometries of constituents. The model suggests that an enhancement in energy dissipation before the material integrity is lost can be achieved by tuning the shear modulus and viscosity of a matrix. Furthermore, our model implies that an appropriately designed staggered microstructure, adopted by many natural composites, can repeatedly activate the energy dissipation process and thus improve dramatically the impact performance. This model demonstrates the role of matrix in energy dissipation, and stimulates new advanced material design concepts for ballistic applications. Biological composites found in nature often possess exceptional mechanical properties that man-made materials haven't be able to achieve. For example, it is predicted that a pencil thick spider silk thread can stop a flying Boeing airplane. Here, by proposing a dynamic shear-lag model, we investigate the relationships between the impact performance of a composite with the dimensions and properties of its constituents. Our analysis suggests that the impact performance of fiber-reinforced composites could improve

  15. Dissipative dynamics of superconducting hybrid qubit systems

    International Nuclear Information System (INIS)

    Montes, Enrique; Calero, Jesus M; Reina, John H

    2009-01-01

    We perform a theoretical study of composed superconducting qubit systems for the case of a coupled qubit configuration based on a hybrid qubit circuit made of both charge and phase qubits, which are coupled via a σ x x σ z interaction. We compute the system's eigen-energies in terms of the qubit transition frequencies and the strength of the inter-qubit coupling, and describe the sensitivity of the energy crossing/anti-crossing features to such coupling. We compute the hybrid system's dissipative dynamics for the cases of i) collective and ii) independent decoherence, whereby the system interacts with one common and two different baths of harmonic oscillators, respectively. The calculations have been performed within the Bloch-Redfield formalism and we report the solutions for the populations and the coherences of the system's reduced density matrix. The dephasing and relaxation rates are explicitly calculated as a function of the heat bath temperature.

  16. Dissipative dynamics of superconducting hybrid qubit systems

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Enrique; Calero, Jesus M; Reina, John H, E-mail: enriquem@univalle.edu.c, E-mail: j.reina-estupinan@physics.ox.ac.u [Departamento de Fisica, Universidad del Valle, A.A. 25360, Cali (Colombia)

    2009-05-01

    We perform a theoretical study of composed superconducting qubit systems for the case of a coupled qubit configuration based on a hybrid qubit circuit made of both charge and phase qubits, which are coupled via a sigma{sub x} x sigma{sub z} interaction. We compute the system's eigen-energies in terms of the qubit transition frequencies and the strength of the inter-qubit coupling, and describe the sensitivity of the energy crossing/anti-crossing features to such coupling. We compute the hybrid system's dissipative dynamics for the cases of i) collective and ii) independent decoherence, whereby the system interacts with one common and two different baths of harmonic oscillators, respectively. The calculations have been performed within the Bloch-Redfield formalism and we report the solutions for the populations and the coherences of the system's reduced density matrix. The dephasing and relaxation rates are explicitly calculated as a function of the heat bath temperature.

  17. Scaling Behaviour of Different Polymer Models in Dissipative Particle Dynamics of Unentangled Melts

    Czech Academy of Sciences Publication Activity Database

    Posel, Zbyšek; Rousseau, B.; Lísal, Martin

    2014-01-01

    Roč. 40, č. 15 (2014), s. 1274-1289 ISSN 0892-7022 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:GA UJEP(CZ) 53222 15 0008 01; CNRS-ASRT(FR) 20206 Institutional support: RVO:67985858 Keywords : coarse-grain potential * dissipative particle dynamics * rouse model Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.133, year: 2014

  18. Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Chattaraj, D.; Dash, Smruti

    2013-01-01

    The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

  19. Shock wave energy dissipation behavior (SWED) in Network forming ionic liquids (NILs): A Molecular dynamics study

    Science.gov (United States)

    Guda Vishnu, Karthik; Strachan, Alejandro

    2017-06-01

    SWED materials play a crucial role in protecting both personnel and structures in close proximity to blasts or ballistic impact. Exposure to shock waves with intensities as low as 1 MPa can cause brain injury in personnel and, hence, it is extremely important to understand the mechanisms operating in SWED materials and help design improved formulations. Recent experimental studies show that NILs containing di-ammonium cations and citrate anions with glass transition temperatures (Tg) below room temperature exhibit shockwave absorption characteristics that outperform polyurea (PU), a benchmark SWED assessment material. The experimentalists further hypothesized that the increased SWED ability in NILs with longer side chains (in di-ammonium cation) is due to a permanent structural ordering and nano-scale segregation. We use molecular dynamics simulations with the Dreiding force field to study shock propagation mechanisms in NILs. Shock propagation mechanisms in these materials are explored by performing both Hugoniostat and large scale non-equilibrium molecular dynamics (NEMD) simulations at 300 K. The simulation results show that the NIL 5-6 (5 C atoms (back bone) and 6 C atoms (side chain)) attenuates shocks better than NIL 5-3 (3 C atoms (side chain) and higher Tg) and PMMA in agreement with experimental observation. The simulations show that under shock loading the structures lose long range order; we find no evidence of nano-segregation nor or permanent structural changes.

  20. General conditions for the existence of non-standard Lagrangians for dissipative dynamical systems

    International Nuclear Information System (INIS)

    Musielak, Z.E.

    2009-01-01

    Equations of motion describing dissipative dynamical systems with coefficients varying either in time or in space are considered. To identify the equations that admit a Lagrangian description, two classes of non-standard Lagrangians are introduced and general conditions required for the existence of these Lagrangians are determined. The conditions are used to obtain some non-standard Lagrangians and derive equations of motion resulting from these Lagrangians.

  1. Dynamics of Rydberg atom lattices in the presence of noise and dissipation

    International Nuclear Information System (INIS)

    Abdussalam, Wildan

    2017-01-01

    The work presented in this dissertation concerns dynamics of Rydberg atom lattices in the presence of noise and dissipation. Rydberg atoms possess a number of exaggerated properties, such as a strong van der Waals interaction. The interplay of that interaction, coherent driving and decoherence leads to intriguing non-equilibrium phenomena. Here, we study the non-equilibrium physics of driven atom lattices in the presence of decoherence caused by either laser phase noise or strong decay. In the first case, we compare between global and local noise and explore their effect on the number of excitations and the full counting statistics. We find that both types of noise give rise to a characteristic distribution of the Rydberg excitation number. The main method employed is the Langevin equation but for the sake of efficiency in certain regimes, we use a Markovian master equation and Monte Carlo rate equations, respectively. In the second case, we consider dissipative systems with more general power-law interactions. We determine the phase diagram in the steady state and analyse its generation dynamics using Monte Carlo rate equations. In contrast to nearest-neighbour models, there is no transition to long-range-ordered phases for realistic interactions and resonant driving. Yet, for finite laser detunings, we show that Rydberg atom lattices can undergo a dissipative phase transition to a long-range-ordered antiferromagnetic phase. We identify the advantages of Monte Carlo rate equations over mean field predictions. Having studied the dynamics of Rydberg atom lattices, we study an application of the strong interactions in such systems for quantum information processing. We investigate the coherent exchange of a single photon between a superconducting microwave cavity and a lattice of strongly interacting Rydberg atoms in the presence of local electric field fluctuations plaguing the cavity surface. We show that despite the increased sensitivity of Rydberg states to

  2. Dynamics of Rydberg atom lattices in the presence of noise and dissipation

    Energy Technology Data Exchange (ETDEWEB)

    Abdussalam, Wildan

    2017-08-07

    The work presented in this dissertation concerns dynamics of Rydberg atom lattices in the presence of noise and dissipation. Rydberg atoms possess a number of exaggerated properties, such as a strong van der Waals interaction. The interplay of that interaction, coherent driving and decoherence leads to intriguing non-equilibrium phenomena. Here, we study the non-equilibrium physics of driven atom lattices in the presence of decoherence caused by either laser phase noise or strong decay. In the first case, we compare between global and local noise and explore their effect on the number of excitations and the full counting statistics. We find that both types of noise give rise to a characteristic distribution of the Rydberg excitation number. The main method employed is the Langevin equation but for the sake of efficiency in certain regimes, we use a Markovian master equation and Monte Carlo rate equations, respectively. In the second case, we consider dissipative systems with more general power-law interactions. We determine the phase diagram in the steady state and analyse its generation dynamics using Monte Carlo rate equations. In contrast to nearest-neighbour models, there is no transition to long-range-ordered phases for realistic interactions and resonant driving. Yet, for finite laser detunings, we show that Rydberg atom lattices can undergo a dissipative phase transition to a long-range-ordered antiferromagnetic phase. We identify the advantages of Monte Carlo rate equations over mean field predictions. Having studied the dynamics of Rydberg atom lattices, we study an application of the strong interactions in such systems for quantum information processing. We investigate the coherent exchange of a single photon between a superconducting microwave cavity and a lattice of strongly interacting Rydberg atoms in the presence of local electric field fluctuations plaguing the cavity surface. We show that despite the increased sensitivity of Rydberg states to

  3. Scalar dissipation rate and dissipative anomaly in isotropic turbulence

    International Nuclear Information System (INIS)

    Donzis, D.A.; Sreenivasan, K.R.; Yeung, P.K.

    2006-12-01

    We examine available data from experiment and recent numerical simulations to explore the supposition that the scalar dissipation rate in turbulence becomes independent of the fluid viscosity when the viscosity is small and of scalar diffusivity when the diffusivity is small. The data are interpreted in the context of semi-empirical spectral theory of Obukhov and Corrsin when the Schmidt number, Sc, is below unity, and of Batchelor's theory when Sc is above unity. Practical limits in terms of the Taylor-microscale Reynolds number, R λ , as well as Sc, are deduced for scalar dissipation to become sensibly independent of molecular properties. In particular, we show that such an asymptotic state is reached if R λ Sc 1/2 >> 1 for Sc λ 1. (author)

  4. AN OVERVIEW OF POWER DISSIPATION AND CONTROL TECHNIQUES IN CMOS TECHNOLOGY

    Directory of Open Access Journals (Sweden)

    N. B. ROMLI

    2015-03-01

    Full Text Available Total power dissipation in CMOS circuits has become a huge challenging in current semiconductor industry due to the leakage current and the leakage power. The exponential growth of both static and dynamic power dissipations in any CMOS process technology option has increased the cost and efficiency of the system. Technology options are used for the execution specifications and usually it depends on the optimisation and the performance constraints over the chip. This article reviews the relevant researches of the source or power dissipation, the mechanism to reduce the dynamic power dissipation as well as static power dissipation and an overview of various circuit techniques to control them. Important device parameters including voltage threshold and switching capacitance impact to the circuit performance in lowering both dynamic and static power dissipation are presented. The demand for the reduction of power dissipation in CMOS technology shall remain a challenging and active area of research for years to come. Thus, this review shall work as a guideline for the researchers who wish to work on power dissipation and control techniques.

  5. Dynamical Origin of Highly Efficient Energy Dissipation in Soft Magnetic Nanoparticles for Magnetic Hyperthermia Applications

    Science.gov (United States)

    Kim, Min-Kwan; Sim, Jaegun; Lee, Jae-Hyeok; Kim, Miyoung; Kim, Sang-Koog

    2018-05-01

    We explore robust magnetization-dynamic behaviors in soft magnetic nanoparticles in single-domain states and find their related high-efficiency energy-dissipation mechanism using finite-element micromagnetic simulations. We also make analytical derivations that provide deeper physical insights into the magnetization dynamics associated with Gilbert damping parameters under applications of time-varying rotating magnetic fields of different strengths and frequencies and static magnetic fields. Furthermore, we find that the mass-specific energy-dissipation rate at resonance in the steady-state regime changes remarkably with the strength of rotating fields and static fields for given damping constants. The associated magnetization dynamics are well interpreted with the help of the numerical calculation of analytically derived explicit forms. The high-efficiency energy-loss power can be obtained using soft magnetic nanoparticles in the single-domain state by tuning the frequency of rotating fields to the resonance frequency; what is more, it is controllable via the rotating and static field strengths for a given intrinsic damping constant. We provide a better and more efficient means of achieving specific loss power that can be implemented in magnetic hyperthermia applications.

  6. Crises in a dissipative bouncing ball model

    Energy Technology Data Exchange (ETDEWEB)

    Livorati, André L.P., E-mail: livorati@usp.br [Departamento de Física, UNESP, Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); School of Mathematics, University of Bristol, Bristol, BS8 1TW (United Kingdom); Instituto de Física, IFUSP, Universidade de São Paulo, USP, Rua do Matão, Tr.R 187, Cidade Universitária, 05314-970, São Paulo, SP (Brazil); Caldas, Iberê L. [Instituto de Física, IFUSP, Universidade de São Paulo, USP, Rua do Matão, Tr.R 187, Cidade Universitária, 05314-970, São Paulo, SP (Brazil); Dettmann, Carl P. [School of Mathematics, University of Bristol, Bristol, BS8 1TW (United Kingdom); Leonel, Edson D. [Departamento de Física, UNESP, Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil)

    2015-11-06

    Highlights: • We studied a dissipative bouncing ball dynamics. • A two-dimensional nonlinear mapping describes the dynamics. • Crises between attractors and its manifolds were characterized. • A new physical crisis between vibrating platform and an attractor was characterized. • The existence of a ‘robust’ chaotic attractor was set. - Abstract: The dynamics of a bouncing ball model under the influence of dissipation is investigated by using a two-dimensional nonlinear mapping. When high dissipation is considered, the dynamics evolves to different attractors. The evolution of the basins of the attracting fixed points is characterized, as we vary the control parameters. Crises between the attractors and their boundaries are observed. We found that the multiple attractors are intertwined, and when the boundary crisis between their stable and unstable manifolds occurs, it creates a successive mechanism of destruction for all attractors originated by the sinks. Also, a physical impact crisis is described, an important mechanism in the reduction of the number of attractors.

  7. Dissipation and spontaneous symmetry breaking in brain dynamics

    International Nuclear Information System (INIS)

    Freeman, Walter J; Vitiello, Giuseppe

    2008-01-01

    We compare the predictions of the dissipative quantum model of the brain with neurophysiological data collected from electroencephalograms resulting from high-density arrays fixed on the surfaces of primary sensory and limbic areas of trained rabbits and cats. Functional brain imaging in relation to behavior reveals the formation of coherent domains of synchronized neuronal oscillatory activity and phase transitions predicted by the dissipative model

  8. Experimental constraints on dynamic fragmentation as a dissipative process during seismic slip.

    Science.gov (United States)

    Barber, Troy; Griffith, W Ashley

    2017-09-28

    Various fault damage fabrics, from gouge in the principal slip zone to fragmented and pulverized rocks in the fault damage zone, have been attributed to brittle deformation at high strain rates during earthquake rupture. Past experimental work has shown that there exists a critical threshold in stress-strain rate space through which rock failure transitions from failure along a few discrete fracture planes to intense fragmentation. We present new experimental results on Arkansas Novaculite (AN) and Westerly Granite (WG) in which we quantify fracture surface area produced by dynamic fragmentation under uniaxial compressive loading and examine the controls of pre-existing mineral anisotropy on dissipative processes at the microscale. Tests on AN produced substantially greater new fracture surface area (approx. 6.0 m 2  g -1 ) than those on WG (0.07 m 2  g -1 ). Estimates of the portion of energy dissipated into brittle fracture were significant for WG (approx. 5%), but appeared substantial in AN (10% to as much as 40%). The results have important implications for the partitioning of dissipated energy under extreme loading conditions expected during earthquakes and the scaling of high-speed laboratory rock mechanics experiments to natural fault zones.This article is part of the themed issue 'Faulting, friction and weakening: from slow to fast motion'. © 2017 The Author(s).

  9. Molecular dynamics simulation of amplitude modulation atomic force microscopy

    International Nuclear Information System (INIS)

    Hu, Xiaoli; Martini, Ashlie; Egberts, Philip; Dong, Yalin

    2015-01-01

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip–substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip–sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement. (paper)

  10. Hamiltonian description and quantization of dissipative systems

    Science.gov (United States)

    Enz, Charles P.

    1994-09-01

    Dissipative systems are described by a Hamiltonian, combined with a “dynamical matrix” which generalizes the simplectic form of the equations of motion. Criteria for dissipation are given and the examples of a particle with friction and of the Lotka-Volterra model are presented. Quantization is first introduced by translating generalized Poisson brackets into commutators and anticommutators. Then a generalized Schrödinger equation expressed by a dynamical matrix is constructed and discussed.

  11. Nonlinear dynamics of drift structures in a magnetized dissipative plasma

    International Nuclear Information System (INIS)

    Aburjania, G. D.; Rogava, D. L.; Kharshiladze, O. A.

    2011-01-01

    A study is made of the nonlinear dynamics of solitary vortex structures in an inhomogeneous magnetized dissipative plasma. A nonlinear transport equation for long-wavelength drift wave structures is derived with allowance for the nonuniformity of the plasma density and temperature equilibria, as well as the magnetic and collisional viscosity of the medium and its friction. The dynamic equation describes two types of nonlinearity: scalar (due to the temperature inhomogeneity) and vector (due to the convectively polarized motion of the particles of the medium). The equation is fourth order in the spatial derivatives, in contrast to the second-order Hasegawa-Mima equations. An analytic steady solution to the nonlinear equation is obtained that describes a new type of solitary dipole vortex. The nonlinear dynamic equation is integrated numerically. A new algorithm and a new finite difference scheme for solving the equation are proposed, and it is proved that the solution so obtained is unique. The equation is used to investigate how the initially steady dipole vortex constructed here behaves unsteadily under the action of the factors just mentioned. Numerical simulations revealed that the role of the vector nonlinearity is twofold: it helps the dispersion or the scalar nonlinearity (depending on their magnitude) to ensure the mutual equilibrium and, thereby, promote self-organization of the vortical structures. It is shown that dispersion breaks the initial dipole vortex into a set of tightly packed, smaller scale, less intense monopole vortices-alternating cyclones and anticyclones. When the dispersion of the evolving initial dipole vortex is weak, the scalar nonlinearity symmetrically breaks a cyclone-anticyclone pair into a cyclone and an anticyclone, which are independent of one another and have essentially the same intensity, shape, and size. The stronger the dispersion, the more anisotropic the process whereby the structures break: the anticyclone is more intense

  12. A Fokker-Planck approach to canonical-dissipative Nambu systems: With an application to human motor control during dynamic haptic perception

    International Nuclear Information System (INIS)

    Frank, T.D.

    2010-01-01

    We formulate Markov diffusion processes for canonical-dissipative systems exhibiting Nambu mechanics. Analytical expressions for stationary canonical-dissipative distributions are obtained. Nambu-Boltzmann distributions are derived as special cases for systems without energy pumping. The Markov short-time propagator is used to derive maximum likelihood estimators for parameters of a model that describes a particular dynamic motor pattern providing haptic cues.

  13. Dynamical entanglement formation and dissipation effects in two double quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Contreras-Pulido, L D [Centro de Investigacion CientIfica y de Educacion Superior de Ensenada, Apartado Postal 2732, Ensenada, BC 22860 (Mexico); Rojas, F [Departamento de Fisica Teorica, Centro de Ciencias de la Materia Condensada, Universidad Nacional Autonoma de Mexico, Ensenada, Baja California 22800 (Mexico)

    2006-11-01

    We study the static and dynamic formation of entanglement in charge states of a two double quantum dot array with two mobile electrons under the effect of an external driving field. We include dissipation via contact with a phonon bath. By using the density matrix formalism and an open quantum system approach, we describe the dynamical behaviour of the charge distribution (polarization), concurrence (measure of the degree of entanglement) and Bell state probabilities (two qubit states with maximum entanglement) of such a system, including the role of dot asymmetry and temperature effects. Our results show that it is possible to obtain entangled states as well as a most probable Bell state, which can be controlled by the driving field. We also evaluate how the entanglement formation based on charge states deteriorates as the temperature or asymmetry increases.

  14. Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

    Science.gov (United States)

    Albaugh, Alex; Head-Gordon, Teresa; Niklasson, Anders M N

    2018-02-13

    Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

  15. Chapter 5: Quantum Dynamics in Dissipative Molecular Systems

    Science.gov (United States)

    Zhang, Hou-Dao; Xu, J.; Xu, Rui-Xue; Yan, Y. J.

    2014-04-01

    The following sections are included: * Introduction * HEOM versus Path Integral Formalism: Background * Generic form and terminology of HEOM * Statistical mechanics description of bath influence * Feynman-Vernon influence functional formalism * General comments * Memory-Frequency Decomposition of Bath Correlation Functions * PSD of Bose function * Brownian oscillators decomposition of bath spectral density function * Optimized HEOM Theory With Accuracy Control * Construction of HEOM via path integral formalism * Accuracy control on white-noise residue ansatz * Efficient HEOM propagator: Numerical filtering and indexing algorithm * HEOM in Quantum Mechanics for Open Systems * The HEOM space and the Schrödinger picture * HEOM in the Heisenberg picture * Mixed Heisenberg-Schrödinger block-matrix dynamics in nonlinear optical response functions * Two-Dimensional Spectroscopy: Model Calculations * Concluding Remarks * Acknowledgments * References

  16. Dissipative fluid mechanics of nuclei

    International Nuclear Information System (INIS)

    Morgenstern, B.

    1987-11-01

    With the aim to describe nucleus-nucleus collisions at low energies in the present thesis for the first time dissipative fluid dynamics for large-amplitude nuclear motion have been formulated. Thereby the collective dynamics are described in a scaling approximation in which the wave function of the system is distorted by a vortex-free velocity field. For infintely extended nuclear matter this scaling of the wave functions leads to a deformation of the Fermi sphere. Two-body collisions destroy the collective deformation of the Fermi sphere and yield so the dissipative contribution of the motion. Equations of motion for a finite set of collective variables and a field equation for the collective velocity potential in the limit of infinitely many degrees of freedom were developed. In the elastic limit oscillations around the equilibrium position are described. For small collective amplitudes and vortex-free velocity fields the integrodifferential equation for the velocity potential in the elastic limit could be transformed to the divergence of the field equation of fluid dynamics. In the dissipative limit an equation results which is similar to the Navier-Stokes equation and transforms to the divergence of the Navier-Stokes equation for vortex-free fields. It was shown that generally the dynamics of the many-body system is described by non-Markovian equations. (orig./HSI) [de

  17. Introduction to practice of molecular simulation molecular dynamics, Monte Carlo, Brownian dynamics, lattice Boltzmann and dissipative particle dynamics

    CERN Document Server

    Satoh, Akira

    2010-01-01

    This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use. Provides tools to develop skills in developing simulations programs Includes sample simulation programs for the reader to use Appendix explains Fortran and C languages in simple terms to allow the non-expert to use them.

  18. Pressure effects on the dissipative behavior of nanocrystalline diamond microelectromechanical resonators

    International Nuclear Information System (INIS)

    Santos, J T; Chu, V; Conde, J P; Holz, T; Fernandes, A J S; Costa, F M

    2015-01-01

    Diamond-based microelectromechanical resonators have the potential of enhanced performance due to the chemical inertness of the diamond structural layer and its high Young’s modulus, high wear resistance, low thermal expansion coefficient, and very high thermal conductivity. In this work, the resonance frequency and quality factor of MEMS resonators based on nanocrystalline diamond films are characterized under different air pressures. The dynamic behavior of 50–300 μm long linear bridges and double ended tuning forks, with resonance frequencies between 0.5 and 15 MHz and quality factors as high as 50 000 are described as a function of measurement pressure from high vacuum(∼10 mTorr) up to atmospheric conditions. The resonance frequencies and quality factors in vacuum show good agreement with the theoretical models including anchor and thermoelastic dissipation (TED). The Young’s moduli for nanocrystalline diamond films extrapolated from experimental data are between 840–920 GPa. The critical pressure values, at which the quality factor starts decreasing due to dissipation in air, are dependent on the resonator length. Longer structures, with quality factors limited by TED and lower resonance frequencies, have low critical pressures, of the order of 1–10 Torr and go from an intrinsic dissipation, to a molecular dissipation regime and finally to a region of viscous dissipation. Shorter resonators, with higher resonance frequencies and quality factors limited by anchor losses, have higher critical pressures, some higher than atmospheric pressure, and enter directly into the viscous dissipation regime from the intrinsic region. (paper)

  19. Memory effects in dissipative nucleus-nucleus collision

    International Nuclear Information System (INIS)

    Yadav, H.L.; Agarwal, K.C.

    2002-01-01

    A macroscopic dynamical model within the framework of a multidimensional Fokker-Planck equation is employed for a theoretical description of low-energy dissipative collisions between two heavy nuclei. The effect of two-body collisions leading to intrinsic equilibrium has been treated phenomenologically using the basic concepts of dissipative diabatic dynamics. The heavy-ion reaction 86 Kr(8.18 MeV/u) + 166 Er has been as a prototype to study and demonstrate the memory effects for dissipation and diffusion processes. Our calculated results for the deflection angle, angular distributions dσ/dθ cm , energy distributions dσ/dΔΕ, and element distributions dσ/dΖ illustrate a remarkable dependence on the memory effects and are consistent with the experimental data

  20. Dynamical Properties of Two Coupled Dissipative QED Cavities Driven by Coherent Fields

    International Nuclear Information System (INIS)

    Hou Bangpin; Sun Weili; Wang Shunjin; Wang Gang

    2007-01-01

    When two identical QED cavities driven by the coherent fields are located in a uniform environment, in addition to dissipation, there appears an indirect coupling between the two cavities induced by the background fields. We investigate the effects of the coherent fields, the dissipation as well as the incoherent coupling on the following dynamical properties of the system: photon transfer, reversible decoherence, and quantum state transfer, etc. We find that the photons in the cavities do not leak completely into the environment due to the collective coupling between the cavities and the environment, and the photons are transferred irreversibly from the cavity with more photons to the cavity with less ones due to the incoherent coupling so that they are equally distributed among the two cavities. The coherent field pumping on the two cavities increases the mean photons, complements the revived magnitude of the reversible decoherence, but hinders the quantum state transfer between the two cavities. The above phenomena may find applications in quantum communication and other basic fields.

  1. 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

  2. Energy Dissipation and Dynamics in Large Guide Field Turbulence Driven Reconnection at the Magnetopause

    Science.gov (United States)

    TenBarge, J. M.; Shay, M. A.; Sharma, P.; Juno, J.; Haggerty, C. C.; Drake, J. F.; Bhattacharjee, A.; Hakim, A.

    2017-12-01

    Turbulence and magnetic reconnection are the primary mechanisms responsible for the conversion of stored magnetic energy into particle energy in many space and astrophysical plasmas. The magnetospheric multiscale mission (MMS) has given us unprecedented access to high cadence particle and field data of turbulence and magnetic reconnection at earth's magnetopause. The observations include large guide field reconnection events generated within the turbulent magnetopause. Motivated by these observations, we present a study of large guide reconnection using the fully kinetic Eulerian Vlasov-Maxwell component of the Gkeyll simulation framework, and we also employ and compare with gyrokinetics to explore the asymptotically large guide field limit. In addition to studying the configuration space dynamics, we leverage the recently developed field-particle correlations to diagnose the dominant sources of dissipation and compare the results of the field-particle correlation to other energy dissipation measures.

  3. Time Dependence of Entropy Flux and Entropy Production of a Dissipative Dynamical System Driven by Non-Gaussian Noise

    International Nuclear Information System (INIS)

    Guo Yongfeng; Xu Wei; Li Dongxi; Xie Wenxian

    2008-01-01

    A stochastic dissipative dynamical system driven by non-Gaussian noise is investigated. A general approximate Fokker-Planck equation of the system is derived through a path-integral approach. Based on the definition of Shannon's information entropy, the exact time dependence of entropy flux and entropy production of the system is calculated both in the absence and in the presence of non-equilibrium constraint. The present calculation can be used to interpret the interplay of the dissipative constant and non-Gaussian noise on the entropy flux and entropy production

  4. Memory effects in dissipative nucleus-nucleus collision

    CERN Document Server

    Yadav, H L

    2002-01-01

    A macroscopic dynamical model within the framework of a multidimensional Fokker-Planck equation is employed for a theoretical description of low-energy dissipative collisions between two heavy nuclei. The effect of two-body collisions leading to intrinsic equilibrium has been treated phenomenologically using the basic concepts of dissipative diabatic dynamics. The heavy-ion reaction sup 8 sup 6 Kr(8.18 MeV/u) + sup 1 sup 6 sup 6 Er has been as a prototype to study and demonstrate the memory effects for dissipation and diffusion processes. Our calculated results for the deflection angle, angular distributions d sigma/d theta sub c sub m , energy distributions d sigma/d DELTA EPSILON, and element distributions d sigma/d ZETA illustrate a remarkable dependence on the memory effects and are consistent with the experimental data

  5. Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

    Science.gov (United States)

    Anderson, Richard L.; Bray, David J.; Ferrante, Andrea S.; Noro, Massimo G.; Stott, Ian P.; Warren, Patrick B.

