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Sample records for nonequilibrium calcium dynamics

  1. 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

  2. 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

  3. Nonequilibrium molecular dynamics: The first 25 years

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments

  4. Linking Equilibrium and Nonequilibrium Dynamics in Glass-Forming Systems

    DEFF Research Database (Denmark)

    Mauro, John C.; Guo, Xiaoju; Smedskjær, Morten Mattrup

    , we show that the nonequilibrium glassy dynamics are intimately connected with the equilibrium liquid dynamics. This is accomplished by deriving a new functional form for the thermal history dependence of nonequilibrium viscosity, which is validated against experimental measurements of industrial...

  5. 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...

  6. Nonequilibrium statistical averages and thermo field dynamics

    International Nuclear Information System (INIS)

    Marinaro, A.; Scarpetta, Q.

    1984-01-01

    An extension of thermo field dynamics is proposed, which permits the computation of nonequilibrium statistical averages. The Brownian motion of a quantum oscillator is treated as an example. In conclusion it is pointed out that the procedure proposed to computation of time-dependent statistical average gives the correct two-point Green function for the damped oscillator. A simple extension can be used to compute two-point Green functions of free particles

  7. Nonequilibrium dynamical mean-field theory

    Energy Technology Data Exchange (ETDEWEB)

    Eckstein, Martin

    2009-12-21

    The aim of this thesis is the investigation of strongly interacting quantum many-particle systems in nonequilibrium by means of the dynamical mean-field theory (DMFT). An efficient numerical implementation of the nonequilibrium DMFT equations within the Keldysh formalism is provided, as well a discussion of several approaches to solve effective single-site problem to which lattice models such as the Hubbard-model are mapped within DMFT. DMFT is then used to study the relaxation of the thermodynamic state after a sudden increase of the interaction parameter in two different models: the Hubbard model and the Falicov-Kimball model. In the latter case an exact solution can be given, which shows that the state does not even thermalize after infinite waiting times. For a slow change of the interaction, a transition to adiabatic behavior is found. The Hubbard model, on the other hand, shows a very sensitive dependence of the relaxation on the interaction, which may be called a dynamical phase transition. Rapid thermalization only occurs at the interaction parameter which corresponds to this transition. (orig.)

  8. Nonequilibrium dynamical mean-field theory

    International Nuclear Information System (INIS)

    Eckstein, Martin

    2009-01-01

    The aim of this thesis is the investigation of strongly interacting quantum many-particle systems in nonequilibrium by means of the dynamical mean-field theory (DMFT). An efficient numerical implementation of the nonequilibrium DMFT equations within the Keldysh formalism is provided, as well a discussion of several approaches to solve effective single-site problem to which lattice models such as the Hubbard-model are mapped within DMFT. DMFT is then used to study the relaxation of the thermodynamic state after a sudden increase of the interaction parameter in two different models: the Hubbard model and the Falicov-Kimball model. In the latter case an exact solution can be given, which shows that the state does not even thermalize after infinite waiting times. For a slow change of the interaction, a transition to adiabatic behavior is found. The Hubbard model, on the other hand, shows a very sensitive dependence of the relaxation on the interaction, which may be called a dynamical phase transition. Rapid thermalization only occurs at the interaction parameter which corresponds to this transition. (orig.)

  9. Nonequilibrium dynamics in an interacting Fe-C nanoparticle system

    DEFF Research Database (Denmark)

    Jönsson, P.; Hansen, Mikkel Fougt; Nordblad, P.

    2000-01-01

    Nonequilibrium dynamics in an interacting Fe-C nanoparticle sample, exhibiting a low-temperature spin-glass-like phase, has been studied by low-frequency ac susceptibility and magnetic relaxation experiments. The nonequilibrium behavior shows characteristic spin-glass features, but some qualitative...