    2017-09-01

    We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e., hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations and mean aggregation numbers of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values.

  6. Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST

    Science.gov (United States)

    Zhu, You-Liang; Pan, Deng; Li, Zhan-Wei; Liu, Hong; Qian, Hu-Jun; Zhao, Yang; Lu, Zhong-Yuan; Sun, Zhao-Yan

    2018-04-01

    We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.

  7. Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

    Science.gov (United States)

    Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

    1987-09-01

    A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

  8. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

    Science.gov (United States)

    Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

    2011-08-01

    Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

  9. Dynamic contact angle of water-based titanium oxide nanofluid

    Science.gov (United States)

    2013-01-01

    This paper presents an investigation into spreading dynamics and dynamic contact angle of TiO2-deionized water nanofluids. Two mechanisms of energy dissipation, (1) contact line friction and (2) wedge film viscosity, govern the dynamics of contact line motion. The primary stage of spreading has the contact line friction as the dominant dissipative mechanism. At the secondary stage of spreading, the wedge film viscosity is the dominant dissipative mechanism. A theoretical model based on combination of molecular kinetic theory and hydrodynamic theory which incorporates non-Newtonian viscosity of solutions is used. The model agreement with experimental data is reasonable. Complex interparticle interactions, local pinning of the contact line, and variations in solid–liquid interfacial tension are attributed to errors. PMID:23759071

  10. Density profiles of granular gases studied by molecular dynamics and Brownian bridges

    Science.gov (United States)

    Peñuñuri, F.; Montoya, J. A.; Carvente, O.

    2018-02-01

    Despite the inherent frictional forces and dissipative collisions, confined granular matter can be regarded as a system in a stationary state if we inject energy continuously. Under these conditions, both the density and the granular temperature are, in general, non-monotonic variables along the height of the container. In consequence, an analytical description of a granular system is hard to conceive. Here, by using molecular dynamics simulations, we measure the packing fraction profiles for a vertically vibrating three-dimensional granular system in several gaseous-like stationary states. We show that by using the Brownian bridge concept, the determined packing fraction profiles can be reproduced accurately and give a complete description of the distribution of the particles inside the simulation box.

  11. Dissipative particle dynamics simulation of fluid motion through an unsaturated fracture and fracture junction

    International Nuclear Information System (INIS)

    Liu Moubin; Meakin, Paul; Huang Hai

    2007-01-01

    Multiphase fluid motion in unsaturated fractures and fracture networks involves complicated fluid dynamics, which is difficult to model using grid-based continuum methods. In this paper, the application of dissipative particle dynamics (DPD), a relatively new mesoscale method to simulate fluid motion in unsaturated fractures is described. Unlike the conventional DPD method that employs a purely repulsive conservative (non-dissipative) particle-particle interaction to simulate the behavior of gases, we used conservative particle-particle interactions that combine short-range repulsive and long-range attractive interactions. This new conservative particle-particle interaction allows the behavior of multiphase systems consisting of gases, liquids and solids to be simulated. Our simulation results demonstrate that, for a fracture with flat parallel walls, the DPD method with the new interaction potential function is able to reproduce the hydrodynamic behavior of fully saturated flow, and various unsaturated flow modes including thin film flow, wetting and non-wetting flow. During simulations of flow through a fracture junction, the fracture junction can be fully or partially saturated depending on the wetting property of the fluid, the injection rate and the geometry of the fracture junction. Flow mode switching from a fully saturated flow to a thin film flow can also be observed in the fracture junction

  12. Nano-colloid electrophoretic transport: Fully explicit modelling via dissipative particle dynamics

    Science.gov (United States)

    Hassanzadeh Afrouzi, Hamid; Farhadi, Mousa; Sedighi, Kurosh; Moshfegh, Abouzar

    2018-02-01

    In present study, a novel fully explicit approach using dissipative particle dynamics (DPD) method is introduced for modelling electrophoretic transport of nano-colloids in an electrolyte solution. Slater type charge smearing function included in 3D Ewald summation method is employed to treat electrostatic interaction. Moreover, capability of different thermostats are challenged to control the system temperature and study the dynamic response of colloidal electrophoretic mobility under practical ranges of external electric field in nano scale application (0.072 600 in DPD units regardless of electric field intensity. Nosé-Hoover-Lowe-Andersen and Lowe-Andersen thermostats are found to function more effectively under high electric fields (E > 0.145 [ v / nm ]) while thermal equilibrium is maintained. Reasonable agreements are achieved by benchmarking the radial distribution function with available electrolyte structure modellings, as well as comparing reduced mobility against conventional Smoluchowski and Hückel theories, and numerical solution of Poisson-Boltzmann equation.

  13. Dissipative particle dynamics: Effects of thermostating schemes on nano-colloid electrophoresis

    Science.gov (United States)

    Hassanzadeh Afrouzi, Hamid; Moshfegh, Abouzar; Farhadi, Mousa; Sedighi, Kurosh

    2018-05-01

    A novel fully explicit approach using dissipative particle dynamics (DPD) method is introduced in the present study to model the electrophoretic transport of nano-colloids in an electrolyte solution. Slater type charge smearing function included in 3D Ewald summation method is employed to treat electrostatic interaction. Performance of various thermostats are challenged to control the system temperature and study the dynamic response of colloidal electrophoretic mobility under practical ranges of external electric field (0 . 072 relationships respectively with electric field and colloidal repulsion; although they each respectively behave direct and inverse trends with salt concentration under various thermostats. Nosé-Hoover-Lowe-Andersen and Lowe-Andersen thermostats are found to function more effectively under high electric fields (E > 0 . 145[v/nm ]) while thermal equilibrium is maintained. Reasonable agreements are achieved by benchmarking the system radial distribution function with available EW3D modellings, as well as comparing reduced mobility against conventional Smoluchowski and Hückel theories, and numerical solution of Poisson-Boltzmann equation.

  14. A dissipative particle dynamics method for arbitrarily complex geometries

    Science.gov (United States)

    Li, Zhen; Bian, Xin; Tang, Yu-Hang; Karniadakis, George Em

    2018-02-01

    Dissipative particle dynamics (DPD) is an effective Lagrangian method for modeling complex fluids in the mesoscale regime but so far it has been limited to relatively simple geometries. Here, we formulate a local detection method for DPD involving arbitrarily shaped geometric three-dimensional domains. By introducing an indicator variable of boundary volume fraction (BVF) for each fluid particle, the boundary of arbitrary-shape objects is detected on-the-fly for the moving fluid particles using only the local particle configuration. Therefore, this approach eliminates the need of an analytical description of the boundary and geometry of objects in DPD simulations and makes it possible to load the geometry of a system directly from experimental images or computer-aided designs/drawings. More specifically, the BVF of a fluid particle is defined by the weighted summation over its neighboring particles within a cutoff distance. Wall penetration is inferred from the value of the BVF and prevented by a predictor-corrector algorithm. The no-slip boundary condition is achieved by employing effective dissipative coefficients for liquid-solid interactions. Quantitative evaluations of the new method are performed for the plane Poiseuille flow, the plane Couette flow and the Wannier flow in a cylindrical domain and compared with their corresponding analytical solutions and (high-order) spectral element solution of the Navier-Stokes equations. We verify that the proposed method yields correct no-slip boundary conditions for velocity and generates negligible fluctuations of density and temperature in the vicinity of the wall surface. Moreover, we construct a very complex 3D geometry - the "Brown Pacman" microfluidic device - to explicitly demonstrate how to construct a DPD system with complex geometry directly from loading a graphical image. Subsequently, we simulate the flow of a surfactant solution through this complex microfluidic device using the new method. Its

  15. Field dissipation of oxyfluorfen in onion and its dynamics in soil under Indian tropical conditions.

    Science.gov (United States)

    Janaki, P; Sathya Priya, R; Chinnusamy, C

    2013-01-01

    Oxyfluorfen, a diphenyl-ether herbicide is being used to control annual and perennial broad-leaved weeds and sedges in a variety of field crops including onion. The present study was aimed to investigate the dynamics and field persistence of oxyfluorfen in onion plant, bulb and soil under Indian tropical conditions. Application of four rates of oxyfluorfen viz., 200, 250, 300 and 400 g AI ha(-1) as pre-emergence gave good weed control in field experiment with onion. The oxyfluorfen residue dissipated faster in plant than in soil respectively, with a mean half-life of 6.1 and 11.2 days. Dissipation followed first-order kinetics. In laboratory column leaching experiments, 17 percent of the applied oxyfluorfen was recovered from the soil and indicates its solubility in water and mobility in sandy clay loam soil was low. A sorption study revealed that the adsorption of oxyfluorfen to the soil was highly influenced by the soil organic carbon with the Koc value of 5450. The study concludes that the dissipation of oxyfluorfen in soil and onion was dependent on the physico-chemical properties of the soil and environmental conditions.

  16. Balance laws and centro velocity in dissipative systems

    NARCIS (Netherlands)

    van Groesen, Embrecht W.C.; Mainardi, F.

    1990-01-01

    Starting with a density that is conserved for a dynamical system when dissipation is ignored, a local conservation law is derived for which the total flux (integrated over the spatial domain) is unique. When dissipation is incorporated, the conservation law becomes a balance law. The contribution

  17. Quantum dynamics of the driven and dissipative Rabi model

    Science.gov (United States)

    Henriet, Loïc; Ristivojevic, Zoran; Orth, Peter P.; Le Hur, Karyn

    2014-08-01

    The Rabi model considers a two-level system (or spin 1/2) coupled to a quantized harmonic oscillator and describes the simplest interaction between matter and light. The recent experimental progress in solid-state circuit quantum electrodynamics has engendered theoretical efforts to quantitatively describe the mathematical and physical aspects of the light-matter interaction beyond the rotating-wave approximation. We develop a stochastic Schrödinger equation approach which enables us to access the strong-coupling limit of the Rabi model and study the effects of dissipation and ac drive in an exact manner. We include the effect of Ohmic noise on the non-Markovian spin dynamics, resulting in Kondo-type correlations, as well as cavity losses. We compute the time evolution of spin variables in various conditions. As a consideration for future work, we discuss the possibility of reaching a steady state with one polariton in realistic experimental conditions.

  18. Drift bifurcation detection for dissipative solitons

    International Nuclear Information System (INIS)

    Liehr, A W; Boedeker, H U; Roettger, M C; Frank, T D; Friedrich, R; Purwins, H-G

    2003-01-01

    We report on the experimental detection of a drift bifurcation for dissipative solitons, which we observe in the form of current filaments in a planar semiconductor-gas-discharge system. By introducing a new stochastic data analysis technique we find that due to a change of system parameters the dissipative solitons undergo a transition from purely noise-driven objects with Brownian motion to particles with a dynamically stabilized finite velocity

  19. Fractional action-like variational problems in holonomic, non-holonomic and semi-holonomic constrained and dissipative dynamical systems

    Energy Technology Data Exchange (ETDEWEB)

    EL-Nabulsi, Ahmad Rami [Department of Nuclear and Energy Engineering, Cheju National University, Ara-dong 1, Jeju 690-756 (Korea, Republic of)], E-mail: nabulsiahmadrami@yahoo.fr

    2009-10-15

    We communicate through this work the fractional calculus of variations and its corresponding Euler-Lagrange equations in 1D constrained holonomic, non-holonomic, and semi-holonomic dissipative dynamical system. The extension of the laws obtained to the 2D space state is done. Some interesting consequences are revealed.

  20. Dissipative effects in Multilevel Systems

    Energy Technology Data Exchange (ETDEWEB)

    Solomon, A I [Department of Physics and Astronomy, Open University, Milton Keynes MK7 6AA (United Kingdom); Schirmer, S G [Department of Applied Maths and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA (United Kingdom)

    2007-11-15

    Dissipation is sometimes regarded as an inevitable and regrettable presence in the real evolution of a quantum system. However, the effects may not always be malign, although often non-intuitive and may even be beneficial. In this note we we display some of these effects for N-level systems, where N = 2,3,4. We start with an elementary introduction to dissipative effects on the Bloch Sphere, and its interior, the Bloch Ball, for a two-level system. We describe explicitly the hamiltonian evolution as well as the purely dissipative dynamics, in the latter case giving the t {yields} {infinity} limits of the motion. This discussion enables us to provide an intuitive feeling for the measures of control-reachable states. For the three-level case we discuss the impossibility of isolating a two-level (qubit) subsystem; this is a Bohm-Aharonov type consequence of dissipation. We finally exemplify the four-level case by giving constraints on the decay of two-qubit entanglement.

  1. Entanglement from dissipation and holographic interpretation

    Science.gov (United States)

    Cantcheff, M. Botta; Gadelha, Alexandre L.; Marchioro, Dáfni F. Z.; Nedel, Daniel Luiz

    2018-02-01

    In this work we study a dissipative field theory where the dissipation process is manifestly related to dynamical entanglement and put it in the holographic context. Such endeavour is realized by further development of a canonical approach to study quantum dissipation, which consists of doubling the degrees of freedom of the original system by defining an auxiliary one. A time dependent entanglement entropy for the vacumm state is calculated and a geometrical interpretation of the auxiliary system and the entropy is given in the context of the AdS/CFT correspondence using the Ryu-Takayanagi formula. We show that the dissipative dynamics is controlled by the entanglement entropy and there are two distinct stages: in the early times the holographic interpretation requires some deviation from classical General Relativity; in the later times the quantum system is described as a wormhole, a solution of the Einstein's equations near to a maximally extended black hole with two asymptotically AdS boundaries. We focus our holographic analysis in this regime, and suggest a mechanism similar to teleportation protocol to exchange (quantum) information between the two CFTs on the boundaries (see Maldacena et al. in Fortschr Phys 65(5):1700034, arXiv:1704.05333 [hep-th], 2017).

  2. Entanglement from dissipation and holographic interpretation

    Energy Technology Data Exchange (ETDEWEB)

    Cantcheff, M.B. [IFLP-CONICET CC 67, La Plata, Buenos Aires (Argentina); Gadelha, Alexandre L. [Universidade Federal da Bahia, Instituto de Fisica, Salvador, BA (Brazil); Marchioro, Dafni F.Z.; Nedel, Daniel Luiz [Universidade Federal da Integracao Latino-Americana, Instituto Latino-Americano de Ciencias da Vida e da Natureza, Foz do Iguacu, PR (Brazil)

    2018-02-15

    In this work we study a dissipative field theory where the dissipation process is manifestly related to dynamical entanglement and put it in the holographic context. Such endeavour is realized by further development of a canonical approach to study quantum dissipation, which consists of doubling the degrees of freedom of the original system by defining an auxiliary one. A time dependent entanglement entropy for the vacuum state is calculated and a geometrical interpretation of the auxiliary system and the entropy is given in the context of the AdS/CFT correspondence using the Ryu-Takayanagi formula. We show that the dissipative dynamics is controlled by the entanglement entropy and there are two distinct stages: in the early times the holographic interpretation requires some deviation from classical General Relativity; in the later times the quantum system is described as a wormhole, a solution of the Einstein's equations near to a maximally extended black hole with two asymptotically AdS boundaries. We focus our holographic analysis in this regime, and suggest a mechanism similar to teleportation protocol to exchange (quantum) information between the two CFTs on the boundaries (see Maldacena et al. in Fortschr Phys 65(5):1700034, arXiv:1704.05333 [hep-th], 2017). (orig.)

  3. Dissipative structures in magnetorotational turbulence

    Science.gov (United States)

    Ross, Johnathan; Latter, Henrik N.

    2018-03-01

    Via the process of accretion, magnetorotational turbulence removes energy from a disk's orbital motion and transforms it into heat. Turbulent heating is far from uniform and is usually concentrated in small regions of intense dissipation, characterised by abrupt magnetic reconnection and higher temperatures. These regions are of interest because they might generate non-thermal emission, in the form of flares and energetic particles, or thermally process solids in protoplanetary disks. Moreover, the nature of the dissipation bears on the fundamental dynamics of the magnetorotational instability (MRI) itself: local simulations indicate that the large-scale properties of the turbulence (e.g. saturation levels, the stress-pressure relationship) depend on the short dissipative scales. In this paper we undertake a numerical study of how the MRI dissipates and the small-scale dissipative structures it employs to do so. We use the Godunov code RAMSES and unstratified compressible shearing boxes. Our simulations reveal that dissipation is concentrated in ribbons of strong magnetic reconnection that are significantly elongated in azimuth, up to a scale height. Dissipative structures are hence meso-scale objects, and potentially provide a route by which large scales and small scales interact. We go on to show how these ribbons evolve over time — forming, merging, breaking apart, and disappearing. Finally, we reveal important couplings between the large-scale density waves generated by the MRI and the small-scale structures, which may illuminate the stress-pressure relationship in MRI turbulence.

  4. From dissipative dynamics to studies of heat transfer at the nanoscale: analysis of the spin-boson model.

    Science.gov (United States)

    Boudjada, Nazim; Segal, Dvira

    2014-11-26

    We study in a unified manner the dissipative dynamics and the transfer of heat in the two-bath spin-boson model. We use the Bloch-Redfield (BR) formalism, valid in the very weak system-bath coupling limit, the noninteracting-blip approximation (NIBA), applicable in the nonadiabatic limit, and iterative, numerically exact path integral tools. These methodologies were originally developed for the description of the dissipative dynamics of a quantum system, and here they are applied to explore the problem of quantum energy transport in a nonequilibrium setting. Specifically, we study the weak-to-intermediate system-bath coupling regime at high temperatures kBT/ħ > ε, with ε as the characteristic frequency of the two-state system. The BR formalism and NIBA can lead to close results for the dynamics of the reduced density matrix (RDM) in a certain range of parameters. However, relatively small deviations in the RDM dynamics propagate into significant qualitative discrepancies in the transport behavior. Similarly, beyond the strict nonadiabatic limit NIBA's prediction for the heat current is qualitatively incorrect: It fails to capture the turnover behavior of the current with tunneling energy and temperature. Thus, techniques that proved meaningful for describing the RDM dynamics, to some extent even beyond their rigorous range of validity, should be used with great caution in heat transfer calculations, because qualitative-serious failures develop once parameters are mildly stretched beyond the techniques' working assumptions.

  5. Dissipation of Alfven waves in compressible inhomogeneous media

    International Nuclear Information System (INIS)

    Malara, F.; Primavera, L.; Veltri, P.

    1997-01-01

    In weakly dissipative media governed by the magnetohydrodynamics (MHD) equations, any efficient mechanism of energy dissipation requires the formation of small scales. Using numerical simulations, we study the properties of Alfven waves propagating in a compressible inhomogeneous medium, with an inhomogeneity transverse to the direction of wave propagation. Two dynamical effects, energy pinching and phase mixing, are responsible for the small-scales formation, similarly to the incompressible case. Moreover, compressive perturbations, slow waves and a static entropy wave are generated; the former are subject to steepening and form shock waves, which efficiently dissipate their energy, regardless of the Reynolds number. Rough estimates show that the dissipation times are consistent with those required to dissipate Alfven waves of photospheric origin inside the solar corona

  6. Quantal and dissipative aspects in nuclear structure and dynamics

    International Nuclear Information System (INIS)

    Lacroix, Denis

    1999-01-01

    This work is devoted to the description of both quantal and statistical aspects in a coherent theoretical framework that goes beyond a mean-field approximation. It is shown that among the possible methods, the Extended mean-field theory (ETDHF) is able to describe relaxation by including correlation effects. This theory is first applied to cold and hot giant resonances. After having developed a extended version of the linear response theory the effect of collisions on the response of 40 Ca is studied. It is shown that collisions contribute to the spreading width of giant resonances and become a dominant decay channel at high temperature. The generalization of these methods through the modelization of the Hamiltonian as a series of couplings in cascade has enabled to go beyond ETDHF. Thus, phenomena as multi-scale Ericson fluctuations and interferences in the nuclear response are predicted. The study of larger amplitudes requires the introduction of transport theories for the nuclear dynamics. Thus the deexcitation of hot and compressed nuclei has been studied with mean-field theories. This analysis has clarified the link between the equation of state and the dynamical expansion in finite Systems. A comparison with semi-classical has further shown the importance of quantum effects and has demonstrated the necessity to take into account nucleon collisions in a quantum framework. The possibility to apply ETDHF to nuclear dynamics in the general case is then discussed. A rapid and reliable method, tested on a schematic model is proposed to solve the extended mean-field. The application of ETDHF to the monopolar expansion of 16 O has finally demonstrated the interesting perspectives of this theory for describing dissipative aspects in quantum dynamics. Finally, the introduction of quantum stochastic approaches is discussed. (author) [fr

  7. Precollisional velocity correlations in a hard-disk fluid with dissipative collisions.

    Science.gov (United States)

    Soto, R; Piasecki, J; Mareschal, M

    2001-09-01

    Velocity correlations are studied in granular fluids, modeled by the inelastic hard sphere gas. Making a density expansion of the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy for the evolution of the reduced distributions, we predict the presence of precollisional velocity correlations. They are created by the propagation through correlated sequences of collisions (ring events) of the velocity correlations generated after dissipative collisions. The correlations have their origin in the dissipative character of collisions, being always present in granular fluids. The correlations, that manifest microscopically as an alignment of the velocities of a colliding pair produce modifications of collisional averages, in particular, the virial pressure. The pressure shows a reduction with respect to the elastic case as a consequence of the velocity alignment. Good qualitative agreement is obtained for the comparison of the numerical evaluations of the obtained analytical expressions and molecular dynamics results that showed evidence of precollisional velocity correlations [R. Soto and M. Mareschal, Phys. Rev. E 63, 041303 (2001)].

  8. Dissipation Assisted Quantum Memory with Coupled Spin Systems

    Science.gov (United States)

    Jiang, Liang; Verstraete, Frank; Cirac, Ignacio; Lukin, Mikhail

    2009-05-01

    Dissipative dynamics often destroys quantum coherences. However, one can use dissipation to suppress decoherence. A well-known example is the so-called quantum Zeno effect, in which one can freeze the evolution using dissipative processes (e.g., frequently projecting the system to its initial state). Similarly, the undesired decoherence of quantum bits can also be suppressed using controlled dissipation. We propose and analyze the use of this generalization of quantum Zeno effect for protecting the quantum information encoded in the coupled spin systems. This new approach may potentially enhance the performance of quantum memories, in systems such as nitrogen-vacancy color-centers in diamond.

  9. Construction of Lyapunov Function for Dissipative Gyroscopic System

    International Nuclear Information System (INIS)

    Xu Wei; Ao Ping; Yuan Bo

    2011-01-01

    We introduce a force decomposition to construct a potential function in deterministic dynamics described by ordinary differential equations in the context of dissipative gyroscopic systems. Such a potential function serves as the corresponding Lyapunov function for the dynamics, hence it gives both quantitative and qualitative descriptions for stability of motion. As an example we apply our force decomposition to a four-dimensional dissipative gyroscopic system. We explicitly obtain the potential function for all parameter regimes in the linear limit, including those regimes where the Lyapunov function was previously believed not to exist. (general)

  10. Dissipative nucleus-nucleus collisions: study of memory effects

    International Nuclear Information System (INIS)

    Agarwal, K.C.; Yadav, H.L.

    2002-01-01

    Dissipative collisions between two heavy nuclei are described in terms of a macroscopic dynamical model within the framework of a multi-dimensional Fokker-Planck equation. The reaction 86 Kr(8.18 MeV/u) + 166 Er has been used as a prototype to study and demonstrate the memory effects for dissipation and diffusion processes

  11. Skyrmionic spin Seebeck effect via dissipative thermomagnonic torques

    Science.gov (United States)

    Kovalev, Alexey A.

    2014-06-01

    We derive thermomagnonic torque and its "β-type" dissipative correction from the stochastic Landau-Lifshitz-Gilbert equation. The β-type dissipative correction describes viscous coupling between magnetic dynamics and magnonic current and it stems from spin mistracking of the magnetic order. We show that thermomagnonic torque is important for describing temperature gradient induced motion of skyrmions in helical magnets while dissipative correction plays an essential role in generating transverse Magnus force. We propose to detect such skyrmionic motion by employing the transverse spin Seebeck effect geometry.

  12. 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)

  13. 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)

  14. 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...

  15. Direct and indirect detection of dissipative dark matter

    Energy Technology Data Exchange (ETDEWEB)

    Fan, JiJi; Katz, Andrey; Shelton, Jessie, E-mail: jijifan1982@gmail.com, E-mail: katz.andrey@gmail.com, E-mail: jshelton137@gmail.com [Department of Physics, Harvard University, Cambridge, MA 02138 (United States)

    2014-06-01

    We study the constraints from direct detection and solar capture on dark matter scenarios with a subdominant dissipative component. This dissipative dark matter component in general has both a symmetric and asymmetric relic abundance. Dissipative dynamics allow this subdominant dark matter component to cool, resulting in its partial or total collapse into a smaller volume inside the halo (e.g., a dark disk) as well as a reduced thermal velocity dispersion compared to that of normal cold dark matter. We first show that these features considerably relax the limits from direct detection experiments on the couplings between standard model (SM) particles and dissipative dark matter. On the other hand, indirect detection of the annihilation of the symmetric dissipative dark matter component inside the Sun sets stringent and robust constraints on the properties of the dissipative dark matter. In particular, IceCube observations force dissipative dark matter particles with mass above 50 GeV to either have a small coupling to the SM or a low local density in the solar system, or to have a nearly asymmetric relic abundance. Possible helioseismology signals associated with purely asymmetric dissipative dark matter are discussed, with no present constraints.

  16. Direct and indirect detection of dissipative dark matter

    International Nuclear Information System (INIS)

    Fan, JiJi; Katz, Andrey; Shelton, Jessie

    2014-01-01

    We study the constraints from direct detection and solar capture on dark matter scenarios with a subdominant dissipative component. This dissipative dark matter component in general has both a symmetric and asymmetric relic abundance. Dissipative dynamics allow this subdominant dark matter component to cool, resulting in its partial or total collapse into a smaller volume inside the halo (e.g., a dark disk) as well as a reduced thermal velocity dispersion compared to that of normal cold dark matter. We first show that these features considerably relax the limits from direct detection experiments on the couplings between standard model (SM) particles and dissipative dark matter. On the other hand, indirect detection of the annihilation of the symmetric dissipative dark matter component inside the Sun sets stringent and robust constraints on the properties of the dissipative dark matter. In particular, IceCube observations force dissipative dark matter particles with mass above 50 GeV to either have a small coupling to the SM or a low local density in the solar system, or to have a nearly asymmetric relic abundance. Possible helioseismology signals associated with purely asymmetric dissipative dark matter are discussed, with no present constraints

  17. 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.

  18. Dissipative light-bullets in the filamentation of femtosecond pulses

    International Nuclear Information System (INIS)

    Porras, M.A.; Gonzalo, I.

    2010-01-01

    Complete text of publication follows. With the growing interest in filamentation in solid and liquid media, the regime of filamentation with anomalous dispersion is receiving more attention. In this work we show that basics aspects of the filament dynamics in this regime can be explained in terms of a novel type of light-bullet, which is not of solitary or of conical types, but a wave-packet that maximizes the energy dissipation into the medium while remaining localized and stationary in propagation. We first show that a nonlinear optical medium at a given carrier wave length at which dispersion is anomalous, supports 'dissipative' light-bullets, i.e., waves localized in space and time and that propagate without change as a result of a balance between nonlinear compression and nonlinear absorption. Among them, the particular dissipative light-bullet with the highest possible dissipation is unique in a given medium, in the sense that all its properties are fixed by the properties of the medium at the carrier wave length. In this light-bullet, self-focusing continuously transports energy towards the pulse center by an amount that just compensates for the nonlinear losses. Figure 1(a) shows the radial profiles of the dissipative light-bullets that maximizes energy dissipation for several orders of multi-photon absorption responsible for the nonlinear losses. We have also found that this dissipative light-bullet tends to be spontaneously formed in the filamentary dynamics in media with anomalous dispersion. Figure 1(b) shows the peak intensity, the total energy and losses of a pulse that undergoes self-focusing and filamentation in an ideal medium with only Kerr nonlinearity and multi-photon absorption. This simple model reproduces the particularly long filament 'segments' and the 'burst' observed in experiments and in more accurate simulations. The peak intensity in the filament is identical to that of the dissipative light-bullet with maximum dissipation, and the

  19. Dissipative preparation of steady Greenberger-Horne-Zeilinger states for Rydberg atoms with quantum Zeno dynamics

    Science.gov (United States)

    Shao, X. Q.; Wu, J. H.; Yi, X. X.; Long, Gui-Lu

    2017-12-01

    Inspired by a recent work [F. Reiter, D. Reeb, and A. S. Sørensen, Phys. Rev. Lett. 117, 040501 (2016), 10.1103/PhysRevLett.117.040501], we present a simplified proposal for dissipatively preparing a Greenberger-Horne-Zeilinger (GHZ) state of three Rydberg atoms in a cavity. The Z pumping is implemented under the action of the spontaneous emission of Λ -type atoms and the quantum Zeno dynamics induced by strong continuous coupling. In the meantime, a dissipative Rydberg pumping breaks up the stability of the state | GHZ+〉 in the process of Z pumping, making | GHZ-〉 the unique steady state of the system. Compared with the former scheme, the number of driving fields acting on atoms is greatly reduced and only a single-mode cavity is required. The numerical simulation of the full master equation reveals that a high fidelity ˜98 % can be obtained with the currently achievable parameters in the Rydberg-atom-cavity system.

  20. Dissipative particle dynamics of diffusion-NMR requires high Schmidt-numbers

    Energy Technology Data Exchange (ETDEWEB)

    Azhar, Mueed; Greiner, Andreas [Laboratory for Simulation, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg (Germany); Korvink, Jan G., E-mail: jan.korvink@kit.edu, E-mail: david.kauzlaric@imtek.uni-freiburg.de [Laboratory for Simulation, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg (Germany); Department of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen (Germany); Kauzlarić, David, E-mail: jan.korvink@kit.edu, E-mail: david.kauzlaric@imtek.uni-freiburg.de [Laboratory for Simulation, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg (Germany); Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, 79104 Freiburg (Germany)

    2016-06-28

    We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. After a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered.

  1. SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Hakamata, Tomoya [Kumamoto Univ., Kumamoto (Japan); Shimamura, Kohei [Kumamoto Univ., Kumamoto (Japan); Univ. of Southern California, Los Angeles, CA (United States); Kobe Univ., Kobe (Japan); Shimojo, Fuyuki [Kumamoto Univ., Kumamoto (Japan); Kalia, Rajiv K. [Univ. of Southern California, Los Angeles, CA (United States); Nakano, Aiichiro [Univ. of Southern California, Los Angeles, CA (United States); Vashishta, Priya [Univ. of Southern California, Los Angeles, CA (United States)

    2017-10-20

    Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH3NH3PbI3. Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH3NH3 sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.

  2. Energy dissipation in multifrequency atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Valentina Pukhova

    2014-04-01

    Full Text Available The instantaneous displacement, velocity and acceleration of a cantilever tip impacting onto a graphite surface are reconstructed. The total dissipated energy and the dissipated energy per cycle of each excited flexural mode during the tip interaction is retrieved. The tip dynamics evolution is studied by wavelet analysis techniques that have general relevance for multi-mode atomic force microscopy, in a regime where few cantilever oscillation cycles characterize the tip–sample interaction.

  3. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    Science.gov (United States)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  4. 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.

  5. The dynamic tidal response of a subsurface ocean on Titan and the associated dissipative heat generated

    Science.gov (United States)

    Tyler, Robert

    2012-04-01

    The tidal flow response and associated dissipative heat generated in a satellite ocean depends strongly on the ocean configuration parameters as these parameters control the form and frequencies of the ocean's natural modes of oscillation; if there is a near match between the form and frequency of one of these natural modes and that of one of the available tidal forcing constituents, the ocean can be resonantly excited, producing strong tidal flow and appreciable dissipative heat. Of primary interest in this study are the ocean parameters that can be expected to evolve (notably, the ocean depth in an ocean attempting to freeze, and the stratification in an ocean attempting to cool) because this evolution can cause an ocean to be pushed into a resonant configuration where the increased dissipative heat of the resonant response halts further evolution and a liquid ocean can be maintained by ocean tidal heat. In this case the resonant ocean tidal response is not only allowed but may be inevitable. Previous work on this topic is extended to describe the resonant configurations in both unstratified and stratified cases for an assumed global ocean on Titan subject to both obliquity and eccentricity tidal forces. Results indicate first that the assumption of an equilibrium tidal response is not justified and the correct dynamical response must be considered. Second, the ocean tidal dissipation will be appreciable if the ocean configuration is near that producing a resonant state. The parameters values required for this resonance are provided in this study, and examples/movies of calculated ocean tidal flow are also presented.

  6. 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.

  7. 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.

  8. Non-Markovian dissipative quantum mechanics with stochastic trajectories

    International Nuclear Information System (INIS)

    Koch, Werner

    2010-01-01

    All fields of physics - be it nuclear, atomic and molecular, solid state, or optical - offer examples of systems which are strongly influenced by the environment of the actual system under investigation. The scope of what is called ''the environment'' may vary, i.e., how far from the system of interest an interaction between the two does persist. Typically, however, it is much larger than the open system itself. Hence, a fully quantum mechanical treatment of the combined system without approximations and without limitations of the type of system is currently out of reach. With the single assumption of the environment to consist of an internally thermalized set of infinitely many harmonic oscillators, the seminal work of Stockburger and Grabert [Chem. Phys., 268:249-256, 2001] introduced an open system description that captures the environmental influence by means of a stochastic driving of the reduced system. The resulting stochastic Liouville-von Neumann equation describes the full non-Markovian dynamics without explicit memory but instead accounts for it implicitly through the correlations of the complex-valued noise forces. The present thesis provides a first application of the Stockburger-Grabert stochastic Liouville-von Neumann equation to the computation of the dynamics of anharmonic, continuous open systems. In particular, it is demonstrated that trajectory based propagators allow for the construction of a numerically stable propagation scheme. With this approach it becomes possible to achieve the tremendous increase of the noise sample count necessary to stochastically converge the results when investigating such systems with continuous variables. After a test against available analytic results for the dissipative harmonic oscillator, the approach is subsequently applied to the analysis of two different realistic, physical systems. As a first example, the dynamics of a dissipative molecular oscillator is investigated. Long time propagation - until

  9. In-flight and collisional dissipation as a mechanism to suppress Fermi acceleration in a breathing Lorentz gas.

    Science.gov (United States)

    Oliveira, Diego F M; Leonel, Edson D

    2012-06-01

    Some dynamical properties for a time dependent Lorentz gas considering both the dissipative and non dissipative dynamics are studied. The model is described by using a four-dimensional nonlinear mapping. For the conservative dynamics, scaling laws are obtained for the behavior of the average velocity for an ensemble of non interacting particles and the unlimited energy growth is confirmed. For the dissipative case, four different kinds of damping forces are considered namely: (i) restitution coefficient which makes the particle experiences a loss of energy upon collisions; and in-flight dissipation given by (ii) F=-ηV(2); (iii) F=-ηV(μ) with μ≠1 and μ≠2 and; (iv) F=-ηV, where η is the dissipation parameter. Extensive numerical simulations were made and our results confirm that the unlimited energy growth, observed for the conservative dynamics, is suppressed for the dissipative case. The behaviour of the average velocity is described using scaling arguments and classes of universalities are defined.

  10. A field theory description of constrained energy-dissipation processes

    International Nuclear Information System (INIS)

    Mandzhavidze, I.D.; Sisakyan, A.N.

    2002-01-01

    A field theory description of dissipation processes constrained by a high-symmetry group is given. The formalism is presented in the example of the multiple-hadron production processes, where the transition to the thermodynamic equilibrium results from the kinetic energy of colliding particles dissipating into hadron masses. The dynamics of these processes is restricted because the constraints responsible for the colour charge confinement must be taken into account. We develop a more general S-matrix formulation of the thermodynamics of nonequilibrium dissipative processes and find a necessary and sufficient condition for the validity of this description; this condition is similar to the correlation relaxation condition, which, according to Bogolyubov, must apply as the system approaches equilibrium. This situation must physically occur in processes with an extremely high multiplicity, at least if the hadron mass is nonzero. We also describe a new strong-coupling perturbation scheme, which is useful for taking symmetry restrictions on the dynamics of dissipation processes into account. We review the literature devoted to this problem

  11. 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....

  12. A mesoscopic simulation of static and dynamic wetting using many-body dissipative particle dynamics

    Science.gov (United States)

    Ghorbani, Najmeh; Pishevar, Ahmadreza

    2018-01-01

    A many-body dissipative particle dynamics simulation is applied here to pave the way for investigating the behavior of mesoscale droplets after impact on horizontal solid substrates. First, hydrophobic and hydrophilic substrates are simulated through tuning the solid-liquid interfacial interaction parameters of an innovative conservative force model. The static contact angles are calculated on homogeneous and several patterned surfaces and compared with the predicted values by the Cassie's law in order to verify the model. The results properly evaluate the amount of increase in surface superhydrophobicity as a result of surface patterning. Then drop impact phenomenon is studied by calculating the spreading factor and dimensionless height versus dimensionless time and the comparisons made between the results and the experimental values for three different static contact angles. The results show the capability of the procedure in calculating the amount of maximum spreading factor, which is a significant concept in ink-jet printing and coating process.

  13. Multiscale Modeling of Blood Flow: Coupling Finite Elements with Smoothed Dissipative Particle Dynamics

    KAUST Repository

    Moreno Chaparro, Nicolas; Vignal, Philippe; Li, Jun; Calo, Victor M.

    2013-01-01

    A variational multi scale approach to model blood flow through arteries is proposed. A finite element discretization to represent the coarse scales (macro size), is coupled to smoothed dissipative particle dynamics that captures the fine scale features (micro scale). Blood is assumed to be incompressible, and flow is described through the Navier Stokes equation. The proposed cou- pling is tested with two benchmark problems, in fully coupled systems. Further refinements of the model can be incorporated in order to explicitly include blood constituents and non-Newtonian behavior. The suggested algorithm can be used with any particle-based method able to solve the Navier-Stokes equation.

  14. Multiscale Modeling of Blood Flow: Coupling Finite Elements with Smoothed Dissipative Particle Dynamics

    KAUST Repository

    Moreno Chaparro, Nicolas

    2013-06-01

    A variational multi scale approach to model blood flow through arteries is proposed. A finite element discretization to represent the coarse scales (macro size), is coupled to smoothed dissipative particle dynamics that captures the fine scale features (micro scale). Blood is assumed to be incompressible, and flow is described through the Navier Stokes equation. The proposed cou- pling is tested with two benchmark problems, in fully coupled systems. Further refinements of the model can be incorporated in order to explicitly include blood constituents and non-Newtonian behavior. The suggested algorithm can be used with any particle-based method able to solve the Navier-Stokes equation.

  15. Modeling non-linear micromechanics of hydrogels using dissipative particle dynamics

    Science.gov (United States)

    Nikolov, Svetoslav; Fernandez-Nieves, Alberto; Alexeev, Alexander

    In response to an appropriate external stimulus microgels are capable of undergoing large and reversible changes in volume (10-20 times) which has made them attractive as microscopic actuators and drug delivery agents. However, the mechanics of microgels is not well understood in part due to inhomogeneities within the network. Full-scale atomistic modeling of micrometer-sized gel networks is currently not possible due to the large length and time scales involved. We develop a mesoscale model based on dissipative particle dynamics to examine the mechanics of microgels in solvent. By varying the osmotic pressure of the gels we probe the changes in bulk modulus for different values of the Flory-Huggins parameter. We examine how the bulk modulus depends on inhomogeneities we introduce within the gel structure by altering the crosslink density and by embedding rigid nanoparticles. Financial support provided by NSF CAREER Award (DMR-1255288) and NSF Graduate Research Fellowship, Grant No. DGE-1650044.

  16. Coronal heating by Alfven waves dissipation in compressible nonuniform media

    International Nuclear Information System (INIS)

    Malara, Francesco; Primavera, Leonardo; Veltri, Pierluigi

    1996-01-01

    The possibility to produce small scales and then to efficiently dissipate energy has been studied by Malara et al. [1992b] in the case of MHD disturbances propagating in an weakly dissipative incompressible and inhomogeneous medium, for a strictly 2D geometry. We extend this work to include both compressibility and the third component for vector quantities. Numerical simulations show that, when an Alfven wave propagates in a compressible nonuniform medium, the two dynamical effects responsible for the small scales formation in the incompressible case are still at work: energy pinching and phase-mixing. These effects give rise to the formation of compressible perturbations (fast and slow waves or a static entropy wave). Some of these compressive fluctuations are subject to the steepening of the wave front and become shock waves, which are extremely efficient in dissipating their energy, their dissipation being independent of the Reynolds number. Rough estimates of the typical times the various dynamical processes take to produce small scales show that these times are consistent with those required to dissipate inside the solar corona the energy of Alfven waves of photospheric origin

  17. 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.

  18. Trajectory approach to dissipative quantum phase space dynamics: Application to barrier scattering

    International Nuclear Information System (INIS)

    Hughes, Keith H.; Wyatt, Robert E.

    2004-01-01

    The Caldeira-Leggett master equation, expressed in Lindblad form, has been used in the numerical study of the effect of a thermal environment on the dynamics of the scattering of a wave packet from a repulsive Eckart barrier. The dynamics are studied in terms of phase space trajectories associated with the distribution function, W(q,p,t). The equations of motion for the trajectories include quantum terms that introduce nonlocality into the motion, which imply that an ensemble of correlated trajectories needs to be propagated. However, use of the derivative propagation method (DPM) allows each trajectory to be propagated individually. This is achieved by deriving equations of motion for the partial derivatives of W(q,p,t) that appear in the master equation. The effects of dissipation on the trajectories are studied and results are shown for the transmission probability. On short time scales, decoherence is demonstrated by a swelling of trajectories into momentum space. For a nondissipative system, a comparison is made of the DPM with the 'exact' transmission probability calculated from a fixed grid calculation

  19. 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.

  20. 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 ...

  1. Dissipative effects in the beam-beam interaction of intersecting storage rings

    International Nuclear Information System (INIS)

    Ford, J.; Vivaldi, F.

    1982-01-01

    This proposal seeks continuing support for an ongoing research investigation of various dynamical instabilities which arise in high energy intersecting storage rings due to the beam-beam interaction. Although the dissipative effect of radiation in beam-beam machines is anticipated to be a dominant feature affecting stability in the dynamics of colliding beams of heavy particles, almost nothing is known regarding the stability problem in many-dimensional dissipative systems. The work proposed here will extend the earlier computations on weak instabilities in many-dimensional beam-beam models to include the effect of dissipation. The object of this research is to obtain conditions for global beam stability over long time scales as a function of the machine parameters

  2. Dissipative Bohmian mechanics within the Caldirola–Kanai framework: A trajectory analysis of wave-packet dynamics in viscid media

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, A.S., E-mail: asanz@iff.csic.es [Instituto de Física Fundamental (IFF-CSIC), Serrano 123, 28006 Madrid (Spain); Martínez-Casado, R. [Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ (United Kingdom); Peñate-Rodríguez, H.C.; Rojas-Lorenzo, G. [Instituto Superior de Tecnologías y Ciencias Aplicadas, Ave. Salvador Allende y Luaces, Quinta de Los Molinos, Plaza, La Habana 10600 (Cuba); Miret-Artés, S. [Instituto de Física Fundamental (IFF-CSIC), Serrano 123, 28006 Madrid (Spain)

    2014-08-15

    Classical viscid media are quite common in our everyday life. However, we are not used to find such media in quantum mechanics, and much less to analyze their effects on the dynamics of quantum systems. In this regard, the Caldirola–Kanai time-dependent Hamiltonian constitutes an appealing model, accounting for friction without including environmental fluctuations (as it happens, for example, with quantum Brownian motion). Here, a Bohmian analysis of the associated friction dynamics is provided in order to understand how a hypothetical, purely quantum viscid medium would act on a wave packet from a (quantum) hydrodynamic viewpoint. To this purpose, a series of paradigmatic contexts have been chosen, such as the free particle, the motion under the action of a linear potential, the harmonic oscillator, or the superposition of two coherent wave packets. Apart from their analyticity, these examples illustrate interesting emerging behaviors, such as localization by “quantum freezing” or a particular type of quantum–classical correspondence. The reliability of the results analytically determined has been checked by means of numerical simulations, which has served to investigate other problems lacking of such analyticity (e.g., the coherent superpositions). - Highlights: • A dissipative Bohmian approach is developed within the Caldirola–Kanai model. • Some simple yet physically insightful systems are then studied analytically. • Dissipation leads to spatial localization in free-force regimes. • Under the action of linear forces, dissipation leads to uniform motion. • In harmonic potentials, the system decays unavoidable to the well minimum.

  3. Dissipative Bohmian mechanics within the Caldirola–Kanai framework: A trajectory analysis of wave-packet dynamics in viscid media

    International Nuclear Information System (INIS)

    Sanz, A.S.; Martínez-Casado, R.; Peñate-Rodríguez, H.C.; Rojas-Lorenzo, G.; Miret-Artés, S.

    2014-01-01

    Classical viscid media are quite common in our everyday life. However, we are not used to find such media in quantum mechanics, and much less to analyze their effects on the dynamics of quantum systems. In this regard, the Caldirola–Kanai time-dependent Hamiltonian constitutes an appealing model, accounting for friction without including environmental fluctuations (as it happens, for example, with quantum Brownian motion). Here, a Bohmian analysis of the associated friction dynamics is provided in order to understand how a hypothetical, purely quantum viscid medium would act on a wave packet from a (quantum) hydrodynamic viewpoint. To this purpose, a series of paradigmatic contexts have been chosen, such as the free particle, the motion under the action of a linear potential, the harmonic oscillator, or the superposition of two coherent wave packets. Apart from their analyticity, these examples illustrate interesting emerging behaviors, such as localization by “quantum freezing” or a particular type of quantum–classical correspondence. The reliability of the results analytically determined has been checked by means of numerical simulations, which has served to investigate other problems lacking of such analyticity (e.g., the coherent superpositions). - Highlights: • A dissipative Bohmian approach is developed within the Caldirola–Kanai model. • Some simple yet physically insightful systems are then studied analytically. • Dissipation leads to spatial localization in free-force regimes. • Under the action of linear forces, dissipation leads to uniform motion. • In harmonic potentials, the system decays unavoidable to the well minimum

  4. Nuclear Dissipation from Fission Time

    International Nuclear Information System (INIS)

    Gontchar, I.; Morjean, M.; Basnary, S.

    2000-01-01

    Fission times, pre-scission neutron multiplicities and GDR pre-scission γ-ray multiplicities measured for uranium or thorium nuclei formed with temperatures T ∼ 1.8 MeV have been compared with calculations performed with CDSM2, a two-dimensional dynamical model combined with a statistical one. Among the three experimental approaches considered, fission times give access to the most precise pieces of information on nuclear dissipation at high excitation energy. For the temperature range under consideration, an agreement between the model and data is achieved if one-body dissipation is used with a strength factor k red ∼ 0.45 ± 0.10 applied to the wall term for the mononuclear configuration. (authors)

  5. Entropy as a Metric Generator of Dissipation in Complete Metriplectic Systems

    Directory of Open Access Journals (Sweden)

    Massimo Materassi

    2016-08-01

    Full Text Available This lecture is a short review on the role entropy plays in those classical dissipative systems whose equations of motion may be expressed via a Leibniz Bracket Algebra (LBA. This means that the time derivative of any physical observable f of the system is calculated by putting this f in a “bracket” together with a “special observable” F, referred to as a Leibniz generator of the dynamics. While conservative dynamics is given an LBA formulation in the Hamiltonian framework, so that F is the Hamiltonian H of the system that generates the motion via classical Poisson brackets or quantum commutation brackets, an LBA formulation can be given to classical dissipative dynamics through the Metriplectic Bracket Algebra (MBA: the conservative component of the dynamics is still generated via Poisson algebra by the total energy H, while S, the entropy of the degrees of freedom statistically encoded in friction, generates dissipation via a metric bracket. The motivation of expressing through a bracket algebra and a motion-generating function F is to endow the theory of the system at hand with all the powerful machinery of Hamiltonian systems in terms of symmetries that become evident and readable. Here a (necessarily partial overview of the types of systems subject to MBA formulation is presented, and the physical meaning of the quantity S involved in each is discussed. Here the aim is to review the different MBAs for isolated systems in a synoptic way. At the end of this collection of examples, the fact that dissipative dynamics may be constructed also in the absence of friction with microscopic degrees of freedom is stressed. This reasoning is a hint to introduce dissipation at a more fundamental level.

  6. 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.

  7. Transient chaotic transport in dissipative drift motion

    Energy Technology Data Exchange (ETDEWEB)

    Oyarzabal, R.S. [Pós-Graduação em Ciências/Física, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Szezech, J.D. [Departamento de Matemática e Estatística, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Batista, A.M., E-mail: antoniomarcosbatista@gmail.com [Departamento de Matemática e Estatística, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR (Brazil); Souza, S.L.T. de [Departamento de Física e Matemática, Universidade Federal de São João del Rei, 36420-000, Ouro Branco, MG (Brazil); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, 05315-970, São Paulo, SP (Brazil); Viana, R.L. [Departamento de Física, Universidade Federal do Paraná, 81531-990, Curitiba, PR (Brazil); Sanjuán, M.A.F. [Departamento de Física, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid (Spain)

    2016-04-22

    Highlights: • We consider a situation for which a chaotic transient is present in the dynamics of the two-wave model with damping. • The damping in plasma models can be a way for study a realistic behavior of confinement due the collisional effect. • The escape time as a function of the damping obey a power-law scaling. • We have made a qualitative transport analysis with a simple model that can be useful for more complete models. • We have shown that the pattern of the basin of attraction depends on the damping parameter. - Abstract: We investigate chaotic particle transport in magnetised plasmas with two electrostatic drift waves. Considering dissipation in the drift motion, we verify that the removed KAM surfaces originate periodic attractors with their corresponding basins of attraction. We show that the properties of the basins depend on the dissipation and the space-averaged escape time decays exponentially when the dissipation increases. We find positive finite time Lyapunov exponents in dissipative drift motion, consequently the trajectories exhibit transient chaotic transport. These features indicate how the transient plasma transport depends on the dissipation.

  8. Crustal control of dissipative ocean tides in Enceladus and other icy moons

    Science.gov (United States)

    Beuthe, Mikael

    2016-12-01

    Could tidal dissipation within Enceladus' subsurface ocean account for the observed heat flow? Earthlike models of dynamical tides give no definitive answer because they neglect the influence of the crust. I propose here the first model of dissipative tides in a subsurface ocean, by combining the Laplace Tidal Equations with the membrane approach. For the first time, it is possible to compute tidal dissipation rates within the crust, ocean, and mantle in one go. I show that oceanic dissipation is strongly reduced by the crustal constraint, and thus contributes little to Enceladus' present heat budget. Tidal resonances could have played a role in a forming or freezing ocean less than 100 m deep. The model is general: it applies to all icy satellites with a thin crust and a shallow ocean. Scaling rules relate the resonances and dissipation rate of a subsurface ocean to the ones of a surface ocean. If the ocean has low viscosity, the westward obliquity tide does not move the crust. Therefore, crustal dissipation due to dynamical obliquity tides can differ from the static prediction by up to a factor of two.

  9. 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.

  10. Signatures of a dissipative phase transition in photon correlation measurements

    Science.gov (United States)

    Fink, Thomas; Schade, Anne; Höfling, Sven; Schneider, Christian; Imamoglu, Ataç

    2018-04-01

    Understanding and characterizing phase transitions in driven-dissipative systems constitutes a new frontier for many-body physics1-8. A generic feature of dissipative phase transitions is a vanishing gap in the Liouvillian spectrum9, which leads to long-lived deviations from the steady state as the system is driven towards the transition. Here, we show that photon correlation measurements can be used to characterize the corresponding critical slowing down of non-equilibrium dynamics. We focus on the extensively studied phenomenon of optical bistability in GaAs cavity polaritons10,11, which can be described as a first-order dissipative phase transition12-14. Increasing the excitation strength towards the bistable range results in an increasing photon-bunching signal along with a decay time that is prolonged by more than nine orders of magnitude as compared with that of single polaritons. In the limit of strong polariton interactions leading to pronounced quantum fluctuations, the mean-field bistability threshold is washed out. Nevertheless, the functional form with which the Liouvillian gap closes as the thermodynamic limit is approached provides a signature of the emerging dissipative phase transition. Our results establish photon correlation measurements as an invaluable tool for studying dynamical properties of dissipative phase transitions without requiring phase-sensitive interferometric measurements.

  11. 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...

  12. Dissipative optomechanics in a Michelson-Sagnac interferometer.

    Science.gov (United States)

    Xuereb, André; Schnabel, Roman; Hammerer, Klemens

    2011-11-18

    Dissipative optomechanics studies the coupling of the motion of an optical element to the decay rate of a cavity. We propose and theoretically explore a realization of this system in the optical domain, using a combined Michelson-Sagnac interferometer, which enables a strong and tunable dissipative coupling. Quantum interference in such a setup results in the suppression of the lower motional sideband, leading to strongly enhanced cooling in the non-sideband-resolved regime. With state-of-the-art parameters, ground-state cooling and low-power quantum-limited position transduction are both possible. The possibility of a strong, tunable dissipative coupling opens up a new route towards observation of such fundamental optomechanical effects as nonlinear dynamics. Beyond optomechanics, the suggested method can be readily transferred to other setups involving nonlinear media, atomic ensembles, or single atoms.

  13. Molecular-dynamics simulation of lateral friction in contact-mode atomic force microscopy of alkane films: The role of molecular flexibility

    DEFF Research Database (Denmark)

    Soza, P.; Hansen, Flemming Yssing; Taub, H.

    2011-01-01

    than on a surface of molecules with the long axis perpendicular to the surface, in agreement with experimental results. A major dissipation mechanism is the molecular flexibility as manifested in the torsional motion about the molecules' C-C bonds. The generation of gauche defects as a result...

  14. Interplay of single particle and collective response in molecular dynamics simulation of dusty plasma system

    Science.gov (United States)

    Maity, Srimanta; Das, Amita; Kumar, Sandeep; Tiwari, Sanat Kumar

    2018-04-01

    The collective response of the plasma medium is well known and has been explored extensively in the context of dusty plasma medium. On the other hand, the individual particle response associated with the collisional character giving rise to the dissipative phenomena has not been explored adequately. In this paper, two-dimensional molecular dynamics simulation of dust particles interacting via Yukawa potential has been considered. It has been shown that disturbances induced in a dust crystal elicit both collective and single particle responses. Generation of a few particles moving at speeds considerably higher than acoustic and/or shock speed (excited by the external disturbance) is observed. This is an indication of a single particle response. Furthermore, as these individual energetic particles propagate, the dust crystal is observed to crack along their path. Initially when the energy is high, these particles generate secondary energetic particles by the collisional scattering process. However, ultimately as these particles slow down they excite a collective response in the dust medium at secondary locations in a region which is undisturbed by the primary external disturbance. The condition when the cracking of the crystal stops and collective excitations get initiated has been identified quantitatively. The trailing collective primary disturbances would thus often encounter a disturbed medium with secondary and tertiary collective perturbations, thereby suffering significant modification in its propagation. It is thus clear that there is an interesting interplay (other than mere dissipation) between the single particle and collective response which governs the dynamics of any disturbance introduced in the medium.

  15. Observation of a Dissipation-Induced Classical to Quantum Transition

    Directory of Open Access Journals (Sweden)

    J. Raftery

    2014-09-01

    Full Text Available Here, we report the experimental observation of a dynamical quantum phase transition in a strongly interacting open photonic system. The system studied, comprising a Jaynes-Cummings dimer realized on a superconducting circuit platform, exhibits a dissipation-driven localization transition. Signatures of the transition in the homodyne signal and photon number reveal this transition to be from a regime of classical oscillations into a macroscopically self-trapped state manifesting revivals, a fundamentally quantum phenomenon. This experiment also demonstrates a small-scale realization of a new class of quantum simulator, whose well-controlled coherent and dissipative dynamics is suited to the study of quantum many-body phenomena out of equilibrium.

  16. Non-Markovian dissipative quantum mechanics with stochastic trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Koch, Werner

    2010-09-09

    All fields of physics - be it nuclear, atomic and molecular, solid state, or optical - offer examples of systems which are strongly influenced by the environment of the actual system under investigation. The scope of what is called ''the environment'' may vary, i.e., how far from the system of interest an interaction between the two does persist. Typically, however, it is much larger than the open system itself. Hence, a fully quantum mechanical treatment of the combined system without approximations and without limitations of the type of system is currently out of reach. With the single assumption of the environment to consist of an internally thermalized set of infinitely many harmonic oscillators, the seminal work of Stockburger and Grabert [Chem. Phys., 268:249-256, 2001] introduced an open system description that captures the environmental influence by means of a stochastic driving of the reduced system. The resulting stochastic Liouville-von Neumann equation describes the full non-Markovian dynamics without explicit memory but instead accounts for it implicitly through the correlations of the complex-valued noise forces. The present thesis provides a first application of the Stockburger-Grabert stochastic Liouville-von Neumann equation to the computation of the dynamics of anharmonic, continuous open systems. In particular, it is demonstrated that trajectory based propagators allow for the construction of a numerically stable propagation scheme. With this approach it becomes possible to achieve the tremendous increase of the noise sample count necessary to stochastically converge the results when investigating such systems with continuous variables. After a test against available analytic results for the dissipative harmonic oscillator, the approach is subsequently applied to the analysis of two different realistic, physical systems. As a first example, the dynamics of a dissipative molecular oscillator is investigated. Long time

  17. Dynamical aspects of particle emission in binary dissipative collisions -effects on hot-nuclei formation

    International Nuclear Information System (INIS)

    Eudes, Ph.; Basrak, Z.; Sebille, F.