  10. Complex Dynamics in Nonequilibrium Economics and Chemistry

    Science.gov (United States)

    Wen, Kehong

    Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator

  11. Non-equilibrium dynamics from RPMD and CMD.

    Science.gov (United States)

    Welsch, Ralph; Song, Kai; Shi, Qiang; Althorpe, Stuart C; Miller, Thomas F

    2016-11-28

    We investigate the calculation of approximate non-equilibrium quantum time correlation functions (TCFs) using two popular path-integral-based molecular dynamics methods, ring-polymer molecular dynamics (RPMD) and centroid molecular dynamics (CMD). It is shown that for the cases of a sudden vertical excitation and an initial momentum impulse, both RPMD and CMD yield non-equilibrium TCFs for linear operators that are exact for high temperatures, in the t = 0 limit, and for harmonic potentials; the subset of these conditions that are preserved for non-equilibrium TCFs of non-linear operators is also discussed. Furthermore, it is shown that for these non-equilibrium initial conditions, both methods retain the connection to Matsubara dynamics that has previously been established for equilibrium initial conditions. Comparison of non-equilibrium TCFs from RPMD and CMD to Matsubara dynamics at short times reveals the orders in time to which the methods agree. Specifically, for the position-autocorrelation function associated with sudden vertical excitation, RPMD and CMD agree with Matsubara dynamics up to O(t 4 ) and O(t 1 ), respectively; for the position-autocorrelation function associated with an initial momentum impulse, RPMD and CMD agree with Matsubara dynamics up to O(t 5 ) and O(t 2 ), respectively. Numerical tests using model potentials for a wide range of non-equilibrium initial conditions show that RPMD and CMD yield non-equilibrium TCFs with an accuracy that is comparable to that for equilibrium TCFs. RPMD is also used to investigate excited-state proton transfer in a system-bath model, and it is compared to numerically exact calculations performed using a recently developed version of the Liouville space hierarchical equation of motion approach; again, similar accuracy is observed for non-equilibrium and equilibrium initial conditions.

  12. Non-equilibrium many body dynamics

    International Nuclear Information System (INIS)

    Creutz, M.; Gyulassy, M.

    1997-01-01

    This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop

  13. Non-equilibrium many body dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Creutz, M.; Gyulassy, M.

    1997-09-22

    This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop.

  14. Nonlinear and Nonequilibrium Dynamics in Geomaterials

    OpenAIRE

    TenCate, James A.; Pasqualini, Donatella; Habib, Salman; Heitmann, Katrin; Higdon, David; Johnson, Paul A.

    2004-01-01

    The transition from linear to nonlinear dynamical elasticity in rocks is of considerable interest in seismic wave propagation as well as in understanding the basic dynamical processes in consolidated granular materials. We have carried out a careful experimental investigation of this transition for Berea and Fontainebleau sandstones. Below a well-characterized strain, the materials behave linearly, transitioning beyond that point to a nonlinear behavior which can be accurately captured by a s...

  15. Exact fluctuations of nonequilibrium steady states from approximate auxiliary dynamics

    OpenAIRE

    Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

    2017-01-01

    We describe a framework to significantly reduce the computational effort to evaluate large deviation functions of time integrated observables within nonequilibrium steady states. We do this by incorporating an auxiliary dynamics into trajectory based Monte Carlo calculations, through a transformation of the system's propagator using an approximate guiding function. This procedure importance samples the trajectories that most contribute to the large deviation function, mitigating the exponenti...

  16. Chaotic Dynamical Ferromagnetic Phase Induced by Nonequilibrium Quantum Fluctuations

    Science.gov (United States)

    Lerose, Alessio; Marino, Jamir; Žunkovič, Bojan; Gambassi, Andrea; Silva, Alessandro

    2018-03-01

    We investigate the robustness of a dynamical phase transition against quantum fluctuations by studying the impact of a ferromagnetic nearest-neighbor spin interaction in one spatial dimension on the nonequilibrium dynamical phase diagram of the fully connected quantum Ising model. In particular, we focus on the transient dynamics after a quantum quench and study the prethermal state via a combination of analytic time-dependent spin wave theory and numerical methods based on matrix product states. We find that, upon increasing the strength of the quantum fluctuations, the dynamical critical point fans out into a chaotic dynamical phase within which the asymptotic ordering is characterized by strong sensitivity to the parameters and initial conditions. We argue that such a phenomenon is general, as it arises from the impact of quantum fluctuations on the mean-field out of equilibrium dynamics of any system which exhibits a broken discrete symmetry.

  17. Quantum Coherent Dynamics Enhanced by Synchronization with Nonequilibrium Environments

    Science.gov (United States)

    Ishikawa, Akira; Okada, Ryo; Uchiyama, Kazuharu; Hori, Hirokazu; Kobayashi, Kiyoshi

    2018-05-01

    We report the discovery of the anomalous enhancement of quantum coherent dynamics (CD) due to a non-Markovian mechanism originating from not thermal-equilibrium phonon baths but nonequilibrium coherent phonons. CD is an elementary process for quantum phenomena in nanosystems, such as excitation transfer (ET) in semiconductor nanostructures and light-harvesting systems. CD occurs in homogeneous nanosystems because system inhomogeneity typically destroys coherence. In real systems, however, nanosystems behave as open systems surrounded by environments such as phonon systems. Typically, CD in inhomogeneous nanosystems is enhanced by the absorption and emission of thermal-equilibrium phonons, and the enhancement is described by the conventional master equation. On the other hand, CD is also enhanced by synchronization between population dynamics in nanosystems and coherent phonons; namely, coherent phonons, which are self-consistently induced by phase matching with Rabi oscillation, are fed back to enhance CD. This anomalous enhancement of CD essentially originates from the nonequilibrium and dynamical non-Markovian nature of coherent phonon environments, and the enhancement is firstly predicted by applying time-dependent projection operators to nonequilibrium and dynamical environments. Moreover, CD is discussed by considering ET from a donor to an acceptor. It is found that the enhancement of ET by synchronization with coherent phonons depends on the competition between the output time from a system to an acceptor and the formation time of coherent phonons. These findings in this study will stimulate the design and manipulation of CD via structured environments from the viewpoint of application to nano-photoelectronic devices.

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

    International Nuclear Information System (INIS)

    Morozov, I V; Norman, G E

    2003-01-01

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

  19. Calcium dynamics in vascular smooth muscle

    OpenAIRE

    Amberg, Gregory C.; Navedo, Manuel F.

    2013-01-01

    Smooth muscle cells are ultimately responsible for determining vascular luminal diameter and blood flow. Dynamic changes in intracellular calcium are a critical mechanism regulating vascular smooth muscle contractility. Processes influencing intracellular calcium are therefore important regulators of vascular function with physiological and pathophysiological consequences. In this review we discuss the major dynamic calcium signals identified and characterized in vascular smooth muscle cells....

  20. Non-equilibrium dynamics of one-dimensional Bose gases

    International Nuclear Information System (INIS)

    Langen, T.

    2013-01-01

    Understanding the non-equilibrium dynamics of isolated quantum many-body systems is an open problem on vastly different energy, length, and time scales. Examples range from the dynamics of the early universe and heavy-ion collisions to the subtle coherence and transport properties in condensed matter physics. However, realizations of such quantum many-body systems, which are both well isolated from the environment and accessible to experimental study are scarce. This thesis presents a series of experiments with ultracold one-dimensional Bose gases. These gases combine a nearly perfect isolation from the environment with many well-established methods to manipulate and probe their quantum states. This makes them an ideal model system to explore the physics of quantum many body systems out of equilibrium. In the experiments, a well-defined non-equilibrium state is created by splitting a single one-dimensional gas coherently into two parts. The relaxation of this state is probed using matter-wave interferometry. The Observations reveal the emergence of a prethermalized steady state which differs strongly from thermal equilibrium. Such thermal-like states had previously been predicted for a large variety of systems, but never been observed directly. Studying the relaxation process in further detail shows that the thermal correlations of the prethermalized state emerge locally in their final form and propagate through the system in a light-cone-like evolution. This provides first experimental evidence for the local relaxation conjecture, which links relaxation processes in quantum many-body systems to the propagation of correlations. Furthermore, engineering the initial state of the evolution demonstrates that the prethermalized state is described by a generalized Gibbs ensemble, an observation which substantiates the importance of this ensemble as an extension of standard statistical mechanics. Finally, an experiment is presented, where pairs of gases with an atom

  1. The effect of pure state structure on nonequilibrium dynamics

    International Nuclear Information System (INIS)

    Newman, C M; Stein, D L

    2008-01-01

    Motivated by short-range Ising spin glasses, we review some rigorous results and their consequences for the relation between the number/nature of equilibrium pure states and nonequilibrium dynamics. Two of the consequences for spin glass dynamics following an instantaneous deep quench to a temperature with broken spin flip symmetry are: (1) almost all initial configurations lie on the boundary between the basins of attraction of multiple pure states; (2) unless there are uncountably many pure states with almost all pairs having zero overlap, there can be no equilibration to a pure state as time t → ∞. We discuss the relevance of these results to the difficulty of equilibration of spin glasses. We also review some results concerning the 'nature versus nurture' problem of whether the large-t behavior of both ferromagnets and spin glasses following a deep quench is determined more by the initial configuration (nature) or by the dynamics realization (nurture)

  2. 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.