    1997-01-01

    Characteristics of charged-particle emission in heavy-ion reactions have been studied in the framework of the semiclassical Landau-Vlasov approach for the 40 Ar + 27 Al collisions at 65 MeV/u. The reaction mechanism is dominated by binary dissipative collisions. After an abundant prompt emission coming from the overlapping region between the target and the projectile, two excited nuclei, the quasi-target and the quasi-projectile, emerge from the collision. To shed some light on the role played by dynamical effects, light-charged particle observables, which are currently used as an experimental signature a of hot equilibrated nucleus, have been carefully investigated. (K.A.)

  18. Non-Markovian electron dynamics in nanostructures coupled to dissipative contacts

    Science.gov (United States)

    Novakovic, B.; Knezevic, I.

    2013-02-01

    In quasiballistic semiconductor nanostructures, carrier exchange between the active region and dissipative contacts is the mechanism that governs relaxation. In this paper, we present a theoretical treatment of transient quantum transport in quasiballistic semiconductor nanostructures, which is based on the open system theory and valid on timescales much longer than the characteristic relaxation time in the contacts. The approach relies on a model interaction between the current-limiting active region and the contacts, given in the scattering-state basis. We derive a non-Markovian master equation for the irreversible evolution of the active region's many-body statistical operator by coarse-graining the exact dynamical map over the contact relaxation time. In order to obtain the response quantities of a nanostructure under bias, such as the potential and the charge and current densities, the non-Markovian master equation must be solved numerically together with the Schr\\"{o}dinger, Poisson, and continuity equations. We discuss how to numerically solve this coupled system of equations and illustrate the approach on the example of a silicon nin diode.

  19. Quantum dissipation from power-law memory

    International Nuclear Information System (INIS)

    Tarasov, Vasily E.

    2012-01-01

    A new quantum dissipation model based on memory mechanism is suggested. Dynamics of open and closed quantum systems with power-law memory is considered. The processes with power-law memory are described by using integration and differentiation of non-integer orders, by methods of fractional calculus. An example of quantum oscillator with linear friction and power-law memory is considered. - Highlights: ► A new quantum dissipation model based on memory mechanism is suggested. ► The generalization of Lindblad equation is considered. ► An exact solution of generalized Lindblad equation for quantum oscillator with linear friction and power-law memory is derived.

  20. 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.

  1. A glimpse of fluid turbulence from the molecular scale

    KAUST Repository

    Komatsu, Teruhisa S.

    2014-08-01

    Large-scale molecular dynamics (MD) simulations of freely decaying turbulence in three-dimensional space are reported. Fluid components are defined from the microscopic states by eliminating thermal components from the coarse-grained fields. The energy spectrum of the fluid components is observed to scale reasonably well according to Kolmogorov scaling determined from the energy dissipation rate and the viscosity of the fluid, even though the Kolmogorov length is of the order of the molecular scale. © 2014 The Authors.

  2. 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.

  3. Induced waveform transitions of dissipative solitons

    Science.gov (United States)

    Kochetov, Bogdan A.; Tuz, Vladimir R.

    2018-01-01

    The effect of an externally applied force upon the dynamics of dissipative solitons is analyzed in the framework of the one-dimensional cubic-quintic complex Ginzburg-Landau equation supplemented by a potential term with an explicit coordinate dependence. The potential accounts for the external force manipulations and consists of three symmetrically arranged potential wells whose depth varies along the longitudinal coordinate. It is found out that under an influence of such potential a transition between different soliton waveforms coexisting under the same physical conditions can be achieved. A low-dimensional phase-space analysis is applied in order to demonstrate that by only changing the potential profile, transitions between different soliton waveforms can be performed in a controllable way. In particular, it is shown that by means of a selected potential, stationary dissipative soliton can be transformed into another stationary soliton as well as into periodic, quasi-periodic, and chaotic spatiotemporal dissipative structures.

  4. 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)

  5. 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...

  6. Dissipative phenomena in condensed matter some applications

    CERN Document Server

    Dattagupta, Sushanta

    2004-01-01

    From the field of nonequilibrium statistical physics, this graduate- and research-level volume treats the modeling and characterization of dissipative phenomena. A variety of examples from diverse disciplines like condensed matter physics, materials science, metallurgy, chemical physics etc. are discussed. Dattagupta employs the broad framework of stochastic processes and master equation techniques to obtain models for a wide range of experimentally relevant phenomena such as classical and quantum Brownian motion, spin dynamics, kinetics of phase ordering, relaxation in glasses, dissipative tunneling. It provides a pedagogical exposition of current research material and will be useful to experimentalists, computational physicists and theorists.

  7. Micro- and macro-scale self-organization in a dissipative plasma

    International Nuclear Information System (INIS)

    Skoric, M.M.; Sato, T.; Maluckov, A.; Jovanovic, M.S.

    1998-10-01

    We study a nonlinear three-wave interaction in an open dissipative model of stimulated Raman backscattering in a plasma. A hybrid kinetic-fluid scheme is proposed to include anomalous kinetic dissipation due to electron trapping and plasma wave breaking. We simulate a finite plasma with open boundaries and vary a transport parameter to examine a route to spatio-temporal complexity. An interplay between self-organization at micro (kinetic) and macro (wave/fluid) scales is revealed through quasi-periodic and intermittent evolution of dynamical variables, dissipative structures and related entropy rates. An evidence that entropy rate extrema correspond to structural transitions is found. (author)

  8. 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...

  9. Artificial biomembrane morphology: a dissipative particle dynamics study.

    Science.gov (United States)

    Becton, Matthew; Averett, Rodney; Wang, Xianqiao

    2017-09-18

    Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamics simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a 'net', or at very low densities, a series of disparate 'clumps' similar to the micelles formed by lipids in nature. When the initial lipid density is high, a membrane forms, but due to the large number of lipids, the naturally formed membrane would be larger than the simulation box, leading to 'rippling' behavior as the excess repulsive force of the membrane interior overcomes the bending energy of the membrane. Once the density reaches a certain point however, 'bubbles' appear inside the membrane, reducing the rippling behavior and eventually generating a relatively flat, but thick, structure with micelles of water inside the membrane itself. Our simulations also demonstrate that the interaction parameter between individual lipids plays a significant role in the formation and behavior of lipid membrane assemblies, creating similar structures as the initial lipid density distribution. This work provides a comprehensive approach to the intricacies of lipid membranes, and offers a guideline to design biological or polymeric membranes through self-assembly processes as well as develop novel cellular manipulation and destruction techniques.

  10. 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

  11. 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 ...

  12. 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).

  13. Power injected in dissipative systems and the fluctuation theorem

    Science.gov (United States)

    Aumaître, S.; Fauve, S.; McNamara, S.; Poggi, P.

    We consider three examples of dissipative dynamical systems involving many degrees of freedom, driven far from equilibrium by a constant or time dependent forcing. We study the statistical properties of the injected and dissipated power as well as the fluctuations of the total energy of these systems. The three systems under consideration are: a shell model of turbulence, a gas of hard spheres colliding inelastically and excited by a vibrating piston, and a Burridge-Knopoff spring-block model. Although they involve different types of forcing and dissipation, we show that the statistics of the injected power obey the ``fluctuation theorem" demonstrated in the case of time reversible dissipative systems maintained at constant total energy, or in the case of some stochastic processes. Although this may be only a consequence of the theory of large deviations, this allows a possible definition of ``temperature" for a dissipative system out of equilibrium. We consider how this ``temperature" scales with the energy and the number of degrees of freedom in the different systems under consideration.

  14. Dissipative preparation of entanglement in quantum optical and solid state systems

    DEFF Research Database (Denmark)

    Reiter, Florentin

    superconducting qubits in a circuit QED setup. Combining resonator photon loss, a dissipative process already present in the setup, with an effective two-photon microwave drive, we engineer an effective decay mechanism which prepares a maximally entangled state of two qubits. We find that high fidelities......” and “dissipative state engineering” suggests to use the interaction with the environment to perform quantum information tasks. Here, decay processes are no longer undesirable, but play an integral part in the dynamics. Following this approach, we consider the dissipative preparation of two-particle and multi...

  15. 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...

  16. Decay of energy and suppression of Fermi acceleration in a dissipative driven stadium-like billiard.

    Science.gov (United States)

    Livorati, André L P; Caldas, Iberê L; Leonel, Edson D

    2012-06-01

    The behavior of the average energy for an ensemble of non-interacting particles is studied using scaling arguments in a dissipative time-dependent stadium-like billiard. The dynamics of the system is described by a four dimensional nonlinear mapping. The dissipation is introduced via inelastic collisions between the particles and the moving boundary. For different combinations of initial velocities and damping coefficients, the long time dynamics of the particles leads them to reach different states of final energy and to visit different attractors, which change as the dissipation is varied. The decay of the average energy of the particles, which is observed for a large range of restitution coefficients and different initial velocities, is described using scaling arguments. Since this system exhibits unlimited energy growth in the absence of dissipation, our results for the dissipative case give support to the principle that Fermi acceleration seems not to be a robust phenomenon.

  17. Magnetization dissipation in ferromagnets from scattering theory

    NARCIS (Netherlands)

    Brataas, A.; Tserkovnyak, Y.; Bauer, G.E.W.

    2011-01-01

    The magnetization dynamics of ferromagnets is often formulated in terms of the Landau-Lifshitz-Gilbert (LLG) equation. The reactive part of this equation describes the response of the magnetization in terms of effective fields, whereas the dissipative part is parametrized by the Gilbert damping

  18. Real-Time Observation of Internal Motion within Ultrafast Dissipative Optical Soliton Molecules

    Science.gov (United States)

    Krupa, Katarzyna; Nithyanandan, K.; Andral, Ugo; Tchofo-Dinda, Patrice; Grelu, Philippe

    2017-06-01

    Real-time access to the internal ultrafast dynamics of complex dissipative optical systems opens new explorations of pulse-pulse interactions and dynamic patterns. We present the first direct experimental evidence of the internal motion of a dissipative optical soliton molecule generated in a passively mode-locked erbium-doped fiber laser. We map the internal motion of a soliton pair molecule by using a dispersive Fourier-transform imaging technique, revealing different categories of internal pulsations, including vibrationlike and phase drifting dynamics. Our experiments agree well with numerical predictions and bring insights to the analogy between self-organized states of lights and states of the matter.

  19. Modeling compaction-induced energy dissipation of granular HMX

    Energy Technology Data Exchange (ETDEWEB)

    Gonthier, K.A. [Lamar Univ., Beaumont, TX (US). Dept. of Mechanical Engineering; Menikoff, R.; Son, S.F.; Asay, B.W. [Los Alamos National Lab., NM (US)

    1998-12-31

    A thermodynamically consistent model is developed for the compaction of granular solids. The model is an extension of the single phase limit of two-phase continuum models used to describe Deflagration-to-Detonation Transition (DDT) experiments. The focus is on the energetics and dissipation of the compaction process. Changes in volume fraction are partitioned into reversible and irreversible components. Unlike conventional DDT models, the model is applicable from the quasi-static to dynamic compaction regimes for elastic, plastic, or brittle materials. When applied to the compaction of granular HMX (a brittle material), the model predicts results commensurate with experiments including stress relaxation, hysteresis, and energy dissipation. The model provides a suitable starting point for the development of thermal energy localization sub-scale models based on compaction-induced dissipation.

  20. 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.

  1. 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

  2. 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

  3. Spontaneous Vesicle Self-Assembly: A Mesoscopic View of Membrane Dynamics

    DEFF Research Database (Denmark)

    Shillcock, J. C.

    2012-01-01

    Amphiphilic vesicles are ubiquitous in living cells and industrially interesting as drug delivery vehicles. Vesicle self-assembly proceeds rapidly from nanometer to micrometer length scales and is too fast to image experimentally but too slow for molecular dynamics simulations. Here, we use...... parallel dissipative particle dynamics (DPD) to follow spontaneous vesicle self-assembly for up to 445 mu s with near-molecular resolution. The mean mass and radius of gyration of growing amphiphilic clusters obey power laws with exponents of 0.85 +/- 0.03 and 0.41 +/- 0.02, respectively. We show that DPD...... provides a computational window onto fluid dynamics on scales unreachable by other explicit-solvent simulations....

  4. 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.

  5. 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.

  6. Energetics and efficiency of a molecular motor model

    DEFF Research Database (Denmark)

    C. Fogedby, Hans; Svane, Axel

    2013-01-01

    The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al. (Phys. Lett. 237, 297 (1998)) is analyzed from an analytical point of view. The model which is based on protein friction with a track is described by coupled Langevin equations for the motion in combination...... when incorporating the full motor dynamics, owing to the strong dissipation associated with the motor action....

  7. Relativistic electrodynamics of dissipative elastic media

    International Nuclear Information System (INIS)

    Kranys, M.

    1980-01-01

    A phenomenological general relativistic electrodynamics is proposed for a dissipative elastic solid which is polarizable and magnetizable and whose governing equations form a hyperbolic system. Non-stationary transport equations are proposed for dissipative fluxes (and constitutive equations of electrodynamics) containing new cross-effect terms, as required for compatibility with an entropy principle expressed by a new balance equation (including a new Gibbs equation). The dynamic equations are deduced from the unified Minkowski-Abraham-Eckart energy-momentum tensor. The theory, formed by a set of 29 (reducible to 23) partial differential equations (in special relativity) governing the material behaviour of the system characterized by generalizing the constitutive equations of quasineutral media, together with Maxwell's equations, may be referred to as the electrodynamics of dissipative elastic media (or fluid). The proposed transport laws for polarization and magnetization generalize the well-known Debye law for relaxation and show the influence of shear and bulk viscosity on polarization and magentization. Besides the form of the entropy function, the free energy function in the non-stationary regime is also formulated. (auth)

  8. 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

  9. 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…

  10. Contact stiffness and damping of liquid films in dynamic atomic force microscope

    International Nuclear Information System (INIS)

    Xu, Rong-Guang; Leng, Yongsheng

    2016-01-01

    The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayer distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film.

  11. Contact stiffness and damping of liquid films in dynamic atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Rong-Guang; Leng, Yongsheng, E-mail: leng@gwu.edu [Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052 (United States)

    2016-04-21

    The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayer distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film.

  12. Identification of energy dissipation mechanisms in CNT-reinforced nanocomposites

    International Nuclear Information System (INIS)

    Gardea, Frank; Lagoudas, Dimitris C; Naraghi, Mohammad; Glaz, Bryan; Riddick, Jaret

    2016-01-01

    In this paper we present our recent findings on the mechanisms of energy dissipation in polymer-based nanocomposites obtained through experimental investigations. The matrix of the nanocomposite was polystyrene (PS) which was reinforced with carbon nanotubes (CNTs). To study the mechanical strain energy dissipation of nanocomposites, we measured the ratio of loss to storage modulus for different CNT concentrations and alignments. CNT alignment was achieved via hot-drawing of PS-CNT. In addition, CNT agglomeration was studied via a combination of SEM imaging and Raman scanning. We found that at sufficiently low strains, energy dissipation in composites with high CNT alignment is not a function of applied strain, as no interfacial slip occurs between the CNTs and PS. However, below the interfacial slip strain threshold, damping scales monotonically with CNT content, which indicates the prevalence of CNT-CNT friction dissipation mechanisms within agglomerates. At higher strains, interfacial slip also contributes to energy dissipation. However, the increase in damping with strain, especially when CNT agglomerates are present, does not scale linearly with the effective interface area between CNTs and PS, suggesting a significant contribution of friction between CNTs within agglomerates to energy dissipation at large strains. In addition, for the first time, a comparison between the energy dissipation in randomly oriented and aligned CNT composites was made. It is inferred that matrix plasticity and tearing caused by misorientation of CNTs with the loading direction is a major cause of energy dissipation. The results of our research can be used to design composites with high energy dissipation capability, especially for applications where dynamic loading may compromise structural stability and functionality, such as rotary wing structures and antennas. (paper)

  13. 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

  14. Brownian motion of classical spins: Anomalous dissipation and generalized Langevin equation

    Science.gov (United States)

    Bandyopadhyay, Malay; Jayannavar, A. M.

    2017-10-01

    In this work, we derive the Langevin equation (LE) of a classical spin interacting with a heat bath through momentum variables, starting from the fully dynamical Hamiltonian description. The derived LE with anomalous dissipation is analyzed in detail. The obtained LE is non-Markovian with multiplicative noise terms. The concomitant dissipative terms obey the fluctuation-dissipation theorem. The Markovian limit correctly produces the Kubo and Hashitsume equation. The perturbative treatment of our equations produces the Landau-Lifshitz equation and the Seshadri-Lindenberg equation. Then we derive the Fokker-Planck equation corresponding to LE and the concept of equilibrium probability distribution is analyzed.

  15. 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

  16. 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)

  17. 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.

  18. Traits of estuarine marsh plants affect wave dissipation

    Science.gov (United States)

    Schulte Ostermann, Tilla; Heuner, Maike; Bouma, Tjeerd

    2017-04-01

    Estuarine vegetation can attenuate hydrodynamic forces such as waves or flow velocities and therefore has an important role in natural tidal bank protection. This function depends on the degree of hydrodynamic forces, bank morphology and on plant traits of the dominant species. The traits vary between the species but also between different marsh sites. Biomass, stem density and biomechanical properties are crucial factors that influence the rate of wave dissipation. These properties illustrate the trade-offs a species is facing in such a dynamic habitat and highlight the ability of dominant species such as Bolboschoenus maritimus and Schoenoplectus tabernaemontani to protect the tidal bank. Along the Elbe estuary, traits of dominant marsh plant species were measured on different sites. The sites vary e.g. in their elevation, salt levels and inundation periods. To analyse the role that plant traits can play in wave dissipation, the structure of the vegetation as well as the composition was recorded. Biomechanical tests helped to understand the species traits regarding stem flexibility and to determine the effects of plant traits on wave dynamics and vice versa. On the conference, we will present how plant traits affect the wave dissipation on tidal marshes and why they vary.

  19. Memory effects in nonadiabatic molecular dynamics at metal surfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Schiøtz, Jakob

    2010-01-01

    We study the effect of temporal correlation in a Langevin equation describing nonadiabatic dynamics at metal surfaces. For a harmonic oscillator, the Langevin equation preserves the quantum dynamics exactly and it is demonstrated that memory effects are needed in order to conserve the ground state...... energy of the oscillator. We then compare the result of Langevin dynamics in a harmonic potential with a perturbative master equation approach and show that the Langevin equation gives a better description in the nonperturbative range of high temperatures and large friction. Unlike the master equation......, this approach is readily extended to anharmonic potentials. Using density functional theory, we calculate representative Langevin trajectories for associative desorption of N-2 from Ru(0001) and find that memory effects lower the dissipation of energy. Finally, we propose an ab initio scheme to calculate...

  20. Entanglement generation through local field and quantum dissipation

    International Nuclear Information System (INIS)

    Stockburger, Jürgen T; Schmidt, Rebecca; Ankerhold, Joachim

    2015-01-01

    Entanglement in a Gaussian two-mode system can be generated by local driving if additional non-local features are introduced to the dynamics. We demonstrate that weak to moderate ohmic friction arising from a dissipative environment can enable entanglement generation in a driven system. This synergy of driving and dissipation is highly sensitive to the pulse shape; several simple pulse shapes fail to produce this effect at all or deposit large amounts of energy in the system as a side effect. Complex pulse shapes, determined by optimal control techniques, however, are effective without detrimental side effects. (paper)

  1. Bead-bead interaction parameters in dissipative particle dynamics: Relation to bead-size, solubility parameter, and surface tension

    Science.gov (United States)

    Maiti, Amitesh; McGrother, Simon

    2004-01-01

    Dissipative particle dynamics (DPD) is a mesoscale modeling method for simulating equilibrium and dynamical properties of polymers in solution. The basic idea has been around for several decades in the form of bead-spring models. A few years ago, Groot and Warren [J. Chem. Phys. 107, 4423 (1997)] established an important link between DPD and the Flory-Huggins χ-parameter theory for polymer solutions. We revisit the Groot-Warren theory and investigate the DPD interaction parameters as a function of bead size. In particular, we show a consistent scheme of computing the interfacial tension in a segregated binary mixture. Results for three systems chosen for illustration are in excellent agreement with experimental results. This opens the door for determining DPD interactions using interfacial tension as a fitting parameter.

  2. Fibrous cartilage of human menisci is less shock-absorbing and energy-dissipating than hyaline cartilage.

    Science.gov (United States)

    Gaugler, Mario; Wirz, Dieter; Ronken, Sarah; Hafner, Mirjam; Göpfert, Beat; Friederich, Niklaus F; Elke, Reinhard

    2015-04-01

    To test meniscal mechanical properties such as the dynamic modulus of elasticity E* and the loss angle δ at two loading frequencies ω at different locations of the menisci and compare it to E* and δ of hyaline cartilage in indentation mode with spherical indenters. On nine pairs of human menisci, the dynamic E*-modulus and loss angle δ (as a measure of the energy dissipation) were determined. The measurements were performed at two different strain rates (slow sinusoidal and fast single impact) to show the strain rate dependence of the material. The measurements were compared to previous similar measurements with the same equipment on human hyaline cartilage. The resultant E* at fast indentation (median 1.16 MPa) was significantly higher, and the loss angle was significantly lower (median 10.2°) compared to slow-loading mode's E* and δ (median 0.18 MPa and 16.9°, respectively). Further, significant differences for different locations are shown. On the medial meniscus, the anterior horn shows the highest resultant dynamic modulus. In dynamic measurements with a spherical indenter, the menisci are much softer and less energy-dissipating than hyaline cartilage. Further, the menisci are stiffer and less energy-dissipating in the middle, intermediate part compared to the meniscal base. In compression, the energy dissipation of meniscus cartilage plays a minor role compared to hyaline cartilage. At high impacts, energy dissipation is less than on low impacts, similar to cartilage.

  3. Dissipative preparation of entanglement in optical cavities

    DEFF Research Database (Denmark)

    Kastoryano, Michael James; Reiter, Florentin; Sørensen, Anders Søndberg

    2011-01-01

    We propose a novel scheme for the preparation of a maximally entangled state of two atoms in an optical cavity. Starting from an arbitrary initial state, a singlet state is prepared as the unique fixed point of a dissipative quantum dynamical process. In our scheme, cavity decay is no longer...

  4. 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

  5. An estimate of energy dissipation due to soil-moisture hysteresis

    KAUST Repository

    McNamara, H.

    2014-01-01

    Processes of infiltration, transport, and outflow in unsaturated soil necessarily involve the dissipation of energy through various processes. Accounting for these energetic processes can contribute to modeling hydrological and ecological systems. The well-documented hysteretic relationship between matric potential and moisture content in soil suggests that one such mechanism of energy dissipation is associated with the cycling between wetting and drying processes, but it is challenging to estimate the magnitude of the effect in situ. The Preisach model, a generalization of the Independent Domain model, allows hysteresis effects to be incorporated into dynamical systems of differential equations. Building on earlier work using such systems with field data from the south-west of Ireland, this work estimates the average rate of hysteretic energy dissipation. Through some straightforward assumptions, the magnitude of this rate is found to be of O(10-5) W m-3. Key Points Hysteresis in soil-water dissipates energy The rate of dissipation can be estimated directly from saturation data The rate of heating caused is significant ©2013. American Geophysical Union. All Rights Reserved.

  6. Artifact-free dynamic atomic force microscopy reveals monotonic dissipation for a simple confined liquid

    Science.gov (United States)

    Kaggwa, G. B.; Kilpatrick, J. I.; Sader, J. E.; Jarvis, S. P.

    2008-07-01

    We present definitive interaction measurements of a simple confined liquid (octamethylcyclotetrasiloxane) using artifact-free frequency modulation atomic force microscopy. We use existing theory to decouple the conservative and dissipative components of the interaction, for a known phase offset from resonance (90° phase shift), that has been deliberately introduced into the experiment. Further we show the qualitative influence on the conservative and dissipative components of the interaction of a phase error deliberately introduced into the measurement, highlighting that artifacts, such as oscillatory dissipation, can be readily observed when the phase error is not compensated for in the force analysis.

  7. Kinetic approach to relativistic dissipation

    Science.gov (United States)

    Gabbana, A.; Mendoza, M.; Succi, S.; Tripiccione, R.

    2017-08-01

    Despite a long record of intense effort, the basic mechanisms by which dissipation emerges from the microscopic dynamics of a relativistic fluid still elude complete understanding. In particular, several details must still be finalized in the pathway from kinetic theory to hydrodynamics mainly in the derivation of the values of the transport coefficients. In this paper, we approach the problem by matching data from lattice-kinetic simulations with analytical predictions. Our numerical results provide neat evidence in favor of the Chapman-Enskog [The Mathematical Theory of Non-Uniform Gases, 3rd ed. (Cambridge University Press, Cambridge, U.K., 1970)] procedure as suggested by recent theoretical analyses along with qualitative hints at the basic reasons why the Chapman-Enskog expansion might be better suited than Grad's method [Commun. Pure Appl. Math. 2, 331 (1949), 10.1002/cpa.3160020403] to capture the emergence of dissipative effects in relativistic fluids.

  8. Effects of dissipation and fluctuation in preheating

    International Nuclear Information System (INIS)

    Vartuli, Rodrigo; Ramos, Rudnei de O.

    2006-01-01

    In this paper, we study the effects of dissipation and fluctuation in preheating after inflation. The effective equation of motion for a scalar field χ interacting with lighter fields is derived using the field theoretical method of closed time path due to Schwinger, winch is suitable to study nonequilibrium and time dependent process. In this derivation the emergent equation is intrinsically dissipative and stochastic in nature. The resulting dynamics is then studied both analytically and numerically. The results obtained are then discussed for then relevance for the reheating epoch right after an inflationary phase(preheating) for the case of the evolution of the scalar field χ and its decay into fermion. (author)

  9. Non-dissipative effects in nonequilibrium systems

    CERN Document Server

    Maes, Christian

    2018-01-01

    This book introduces and discusses both the fundamental aspects and the measurability of applications of time-symmetric kinetic quantities, outlining the features that constitute the non-dissipative branch of non-equilibrium physics. These specific features of non-equilibrium dynamics have largely been ignored in standard statistical mechanics texts. This introductory-level book offers novel material that does not take the traditional line of extending standard thermodynamics to the irreversible domain. It shows that although stationary dissipation is essentially equivalent with steady non-equilibrium and ubiquitous in complex phenomena, non-equilibrium is not determined solely by the time-antisymmetric sector of energy-entropy considerations. While this should not be very surprising, this book provides timely, simple reminders of the role of time-symmetric and kinetic aspects in the construction of non-equilibrium statistical mechanics.

  10. Critical behavior in earthquake energy dissipation

    Science.gov (United States)

    Wanliss, James; Muñoz, Víctor; Pastén, Denisse; Toledo, Benjamín; Valdivia, Juan Alejandro

    2017-09-01

    We explore bursty multiscale energy dissipation from earthquakes flanked by latitudes 29° S and 35.5° S, and longitudes 69.501° W and 73.944° W (in the Chilean central zone). Our work compares the predictions of a theory of nonequilibrium phase transitions with nonstandard statistical signatures of earthquake complex scaling behaviors. For temporal scales less than 84 hours, time development of earthquake radiated energy activity follows an algebraic arrangement consistent with estimates from the theory of nonequilibrium phase transitions. There are no characteristic scales for probability distributions of sizes and lifetimes of the activity bursts in the scaling region. The power-law exponents describing the probability distributions suggest that the main energy dissipation takes place due to largest bursts of activity, such as major earthquakes, as opposed to smaller activations which contribute less significantly though they have greater relative occurrence. The results obtained provide statistical evidence that earthquake energy dissipation mechanisms are essentially "scale-free", displaying statistical and dynamical self-similarity. Our results provide some evidence that earthquake radiated energy and directed percolation belong to a similar universality class.