  3. 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

  4. NATO Advanced Study Institute on Nonequilibrium Phonon Dynamics

    CERN Document Server

    1985-01-01

    Phonons are always present in the solid state even at an absolute temperature of 0 K where zero point vibrations still abound. Moreover, phonons interact with all other excitations of the solid state and, thereby, influence most of its properties. Historically experimental information on phonon transport came from measurements of thermal conductivity. Over the past two decades much more, and much more detailed, information on phonon transport and on many of the inherent phonon interaction processes have come to light from experiments which use nonequilibrium phonons to study their dynamics. The resultant research field has most recently blossomed with the development of ever more sophisticated experimental and theoretical methods which can be applied to it. In fact, the field is moving so rapidly that new members of the research community have difficulties in keeping up to date. This NATO Advanced Study Institute (ASI) was organized with the objective of overcoming the information barrier between those expert...

  5. Non-equilibrium dynamics near a quantum multicritical point

    International Nuclear Information System (INIS)

    Patra, Ayoti; Mukherjee, Victor; Dutta, Amit

    2011-01-01

    We study the non-equilibrium dynamics of a quantum system close to a quantum multi-critical point (MCP) using the example of a one-dimensional spin-1/2 transverse XY spin chain. We summarize earlier results of defect generenation and fidelity susceptibility for quenching through MCP and close to the MCP, respectively. For a quenching scheme which enables the system to hit the MCP along different paths, we emphasize the role of path on exponents associated with quasicritical points which appear in the scaling relations. Finally, we explicitly derive the scaling of concurrence and negativity for two spin entanglement generated following a slow quenching across the MCP and enlist the results for different quenching schemes. We explicity show the dependence of the scaling on the quenching path and dicuss the limiting situations.

  6. Dynamical Symmetries and Causality in Non-Equilibrium Phase Transitions

    Directory of Open Access Journals (Sweden)

    Malte Henkel

    2015-11-01

    Full Text Available Dynamical symmetries are of considerable importance in elucidating the complex behaviour of strongly interacting systems with many degrees of freedom. Paradigmatic examples are cooperative phenomena as they arise in phase transitions, where conformal invariance has led to enormous progress in equilibrium phase transitions, especially in two dimensions. Non-equilibrium phase transitions can arise in much larger portions of the parameter space than equilibrium phase transitions. The state of the art of recent attempts to generalise conformal invariance to a new generic symmetry, taking into account the different scaling behaviour of space and time, will be reviewed. Particular attention will be given to the causality properties as they follow for co-variant n-point functions. These are important for the physical identification of n-point functions as responses or correlators.

  7. Equilibrium and nonequilibrium dynamics of soft sphere fluids.

    Science.gov (United States)

    Ding, Yajun; Mittal, Jeetain

    2015-07-14

    We use computer simulations to test the freezing-point scaling relationship between equilibrium transport coefficients (self-diffusivity, viscosity) and thermodynamic parameters for soft sphere fluids. The fluid particles interact via the inverse-power potential (IPP), and the particle softness is changed by modifying the exponent of the distance-dependent potential term. In the case of IPP fluids, density and temperature are not independent variables and can be combined to obtain a coupling parameter to define the thermodynamic state of the system. We find that the rescaled coupling parameter, based on its value at the freezing point, can approximately collapse the diffusivity and viscosity data for IPP fluids over a wide range of particle softness. Even though the collapse is far from perfect, the freezing-point scaling relationship provides a convenient and effective way to compare the structure and dynamics of fluid systems with different particle softness. We further show that an alternate scaling relationship based on two-body excess entropy can provide an almost perfect collapse of the diffusivity and viscosity data below the freezing transition. Next, we perform nonequilibrium molecular dynamics simulations to calculate the shear-dependent viscosity and to identify the distinct role of particle softness in underlying structural changes associated with rheological properties. Qualitatively, we find a similar shear-thinning behavior for IPP fluids with different particle softness, though softer particles exhibit stronger shear-thinning tendency. By investigating the distance and angle-dependent pair correlation functions in these systems, we find different structural features in the case of IPP fluids with hard-sphere like and softer particle interactions. Interestingly, shear-thinning in hard-sphere like fluids is accompanied by enhanced translational order, whereas softer fluids exhibit loss of order with shear. Our results provide a systematic evaluation

  8. On the definition of equilibrium and non-equilibrium states in dynamical systems

    OpenAIRE

    Akimoto, Takuma

    2008-01-01

    We propose a definition of equilibrium and non-equilibrium states in dynamical systems on the basis of the time average. We show numerically that there exists a non-equilibrium non-stationary state in the coupled modified Bernoulli map lattice.