  11. Transient Changes in Molecular Geometries and How to Model Them

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard

    Light-induced chemical processes are accompanied by molecular motion on the femtosecond time scale. Uncovering this dynamical motion is central to understanding the chemical reaction on a fundamental level. This thesis focuses on the aspects of excess excitation energy dissipation via dynamic...... observe how the wide distribution of ground state geometries is responsible for decoherence, and that the solvent cage actually facilitates coherent motion, by blocking the newly discovered vibrational mode. We furthermore observe a non-specific, rotational solvent response to the excitation. The second...

  12. 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

  13. 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.

  14. Dissipative particle dynamics simulation of flow generated by two rotating concentric cylinders: II. Lateral dissipative and random forces

    International Nuclear Information System (INIS)

    Filipovic, N; Haber, S; Kojic, M; Tsuda, A

    2008-01-01

    Traditional DPD methods address dissipative and random forces exerted along the line connecting neighbouring particles. Espanol (1998 Phys. Rev. E 57 2930-48) suggested adding dissipative and random force components in a direction perpendicular to this line. This paper focuses on the advantages and disadvantages of such an addition as compared with the traditional DPD method. Our benchmark system comprises fluid initially at rest occupying the space between two concentric cylinders rotating with various angular velocities. The effect of the lateral force components on the time evolution of the simulated velocity profile was also compared with that of the known analytical solution. The results show that (i) the solution accuracy at steady state has improved and the error has been reduced by at least 30% (in one case by 75%), (ii) the DPD time to reach steady state has been halved, (iii) the CPU time has increased by only 30%, and (iv) no significant differences exist in density and temperature distributions

  15. Robustness of Linear Systems towards Multi-Dissipative Pertubations

    DEFF Research Database (Denmark)

    Thygesen, Uffe Høgsbro; Poulsen, Niels Kjølstad

    1997-01-01

    We consider the question of robust stability of a linear time invariant plant subject to dynamic perturbations, which are dissipative in the sense of Willems with respect to several quadratic supply rates. For instance, parasitic dynamics are often both small gain and passive. We reduce several...... robustness analysis questions to linear matrix inequalities: robust stability, robust H2 performance and robust performance in presence of disturbances with finite signal-to-noise ratios...

  16. Fluctuation and dissipation in nonequilibrium quantum field theory

    International Nuclear Information System (INIS)

    Ramos, Rudnei O.

    1994-01-01

    The nonequilibrium dynamics of a scalar field is studied using perturbation theory and a real time finite temperature formulation. The evolution equation for the scalar field is explicitly obtained, and terms responsible for noise (fluctuations) and dissipation are identified and studied in the high temperature limit. (author)

  17. 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.

  18. Dissipative relativistic hydrodynamics

    International Nuclear Information System (INIS)

    Imshennik, V.S.; Morozov, Yu.I.

    1989-01-01

    Using the comoving reference frame in the general non-inertial case, the relativistic hydrodynamics equations are derived with an account for dissipative effects in the matter. From the entropy production equation, the exact from for the dissipative tensor components is obtained. As a result, the closed system of equations of dissipative relativistic hydrodynamics is obtained in the comoving reference frame as a relativistic generalization of the known Navier-Stokes equations for Lagrange coordinates. Equations of relativistic hydrodynamics with account for dissipative effects in the matter are derived using the assocoated reference system in general non-inertial case. True form of the dissipative tensor components is obtained from entropy production equation. Closed system of equations for dissipative relativistic hydrodynamics is obtained as a result in the assocoated reference system (ARS) - relativistic generalization of well-known Navier-Stokes equations for Lagrange coordinates. Equation system, obtained in this paper for ARS, may be effectively used in numerical models of explosive processes with 10 51 erg energy releases which are characteristic for flashes of supernovae, if white dwarf type compact target suggested as presupernova

  19. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  20. Water Dynamics in the Hydration Shells of Biomolecules

    Science.gov (United States)

    2017-01-01

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

  1. 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)

  2. 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.

  3. 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

  4. 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

  5. Modeling and simulations for molecular scale hydrodynamics of the moving contact line in immiscible two-phase flows

    KAUST Repository

    Qian, Tiezheng

    2009-10-29

    This paper starts with an introduction to the Onsager principle of minimum energy dissipation which governs the optimal paths of deviation and restoration to equilibrium. Then there is a review of the variational approach to moving contact line hydrodynamics. To demonstrate the validity of our continuum hydrodynamic model, numerical results from model calculations and molecular dynamics simulations are presented for immiscible Couette and Poiseuille flows past homogeneous solid surfaces, with remarkable overall agreement. Our continuum model is also used to study the contact line motion on surfaces patterned with stripes of different contact angles (i.e. surfaces of varying wettability). Continuum calculations predict the stick-slip motion for contact lines moving along these patterned surfaces, in quantitative agreement with molecular dynamics simulation results. This periodic motion is tunable through pattern period (geometry) and contrast in wetting property (chemistry). The consequence of stick-slip contact line motion on energy dissipation is discussed. © 2009 IOP Publishing Ltd.

  6. 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...

  7. Natural approach to quantum dissipation

    Science.gov (United States)

    Taj, David; Öttinger, Hans Christian

    2015-12-01

    The dissipative dynamics of a quantum system weakly coupled to one or several reservoirs is usually described in terms of a Lindblad generator. The popularity of this approach is certainly due to the linear character of the latter. However, while such linearity finds justification from an underlying Hamiltonian evolution in some scaling limit, it does not rely on solid physical motivations at small but finite values of the coupling constants, where the generator is typically used for applications. The Markovian quantum master equations we propose are instead supported by very natural thermodynamic arguments. They themselves arise from Markovian master equations for the system and the environment which preserve factorized states and mean energy and generate entropy at a non-negative rate. The dissipative structure is driven by an entropic map, called modular, which introduces nonlinearity. The generated modular dynamical semigroup (MDS) guarantees for the positivity of the time evolved state the correct steady state properties, the positivity of the entropy production, and a positive Onsager matrix with symmetry relations arising from Green-Kubo formulas. We show that the celebrated Davies Lindblad generator, obtained through the Born and the secular approximations, generates a MDS. In doing so we also provide a nonlinear MDS which is supported by a weak coupling argument and is free from the limitations of the Davies generator.

  8. Single-molecule spectroscopy of LHCSR1 protein dynamics identifies two distinct states responsible for multi-timescale photosynthetic photoprotection

    Science.gov (United States)

    Kondo, Toru; Pinnola, Alberta; Chen, Wei Jia; Dall'Osto, Luca; Bassi, Roberto; Schlau-Cohen, Gabriela S.

    2017-08-01

    In oxygenic photosynthesis, light harvesting is regulated to safely dissipate excess energy and prevent the formation of harmful photoproducts. Regulation is known to be necessary for fitness, but the molecular mechanisms are not understood. One challenge has been that ensemble experiments average over active and dissipative behaviours, preventing identification of distinct states. Here, we use single-molecule spectroscopy to uncover the photoprotective states and dynamics of the light-harvesting complex stress-related 1 (LHCSR1) protein, which is responsible for dissipation in green algae and moss. We discover the existence of two dissipative states. We find that one of these states is activated by pH and the other by carotenoid composition, and that distinct protein dynamics regulate these states. Together, these two states enable the organism to respond to two types of intermittency in solar intensity—step changes (clouds and shadows) and ramp changes (sunrise), respectively. Our findings reveal key control mechanisms underlying photoprotective dissipation, with implications for increasing biomass yields and developing robust solar energy devices.

  9. 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

  10. Dissipative dark matter halos: The steady state solution

    Science.gov (United States)

    Foot, R.

    2018-02-01

    Dissipative dark matter, where dark matter particle properties closely resemble familiar baryonic matter, is considered. Mirror dark matter, which arises from an isomorphic hidden sector, is a specific and theoretically constrained scenario. Other possibilities include models with more generic hidden sectors that contain massless dark photons [unbroken U (1 ) gauge interactions]. Such dark matter not only features dissipative cooling processes but also is assumed to have nontrivial heating sourced by ordinary supernovae (facilitated by the kinetic mixing interaction). The dynamics of dissipative dark matter halos around rotationally supported galaxies, influenced by heating as well as cooling processes, can be modeled by fluid equations. For a sufficiently isolated galaxy with a stable star formation rate, the dissipative dark matter halos are expected to evolve to a steady state configuration which is in hydrostatic equilibrium and where heating and cooling rates locally balance. Here, we take into account the major cooling and heating processes, and numerically solve for the steady state solution under the assumptions of spherical symmetry, negligible dark magnetic fields, and that supernova sourced energy is transported to the halo via dark radiation. For the parameters considered, and assumptions made, we were unable to find a physically realistic solution for the constrained case of mirror dark matter halos. Halo cooling generally exceeds heating at realistic halo mass densities. This problem can be rectified in more generic dissipative dark matter models, and we discuss a specific example in some detail.

  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. 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.

  13. 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.)

  14. 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.

  15. Dissipative dynamics with the corrected propagator method. Numerical comparison between fully quantum and mixed quantum/classical simulations

    International Nuclear Information System (INIS)

    Gelman, David; Schwartz, Steven D.

    2010-01-01

    The recently developed quantum-classical method has been applied to the study of dissipative dynamics in multidimensional systems. The method is designed to treat many-body systems consisting of a low dimensional quantum part coupled to a classical bath. Assuming the approximate zeroth order evolution rule, the corrections to the quantum propagator are defined in terms of the total Hamiltonian and the zeroth order propagator. Then the corrections are taken to the classical limit by introducing the frozen Gaussian approximation for the bath degrees of freedom. The evolution of the primary part is governed by the corrected propagator yielding the exact quantum dynamics. The method has been tested on two model systems coupled to a harmonic bath: (i) an anharmonic (Morse) oscillator and (ii) a double-well potential. The simulations have been performed at zero temperature. The results have been compared to the exact quantum simulations using the surrogate Hamiltonian approach.

  16. Molecular-scale noncontact atomic force microscopy contrasts in topography and energy dissipation on c(4x2) superlattice structures of alkanethiol self-assembled monolayers

    OpenAIRE

    Fukuma, Takeshi; Ichii, Takashi; Kobayashi, Kei; Yamada, Hirofumi; Matsushige, Kazumi

    2004-01-01

    Alkanethiol self-assembledmonolayers formed on Au(111) surfaces were investigated by noncontact atomic force microscopy (NC-AFM). Dodecanethiol monolayers prepared at 78 °C were imaged by NC-AFM, which revealed that the film is composed predominantly of two different phases of c(4×2)superlattice structures. The obtained molecular-scale NC-AFM contrasts are discussed in comparison with previously reported scanning tunneling microscopy images. We found that the energy dissipation image exhibits...

  17. Defect-related internal dissipation in mechanical resonators and the study of coupled mechanical systems.

    Energy Technology Data Exchange (ETDEWEB)

    Friedmann, Thomas Aquinas; Czaplewski, David A.; Sullivan, John Patrick; Modine, Normand Arthur; Wendt, Joel Robert; Aslam, Dean (Michigan State University, Lansing, MI); Sepulveda-Alancastro, Nelson (University of Puerto Rico, Mayaguez, PR)

    2007-01-01

    Understanding internal dissipation in resonant mechanical systems at the micro- and nanoscale is of great technological and fundamental interest. Resonant mechanical systems are central to many sensor technologies, and microscale resonators form the basis of a variety of scanning probe microscopies. Furthermore, coupled resonant mechanical systems are of great utility for the study of complex dynamics in systems ranging from biology to electronics to photonics. In this work, we report the detailed experimental study of internal dissipation in micro- and nanomechanical oscillators fabricated from amorphous and crystalline diamond materials, atomistic modeling of dissipation in amorphous, defect-free, and defect-containing crystalline silicon, and experimental work on the properties of one-dimensional and two-dimensional coupled mechanical oscillator arrays. We have identified that internal dissipation in most micro- and nanoscale oscillators is limited by defect relaxation processes, with large differences in the nature of the defects as the local order of the material ranges from amorphous to crystalline. Atomistic simulations also showed a dominant role of defect relaxation processes in controlling internal dissipation. Our studies of one-dimensional and two-dimensional coupled oscillator arrays revealed that it is possible to create mechanical systems that should be ideal for the study of non-linear dynamics and localization.

  18. 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.

  19. 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 ...

  20. A molecular dynamics (MD simulation on tire-aggregate friction

    Directory of Open Access Journals (Sweden)

    Fengyan Sun

    2017-07-01

    Full Text Available The friction between tire and road surface is fundamentally depending on the molecular forces. In this paper, the nanoscale 3D contact model is employed to investigate the tire-aggregate friction mechanism. The tire and aggregate micro-structure are both constructed to evaluate the microscopic performance of tire-aggregate friction influence. Simulation results show for a high velocity, the energy dissipation of sliding on crystal structure is small, which results in a small friction coefficient; temperature will have influences on the friction coefficient, and with the increasing of velocity, the effect will gradually reduce. Keywords: Tire, Aggregate, Friction coefficient, Microscopic mechanism, MD simulation

  1. Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

    Science.gov (United States)

    Klinkusch, Stefan; Tremblay, Jean Christophe

    2016-05-14

    In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

  2. Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields

    Energy Technology Data Exchange (ETDEWEB)

    Klinkusch, Stefan; Tremblay, Jean Christophe [Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany)

    2016-05-14

    In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

  3. Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

    Science.gov (United States)

    Plimpton, Steve

    Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

  4. Electroviscous dissipation in aqueous electrolyte films with overlapping electric double layers

    OpenAIRE

    Liu, Fei; Klaassen, Aram Harold; Zhao, Cunlu; Mugele, Friedrich Gunther; van den Ende, Henricus T.M.

    2018-01-01

    We use dynamic atomic force microscopy (AFM) to investigate the forces involved in squeezing out thin films of aqueous electrolyte between an AFM tip and silica substrates at variable pH and salt concentration. From amplitude and phase of the AFM signal we determine both conservative and dissipative components of the tip sample interaction forces. The measured dissipation is enhanced by up to a factor of 5 at tip–sample separations of ≈ one Debye length compared to the expectations based on c...

  5. 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.

  6. 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.

  7. On the Lagrangian description of dissipative systems

    Science.gov (United States)

    Martínez-Pérez, N. E.; Ramírez, C.

    2018-03-01

    We consider the Lagrangian formulation with duplicated variables of dissipative mechanical systems. The application of Noether theorem leads to physical observable quantities which are not conserved, like energy and angular momentum, and conserved quantities, like the Hamiltonian, that generate symmetry transformations and do not correspond to observables. We show that there are simple relations among the equations satisfied by these two types of quantities. In the case of the damped harmonic oscillator, from the quantities obtained by the Noether theorem follows the algebra of Feshbach and Tikochinsky. Furthermore, if we consider the whole dynamics, the degrees of freedom separate into a physical and an unphysical sector. We analyze several cases, with linear and nonlinear dissipative forces; the physical consistency of the solutions is ensured, observing that the unphysical sector has always the trivial solution.

  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. Variational principles for dissipative waves

    Science.gov (United States)

    Dodin, I. Y.; Ruiz, D. E.

    2016-10-01

    Variational methods are a powerful tool in plasma theory. However, their applications are typically restricted to conservative systems or require doubling of variables, which often contradicts the purpose of the variational approach altogether. We show that these restrictions can be relaxed for some classes of dynamical systems that are of practical interest in plasma physics, particularly including dissipative plasma waves. Applications will be discussed to calculating dispersion relations and modulational dynamics of individual plasma waves and wave ensembles. The work was supported by the NNSA SSAA Program through DOE Research Grant No. DE-NA0002948, by the U.S. DOE through Contract No. DE-AC02-09CH11466, and by the U.S. DOD NDSEG Fellowship through Contract No. 32-CFR-168a.

  10. Dissipative Effects in the Effective Field Theory of Inflation

    Energy Technology Data Exchange (ETDEWEB)

    Lopez Nacir, Diana; /Buenos Aires, CONICET /Buenos Aires U.; Porto, Rafael A.; /Princeton, Inst. Advanced Study /ISCAP, New York /Columbia U.; Senatore, Leonardo; /Stanford U., ITP /SLAC /KIPAC, Menlo Park; Zaldarriaga, Matias; /Princeton, Inst. Advanced Study

    2012-09-14

    We generalize the effective field theory of single clock inflation to include dissipative effects. Working in unitary gauge we couple a set of composite operators, {Omicron}{sub {mu}{nu}}..., in the effective action which is constrained solely by invariance under time-dependent spatial diffeomorphisms. We restrict ourselves to situations where the degrees of freedom responsible for dissipation do not contribute to the density perturbations at late time. The dynamics of the perturbations is then modified by the appearance of 'friction' and noise terms, and assuming certain locality properties for the Green's functions of these composite operators, we show that there is a regime characterized by a large friction term {gamma} >> H in which the {zeta}-correlators are dominated by the noise and the power spectrum can be significantly enhanced. We also compute the three point function <{zeta}{zeta}{zeta}> for a wide class of models and discuss under which circumstances large friction leads to an increased level of non-Gaussianities. In particular, under our assumptions, we show that strong dissipation together with the required non-linear realization of the symmetries implies |f{sub NL}| {approx} {gamma}/c{sub s}{sup 2} H >> 1. As a paradigmatic example we work out a variation of the 'trapped inflation' scenario with local response functions and perform the matching with our effective theory. A detection of the generic type of signatures that result from incorporating dissipative effects during inflation, as we describe here, would teach us about the dynamics of the early universe and also extend the parameter space of inflationary models.

  11. Optimal design of base isolation and energy dissipation system for nuclear power plant structures

    International Nuclear Information System (INIS)

    Zhou Fulin

    1991-01-01

    This paper suggests the method of optimal design of base isolation and energy dissipation system for earthquake resistant nuclear power plant structures. This method is based on dynamic analysis, shaking table tests for a 1/4 scale model, and a great number of low cycle fatigue failure tests for energy dissipating elements. A set of calculation formulas for optimal design of structures with base isolation and energy dissipation system were introduced, which are able to be used in engineering design for earthquake resistant nuclear power plant structures or other kinds of structures. (author)

  12. Energy density of a dissipative polarizable solid by a Lagrangean formalism

    International Nuclear Information System (INIS)

    Englman, R.; Yahalom, A.

    2003-01-01

    A Lagrangean for the dynamics of an electromagnetic field in a dispersive and dissipative material is constructed (adapting some ideas by Bekenstein and Hannay) and an expression for the energy density that is positive is obtained from it. The expression contains extra (sink) degrees of freedom that represent dissipating modes. In simplified cases the sink modes can be eliminated to yield an energy density expression in terms of the electromagnetic fields, the polarization and the magnetization only, but which contains parameters associated with the sink modes. The method of adding extra modes can be used to set up a Lagrangean formalism for dissipative systems in general, such that will reinstate time-translation invariance and will yield a unique energy density

  13. 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

  14. 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

  15. Anelastic tidal dissipation in multi-layer planets

    Science.gov (United States)

    Remus, F.; Mathis, S.; Zahn, J.-P.; Lainey, V.

    2012-09-01

    Earth-like planets have anelastic mantles, whereas giant planets may have anelastic cores. As for the fluid parts of a body, the tidal dissipation of such solid regions, gravitationally perturbed by a companion body, highly depends on its internal friction, and thus on its internal structure. Therefore, modelling this kind of interaction presents a high interest to provide constraints on planets interiors, whose properties are still quite uncertain. Here, we examine the equilibrium tide in the solid part of a planet, taking into account the presence of a fluid envelope. We derive the different Love numbers that describe its deformation and discuss the dependence of the quality factor Q on the chosen anelastic model and the size of the core. Taking plausible values for the anelastic parameters, and discussing the frequency-dependence of the solid dissipation, we show how this mechanism may compete with the dissipation in fluid layers, when applied to Jupiter- and Saturn-like planets. We also discuss the case of the icy giants Uranus and Neptune. Finally, we present the way to implement the results in the equations that describe the dynamical evolution of planetary systems.

  16. Dissipation and fluctuation of quantum fields in expanding universes

    International Nuclear Information System (INIS)

    Morikawa, M.

    1990-01-01

    A stochastic dynamics of a long-wavelength part of a scalar field in an expanding universe is derived by using the influence functional method. Dissipation as well as fluctuation are derived for general parameters: a mass, a coupling to the scalar curvature, and a cutoff scale parameter. A dissipation-fluctuation relation is found with a temperature which is proportional to the Hawking temperature, but system dependent. The method is further applied to an expanding universe with a power law and yields the dispersion which agrees with that obtained by the regularization method. The back reaction to the background de Sitter space itself is also obtained

  17. Universality in driven-dissipative quantum many-body systems

    International Nuclear Information System (INIS)

    Sieberer, L.M.

    2015-01-01

    Recent experimental investigations of condensation phenomena in driven-dissipative quantum many-body systems raise the question of what kind of novel universal behavior can emerge under non-equilibrium conditions. We explore various aspects of universality in this context. Our results are of relevance for a variety of open quantum systems on the interface of quantum optics and condensed matter physics, ranging from exciton-polariton condensates to cold atomic gases. In Part I we characterize the dynamical critical behavior at the Bose-Einstein condensation phase transition in driven open quantum systems in three spatial dimensions. Although thermodynamic equilibrium conditions are emergent at low frequencies, the approach to this thermalized low-frequency regime is described by a critical exponent which is specific to the non-equilibrium transition, and places the latter beyond the standard classification of equilibrium dynamical critical behavior. Our theoretical approach is based on the functional renormalization group within the framework of Keldysh non-equilibrium field theory, which is equivalent to a microscopic description of the open system dynamics in terms of a many-body quantum master equation. Universal behavior in the coherence properties of driven-dissipative condensates in reduced dimensions is investigated in Part II. We show that driven two-dimensional Bose systems cannot exhibit algebraic order as in thermodynamic equilibrium, unless they are sufficiently anisotropic. However, we find evidence that even isotropic systems may have a finite superfluidity fraction. In one-dimensional systems, non-equilibrium conditions are traceable in the behavior of the autocorrelation function. We obtain these results by mapping the long-wavelength condensate dynamics onto the Kardar-Parisi-Zhang equation. In Part III we show that systems in thermodynamic equilibrium have a specific symmetry, which makes them distinct from generic driven open systems. The novel

  18. 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)

  19. 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

  20. Transport phenomena in dissipative heavy-ion collisions: the one-body dissipation approach

    International Nuclear Information System (INIS)

    Feldmeier, H.

    1987-01-01

    The paper reviews dissipative collisions between two atomic nuclei, with the help of the classical description of Brownian movement and the Langevin equation. The 'one-body dissipation model' for dissipative heavy-ion collisions is discussed, and its predictions are compared with measured data. Special attention is paid to the non-equilibrium relation between friction and diffusion. (U.K.)

  1. 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)

  2. Quantum tight-binding chains with dissipative coupling

    International Nuclear Information System (INIS)

    Mogilevtsev, D; Slepyan, G Ya; Garusov, E; Kilin, S Ya; Korolkova, N

    2015-01-01

    We present a one-dimensional tight-binding chain of two-level systems coupled only through common dissipative Markovian reservoirs. This quantum chain can demonstrate anomalous thermodynamic behavior contradicting Fourier law. Population dynamics of individual systems of the chain is polynomial with the order determined by the initial state of the chain. The chain can simulate classically hard problems, such as multi-dimensional random walks. (paper)

  3. 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

  4. 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.

  5. 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.

  6. On local Hamiltonians and dissipative systems

    Energy Technology Data Exchange (ETDEWEB)

    Castagnino, M. [CONICET-Institutos de Fisica Rosario y de Astronomia y Fisica del Espacio Casilla de Correos 67, Sucursal 28, 1428, Buenos Aires (Argentina); Gadella, M. [Facultad de Ciencias Exactas, Ingenieria y Agrimensura UNR, Rosario (Argentina) and Departamento de Fisica Teorica, Facultad de Ciencias c. Real de Burgos, s.n., 47011 Valladolid (Spain)]. E-mail: manuelgadella@yahoo.com.ar; Lara, L.P. [Facultad de Ciencias Exactas, Ingenieria y Agrimensura UNR, Rosario (Argentina)

    2006-11-15

    We study a type of one-dimensional dynamical systems on the corresponding two-dimensional phase space. By using arguments related to the existence of integrating factors for Pfaff equations, we show that some one-dimensional non-Hamiltonian systems like dissipative systems, admit a Hamiltonian description by sectors on the phase plane. This picture is not uniquely defined and is coordinate dependent. A simple example is exhaustively discussed. The method, is not always applicable to systems with higher dimensions.

  7. 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

  8. Non-linear quantum critical dynamics and fluctuation-dissipation ratios far from equilibrium

    Energy Technology Data Exchange (ETDEWEB)

    Zamani, Farzaneh [Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden (Germany); Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Str. 40, 01187 Dresden (Germany); Ribeiro, Pedro [CeFEMA, Instituto Superior Tcnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Russian Quantum Center, Novaya Street 100 A, Skolkovo, Moscow Area, 143025 (Russian Federation); Kirchner, Stefan, E-mail: stefan.kirchner@correlated-matter.com [Center for Correlated Matter, Zhejiang University, Hangzhou, Zhejiang 310058 (China)

    2016-02-15

    Non-thermal correlations of strongly correlated electron systems and the far-from-equilibrium properties of phases of condensed matter have become a topical research area. Here, an overview of the non-linear dynamics found near continuous zero-temperature phase transitions within the context of effective temperatures is presented. In particular, we focus on models of critical Kondo destruction. Such a quantum critical state, where Kondo screening is destroyed in a critical fashion, is realized in a number of rare earth intermetallics. This raises the possibility of experimentally testing for the existence of fluctuation-dissipation relations far from equilibrium in terms of effective temperatures. Finally, we present an analysis of a non-interacting, critical reference system, the pseudogap resonant level model, in terms of effective temperatures and contrast these results with those obtained near interacting quantum critical points. - Highlights: • Critical Kondo destruction explains the unusual properties of quantum critical heavy fermion compounds. • We review the concept of effective temperatures in models of critical Kondo destruction. • We compare effective temperatures found near non-interacting and fully interacting fixed points. • A comparison with non-interacting quantum impurity models is presented.

  9. Dissipative time-dependent quantum transport theory.

    Science.gov (United States)

    Zhang, Yu; Yam, Chi Yung; Chen, GuanHua

    2013-04-28

    A dissipative time-dependent quantum transport theory is developed to treat the transient current through molecular or nanoscopic devices in presence of electron-phonon interaction. The dissipation via phonon is taken into account by introducing a self-energy for the electron-phonon coupling in addition to the self-energy caused by the electrodes. Based on this, a numerical method is proposed. For practical implementation, the lowest order expansion is employed for the weak electron-phonon coupling case and the wide-band limit approximation is adopted for device and electrodes coupling. The corresponding hierarchical equation of motion is derived, which leads to an efficient and accurate time-dependent treatment of inelastic effect on transport for the weak electron-phonon interaction. The resulting method is applied to a one-level model system and a gold wire described by tight-binding model to demonstrate its validity and the importance of electron-phonon interaction for the quantum transport. As it is based on the effective single-electron model, the method can be readily extended to time-dependent density functional theory.

  10. Irreversibility and dissipation in finite-state automata

    International Nuclear Information System (INIS)

    Ganesh, Natesh; Anderson, Neal G.

    2013-01-01

    Irreversibility and dissipation in finite-state automata (FSA) are considered from a physical-information-theoretic perspective. A quantitative measure for the computational irreversibility of finite automata is introduced, and a fundamental lower bound on the average energy dissipated per state transition is obtained and expressed in terms of FSA irreversibility. The irreversibility measure and energy bound are germane to any realization of a deterministic automaton that faithfully registers abstract FSA states in distinguishable states of a physical system coupled to a thermal environment, and that evolves via a sequence of interactions with an external system holding a physical instantiation of a random input string. The central result, which is shown to follow from quantum dynamics and entropic inequalities alone, can be regarded as a generalization of Landauer's Principle applicable to FSAs and tailorable to specified automata. Application to a simple FSA is illustrated.

  11. Velocity and stress autocorrelation decay in isothermal dissipative particle dynamics

    Science.gov (United States)

    Chaudhri, Anuj; Lukes, Jennifer R.

    2010-02-01

    The velocity and stress autocorrelation decay in a dissipative particle dynamics ideal fluid model is analyzed in this paper. The autocorrelation functions are calculated at three different friction parameters and three different time steps using the well-known Groot/Warren algorithm and newer algorithms including self-consistent leap-frog, self-consistent velocity Verlet and Shardlow first and second order integrators. At low friction values, the velocity autocorrelation function decays exponentially at short times, shows slower-than exponential decay at intermediate times, and approaches zero at long times for all five integrators. As friction value increases, the deviation from exponential behavior occurs earlier and is more pronounced. At small time steps, all the integrators give identical decay profiles. As time step increases, there are qualitative and quantitative differences between the integrators. The stress correlation behavior is markedly different for the algorithms. The self-consistent velocity Verlet and the Shardlow algorithms show very similar stress autocorrelation decay with change in friction parameter, whereas the Groot/Warren and leap-frog schemes show variations at higher friction factors. Diffusion coefficients and shear viscosities are calculated using Green-Kubo integration of the velocity and stress autocorrelation functions. The diffusion coefficients match well-known theoretical results at low friction limits. Although the stress autocorrelation function is different for each integrator, fluctuates rapidly, and gives poor statistics for most of the cases, the calculated shear viscosities still fall within range of theoretical predictions and nonequilibrium studies.