  9. Stochastic Simulation of Cardiac Ventricular Myocyte Calcium Dynamics and Waves

    OpenAIRE

    Tuan, Hoang-Trong Minh; Williams, George S. B.; Chikando, Aristide C.; Sobie, Eric A.; Lederer, W. Jonathan; Jafri, M. Saleet

    2011-01-01

    A three dimensional model of calcium dynamics in the rat ventricular myocyte was developed to study the mechanism of calcium homeostasis and pathological calcium dynamics during calcium overload. The model contains 20,000 calcium release units (CRUs) each containing 49 ryanodine receptors. The model simulates calcium sparks with a realistic spontaneous calcium spark rate. It suggests that in addition to the calcium spark-based leak, there is an invisible calcium leak caused by the stochastic ...

  10. Unstable dynamics, nonequilibrium phases, and criticality in networked excitable media

    International Nuclear Information System (INIS)

    Franciscis, S. de; Torres, J. J.; Marro, J.

    2010-01-01

    Excitable systems are of great theoretical and practical interest in mathematics, physics, chemistry, and biology. Here, we numerically study models of excitable media, namely, networks whose nodes may occasionally be dormant and the connection weights are allowed to vary with the system activity on a short-time scale, which is a convenient and realistic representation. The resulting global activity is quite sensitive to stimuli and eventually becomes unstable also in the absence of any stimuli. Outstanding consequences of such unstable dynamics are the spontaneous occurrence of various nonequilibrium phases--including associative-memory phases and one in which the global activity wanders irregularly, e.g., chaotically among all or part of the dynamic attractors--and 1/f noise as the system is driven into the phase region corresponding to the most irregular behavior. A net result is resilience which results in an efficient search in the model attractor space that can explain the origin of some observed behavior in neural, genetic, and ill-condensed matter systems. By extensive computer simulation we also address a previously conjectured relation between observed power-law distributions and the possible occurrence of a ''critical state'' during functionality of, e.g., cortical networks, and describe the precise nature of such criticality in the model which may serve to guide future experiments.

  11. Step-wise pulling protocols for non-equilibrium dynamics

    Science.gov (United States)

    Ngo, Van Anh

    The fundamental laws of thermodynamics and statistical mechanics, and the deeper understandings of quantum mechanics have been rebuilt in recent years. It is partly because of the increasing power of computing resources nowadays, that allow shedding direct insights into the connections among the thermodynamics laws, statistical nature of our world, and the concepts of quantum mechanics, which have not yet been understood. But mostly, the most important reason, also the ultimate goal, is to understand the mechanisms, statistics and dynamics of biological systems, whose prevailing non-equilibrium processes violate the fundamental laws of thermodynamics, deviate from statistical mechanics, and finally complicate quantum effects. I believe that investigations of the fundamental laws of non-equilibrium dynamics will be a frontier research for at least several more decades. One of the fundamental laws was first discovered in 1997 by Jarzynski, so-called Jarzynski's Equality. Since then, different proofs, alternative descriptions of Jarzynski's Equality, and its further developments and applications have been quickly accumulated. My understandings, developments and applications of an alternative theory on Jarzynski's Equality form the bulk of this dissertation. The core of my theory is based on stepwise pulling protocols, which provide deeper insight into how fluctuations of reaction coordinates contribute to free-energy changes along a reaction pathway. We find that the most optimal pathways, having the largest contribution to free-energy changes, follow the principle of detailed balance. This is a glimpse of why the principle of detailed balance appears so powerful for sampling the most probable statistics of events. In a further development on Jarzynski's Equality, I have been trying to use it in the formalism of diagonal entropy to propose a way to extract useful thermodynamic quantities such temperature, work and free-energy profiles from far

  12. Non-equilibrium transport in the quantum dot: quench dynamics and non-equilibrium steady state

    Science.gov (United States)

    Culver, Adrian; Andrei, Natan

    We present an exact method of calculating the non-equilibrium current driven by a voltage drop across a quantum dot. The system is described by the two lead Anderson model at zero temperature with on-site Coulomb repulsion and non-interacting, linearized leads. We prepare the system in an initial state consisting of a free Fermi sea in each lead with the voltage drop given as the difference between the two Fermi levels. We quench the system by coupling the dot to the leads at t = 0 and following the time evolution of the wavefunction. In the long time limit a new type of Bethe Ansatz wavefunction emerges, which satisfies the Lippmann-Schwinger equation with the two Fermi seas serving as the boundary conditions. This exact, non-perturbative solution describes the non-equilibrium steady state of the system. We describe how to use this solution to compute the infinite time limit of the expectation value of the current operator at a given voltage, which would yield the I-V characteristic of the dot. Research supported by NSF Grant DMR 1410583.