  12. Cavity-assisted mesoscopic transport of fermions: Coherent and dissipative dynamics

    Science.gov (United States)

    Hagenmüller, David; Schütz, Stefan; Schachenmayer, Johannes; Genes, Claudiu; Pupillo, Guido

    2018-05-01

    We study the interplay between charge transport and light-matter interactions in a confined geometry by considering an open, mesoscopic chain of two-orbital systems resonantly coupled to a single bosonic mode close to its vacuum state. We introduce and benchmark different methods based on self-consistent solutions of nonequilibrium Green's functions and numerical simulations of the quantum master equation, and derive both analytical and numerical results. It is shown that in the dissipative regime where the cavity photon decay rate is the largest parameter, the light-matter coupling is responsible for a steady-state current enhancement scaling with the cooperativity parameter. We further identify different regimes of interest depending on the ratio between the cavity decay rate and the electronic bandwidth. Considering the situation where the lower band has a vanishing bandwidth, we show that for a high-finesse cavity, the properties of the resonant Bloch state in the upper band are transferred to the lower one, giving rise to a delocalized state along the chain. Conversely, in the dissipative regime with low-cavity quality factors, we find that the current enhancement is due to a collective decay of populations from the upper to the lower band.

  13. 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

  14. 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...

  15. 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.

  16. Dynamical tides in highly eccentric binaries: chaos, dissipation, and quasi-steady state

    Science.gov (United States)

    Vick, Michelle; Lai, Dong

    2018-05-01

    Highly eccentric binary systems appear in many astrophysical contexts, ranging from tidal capture in dense star clusters, precursors of stellar disruption by massive black holes, to high-eccentricity migration of giant planets. In a highly eccentric binary, the tidal potential of one body can excite oscillatory modes in the other during a pericentre passage, resulting in energy exchange between the modes and the binary orbit. These modes exhibit one of three behaviours over multiple passages: low-amplitude oscillations, large-amplitude oscillations corresponding to a resonance between the orbital frequency and the mode frequency, and chaotic growth, with the mode energy reaching a level comparable to the orbital binding energy. We study these phenomena with an iterative map that includes mode dissipation, fully exploring how the mode evolution depends on the orbital and mode properties of the system. The dissipation of mode energy drives the system towards a quasi-steady state, with gradual orbital decay punctuated by resonances. We quantify the quasi-steady state and the long-term evolution of the system. A newly captured star around a black hole can experience significant orbital decay and heating due to the chaotic growth of the mode amplitude and dissipation. A giant planet pushed into a high-eccentricity orbit may experience a similar effect and become a hot or warm Jupiter.

  17. 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)

  18. 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.

  19. 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.

  20. 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....

  1. 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.

  2. Quantum dissipation theory and applications to quantum transport and quantum measurement in mesoscopic systems

    Science.gov (United States)

    Cui, Ping

    The thesis comprises two major themes of quantum statistical dynamics. One is the development of quantum dissipation theory (QDT). It covers the establishment of some basic relations of quantum statistical dynamics, the construction of several nonequivalent complete second-order formulations, and the development of exact QDT. Another is related to the applications of quantum statistical dynamics to a variety of research fields. In particular, unconventional but novel theories of the electron transfer in Debye solvents, quantum transport, and quantum measurement are developed on the basis of QDT formulations. The thesis is organized as follows. In Chapter 1, we present some background knowledge in relation to the aforementioned two themes of this thesis. The key quantity in QDT is the reduced density operator rho(t) ≡ trBrho T(t); i.e., the partial trace of the total system and bath composite rhoT(t) over the bath degrees of freedom. QDT governs the evolution of reduced density operator, where the effects of bath are treated in a quantum statistical manner. In principle, the reduced density operator contains all dynamics information of interest. However, the conventional quantum transport theory is formulated in terms of nonequilibrium Green's function. The newly emerging field of quantum measurement in relation to quantum information and quantum computing does exploit a sort of QDT formalism. Besides the background of the relevant theoretical development, some representative experiments on molecular nanojunctions are also briefly discussed. In chapter 2, we outline some basic (including new) relations that highlight several important issues on QDT. The content includes the background of nonequilibrium quantum statistical mechanics, the general description of the total composite Hamiltonian with stochastic system-bath interaction, a novel parameterization scheme for bath correlation functions, a newly developed exact theory of driven Brownian oscillator (DBO

  3. Theoretical Consolidation of Acoustic Dissipation

    Science.gov (United States)

    Casiano, M. J.; Zoladz, T. F.

    2012-01-01

    In many engineering problems, the effects of dissipation can be extremely important. Dissipation can be represented by several parameters depending on the context and the models that are used. Some examples of dissipation-related parameters are damping ratio, viscosity, resistance, absorption coefficients, pressure drop, or damping rate. This Technical Memorandum (TM) describes the theoretical consolidation of the classic absorption coefficients with several other dissipation parameters including linearized resistance. The primary goal of this TM is to theoretically consolidate the linearized resistance with the absorption coefficient. As a secondary goal, other dissipation relationships are presented.

  4. Low-Dissipation Advection Schemes Designed for Large Eddy Simulations of Hypersonic Propulsion Systems

    Science.gov (United States)

    White, Jeffrey A.; Baurle, Robert A.; Fisher, Travis C.; Quinlan, Jesse R.; Black, William S.

    2012-01-01

    The 2nd-order upwind inviscid flux scheme implemented in the multi-block, structured grid, cell centered, finite volume, high-speed reacting flow code VULCAN has been modified to reduce numerical dissipation. This modification was motivated by the desire to improve the codes ability to perform large eddy simulations. The reduction in dissipation was accomplished through a hybridization of non-dissipative and dissipative discontinuity-capturing advection schemes that reduces numerical dissipation while maintaining the ability to capture shocks. A methodology for constructing hybrid-advection schemes that blends nondissipative fluxes consisting of linear combinations of divergence and product rule forms discretized using 4th-order symmetric operators, with dissipative, 3rd or 4th-order reconstruction based upwind flux schemes was developed and implemented. A series of benchmark problems with increasing spatial and fluid dynamical complexity were utilized to examine the ability of the candidate schemes to resolve and propagate structures typical of turbulent flow, their discontinuity capturing capability and their robustness. A realistic geometry typical of a high-speed propulsion system flowpath was computed using the most promising of the examined schemes and was compared with available experimental data to demonstrate simulation fidelity.

  5. Continuum kinetic methods for analyzing wave physics and distribution function dynamics in the turbulence dissipation challenge

    Science.gov (United States)

    Juno, J.; Hakim, A.; TenBarge, J.; Dorland, W.

    2015-12-01

    We present for the first time results for the turbulence dissipation challenge, with specific focus on the linear wave portion of the challenge, using a variety of continuum kinetic models: hybrid Vlasov-Maxwell, gyrokinetic, and full Vlasov-Maxwell. As one of the goals of the wave problem as it is outlined is to identify how well various models capture linear physics, we compare our results to linear Vlasov and gyrokinetic theory. Preliminary gyrokinetic results match linear theory extremely well due to the geometry of the problem, which eliminates the dominant nonlinearity. With the non-reduced models, we explore how the subdominant nonlinearities manifest and affect the evolution of the turbulence and the energy budget. We also take advantage of employing continuum methods to study the dynamics of the distribution function, with particular emphasis on the full Vlasov results where a basic collision operator has been implemented. As the community prepares for the next stage of the turbulence dissipation challenge, where we hope to do large 3D simulations to inform the next generation of observational missions such as THOR (Turbulence Heating ObserveR), we argue for the consideration of hybrid Vlasov and full Vlasov as candidate models for these critical simulations. With the use of modern numerical algorithms, we demonstrate the competitiveness of our code with traditional particle-in-cell algorithms, with a clear plan for continued improvements and optimizations to further strengthen the code's viability as an option for the next stage of the challenge.

  6. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  7. 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

  8. Monte Carlo-molecular dynamics simulations for two-dimensional magnets

    International Nuclear Information System (INIS)

    Kawabata, C.; takeuchi, M.; Bishop, A.R.

    1985-01-01

    A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

  9. Detachment of semiflexible polymer chains from a substrate: A molecular dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Paturej, J. [Leibniz-Institut of Poslymer Research Dresden, 01069 Dresden (Germany); Institute of Physics, University of Szczecin, Wielkopolska 15, 70451 Szczecin (Poland); Erbas, A. [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Milchev, A. [Institute for Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Rostiashvili, V. G. [Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2014-12-07

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force 〈f〉 vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the 〈f〉-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the 〈f〉-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε{sub s}{sup B}/ε{sub s}{sup A} of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the 〈f〉-D profile whereby the B-spikes vanish when ε{sub s}{sup B}/ε{sub s}{sup A}<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  10. Dissipation in nucleus-nucleus collisions

    International Nuclear Information System (INIS)

    Santanu Pal

    1984-01-01

    This paper deals with the mechanism of one- and two-body dissipations in nucleus-nucleus collisions. The average energy transferred to nuclear excitations is calculated using a time-dependent density matrix approach with lowest-order approximations. Considering the nuclei as Fermi gases, and using a gaussian-type NN interaction as the basic perturbation, simplified expressions are obtained for energy dissipations. These expressions are quite instructive to follow a number of interesting aspects of one- and two-body dissipations. It is theoretically observed that the memory time for the two-body dissipation is significantly smaller than that of one-body dissipation. A threshold-type dependence of the transferred energy on the relative velocity between the two nuclei is also observed. This threshold velocity is found to be related with the intrinsic nucleon kinetic energy for two-body dissipation and with the nuclear size for the one-body case. This observation further suggests that the total dissipated energy is shared between the two nuclei approximately in the ratio of their masses. The physical origin of these observations is also explained. Numerical calculations further illustrate some characteristic features of one- and two-body dissipations. (orig.)

  11. 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.

  12. Molecular dynamics and Monte Carlo calculations in statistical mechanics

    International Nuclear Information System (INIS)

    Wood, W.W.; Erpenbeck, J.J.

    1976-01-01

    Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

  13. Dissipation of Turbulence in the Solar Wind as Measured by Cluster

    Science.gov (United States)

    Goldstein, Melvyn

    2012-01-01

    Turbulence in fluids and plasmas is a scale-dependent process that generates fluctuations towards ever-smaller scales until dissipation occurs. Recent Cluster observations in the solar wind demonstrate the existence of a cascade of magnetic energy from the scale of the proton Larmor radius, where kinetic properties of ions invalidate fluid approximations, down to the electron Larmor radius, where electrons become demagnetized. The cascade is quasi-two-dimensional and has been interpreted as consisting of highly oblique kinetic Alfvenic fluctuations that dissipate near at the electron gyroradius scale via proton and electron Landau damping. Here we investigate for the first time the spatial properties of the turbulence at these scales. We report the presence of thin current sheets and discontinuities with spatial sizes greater than or approximately equal to the proton Larmor radius. These isolated structures may be manifestations of intermittency, and such would localize sites of turbulent dissipation. Studying the relationship between turbulent dissipation, reconnection and intermittency is crucial for understanding the dynamics of laboratory and astrophysical plasmas.

  14. Engineering dissipation with phononic spectral hole burning

    Science.gov (United States)

    Behunin, R. O.; Kharel, P.; Renninger, W. H.; Rakich, P. T.

    2017-03-01

    Optomechanics, nano-electromechanics, and integrated photonics have brought about a renaissance in phononic device physics and technology. Central to this advance are devices and materials supporting ultra-long-lived photonic and phononic excitations that enable novel regimes of classical and quantum dynamics based on tailorable photon-phonon coupling. Silica-based devices have been at the forefront of such innovations for their ability to support optical excitations persisting for nearly 1 billion cycles, and for their low optical nonlinearity. While acoustic phonon modes can persist for a similar number of cycles in crystalline solids at cryogenic temperatures, it has not been possible to achieve such performance in silica, as silica becomes acoustically opaque at low temperatures. We demonstrate that these intrinsic forms of phonon dissipation are greatly reduced (by >90%) by nonlinear saturation using continuous drive fields of disparate frequencies. The result is a form of steady-state phononic spectral hole burning that produces a wideband transparency window with optically generated phonon fields of modest (nW) powers. We developed a simple model that explains both dissipative and dispersive changes produced by phononic saturation. Our studies, conducted in a microscale device, represent an important step towards engineerable phonon dynamics on demand and the use of glasses as low-loss phononic media.

  15. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  16. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  17. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  18. Optimal coherent control of dissipative N-level systems

    International Nuclear Information System (INIS)

    Jirari, H.; Poetz, W.

    2005-01-01

    General optimal coherent control of dissipative N-level systems in the Markovian time regime is formulated within Pointryagin's principle and the Lindblad equation. In the present paper, we study feasibility and limitations of steering of dissipative two-, three-, and four-level systems from a given initial pure or mixed state into a desired final state under the influence of an external electric field. The time evolution of the system is computed within the Lindblad equation and a conjugate gradient method is used to identify optimal control fields. The influence of both field-independent population and polarization decay on achieving the objective is investigated in systematic fashion. It is shown that, for realistic dephasing times, optimum control fields can be identified which drive the system into the target state with very high success rate and in economical fashion, even when starting from a poor initial guess. Furthermore, the optimal fields obtained give insight into the system dynamics. However, if decay rates of the system cannot be subjected to electromagnetic control, the dissipative system cannot be maintained in a specific pure or mixed state, in general

  19. Molecular energy dissipation in nanoscale networks of Dentin Matrix Protein 1 is strongly dependent on ion valence

    Science.gov (United States)

    Adams, J; Fantner, G E; Fisher, L W; Hansma, P K

    2008-01-01

    The fracture resistance of biomineralized tissues such as bone, dentin, and abalone is greatly enhanced through the nanoscale interactions of stiff inorganic mineral components with soft organic adhesive components. A proper understanding of the interactions that occur within the organic component, and between the organic and inorganic components, is therefore critical for a complete understanding of the mechanics of these tissues. In this paper, we use Atomic Force Microscope (AFM) force spectroscopy and dynamic force spectroscopy to explore the effect of ionic interactions within a nanoscale system consisting of networks of Dentin Matrix Protein 1 (DMP1) (a component of both bone and dentin organic matrix), a mica surface, and an AFM tip. We find that DMP1 is capable of dissipating large amounts of energy through an ion-mediated mechanism, and that the effectiveness increases with increasing ion valence. PMID:18843380

  20. Molecular energy dissipation in nanoscale networks of dentin matrix protein 1 is strongly dependent on ion valence

    International Nuclear Information System (INIS)

    Adams, J; Fantner, G E; Hansma, P K; Fisher, L W

    2008-01-01

    The fracture resistance of biomineralized tissues such as bone, dentin, and abalone is greatly enhanced through the nanoscale interactions of stiff inorganic mineral components with soft organic adhesive components. A proper understanding of the interactions that occur within the organic component, and between the organic and inorganic components, is therefore critical for a complete understanding of the mechanics of these tissues. In this paper, we use atomic force microscope (AFM) force spectroscopy and dynamic force spectroscopy to explore the effect of ionic interactions within a nanoscale system consisting of networks of dentin matrix protein 1 (DMP1) (a component of both bone and dentin organic matrix), a mica surface and an AFM tip. We find that DMP1 is capable of dissipating large amounts of energy through an ion-mediated mechanism, and that the effectiveness increases with increasing ion valence

  1. Molecular energy dissipation in nanoscale networks of dentin matrix protein 1 is strongly dependent on ion valence

    Energy Technology Data Exchange (ETDEWEB)

    Adams, J; Fantner, G E; Hansma, P K [Department of Physics, Broida Hall, University of California, Santa Barbara, CA 93106 (United States); Fisher, L W [Craniofacial and Skeletal Diseases Branch, NIDCR, NIH, DHHS, Bethesda, MD 20892 (United States)], E-mail: adams@physics.ucsb.edu, E-mail: fantner@physics.ucsb.edu, E-mail: lfisher@dir.nidcr.nih.gov, E-mail: prasant@physics.ucsb.edu

    2008-09-24

    The fracture resistance of biomineralized tissues such as bone, dentin, and abalone is greatly enhanced through the nanoscale interactions of stiff inorganic mineral components with soft organic adhesive components. A proper understanding of the interactions that occur within the organic component, and between the organic and inorganic components, is therefore critical for a complete understanding of the mechanics of these tissues. In this paper, we use atomic force microscope (AFM) force spectroscopy and dynamic force spectroscopy to explore the effect of ionic interactions within a nanoscale system consisting of networks of dentin matrix protein 1 (DMP1) (a component of both bone and dentin organic matrix), a mica surface and an AFM tip. We find that DMP1 is capable of dissipating large amounts of energy through an ion-mediated mechanism, and that the effectiveness increases with increasing ion valence.

  2. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  3. Designing Biomimetic, Dissipative Material Systems

    Energy Technology Data Exchange (ETDEWEB)

    Balazs, Anna C. [Univ. of Pittsburgh, PA (United States). Chemical Engineering Dept.; Whitesides, George M. [Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology; Brinker, C. Jeffrey [Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Chemical and Nuclear Engineering. Dept. of Chemistry. Dept. of Molecular Genetics and Microbiology. Center for Micro-Engineered Materials; Aranson, Igor S. [UChicago, LLC., Argonne, IL (United States); Chaikin, Paul [New York Univ. (NYU), NY (United States). Dept. of Physics; Dogic, Zvonimir [Brandeis Univ., Waltham, MA (United States). Dept. of Physics; Glotzer, Sharon [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemical Engineering. Dept. of Materials Science and Engineering. Dept. of Macromolecular Science and Engineering Physics; Hammer, Daniel [Univ. of Pennsylvania, Philadelphia, PA (United States). School of Engineering and Applied Science; Irvine, Darrell [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Materials Science and Engineering and Biological Engineering; Little, Steven R. [Univ. of Pittsburgh, PA (United States). Chemical Engineering Dept.; Olvera de la Cruz, Monica [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering; Parikh, Atul N. [Univ. of California, Davis, CA (United States). Dept. of Biomedical Engineering. Dept. of Chemical Engineering and Materials Science; Stupp, Samuel [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering. Dept. of Chemistry. Dept. of Medicine. Dept. of Biomedical Engineering; Szostak, Jack [Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology

    2016-01-21

    Throughout human history, new materials have been the foundation of transformative technologies: from bronze, paper, and ceramics to steel, silicon, and polymers, each material has enabled far-reaching advances. Today, another new class of materials is emerging—one with both the potential to provide radically new functions and to challenge our notion of what constitutes a “material”. These materials would harvest, transduce, or dissipate energy to perform autonomous, dynamic functions that mimic the behaviors of living organisms. Herein, we discuss the challenges and benefits of creating “dissipative” materials that can potentially blur the boundaries between living and non-living matter.

  4. Multi-scale coarse-graining of non-conservative interactions in molecular liquids

    International Nuclear Information System (INIS)

    Izvekov, Sergei; Rice, Betsy M.

    2014-01-01

    A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

  5. Multi-scale coarse-graining of non-conservative interactions in molecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

    2014-03-14

    A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

  6. Dissipative particle dynamics simulations for biological tissues: rheology and competition

    International Nuclear Information System (INIS)

    Basan, Markus; Prost, Jacques; Joanny, Jean-François; Elgeti, Jens

    2011-01-01

    In this work, we model biological tissues using a simple, mechanistic simulation based on dissipative particle dynamics. We investigate the continuum behavior of the simulated tissue and determine its dependence on the properties of the individual cell. Cells in our simulation adhere to each other, expand in volume, divide after reaching a specific size checkpoint and undergo apoptosis at a constant rate, leading to a steady-state homeostatic pressure in the tissue. We measure the dependence of the homeostatic state on the microscopic parameters of our model and show that homeostatic pressure, rather than the unconfined rate of cell division, determines the outcome of tissue competitions. Simulated cell aggregates are cohesive and round up due to the effect of tissue surface tension, which we measure for different tissues. Furthermore, mixtures of different cells unmix according to their adhesive properties. Using a variety of shear and creep simulations, we study tissue rheology by measuring yield stresses, shear viscosities, complex viscosities as well as the loss tangents as a function of model parameters. We find that cell division and apoptosis lead to a vanishing yield stress and fluid-like tissues. The effects of different adhesion strengths and levels of noise on the rheology of the tissue are also measured. In addition, we find that the level of cell division and apoptosis drives the diffusion of cells in the tissue. Finally, we present a method for measuring the compressibility of the tissue and its response to external stress via cell division and apoptosis

  7. Modeling ramp compression experiments using large-scale molecular dynamics simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

    2011-10-01

    Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

  8. Effective temperature and fluctuation-dissipation theorem in athermal granular systems: A review

    International Nuclear Information System (INIS)

    Chen Qiong; Hou Mei-Ying

    2014-01-01

    The definition and the previous measurements of a dynamics-relevant temperature-like quantity in granular media are reviewed for slow and fast particle systems. Especially, the validity of the fluctuation-dissipation theorem in such an athermal system is explored. Experimental evidences for the fluctuation-dissipation theorem relevant effect temperature support the athermal statistical mechanics, which has been widely explored in recent years by physicists. Difficulties encountered in defining temperature or establishing thermodynamics or statistical mechanics in non-equilibrium situations are discussed. (topical review - statistical physics and complex systems)

  9. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp; Tchipev, Nikola

    2012-01-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

  10. Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

    KAUST Repository

    Yoon, Seyoon; Monteiro, Paulo J.M.

    2013-01-01

    The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

  11. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  12. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  13. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  14. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    International Nuclear Information System (INIS)

    Aradi, Balint; Frauenheim, Thomas

    2015-01-01

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

  15. Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

    Science.gov (United States)

    Dizkirici, Ayten; Tekpinar, Mustafa

    2015-03-01

    GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

  16. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

    Science.gov (United States)

    Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

    2015-07-14

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

  17. 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.

  18. 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.

  19. The nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-03-01

    MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

  20. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  1. Dissipative hidden sector dark matter

    Science.gov (United States)

    Foot, R.; Vagnozzi, S.

    2015-01-01

    A simple way of explaining dark matter without modifying known Standard Model physics is to require the existence of a hidden (dark) sector, which interacts with the visible one predominantly via gravity. We consider a hidden sector containing two stable particles charged under an unbroken U (1 )' gauge symmetry, hence featuring dissipative interactions. The massless gauge field associated with this symmetry, the dark photon, can interact via kinetic mixing with the ordinary photon. In fact, such an interaction of strength ε ˜10-9 appears to be necessary in order to explain galactic structure. We calculate the effect of this new physics on big bang nucleosynthesis and its contribution to the relativistic energy density at hydrogen recombination. We then examine the process of dark recombination, during which neutral dark states are formed, which is important for large-scale structure formation. Galactic structure is considered next, focusing on spiral and irregular galaxies. For these galaxies we modeled the dark matter halo (at the current epoch) as a dissipative plasma of dark matter particles, where the energy lost due to dissipation is compensated by the energy produced from ordinary supernovae (the core-collapse energy is transferred to the hidden sector via kinetic mixing induced processes in the supernova core). We find that such a dynamical halo model can reproduce several observed features of disk galaxies, including the cored density profile and the Tully-Fisher relation. We also discuss how elliptical and dwarf spheroidal galaxies could fit into this picture. Finally, these analyses are combined to set bounds on the parameter space of our model, which can serve as a guideline for future experimental searches.

  2. Fractal and chaotic laws on seismic dissipated energy in an energy system of engineering structures

    Science.gov (United States)

    Cui, Yu-Hong; Nie, Yong-An; Yan, Zong-Da; Wu, Guo-You

    1998-09-01

    Fractal and chaotic laws of engineering structures are discussed in this paper, it means that the intrinsic essences and laws on dynamic systems which are made from seismic dissipated energy intensity E d and intensity of seismic dissipated energy moment I e are analyzed. Based on the intrinsic characters of chaotic and fractal dynamic system of E d and I e, three kinds of approximate dynamic models are rebuilt one by one: index autoregressive model, threshold autoregressive model and local-approximate autoregressive model. The innate laws, essences and systematic error of evolutional behavior I e are explained over all, the short-term behavior predictability and long-term behavior probability of which are analyzed in the end. That may be valuable for earthquake-resistant theory and analysis method in practical engineering structures.

  3. Cooperative and submolecular dissipation mechanisms of sliding friction in complex organic systems.

    Science.gov (United States)

    Knorr, Daniel B; Gray, Tomoko O; Overney, René M

    2008-08-21

    Energy dissipation in single asperity sliding friction was directly linked to submolecular modes of mobility by intrinsic friction analysis, involving time-temperature superposition along with thermodynamic stress and reaction rate models. Thereby, polystyrene served as a representative tribological sample for organic and amorphous complex systems. This study reveals the significance of surface and subsurface (alpha-, beta-, and gamma-) relaxational modes, which couple under appropriate external conditions (load, temperature, and rate) with shear induced disturbances, and thus gives rise to material specific frictional dissipation. At low pressures and temperatures below the glass transition point, the phenyl pendant side groups of polystyrene, known for their preferential orientation at the free surface, were noticed to be the primary channel for dissipation of kinetic sliding-energy. While this process was found to be truly enthalpic (activation energy of 8 kcalmol), energy dissipation was shown to possess both enthalpic and cooperative entropic contributions above the loading capacity of the surface phenyl groups (9.9 kcalmol) or above the glass transition. Apparent Arrhenius activation energies of frictional dissipation of 22 and 90 kcalmol, respectively, and cooperative contributions up to 80% were found. As such, this study highlights issues critical to organic lubricant design, i.e., the intrinsic enthalpic activation barriers of mobile linker groups, the evaluation of cooperative mobility phenomena, and critical tribological parameters to access or avoid coupling between shear disturbances and molecular actuators.

  4. State-to-state dynamics of molecular energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  5. Line-shape theory and molecular dynamics in collision-induced light scattering

    International Nuclear Information System (INIS)

    Balucani, U.; Tognetti, V.; Vallauri, R.

    1979-01-01

    Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

  6. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  7. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  8. Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

    Science.gov (United States)

    Hu, Hao; Liu, Haiyan

    2013-05-30

    Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

  9. Inferring energy dissipation from violation of the fluctuation-dissipation theorem

    Science.gov (United States)

    Wang, Shou-Wen

    2018-05-01

    The Harada-Sasa equality elegantly connects the energy dissipation rate of a moving object with its measurable violation of the Fluctuation-Dissipation Theorem (FDT). Although proven for Langevin processes, its validity remains unclear for discrete Markov systems whose forward and backward transition rates respond asymmetrically to external perturbation. A typical example is a motor protein called kinesin. Here we show generally that the FDT violation persists surprisingly in the high-frequency limit due to the asymmetry, resulting in a divergent FDT violation integral and thus a complete breakdown of the Harada-Sasa equality. A renormalized FDT violation integral still well predicts the dissipation rate when each discrete transition produces a small entropy in the environment. Our study also suggests a way to infer this perturbation asymmetry based on the measurable high-frequency-limit FDT violation.

  10. Derivation of exact master equation with stochastic description: dissipative harmonic oscillator.

    Science.gov (United States)

    Li, Haifeng; Shao, Jiushu; Wang, Shikuan

    2011-11-01

    A systematic procedure for deriving the master equation of a dissipative system is reported in the framework of stochastic description. For the Caldeira-Leggett model of the harmonic-oscillator bath, a detailed and elementary derivation of the bath-induced stochastic field is presented. The dynamics of the system is thereby fully described by a stochastic differential equation, and the desired master equation would be acquired with statistical averaging. It is shown that the existence of a closed-form master equation depends on the specificity of the system as well as the feature of the dissipation characterized by the spectral density function. For a dissipative harmonic oscillator it is observed that the correlation between the stochastic field due to the bath and the system can be decoupled, and the master equation naturally results. Such an equation possesses the Lindblad form in which time-dependent coefficients are determined by a set of integral equations. It is proved that the obtained master equation is equivalent to the well-known Hu-Paz-Zhang equation based on the path-integral technique. The procedure is also used to obtain the master equation of a dissipative harmonic oscillator in time-dependent fields.