  13. Adiabatic Hamiltonian deformation, linear response theory, and nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1980-01-01

    Although Hamiltonians of various kinds have previously been used to derive Green-Kubo relations for the transport coefficients, the particular choice described is uniquely related to thermodynamics. This nonequilibrium Hamiltonian formulation of fluid flow provides pedagogically simple routes to nonequilibrium fluxes and distribution functions, to theoretical understanding of long-time effects, and to new numerical methods for simulating systems far from equilibrium. The same methods are now being applied to solid-phase problems. At the relatively high frequencies used in the viscous fluid calculations described, solids typically behave elastically. Lower frequencies lead to the formation of dislocations and other defects, making it possible to study plastic flow. A property of the nonequilibrium equations of motion which might be profitably explored is their effective irreversibility. Because only a few particles are necessary to generate irreversible behavior, simulations using adiabatic deformations of the kind described here could perhaps elucidate the instability in the equations of motion responsible for irreversibility

  14. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics

    International Nuclear Information System (INIS)

    Crooks, Gavin E; Sivak, David A

    2011-01-01

    Many interesting divergence measures between conjugate ensembles of nonequilibrium trajectories can be experimentally determined from the work distribution of the process. Herein, we review the statistical and physical significance of several of these measures, in particular the relative entropy (dissipation), Jeffreys divergence (hysteresis), Jensen–Shannon divergence (time-asymmetry), Chernoff divergence (work cumulant generating function), and Rényi divergence

  15. Understanding calcium dynamics experiments and theory

    CERN Document Server

    Malchow, Dieter

    2003-01-01

    Intracellular Calcium is an important messenger in living cells. Calcium dynamics display complex temporal and spatial structures created by the concentration patterns which are characteristic for a nonlinear system operating far from thermodynamic equilibrium. Written as a set of tutorial reviews on both experimental facts and theoretical modelling, this volume is intended as an introduction and modern reference in the field for graduate students and researchers in biophysics, biochemistry and applied mathematics.

  16. Numerical fluid dynamics calculations of nonequilibrium steam-water flows with entrained droplets

    International Nuclear Information System (INIS)

    Williams, K.A.

    1984-01-01

    The present work has developed a computational fluid dynamics formulation that efficiently solves the conservation laws for a vapor field, a continuous liquid field, and two dispersed droplet fields. The thermal-hydraulic effects resulting from the exchange of mass, momentum and energy between the vapor and the dispersed droplet phases has been accurately modeled. This work is an advancement of the state-of-the-art for engineering analyses of nonequilibrium steam-water-droplet flows in heated channels. It is particularly applicable for boiling steam-water flows in which it is important to represent the effects of significant thermal nonequilibrium between the vapor and the liquid phases. This work was shown to be in good agreement with unique experimental measurements of significant thermal nonequilibrium between the vapor and dispersed droplets. The tests analyzed covered a range of mass fluxes and wall heating rates, and were all at low pressures where nonequilibrium effects are most pronounced

  17. Nonequilibrium statistical physics of small systems: fluctuation relations and beyond (annual reviews of nonlinear dynamics and complexity (vch))

    CERN Document Server

    2013-01-01

    This book offers a comprehensive picture of nonequilibrium phenomena in nanoscale systems. Written by internationally recognized experts in the field, this book strikes a balance between theory and experiment, and includes in-depth introductions to nonequilibrium fluctuation relations, nonlinear dynamics and transport, single molecule experiments, and molecular diffusion in nanopores. The authors explore the application of these concepts to nano- and biosystems by cross-linking key methods and ideas from nonequilibrium statistical physics, thermodynamics, stochastic theory, and dynamical s

  18. Non-equilibrium Dynamics, Thermalization and Entropy Production

    International Nuclear Information System (INIS)

    Hinrichsen, Haye; Janotta, Peter; Gogolin, Christian

    2011-01-01

    This paper addresses fundamental aspects of statistical mechanics such as the motivation of a classical state space with spontaneous transitions, the meaning of non-equilibrium in the context of thermalization, and the justification of these concepts from the quantum-mechanical point of view. After an introductory part we focus on the problem of entropy production in non-equilibrium systems. In particular, the generally accepted formula for entropy production in the environment is analyzed from a critical perspective. It is shown that this formula is only valid in the limit of separated time scales of the system's and the environmental degrees of freedom. Finally, we present an alternative simple proof of the fluctuation theorem.

  19. 14th International Conference on Nonequilibrium Carrier Dynamics in Semiconductors

    CERN Document Server

    Saraniti, M; Nonequilibrium Carrier Dynamics in Semiconductors

    2006-01-01

    International experts gather every two years at this established conference to discuss recent developments in theory and experiment in non-equilibrium transport phenomena. These developments have been the driving force behind the spectacular advances in semiconductor physics and devices over the last few decades. Originally known as "Hot Carriers in Semiconductors," the 14th conference in the series covered a wide spectrum of traditional topics dealing with non-equilibrium phenomena, ranging from quantum transport to optical phenomena in mesoscopic and nano-scale structures. Particular attention was given this time to emerging areas of this rapidly evolving field, with many sessions covering terahertz devices, high field transport in nitride semiconductors, spintronics, molecular electronics, and bioelectronics applications.

  20. Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

    International Nuclear Information System (INIS)

    Mottola, E.; Bhattacharya, T.; Cooper, F.

    1998-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys

  1. Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

    Energy Technology Data Exchange (ETDEWEB)

    Mottola, E.; Bhattacharya, T.; Cooper, F. [and others

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys.

  2. 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

  3. Exploring the nonequilibrium dynamics of ultracold quantum gases by using numerical tools

    Science.gov (United States)

    Heidrich-Meisner, Fabian

    Numerical tools such as exact diagonalization or the density matrix renormalization group method have been vital for the study of the nonequilibrium dynamics of strongly correlated many-body systems. Moreover, they provided unique insight for the interpretation of quantum gas experiments, whenever a direct comparison with theory is possible. By considering the example of the experiment by Ronzheimer et al., in which both an interaction quench and the release of bosons from a trap into an empty optical lattice (sudden expansion) was realized, I discuss several nonequilibrium effects of strongly interacting quantum gases. These include the thermalization of a closed quantum system and its connection to the eigenstate thermalization hypothesis, nonequilibrium mass transport, dynamical fermionization, and transient phenomena such as quantum distillation or dynamical quasicondensation. I highlight the role of integrability in giving rise to ballistic transport in strongly interacting 1D systems and in determining the asymptotic state after a quantum quench. The talk concludes with a perspective on open questions concerning 2D systems and the numerical simulation of their nonequilibrium dynamics. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 801.

  4. Non-equilibrium dynamics of single polymer adsorption to solid surfaces

    NARCIS (Netherlands)

    Panja, D.; Barkema, G.T.; Kolomeisky, A.B.

    2009-01-01

    The adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption of a single polymer of length N to a planar solid surface

  5. A general theory of non-equilibrium dynamics of lipid-protein fluid membranes

    DEFF Research Database (Denmark)

    Lomholt, Michael Andersen; Hansen, Per Lyngs; Miao, L.

    2005-01-01

    We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of statistical physics and designed to be a meso...

  6. Kinetic equations within the formalism of non-equilibrium thermo field dynamics

    International Nuclear Information System (INIS)

    Arimitsu, Toshihico

    1988-01-01

    After reviewing the real-time formalism of dissipative quantum field theory, i.e. non-equilibrium thermo field dynamics (NETFD), a kinetic equation, a self-consistent equation for the dissipation coefficient and a ''mass'' or ''chemical potential'' renormalization equation for non-equilibrium transient situations are extracted out of the two-point Green's function of the Heisenberg field, in their most general forms upon the basic requirements of NETFD. The formulation is applied to the electron-phonon system, as an example, where the gradient expansion and the quasi-particle approximation are performed. The formalism of NETFD is reinvestigated in connection with the kinetic equations. (orig.)

  7. One-loop calculation in time-dependent non-equilibrium thermo field dynamics

    International Nuclear Information System (INIS)

    Umezawa, H.; Yamanaka, Y.