  11. Ab initio molecular dynamics in a finite homogeneous electric field.

    Science.gov (United States)

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  12. ENERGY DISSIPATION PROCESSES IN SOLAR WIND TURBULENCE

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.; Wei, F. S.; Feng, X. S.; Sun, T. R.; Zuo, P. B. [SIGMA Weather Group, State Key Laboratory for Space Weather, National Space Science Center, Chinese Academy of Sciences, Beijing 100190 (China); Xu, X. J. [Space Science Institute, Macau University of Science and Technology, Macao (China); Zhang, J., E-mail: yw@spaceweather.ac.cn [School of Physics, Astronomy and Computational Sciences, George Mason University, 4400 University Drive, MSN 3F3, Fairfax, Virginia 22030 (United States)

    2015-12-15

    Turbulence is a chaotic flow regime filled by irregular flows. The dissipation of turbulence is a fundamental problem in the realm of physics. Theoretically, dissipation ultimately cannot be achieved without collisions, and so how turbulent kinetic energy is dissipated in the nearly collisionless solar wind is a challenging problem. Wave particle interactions and magnetic reconnection (MR) are two possible dissipation mechanisms, but which mechanism dominates is still a controversial topic. Here we analyze the dissipation region scaling around a solar wind MR region. We find that the MR region shows unique multifractal scaling in the dissipation range, while the ambient solar wind turbulence reveals a monofractal dissipation process for most of the time. These results provide the first observational evidences for intermittent multifractal dissipation region scaling around a MR site, and they also have significant implications for the fundamental energy dissipation process.

  13. Kinetic energy spectra, vertical resolution and dissipation in high-resolution atmospheric simulations.

    Science.gov (United States)

    Skamarock, W. C.

    2017-12-01

    We have performed week-long full-physics simulations with the MPAS global model at 15 km cell spacing using vertical mesh spacings of 800, 400, 200 and 100 meters in the mid-troposphere through the mid-stratosphere. We find that the horizontal kinetic energy spectra in the upper troposphere and stratosphere does not converge with increasing vertical resolution until we reach 200 meter level spacing. Examination of the solutions indicates that significant inertia-gravity waves are not vertically resolved at the lower vertical resolutions. Diagnostics from the simulations indicate that the primary kinetic energy dissipation results from the vertical mixing within the PBL parameterization and from the gravity-wave drag parameterization, with smaller but significant contributions from damping in the vertical transport scheme and from the horizontal filters in the dynamical core. Most of the kinetic energy dissipation in the free atmosphere occurs within breaking mid-latitude baroclinic waves. We will briefly review these results and their implications for atmospheric model configuration and for atmospheric dynamics, specifically that related to the dynamics associated with the mesoscale kinetic energy spectrum.

  14. Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bresme, F.; Armstrong, J.

    2014-01-01

    We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

  15. Dissipative neutrino oscillations in randomly fluctuating matter

    International Nuclear Information System (INIS)

    Benatti, F.; Floreanini, R.

    2005-01-01

    The generalized dynamics describing the propagation of neutrinos in randomly fluctuating media is analyzed: It takes into account matter-induced, decoherence phenomena that go beyond the standard Mikheyev-Smirnov-Wolfenstein (MSW) effect. A widely adopted density fluctuation pattern is found to be physically untenable: A more general model needs to be instead considered, leading to flavor changing effective neutrino-matter interactions. They induce new, dissipative effects that modify the neutrino oscillation pattern in a way amenable to a direct experimental analysis

  16. Dissipative neutrino oscillations in randomly fluctuating matter

    Science.gov (United States)

    Benatti, F.; Floreanini, R.

    2005-01-01

    The generalized dynamics describing the propagation of neutrinos in randomly fluctuating media is analyzed: It takes into account matter-induced, decoherence phenomena that go beyond the standard Mikheyev-Smirnov-Wolfenstein (MSW) effect. A widely adopted density fluctuation pattern is found to be physically untenable: A more general model needs to be instead considered, leading to flavor changing effective neutrino-matter interactions. They induce new, dissipative effects that modify the neutrino oscillation pattern in a way amenable to a direct experimental analysis.

  17. A non-equilibrium phase transition in a dissipative forest model

    International Nuclear Information System (INIS)

    Messer, Joachim A.

    2009-01-01

    The shape of the biostress force for a stressed Lotka-Volterra network is for the first time derived from Lindblad's dissipative dynamics. Numerical solutions for stressed prey-predator systems with limited resources show a threshold. A non-equilibrium phase transition to a phase with ecosystem dying after a few enforced oscillations (waldsterben phase) occurs.

  18. Fermionic molecular dynamics for colliding and decaying nuclei

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    1993-11-01

    Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

  19. Optical spectra and lattice dynamics of molecular crystals

    CERN Document Server

    Zhizhin, GN

    1995-01-01

    The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

  20. A modal approach to modeling spatially distributed vibration energy dissipation.

    Energy Technology Data Exchange (ETDEWEB)

    Segalman, Daniel Joseph

    2010-08-01

    The nonlinear behavior of mechanical joints is a confounding element in modeling the dynamic response of structures. Though there has been some progress in recent years in modeling individual joints, modeling the full structure with myriad frictional interfaces has remained an obstinate challenge. A strategy is suggested for structural dynamics modeling that can account for the combined effect of interface friction distributed spatially about the structure. This approach accommodates the following observations: (1) At small to modest amplitudes, the nonlinearity of jointed structures is manifest primarily in the energy dissipation - visible as vibration damping; (2) Correspondingly, measured vibration modes do not change significantly with amplitude; and (3) Significant coupling among the modes does not appear to result at modest amplitudes. The mathematical approach presented here postulates the preservation of linear modes and invests all the nonlinearity in the evolution of the modal coordinates. The constitutive form selected is one that works well in modeling spatially discrete joints. When compared against a mathematical truth model, the distributed dissipation approximation performs well.

  1. Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

    International Nuclear Information System (INIS)

    De Leeuw, S.W.; Brakkee, M.J.D.

    1990-01-01

    Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

  2. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  3. Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

    Science.gov (United States)

    Cooke, Ben; Schmidler, Scott C

    2008-10-28

    We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

  4. Electroviscous dissipation in aqueous electrolyte films with overlapping electric double layers

    NARCIS (Netherlands)

    Liu, Fei; Klaassen, Aram Harold; Zhao, Cunlu; Mugele, Friedrich Gunther; van den Ende, Henricus T.M.

    2018-01-01

    We use dynamic atomic force microscopy (AFM) to investigate the forces involved in squeezing out thin films of aqueous electrolyte between an AFM tip and silica substrates at variable pH and salt concentration. From amplitude and phase of the AFM signal we determine both conservative and dissipative

  5. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  6. Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

    Energy Technology Data Exchange (ETDEWEB)

    Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

    2017-04-04

    The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

  7. Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

    NARCIS (Netherlands)

    Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

    2007-01-01

    This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

  8. A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

    Science.gov (United States)

    Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

    2017-11-01

    In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space

  9. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  10. Entanglement replication in driven dissipative many-body systems.

    Science.gov (United States)

    Zippilli, S; Paternostro, M; Adesso, G; Illuminati, F

    2013-01-25

    We study the dissipative dynamics of two independent arrays of many-body systems, locally driven by a common entangled field. We show that in the steady state the entanglement of the driving field is reproduced in an arbitrarily large series of inter-array entangled pairs over all distances. Local nonclassical driving thus realizes a scale-free entanglement replication and long-distance entanglement distribution mechanism that has immediate bearing on the implementation of quantum communication networks.

  11. The semi-diurnal cycle of dissipation in a ROFI: model-measurement comparisons

    Science.gov (United States)

    Simpson, John H.; Burchard, Hans; Fisher, Neil R.; Rippeth, Tom P.

    2002-07-01

    The Liverpool Bay Region of Freshwater Influence in the Irish Sea exhibits strong horizontal gradients which interact with the dominant tidal flow. A 25 h series of measurements of the cycle of turbulent dissipation with the FLY dissipation profiler shows a strong asymmetry between ebb and flood which is associated with a cycle of increasing stratification on the ebb and progressive mixing on the flood which results in vertical homogeneity as high water is approached. At this time strong dissipation extends throughout the water column in contrast to the ebb when there is a near shutdown of dissipation in the upper half of the column. The cycle of stratification and dissipation is closely consistent for the two semi-diurnal tidal cycles observed. We have attempted to simulate this situation, which involves a complex suite of processes including tidal straining and mixing, using a version of the k-ɛ closure scheme in a 1-d dynamical model which is forced by a combination of the observed tidal flow and horizontal temperature and salinity gradients. The latter were measured directly at the end of the observational series but, in order to focus on the cycle of dissipation, the correct reproduction of the temperature and salinity cycle can be assured by a nudging procedure which obliges the model temperature and salinity values to track the observations. With or without this procedure, the model gives a reasonable account of the dissipation and its asymmetric behaviour on ebb and flood although nudging improves the timing of peak dissipation in the upper part of the water column near highwater. The model has also been used to examine the ratio of shear production (P/ɛ) and buoyancy inputs to dissipation (B/ɛ). The variation of these quantities over the tidal cycle confirms the important role of convective motions forced by tidal straining near the end of the flood phase of the tide.

  12. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  13. A generalized model for optimal transport of images including dissipation and density modulation

    KAUST Repository

    Maas, Jan; Rumpf, Martin; Schö nlieb, Carola; Simon, Stefan

    2015-01-01

    transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals

  14. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  15. A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

    NARCIS (Netherlands)

    Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

    2010-01-01

    In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

  16. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

    NARCIS (Netherlands)

    van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  17. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

    NARCIS (Netherlands)

    van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  18. Essential equivalence of the general equation for the nonequilibrium reversible-irreversible coupling (GENERIC) and steepest-entropy-ascent models of dissipation for nonequilibrium thermodynamics.

    Science.gov (United States)

    Montefusco, Alberto; Consonni, Francesco; Beretta, Gian Paolo

    2015-04-01

    By reformulating the steepest-entropy-ascent (SEA) dynamical model for nonequilibrium thermodynamics in the mathematical language of differential geometry, we compare it with the primitive formulation of the general equation for the nonequilibrium reversible-irreversible coupling (GENERIC) model and discuss the main technical differences of the two approaches. In both dynamical models the description of dissipation is of the "entropy-gradient" type. SEA focuses only on the dissipative, i.e., entropy generating, component of the time evolution, chooses a sub-Riemannian metric tensor as dissipative structure, and uses the local entropy density field as potential. GENERIC emphasizes the coupling between the dissipative and nondissipative components of the time evolution, chooses two compatible degenerate structures (Poisson and degenerate co-Riemannian), and uses the global energy and entropy functionals as potentials. As an illustration, we rewrite the known GENERIC formulation of the Boltzmann equation in terms of the square root of the distribution function adopted by the SEA formulation. We then provide a formal proof that in more general frameworks, whenever all degeneracies in the GENERIC framework are related to conservation laws, the SEA and GENERIC models of the dissipative component of the dynamics are essentially interchangeable, provided of course they assume the same kinematics. As part of the discussion, we note that equipping the dissipative structure of GENERIC with the Leibniz identity makes it automatically SEA on metric leaves.

  19. Mechanism of nuclear dissipation in fission and heavy-ion reactions

    International Nuclear Information System (INIS)

    Nix, J.R.; Sierk, A.J.

    1986-01-01

    Recent advances in the theoretical understanding of nuclear dissipation at intermediate excitation energies are reviewed, with particular emphasis on a new surface-plus-window mechanism that involves interactions of either one or two nucleons with the moving nuclear surface and also, for dumbbell-like shapes encountered in fission and heavy-ion reactions, the transfer of nucleons through the window separating the two portions of the system. This novel dissipation mechanism provides a unified macroscopic description of such diverse phenomena as widths of isoscalar giant quadrupole and giant octupole resonances, mean fission-fragment kinetic energies and excitation energies, dynamical thresholds for compound-nucleus formation, enhancement in neutron emission prior to fission, and widths of mass and charge distributions in deep-inelastic heavy-ion reactions. 41 refs., 8 figs

  20. Capillary Rise: Validity of the Dynamic Contact Angle Models.

    Science.gov (United States)

    Wu, Pingkeng; Nikolov, Alex D; Wasan, Darsh T

    2017-08-15

    The classical Lucas-Washburn-Rideal (LWR) equation, using the equilibrium contact angle, predicts a faster capillary rise process than experiments in many cases. The major contributor to the faster prediction is believed to be the velocity dependent dynamic contact angle. In this work, we investigated the dynamic contact angle models for their ability to correct the dynamic contact angle effect in the capillary rise process. We conducted capillary rise experiments of various wetting liquids in borosilicate glass capillaries and compared the model predictions with our experimental data. The results show that the LWR equations modified by the molecular kinetic theory and hydrodynamic model provide good predictions on the capillary rise of all the testing liquids with fitting parameters, while the one modified by Joos' empirical equation works for specific liquids, such as silicone oils. The LWR equation modified by molecular self-layering model predicts well the capillary rise of carbon tetrachloride, octamethylcyclotetrasiloxane, and n-alkanes with the molecular diameter or measured solvation force data. The molecular self-layering model modified LWR equation also has good predictions on the capillary rise of silicone oils covering a wide range of bulk viscosities with the same key parameter W(0), which results from the molecular self-layering. The advantage of the molecular self-layering model over the other models reveals the importance of the layered molecularly thin wetting film ahead of the main meniscus in the energy dissipation associated with dynamic contact angle. The analysis of the capillary rise of silicone oils with a wide range of bulk viscosities provides new insights into the capillary dynamics of polymer melts.

  1. Diffusion in randomly perturbed dissipative dynamics

    Science.gov (United States)

    Rodrigues, Christian S.; Chechkin, Aleksei V.; de Moura, Alessandro P. S.; Grebogi, Celso; Klages, Rainer

    2014-11-01

    Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no longer invariant and there is the possibility of transport among them. Here we introduce a basic theoretical setting which enables us to study this hopping process from the perspective of anomalous transport using the concept of a random dynamical system with holes. We apply it to a simple model by investigating the role of hyperbolicity for the transport among basins. We show numerically that our system exhibits non-Gaussian position distributions, power-law escape times, and subdiffusion. Our simulation results are reproduced consistently from stochastic continuous time random walk theory.

  2. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  3. Dissipation and oscillatory solvation forces in confined liquids studied by small amplitude atomic force spectroscopy

    NARCIS (Netherlands)

    de Beer, Sissi; van den Ende, Henricus T.M.; Mugele, Friedrich

    2010-01-01

    We determine conservative and dissipative tip–sample interaction forces from the amplitude and phase response of acoustically driven atomic force microscope (AFM) cantilevers using a non-polar model fluid (octamethylcyclotetrasiloxane, which displays strong molecular layering) and atomically flat

  4. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  5. Molecular dynamics simulation of displacement cascades in iron-alpha

    International Nuclear Information System (INIS)

    Vascon, R.

    1997-01-01

    Radiation damage by neutrons or ions in bcc iron has been investigated by molecular dynamics simulations using an embedded atom type many-body potential (EAM). Displacement cascades with energies of 1 to 30 keV were generated in the microcanonical system where the number of atoms (up to 1.5 million) is chosen high enough to compensate the fact that the dissipation of energy is not taken into account in our model. The defect number at the end of cascade lifetime was found to be 60 percent of the NRT standard value. This tendency is in good agreement with experimental data. However, compared with other simulations in iron, we found significant differences in the defect production and distribution. The comparison with results obtained form simulations of cascades in other metals, leads on the one hand to a higher value of the defect number in bcc iron than in fcc metals like copper or nickel, and on the other hand to a ratio, between the number of replacements and the number of defects, lower in iron ( 100). We observed the transient melting of the core of the cascade during simulations. We showed that a higher value of the initial iron crystal temperature, as the mass difference between the components of an artificial binary alloy Fe-X(X=Al,Sb,Au,U) both produce a 'cascade effect': a decrease of the number of defects and an increase of the number of replacements. We also showed up the quasi-channeling of some atoms in high energy cascades. They are at the origin of sub-cascades formation; as a result they induce an opposite effect to the 'cascade effect'. (author)

  6. Implementation of surface hopping molecular dynamics using semiempirical methods

    International Nuclear Information System (INIS)

    Fabiano, E.; Keal, T.W.; Thiel, W.

    2008-01-01

    A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

  7. Investigation of the dynamics of dissipative U+Au collisions with δ-electron spectroscopy

    International Nuclear Information System (INIS)

    Stroth, J.; Dahlinger, M.; Konen, W.; Stiebing, K.

    1997-01-01

    δ-electron emission in elastic and dissipative collisions of U+Au at E/A=8.65 MeV has been investigated. The velocity vectors of the reaction products were measured in coincidence with electrons of energies up to 3.2 MeV. The δ-electron yield measured for elastic collisions is in good agreement with coupled-channel calculations. The δ-electron spectra of dissipative reactions show a clear dependence on the violence of the collision, i.e. the total kinetic energy loss (TKEL). The shape of the spectra are analysed with an atomic model by a fitting procedure using phenomenological trajectories. The results indicate an increasing contact time of the united system with increasing total kinetic energy loss reaching 1.16(4) x 10 -21 s at left angle TKEL right angle =375 MeV. (orig.). With 2 figs

  8. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  9. Molecular dynamics coupled with a virtual system for effective conformational sampling.

    Science.gov (United States)

    Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

    2018-07-15

    An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  10. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

  11. Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems.

    Science.gov (United States)

    Ge, Hao; Qian, Hong

    2013-06-01

    Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further

  12. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  13. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  14. Molecular dynamics simulation of self-diffusion coefficients for liquid metals

    International Nuclear Information System (INIS)

    Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

    2013-01-01

    The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)

  15. Electrostatic shock structures in dissipative multi-ion dusty plasmas

    Science.gov (United States)

    Elkamash, I. S.; Kourakis, I.

    2018-06-01

    A comprehensive analytical model is introduced for shock excitations in dusty bi-ion plasma mixtures, taking into account collisionality and kinematic (fluid) viscosity. A multicomponent plasma configuration is considered, consisting of positive ions, negative ions, electrons, and a massive charged component in the background (dust). The ionic dynamical scale is focused upon; thus, electrons are assumed to be thermalized, while the dust is stationary. A dissipative hybrid Korteweg-de Vries/Burgers equation is derived. An analytical solution is obtained, in the form of a shock structure (a step-shaped function for the electrostatic potential, or an electric field pulse) whose maximum amplitude in the far downstream region decays in time. The effect of relevant plasma configuration parameters, in addition to dissipation, is investigated. Our work extends earlier studies of ion-acoustic type shock waves in pure (two-component) bi-ion plasma mixtures.

  16. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

  17. Catalysis and communication in dynamic molecular networks

    NARCIS (Netherlands)

    Fanlo Virgos, Hugo

    2015-01-01

    The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

  18. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  19. 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.

  20. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  1. Hyperbolic theory of relativistic conformal dissipative fluids

    Science.gov (United States)

    Lehner, Luis; Reula, Oscar A.; Rubio, Marcelo E.

    2018-01-01

    We develop a complete description of the class of conformal relativistic dissipative fluids of divergence form, following the formalism described in [R. Geroch and L. Lindblom, Phys. Rev. D 41, 1855 (1990), 10.1103/PhysRevD.41.1855, S. Pennisi, Some considerations on a non linear approach to extended thermodynamics and in Proceedings of Symposium of Kinetic Theory and Extended Thermodynamics, Bologna, 1987.]. This type of theory is fully described in terms of evolution variables whose dynamics are governed by total divergence-type conservation laws. Specifically, we give a characterization of the whole family of conformal fluids in terms of a single master scalar function defined up to second-order corrections in dissipative effects, which we explicitly find in general form. This allows us to identify the equilibrium states of the theory and derive constitutive relations and a Fourier-like law for the corresponding first-order theory heat flux. Finally, we show that among this class of theories—and near equilibrium configurations—there exist symmetric hyperbolic ones, implying that for them one can define well-posed initial value problems.

  2. Laser Controlled Molecular Orientation Dynamics

    International Nuclear Information System (INIS)

    Atabek, O.

    2004-01-01

    Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

  3. Analysis of microstructure-dependent shock dissipation and hot-spot formation in granular metalized explosive

    Science.gov (United States)

    Chakravarthy, Sunada; Gonthier, Keith A.

    2016-07-01

    Variations in the microstructure of granular explosives (i.e., particle packing density, size, shape, and composition) can affect their shock sensitivity by altering thermomechanical fields at the particle-scale during pore collapse within shocks. If the deformation rate is fast, hot-spots can form, ignite, and interact, resulting in burn at the macro-scale. In this study, a two-dimensional finite and discrete element technique is used to simulate and examine shock-induced dissipation and hot-spot formation within low density explosives (68%-84% theoretical maximum density (TMD)) consisting of large ensembles of HMX (C4H8N8O8) and aluminum (Al) particles (size ˜ 60 -360 μm). Emphasis is placed on identifying how the inclusion of Al influences effective shock dissipation and hot-spot fields relative to equivalent ensembles of neat/pure HMX for shocks that are sufficiently strong to eliminate porosity. Spatially distributed hot-spot fields are characterized by their number density and area fraction enabling their dynamics to be described in terms of nucleation, growth, and agglomeration-dominated phases with increasing shock strength. For fixed shock particle speed, predictions indicate that decreasing packing density enhances shock dissipation and hot-spot formation, and that the inclusion of Al increases dissipation relative to neat HMX by pressure enhanced compaction resulting in fewer but larger HMX hot-spots. Ensembles having bimodal particle sizes are shown to significantly affect hot-spot dynamics by altering the spatial distribution of hot-spots behind shocks.

  4. Molecular dynamics simulations of the effect of waviness and agglomeration of CNTs on interface strength of thermoset nanocomposites.

    Science.gov (United States)

    Alian, A R; Meguid, S A

    2017-02-08

    Most existing molecular dynamics simulations in nanoreinforced composites assume carbon nanotubes (CNTs) to be straight and uniformly dispersed within thermoplastics. In reality, however, CNTs are typically curved, agglomerated and aggregated as a result of van der Waal interactions and electrostatic forces. In this paper, we account for both curvature and agglomeration of CNTs in extensive molecular dynamic (MD) simulations. The purpose of these simulations is to evaluate the influence of waviness and agglomeration of these curved and agglomerated CNTs on the interfacial strength of thermoset nanocomposite and upon their load transfer capability. Two aspects of the work were accordingly examined. In the first, realistic carbon nanotubes (CNTs) of the same length but varied curvatures were embedded in thermoset polymer composites and simulations of pull-out tests were conducted to evaluate the corresponding interfacial shear strength (ISS). In the second, the effect of the agglomerate size upon the ISS was determined using bundles of CNTs of different diameters. The results of our MD simulations revealed the following. The pull-out force of the curved CNTs is significantly higher than its straight counterpart and increases further with the increase in the waviness of the CNTs. This is attributed to the added pull-out energy dissipated in straightening the CNTs during the pull-out process. It also reveals that agglomeration of CNTs leads to a reduction in the ISS and poor load transferability, and that this reduction is governed by the size of the agglomerate. The simulation results were also used to develop a generalized relation for the ISS that takes into consideration the effect of waviness and agglomeration of CNTs of CNT-polymer composites.

  5. 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

  6. Nanoscale thermal imaging of dissipation in quantum systems and in encapsulated graphene

    Science.gov (United States)

    Halbertal, Dorri

    Energy dissipation is a fundamental process governing the dynamics of physical systems. In condensed matter physics, in particular, scattering mechanisms, loss of quantum information, or breakdown of topological protection are deeply rooted in the intricate details of how and where the dissipation occurs. Despite its vital importance the microscopic behavior of a system is usually not formulated in terms of dissipation because the latter is not a readily measureable quantity on the microscale. While the motivation is clear, existing thermal imaging methods lack the necessary sensitivity and are unsuitable for low temperature operation required for the study of quantum systems. We developed a superconducting quantum interference nano thermometer device with sub 50 nm diameter that resides at the apex of a sharp pipette and provides scanning cryogenic thermal sensing with four orders of magnitude improved thermal sensitivity of below 1 uK/sqrtHz. The noncontact noninvasive thermometry allows thermal imaging of very low nanoscale energy dissipation down to the fundamental Landauer limitý of 40 fW for continuous readout of a single qubit at 1 GHz at 4.2 K. These advances enable observation of dissipation due to single electron charging of individual quantum dots in carbon nanotubes, opening the door to direct imaging of nanoscale dissipation processes in quantum matter. In this talk I will describe the technique and present a study of hBN encapsulated graphene which reveals a novel dissipation mechanism due to atomic-scale resonant localized states at the edges of graphene. These results provide a direct valuable glimpse into the electron thermalization process in systems with weak electron-phonon interactions. Funded by European Research Council (ERC) under the European Union's Horizon 2020 programme (Grant No. 655416), Minerva Foundation with funding from the Federal German Ministry of Education and Research, Rosa and Emilio Segré Research Award, and the MISTI.

  7. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  8. The 2011 Dynamics of Molecular Collisions Conference

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [JILA, NIST

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  9. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  10. Dynamical quenching of tunneling in molecular magnets

    International Nuclear Information System (INIS)

    José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

    2015-01-01

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

  11. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

    2015-12-15

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

  12. Perturbative Field-Theoretical Renormalization Group Approach to Driven-Dissipative Bose-Einstein Criticality

    Directory of Open Access Journals (Sweden)

    Uwe C. Täuber

    2014-04-01

    Full Text Available The universal critical behavior of the driven-dissipative nonequilibrium Bose-Einstein condensation transition is investigated employing the field-theoretical renormalization group method. Such criticality may be realized in broad ranges of driven open systems on the interface of quantum optics and many-body physics, from exciton-polariton condensates to cold atomic gases. The starting point is a noisy and dissipative Gross-Pitaevski equation corresponding to a complex-valued Landau-Ginzburg functional, which captures the near critical nonequilibrium dynamics, and generalizes model A for classical relaxational dynamics with nonconserved order parameter. We confirm and further develop the physical picture previously established by means of a functional renormalization group study of this system. Complementing this earlier numerical analysis, we analytically compute the static and dynamical critical exponents at the condensation transition to lowest nontrivial order in the dimensional ε expansion about the upper critical dimension d_{c}=4 and establish the emergence of a novel universal scaling exponent associated with the nonequilibrium drive. We also discuss the corresponding situation for a conserved order parameter field, i.e., (subdiffusive model B with complex coefficients.

  13. Dynamical critical phenomena in driven-dissipative systems.

    Science.gov (United States)

    Sieberer, L M; Huber, S D; Altman, E; Diehl, S

    2013-05-10

    We explore the nature of the Bose condensation transition in driven open quantum systems, such as exciton-polariton condensates. Using a functional renormalization group approach formulated in the Keldysh framework, we characterize the dynamical critical behavior that governs decoherence and an effective thermalization of the low frequency dynamics. We identify a critical exponent special to the driven system, showing that it defines a new dynamical universality class. Hence critical points in driven systems lie beyond the standard classification of equilibrium dynamical phase transitions. We show how the new critical exponent can be probed in experiments with driven cold atomic systems and exciton-polariton condensates.

  14. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  15. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik; Szepessy, Anders

    2010-01-01

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  16. CH+ and SH+ in the diffuse interstellar medium: Tracers of turbulent dissipation

    International Nuclear Information System (INIS)

    Edith, Falgarone; Maryvonne, Gerin; Massimo, De Luca; Benjamin, Godard

    2015-01-01

    Absorption spectroscopy performed with Herschel/HIFI against the dust continuum emission of bright galactic star-forming regions has allowed the detection of the ground-state transitions of several hydride cations, CH + , OH + , H 2 O + , and SH + in the intervening diffuse medium. These hydrides, that need H 2 to form but are also destroyed by H 2 , appear to be most sensitive tracers of a poorly known component of the interstellar medium (ISM): molecular gas weakly shielded from UV radiation. Among them, because their formation routes are so highly endoenergic, the CH + and SH + cations are proposed to be specific tracers of turbulent dissipation occurring in diffuse gas. Their elusive origin in the diffuse ISM is therefore much more than a chemical riddle: it is rooted in the physics of the diffuse ISM, its turbulent dissipation rate and connects with the far broader issue of galaxy evolution. The Herschel/HIFI observations of CH + and SH + are compared with the predictions of chemical models that include the non-equilibrium effects of turbulent dissipation

  17. Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

    Science.gov (United States)

    Tsukanov, A. A.; Psakhie, S. G.

    2017-12-01

    The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

  18. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-01-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

  19. The use of molecular dynamics for the thermodynamic properties of simple and transition metals

    International Nuclear Information System (INIS)

    Straub, G.K.

    1987-04-01

    The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated

  20. Tully-Fisher relation, galactic rotation curves and dissipative mirror dark matter

    Energy Technology Data Exchange (ETDEWEB)

    Foot, R., E-mail: rfoot@unimelb.edu.au [ARC Centre of Excellence for Particle Physics at the Terascale, School of Physics, University of Melbourne, Victoria 3010 Australia (Australia)

    2014-12-01

    If dark matter is dissipative then the distribution of dark matter within galactic halos can be governed by dissipation, heating and hydrostatic equilibrium. Previous work has shown that a specific model, in the framework of mirror dark matter, can explain several empirical galactic scaling relations. It is shown here that this dynamical halo model implies a quasi-isothermal dark matter density, ρ(r) ≅ ρ{sub 0}r{sub 0}{sup 2}/(r{sup 2}+r{sub 0}{sup 2}), where the core radius, r{sub 0}, scales with disk scale length, r{sub D}, via r{sub 0}/kpc ≈ 1.4(r{sub D}/kpc). Additionally, the product ρ{sub 0}r{sub 0} is roughly constant, i.e. independent of galaxy size (the constant is set by the parameters of the model). The derived dark matter density profile implies that the galactic rotation velocity satisfies the Tully-Fisher relation, L{sub B}∝v{sup 3}{sub max}, where v{sub max} is the maximal rotational velocity. Examples of rotation curves resulting from this dynamics are given.

  1. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

    Energy Technology Data Exchange (ETDEWEB)

    Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  2. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  3. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  4. Tracking Dissipation Reduction, Externalities, Stability and Sustainability for Environmental Management of New Orleans

    Science.gov (United States)

    McNamara, D.; Werner, B. T.

    2014-12-01

    Sustainability requires stability, but in promoting economic development, modern economies and political systems reduce stabilizing dissipation by facilitating use and management of the environment through engineered mitigation of disturbances, which externalizes dissipation over the short to medium term. To quantitatively investigate the relationship between a range of environmental management approaches and sustainability, and the implications for Earth's future, we track the impact of management strategies on dissipation within the system and its externalities in a numerical model for the coupled economic, political/management and flooding dynamics of New Orleans. The model simulates river floods, hurricane storm-surge-induced floods, subsidence, and agent-based market interactions leading to development of port services, hotels, homes and labor relations. Flood protection decisions for levee construction based on the baseline case of cost-benefit analyses designed to prevent short-term economic loss from future floods qualitatively reproduce historical expansion of New Orleans and increases in levee height. Alternative management strategies explored include majority voting, consensus-based decision-making, and variations in discounting of costs and benefits. Enhanced dissipation is measured relative to optimal economic development without floods. The focus of modern economies on commodification is exploited to track dissipation as a scalar representing value or power, but this approach might not be applicable to more complicated traditional/indigenous cultures or cultures of resistance. For the baseline case, short-to-medium-term reductions in dissipation destabilize the coupled system, resulting in episodic bursts of externalized dissipation during flooding. Comparisons of results for a range of management options and generalizations of this approach for alternative cultural systems will be discussed.

  5. Double-beam optical method and apparatus for measuring thermal diffusivity and other molecular dynamic processes in utilizing the transient thermal lens effect

    International Nuclear Information System (INIS)

    Gupta, A.; Hong, S.; Moacanin, J.

    1981-01-01

    A method and apparatus for measuring thermal diffusivity and molecular relaxation processes in a sample material utilizing two light beams, one being a pulsed laser light beam for forming a thermal lens in the sample material, and the other being a relatively low power probe light beam for measuring changes in the refractive index of the sample material during formation and dissipation of the thermal lens. More specifically, a sample material is irradiated by relatively high power, short pulses from a dye laser. Energy from the pulses is absorbed by the sample material, thereby forming a thermal lens in the area of absorption. The pulse repetition rate is chosen so that the thermal lens is substantially dissipated by the time the next pulse reaches the sample material. A probe light beam, which in a specific embodiment is a relatively low power, continuous wave (Cw) laser beam, irradiates the thermal lens formed in the sample material. The intensity characteristics of the probe light beam subsequent to irradiation of the thermal lens is related to changes in the refractive index of the sample material as the thermal lens is formed and dissipated. A plot of the changes in refractive index as a function of time during formation of the thermal lens as reflected by changes in intensity of the probe beam, provides a curve related to molecular relaxation characteristics of the material, and a plot during dissipation of the thermal lens provides a curve related to the thermal diffusivity of the sample material

  6. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    International Nuclear Information System (INIS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

  7. Topology of a dissipative spin: Dynamical Chern number, bath-induced nonadiabaticity, and a quantum dynamo effect

    Science.gov (United States)

    Henriet, Loïc; Sclocchi, Antonio; Orth, Peter P.; Le Hur, Karyn

    2017-02-01

    We analyze the topological deformations of the ground state manifold of a quantum spin-1/2 in a magnetic field H =H (sinθ cosϕ ,sinθ sinϕ ,cosθ ) induced by a coupling to an ohmic quantum dissipative environment at zero temperature. From Bethe ansatz results and a variational approach, we confirm that the Chern number associated with the geometry of the reduced spin ground state manifold is preserved in the delocalized phase for α <1 . We report a divergence of the Berry curvature at αc=1 for magnetic fields aligned along the equator θ =π /2 . This divergence is caused by the complete quenching of the transverse magnetic field by the bath associated with a gap closing that occurs at the localization Kosterlitz-Thouless quantum phase transition in this model. Recent experiments in quantum circuits have engineered nonequilibrium protocols to access topological properties from a measurement of a dynamical Chern number defined via the out-of-equilibrium spin expectation values. Applying a numerically exact stochastic Schrödinger approach we find that, for a fixed field sweep velocity θ (t )=v t , the bath induces a crossover from (quasi)adiabatic to nonadiabatic dynamical behavior when the spin bath coupling α increases. We also investigate the particular regime H /ωc≪v /H ≪1 with large bath cutoff frequency ωc, where the dynamical Chern number vanishes already at α =1 /2 . In this regime, the mapping to an interacting resonance level model enables us to analytically describe the behavior of the dynamical Chern number in the vicinity of α =1 /2 . We further provide an intuitive physical explanation of the bath-induced breakdown of adiabaticity in analogy to the Faraday effect in electromagnetism. We demonstrate that the driving of the spin leads to the production of a large number of bosonic excitations in the bath, which strongly affect the spin dynamics. Finally, we quantify the spin-bath entanglement and formulate an analogy with an effective

  8. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  9. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  10. Synthesis of dexterity measure of mechanisms by evolution of dissipative system

    Directory of Open Access Journals (Sweden)

    Grešl M.

    2007-11-01

    Full Text Available The paper deals with the new approach of solving traditional kinematical synthesis of mechanisms. The kinematical synthesis is reformulated as nonlinear dynamical problem. All searched parameters of the mechanism are in this dynamical dissipative system introduced as time-varying during motion of mechanism’s dimension iteration. The synthesis process is realized as the time evolution of such system. One of the most important objectives of the machine synthesis is the dexterity measure. The new approach is applied to optimization of this property.

  11. PREFACE: Dynamics of wetting Dynamics of wetting

    Science.gov (United States)

    Grest, Gary S.; Oshanin, Gleb; Webb, Edmund B., III

    2009-11-01

    Capillary phenomena associated with fluids wetting other condensed matter phases have drawn great scientific interest for hundreds of years; consider the recent bicentennial celebration of Thomas Young's paper on equilibrium contact angles, describing the geometric shape assumed near a three phase contact line in terms of the relevant surface energies of the constituent phases [1]. Indeed, nearly a century has passed since the seminal papers of Lucas and Washburn, describing dynamics of capillary imbibition [2, 3]. While it is generally appreciated that dynamics of fluid wetting processes are determined by the degree to which a system is out of capillary equilibrium, myriad complications exist that challenge the fundamental understanding of dynamic capillary phenomena. The topic has gathered much interest from recent Nobel laureate Pierre-Gilles de Gennes, who provided a seminal review of relevant dissipation mechanisms for fluid droplets spreading on solid surfaces [4] Although much about the dynamics of wetting has been revealed, much remains to be learned and intrinsic technological and fundamental interest in the topic drives continuing high levels of research activity. This is enabled partly by improved experimental capabilities for resolving wetting processes at increasingly finer temporal, spatial, and chemical resolution. Additionally, dynamic wetting research advances via higher fidelity computational modeling capabilities, which drive more highly refined theory development. The significance of this topic both fundamentally and technologically has resulted in a number of reviews of research activity in wetting dynamics. One recent example addresses the evaluation of existing wetting dynamics theories from an experimentalist's perspective [5]. A Current Opinion issue was recently dedicated to high temperature capillarity, including dynamics of high temperature spreading [6]. New educational tools have recently emerged for providing instruction in wetting

  12. Critical slowing down in driven-dissipative Bose-Hubbard lattices

    Science.gov (United States)

    Vicentini, Filippo; Minganti, Fabrizio; Rota, Riccardo; Orso, Giuliano; Ciuti, Cristiano

    2018-01-01

    We explore theoretically the dynamical properties of a first-order dissipative phase transition in coherently driven Bose-Hubbard systems, describing, e.g., lattices of coupled nonlinear optical cavities. Via stochastic trajectory calculations based on the truncated Wigner approximation, we investigate the dynamical behavior as a function of system size for one-dimensional (1D) and 2D square lattices in the regime where mean-field theory predicts nonlinear bistability. We show that a critical slowing down emerges for increasing number of sites in 2D square lattices, while it is absent in 1D arrays. We characterize the peculiar properties of the collective phases in the critical region.

  13. Modified fluctuation-dissipation theorem for general non-stationary states and application to the Glauber–Ising chain

    International Nuclear Information System (INIS)

    Verley, Gatien; Lacoste, David; Chétrite, Raphaël

    2011-01-01

    In this paper, we present a general derivation of a modified fluctuation-dissipation theorem (MFDT) valid near an arbitrary non-stationary state for a system obeying Markovian dynamics. We show that the method for deriving modified fluctuation-dissipation theorems near non-equilibrium stationary states used by Prost et al (2009 Phys. Rev. Lett. 103 090601) is generalizable to non-stationary states. This result follows from both standard linear response theory and from a transient fluctuation theorem, analogous to the Hatano–Sasa relation. We show that this modified fluctuation-dissipation theorem can be interpreted at the trajectory level using the notion of stochastic trajectory entropy, in a way which is similar to what has been done recently in the case of the MFDT near non-equilibrium steady states (NESS). We illustrate this framework with two solvable examples: the first example corresponds to a Brownian particle in a harmonic trap subjected to a quench of temperature and to a time-dependent stiffness; the second example is a classic model of coarsening systems, namely the 1D Ising model with Glauber dynamics

  14. Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

  15. Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

    Science.gov (United States)

    Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

    2017-08-22

    A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

  16. Analytical study of dissipative solitary waves

    Energy Technology Data Exchange (ETDEWEB)

    Dini, Fatemeh [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Emamzadeh, Mehdi Molaie [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Khorasani, Sina [School of Electrical Engineering, Sharif University of Technology, PO Box 11365-363, Tehran (Iran, Islamic Republic of); Bobin, Jean Louis [Universite Pierre et Marie Curie, Paris (France); Amrollahi, Reza [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Sodagar, Majid [School of Electrical Engineering, Sharif University of Technology, PO Box 11365-363, Tehran (Iran, Islamic Republic of); Khoshnegar, Milad [School of Electrical Engineering, Sharif University of Technology, PO Box 11365-363, Tehran (Iran, Islamic Republic of)

    2008-02-15

    In this paper, the analytical solution to a new class of nonlinear solitons is presented with cubic nonlinearity, subject to a dissipation term arising as a result of a first-order derivative with respect to time, in the weakly nonlinear regime. Exact solutions are found using the combination of the perturbation and Green's function methods up to the third order. We present an example and discuss the asymptotic behavior of the Green's function. The dissipative solitary equation is also studied in the phase space in the non-dissipative and dissipative forms. Bounded and unbounded solutions of this equation are characterized, yielding an energy conversation law for non-dissipative waves. Applications of the model include weakly nonlinear solutions of terahertz Josephson plasma waves in layered superconductors and ablative Rayleigh-Taylor instability.

  17. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  18. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

    2013-12-21

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

  19. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    International Nuclear Information System (INIS)

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2013-01-01

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective

  20. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2013-12-01

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

  1. Dissipative tunneling and orthogonality catastrophe in molecular transistors

    DEFF Research Database (Denmark)

    Braig, S.; Flensberg, Karsten

    2004-01-01

    Transport through molecular devices with weak tunnel coupling to the leads but with strong coupling to a single vibrational mode is considered in the case where the vibration is damped by coupling to the environment. In particular, we investigate what influence the electrostatic coupling of the c......Transport through molecular devices with weak tunnel coupling to the leads but with strong coupling to a single vibrational mode is considered in the case where the vibration is damped by coupling to the environment. In particular, we investigate what influence the electrostatic coupling...

  2. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    International Nuclear Information System (INIS)

    Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

    2015-01-01

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

  3. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

    DEFF Research Database (Denmark)

    Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

    -up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

  4. Energy dissipation effects on imaging of soft materials by dynamic atomic force microscopy: A DNA-chip study

    Energy Technology Data Exchange (ETDEWEB)

    Phaner-Goutorbe, M., E-mail: magali.phaner@ec-lyon.fr [Université de Lyon, Institut des Nanotechnologies de Lyon (INL) UMR CNRS 5270, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully (France); Iazykov, M. [Université de Lyon, laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d' Italie 69364 Lyon cedex 07 (France); Villey, R. [Université de Lyon, Institut des Nanotechnologies de Lyon (INL) UMR CNRS 5270, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully (France); Université de Lyon, laboratoire de Physique de la Matière Condensée et Nanostructures, Université Claude Bernard Lyon 1, Domaine Scientifique de la Doua, Bâtiment Léon Brillouin 43 boulevard du 11 Novembre 1918, F 69622 Villeurbanne (France); Sicard, D.; Robach, Y. [Université de Lyon, Institut des Nanotechnologies de Lyon (INL) UMR CNRS 5270, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully (France)

    2013-05-01

    Using amplitude-mode AFM (AM-AFM), we have obtained valuable information during these recent years through the study of amplitude and phase shift dependence on tip–sample separation, leading to a comprehensive understanding of the interaction processes. Two imaging regimes, attractive and repulsive, have been identified and a relationship between phase and dissipative energy was established, providing information on observed material properties. Most of the previous studies have concerned model systems: either hard or soft materials. In this paper, we present the analysis of a mixed system of soft structures on a hard substrate. This is a DNA chip for biological applications consisting of oligonucleotides covalently linked by a layer of silane to a silicon substrate. A detailed study of amplitude-phase curves as a function of the tip–sample separation allowed us to define the best experimental conditions to obtain specific information: we got reliable conditions to minimize noise during topographic imaging and an understanding of the processes of energy dissipation involved in the DNA breaking for DNA arrays. By calculating the energy dissipated as a function of the amplitude of oscillation, we have demonstrated a transition from an energy dissipation process governed by localized viscoelastic interactions (due to the soft layer) to a process governed by extended irreversible deformations (due to the hard substrate). Highlights: ► Amplitude mode AFM analysis of a DNA array is presented. ► Reliable conditions for noise minimization on topographic images are presented. ► Phase, amplitude vs distance curves are analyzed for different setpoint amplitudes. ► Energy dissipation processes are described from viscoelasticity to DNA breaking.

  5. 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).

  6. Decay of Kadomtsev-Petviashvili lumps in dissipative media

    Science.gov (United States)

    Clarke, S.; Gorshkov, K.; Grimshaw, R.; Stepanyants, Y.

    2018-03-01

    The decay of Kadomtsev-Petviashvili lumps is considered for a few typical dissipations-Rayleigh dissipation, Reynolds dissipation, Landau damping, Chezy bottom friction, viscous dissipation in the laminar boundary layer, and radiative losses caused by large-scale dispersion. It is shown that the straight-line motion of lumps is unstable under the influence of dissipation. The lump trajectories are calculated for two most typical models of dissipation-the Rayleigh and Reynolds dissipations. A comparison of analytical results obtained within the framework of asymptotic theory with the direct numerical calculations of the Kadomtsev-Petviashvili equation is presented. Good agreement between the theoretical and numerical results is obtained.

  7. Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko

    1998-03-01

    This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)

  8. Highly dissipative Hénon map behavior in the four-level model of the CO 2 laser with modulated losses

    Science.gov (United States)

    Pando L., C. L.; Acosta, G. A. Luna; Meucci, R.; Ciofini, M.

    1995-02-01

    We show that the four-level model for the CO 2 laser with modulated losses behaves in a qualitatively similar way as the highly dissipative Hénon map. The ubiquity of elements of the universal sequence, their related symbolic dynamics, and the presence of reverse bifurcations of chaotic bands in the model are reminiscent of the logistic map which is the limit of the Hénon map when the Jacobian equals zero. The coexistence of attractors, its dynamics related to contraction of volumes in phase space and the associated return maps can be correlated with those of the highly dissipative Hénon map.

  9. Estimation of viscous dissipative stresses induced by a mechanical heart valve using PIV data.

    Science.gov (United States)

    Li, Chi-Pei; Lo, Chi-Wen; Lu, Po-Chien

    2010-03-01

    Among the clinical complications of mechanical heart valves (MHVs), hemolysis was previously thought to result from Reynolds stresses in turbulent flows. A more recent hypothesis suggests viscous dissipative stresses at spatial scales similar in size to red blood cells may be related to hemolysis in MHVs, but the resolution of current instrumentation is insufficient to measure the smallest eddy sizes. We studied the St. Jude Medical (SJM) 27 mm valve in the aortic position of a pulsatile circulatory mock loop under physiologic conditions with particle image velocimetry (PIV). Assuming a dynamic equilibrium assumption between the resolved and sub-grid-scale (SGS) energy flux, the SGS energy flux was calculated from the strain rate tensor computed from the resolved velocity fields and the SGS stress was determined by the Smagorinsky model, from which the turbulence dissipation rate and then the viscous dissipative stresses were estimated. Our results showed Reynolds stresses up to 80 N/m2 throughout the cardiac cycle, and viscous dissipative stresses below 12 N/m2. The viscous dissipative stresses remain far below the threshold of red blood cell hemolysis, but could potentially damage platelets, implying the need for further study in the phenomenon of MHV hemolytic complications.

  10. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  11. DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

    NARCIS (Netherlands)

    JUFFER, AH; BERENDSEN, HJC

    1993-01-01

    A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

  12. Quantum Dissipative Systems

    CERN Document Server

    Weiss, Ulrich

    2008-01-01

    Major advances in the quantum theory of macroscopic systems, in combination with stunning experimental achievements, have brightened the field and brought it to the attention of the general community in natural sciences. Today, working knowledge of dissipative quantum mechanics is an essential tool for many physicists. This book - originally published in 1990 and republished in 1999 as an enlarged second edition - delves much deeper than ever before into the fundamental concepts, methods, and applications of quantum dissipative systems, including the most recent developments. In this third edi

  13. Conservation laws shape dissipation

    Science.gov (United States)

    Rao, Riccardo; Esposito, Massimiliano

    2018-02-01

    Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs—we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.

  14. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  15. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

    NARCIS (Netherlands)

    Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

    2007-01-01

    A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

  16. Droplet spreading driven by van der Waals force: a molecular dynamics study

    KAUST Repository

    Wu, Congmin

    2010-07-07

    The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

  17. Modulation instability and dissipative rogue waves in ion-beam plasma: Roles of ionization, recombination, and electron attachment

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Shimin, E-mail: gsm861@126.com; Mei, Liquan, E-mail: lqmei@mail.xjtu.edu.cn [School of Mathematics and Statistics, Xi' an Jiaotong University, Xi' an 710049 (China)

    2014-11-15

    The amplitude modulation of ion-acoustic waves is investigated in an unmagnetized plasma containing positive ions, negative ions, and electrons obeying a kappa-type distribution that is penetrated by a positive ion beam. By considering dissipative mechanisms, including ionization, negative-positive ion recombination, and electron attachment, we introduce a comprehensive model for the plasma with the effects of sources and sinks. Via reductive perturbation theory, the modified nonlinear Schrödinger equation with a dissipative term is derived to govern the dynamics of the modulated waves. The effect of the plasma parameters on the modulation instability criterion for the modified nonlinear Schrödinger equation is numerically investigated in detail. Within the unstable region, first- and second-order dissipative ion-acoustic rogue waves are present. The effect of the plasma parameters on the characteristics of the dissipative rogue waves is also discussed.

  18. Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry

    International Nuclear Information System (INIS)

    Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo

    2012-01-01

    Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.

  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. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  1. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    Directory of Open Access Journals (Sweden)

    Dirk-Sören Lühmann

    2015-08-01

    Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  2. Moving contact lines: linking molecular dynamics and continuum-scale modelling.

    Science.gov (United States)

    Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

    2018-05-04

    Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

  3. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  4. Dissipative open systems theory as a foundation for the thermodynamics of linear systems.

    Science.gov (United States)

    Delvenne, Jean-Charles; Sandberg, Henrik

    2017-03-06

    In this paper, we advocate the use of open dynamical systems, i.e. systems sharing input and output variables with their environment, and the dissipativity theory initiated by Jan Willems as models of thermodynamical systems, at the microscopic and macroscopic level alike. We take linear systems as a study case, where we show how to derive a global Lyapunov function to analyse networks of interconnected systems. We define a suitable notion of dynamic non-equilibrium temperature that allows us to derive a discrete Fourier law ruling the exchange of heat between lumped, discrete-space systems, enriched with the Maxwell-Cattaneo correction. We complete these results by a brief recall of the steps that allow complete derivation of the dissipation and fluctuation in macroscopic systems (i.e. at the level of probability distributions) from lossless and deterministic systems.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

  5. A study of energy dissipation and critical speed of granular flow in a rotating cylinder

    Science.gov (United States)

    Dragomir, Sergiu C.; Sinnott, Mathew D.; Semercigil, S. Eren; Turan, Özden F.

    2014-12-01

    Tuned vibration absorbers may improve the safety of flexible structures which are prone to excessive oscillation magnitudes under dynamic loads. A novel absorber design proposes sloshing of granular material in a rotating cylinder where the granular material is the energy dissipating agent. As the conventional dissipative elements require maintenance due to the nature of their function, the new design may represent a virtually maintenance free alternative. The angular speed of the cylinder containing particles has a critical centrifuging speed, after which particles remain permanently in contact with the walls and there can be no further dissipation. Until the critical speed, however, dissipation increases proportionally with the angular speed. It is then vital to know the value of the critical speed as the limit of dissipation. The focus of the present study is on determination of the critical centrifuge speed. This critical speed is also of practical importance in bulk-material handling rotary mills, such as dryers and crushers. Experiments and numerical simulations, using Discrete Element Method, are used to determine the critical centrifuging speed. In addition, predictions are given and guidelines are offered for the choice of material properties to maximize the energy dissipation. As a result of a parametric study, the coefficient of friction is found to have the greatest significance on the centrifuging speed.

  6. Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

    International Nuclear Information System (INIS)

    More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

    2012-01-01

    Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

  7. Space dissipative structures

    International Nuclear Information System (INIS)

    Chernousenko, V.M.; Kuklin, V.M.; Panachenko, I.P.; Vorob'yov, V.M.

    1990-01-01

    This paper reports on a wide spectrum of oscillations that is excited due to the evolution instabilities, being in a weak above-threshold state, in the inequilibrium media with decaying spectrum. In this case the pumping, whose part is played by an intensive wave or occupation inversion in the active medium, synchronized the phases of excited modes and, thus, forms the space dissipative structure of the field. In dissipative nonlinear media with nondecaying spectrum the space structures, formed due to the development of instability, experience small-scale hexagonal modulation

  8. Quantum interference and coherent control in dissipative atomic systems

    International Nuclear Information System (INIS)

    Paspalakis, E.

    1999-01-01

    In this thesis we study the effects of quantum interference arising from dissipative processes in atomic systems. First, we identify quantum interference phenomena arising from decay mechanisms. Second, we use dynamical methods (the properties of laser fields) to obtain a tailored response of systems in which such interferences are present. We are mainly concerned with two dissipative processes: spontaneous emission and ionization. First, we study the effects of quantum interference arising from spontaneous emission on the population dynamics and the spontaneous emission spectrum of several multi-level systems. Coherent 'phase' control methods for manipulating the response of systems involving spontaneous emission interference are also proposed. Several interesting phenomena are identified such as partial and total quenching of spontaneous emission, phase dependent population dynamics and coherent population trapping. Next, we consider the process of laser-induced continuum structure, where an atom is coupled by two laser fields to the same electronic continuum. An {it ab initio}, non-perturbative study of this process in helium using the R-Matrix Floquet theory is presented. The results of our numerical calculations are compared with those obtained by simple perturbative models and with recent experimental results. The possibility of coherent population transfer via a continuum of states is then analyzed. We study two distinct atomic systems. A laser-induced continuum structure scheme (unstructured continuum) and a bichromatically driven autoionizing scheme (structured continuum). We find that the same conditions which lead to 'dark' states in these systems lead to efficient population transfer. We also identify parameters detrimental to the transfer efficiency and propose methods to overcome them. Finally, we study short pulse propagation in systems involving interfering dissipation mechanisms. We show that the existence of dark states can lead to loss-free and

  9. Strain energy storage and dissipation rate in active cell mechanics

    Science.gov (United States)

    Agosti, A.; Ambrosi, D.; Turzi, S.

    2018-05-01

    When living cells are observed at rest on a flat substrate, they can typically exhibit a rounded (symmetric) or an elongated (polarized) shape. Although the cells are apparently at rest, the active stress generated by the molecular motors continuously stretches and drifts the actin network, the cytoskeleton of the cell. In this paper we theoretically compare the energy stored and dissipated in this active system in two geometric configurations of interest: symmetric and polarized. We find that the stored energy is larger for a radially symmetric cell at low activation regime, while the polar configuration has larger strain energy when the active stress is beyond a critical threshold. Conversely, the dissipation of energy in a symmetric cell is always larger than that of a nonsymmetric one. By a combination of symmetry arguments and competition between surface and bulk stress, we argue that radial symmetry is an energetically expensive metastable state that provides access to an infinite number of lower-energy states, the polarized configurations.

  10. Fluctuation-dissipation theorem in an isolated system of quantum dipolar bosons after a quench.

    Science.gov (United States)

    Khatami, Ehsan; Pupillo, Guido; Srednicki, Mark; Rigol, Marcos

    2013-08-02

    We examine the validity of fluctuation-dissipation relations in isolated quantum systems taken out of equilibrium by a sudden quench. We focus on the dynamics of trapped hard-core bosons in one-dimensional lattices with dipolar interactions whose strength is changed during the quench. We find indications that fluctuation-dissipation relations hold if the system is nonintegrable after the quench, as well as if it is integrable after the quench if the initial state is an equilibrium state of a nonintegrable Hamiltonian. On the other hand, we find indications that they fail if the system is integrable both before and after quenching.

  11. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  12. Architected squirt-flow materials for energy dissipation

    Science.gov (United States)

    Cohen, Tal; Kurzeja, Patrick; Bertoldi, Katia

    2017-12-01

    In the present study we explore material architectures that lead to enhanced dissipation properties by taking advantage of squirt-flow - a local flow mechanism triggered by heterogeneities at the pore level. While squirt-flow is a known dominant source of dissipation and seismic attenuation in fluid saturated geological materials, we study its untapped potential to be incorporated in highly deformable elastic materials with embedded fluid-filled cavities for future engineering applications. An analytical investigation, that isolates the squirt-flow mechanism from other potential dissipation mechanisms and considers an idealized setting, predicts high theoretical levels of dissipation achievable by squirt-flow and establishes a set of guidelines for optimal dissipation design. Particular architectures are then investigated via numerical simulations showing that a careful design of the internal voids can lead to an increase of dissipation levels by an order of magnitude, compared with equivalent homogeneous void distributions. Therefore, we suggest squirt-flow as a promising mechanism to be incorporated in future architected materials to effectively and reversibly dissipate energy.

  13. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  14. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

    NARCIS (Netherlands)

    Marrink, SJ; Mark, AE

    2003-01-01

    Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

  15. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

    NARCIS (Netherlands)

    Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

    2007-01-01

    We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

  16. Energy dissipators

    National Research Council Canada - National Science Library

    Vischer, D. L; Hager, Willi H; Hager, W. H

    1995-01-01

    .... the book comprises chapters in farious fields such as hydraulic jump, stilling basins, ski jumps and plunge pools but introduces also a general account on various methods of dissipation, as well...

  17. Quantum molecular dynamics study of the Su-Schrieffer-Heeger model

    NARCIS (Netherlands)

    Michielsen, Kristel; Raedt, Hans De

    A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to

  18. A comparative molecular dynamics study of diffusion of n-decane ...

    Indian Academy of Sciences (India)

    Administrator

    Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.

  19. Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

    National Research Council Canada - National Science Library

    Johnston, K

    1998-01-01

    .... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

  20. Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

    Czech Academy of Sciences Publication Activity Database

    Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

    2012-01-01

    Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012