    1989-01-01

    This paper is a review on the structure of thermo field dynamics (TFD) in which the basic concepts such as the thermal doublets, the quasi-particles and the self-consistent renormalization are presented in detail. A strong emphasis is put on the computational scheme. A detailed structure of this scheme is illustrated by the one-loop calculation in a non-equilibrium time-dependent process. A detailed account of the one-loop calculation has never been reported anywhere. The role of the self-consistent renormalization is explained. The equilibrium TFD is obtained as the long-time limit of non-equilibrium TFD. (author)

  8. Elements of non-equilibrium (ℎ, k)-dynamics at zero and finite temperatures

    International Nuclear Information System (INIS)

    Golubeva, O.N.; Sukhanov, A.D.

    2011-01-01

    We suggest a method which allows developing some elements of non-equilibrium (ℎ, k)-dynamics without use of Schroedinger equation. It is based on the generalization pf Fokker-Planck and Hamilton-Jacobi equations. Sequential considering of stochastic influence of vacuum is realized in the quantum heat bath model. We show that at the presence of quantum-thermal diffusion non-equilibrium wave functions describe the process of nearing to generalized state of thermal equilibrium at zero and finite temperatures. They can be used as a ground for universal description of transport phenomena

  9. Quantum gases finite temperature and non-equilibrium dynamics

    CERN Document Server

    Szymanska, Marzena; Davis, Matthew; Gardiner, Simon

    2013-01-01

    The 1995 observation of Bose-Einstein condensation in dilute atomic vapours spawned the field of ultracold, degenerate quantum gases. Unprecedented developments in experimental design and precision control have led to quantum gases becoming the preferred playground for designer quantum many-body systems. This self-contained volume provides a broad overview of the principal theoretical techniques applied to non-equilibrium and finite temperature quantum gases. Covering Bose-Einstein condensates, degenerate Fermi gases, and the more recently realised exciton-polariton condensates, it fills a gap by linking between different methods with origins in condensed matter physics, quantum field theory, quantum optics, atomic physics, and statistical mechanics. Thematically organised chapters on different methodologies, contributed by key researchers using a unified notation, provide the first integrated view of the relative merits of individual approaches, aided by pertinent introductory chapters and the guidance of ed...

  10. Stochastic linearization of turbulent dynamics of dispersive waves in equilibrium and non-equilibrium state

    International Nuclear Information System (INIS)

    Jiang, Shixiao W; Lu, Haihao; Zhou, Douglas; Cai, David

    2016-01-01

    Characterizing dispersive wave turbulence in the long time dynamics is central to understanding of many natural phenomena, e.g., in atmosphere ocean dynamics, nonlinear optics, and plasma physics. Using the β -Fermi–Pasta–Ulam nonlinear system as a prototypical example, we show that in thermal equilibrium and non-equilibrium steady state the turbulent state even in the strongly nonlinear regime possesses an effective linear stochastic structure in renormalized normal variables. In this framework, we can well characterize the spatiotemporal dynamics, which are dominated by long-wavelength renormalized waves. We further demonstrate that the energy flux is nearly saturated by the long-wavelength renormalized waves in non-equilibrium steady state. The scenario of such effective linear stochastic dynamics can be extended to study turbulent states in other nonlinear wave systems. (paper)

  11. Approximate but accurate quantum dynamics from the Mori formalism: I. Nonequilibrium dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Montoya-Castillo, Andrés, E-mail: am3720@columbia.edu; Reichman, David R., E-mail: drr2103@columbia.edu [Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-05-14

    We present a formalism that explicitly unifies the commonly used Nakajima-Zwanzig approach for reduced density matrix dynamics with the more versatile Mori theory in the context of nonequilibrium dynamics. Employing a Dyson-type expansion to circumvent the difficulty of projected dynamics, we obtain a self-consistent equation for the memory kernel which requires only knowledge of normally evolved auxiliary kernels. To illustrate the properties of the current approach, we focus on the spin-boson model and limit our attention to the use of a simple and inexpensive quasi-classical dynamics, given by the Ehrenfest method, for the calculation of the auxiliary kernels. For the first time, we provide a detailed analysis of the dependence of the properties of the memory kernels obtained via different projection operators, namely, the thermal (Redfield-type) and population based (NIBA-type) projection operators. We further elucidate the conditions that lead to short-lived memory kernels and the regions of parameter space to which this program is best suited. Via a thorough analysis of the different closures available for the auxiliary kernels and the convergence properties of the self-consistently extracted memory kernel, we identify the mechanisms whereby the current approach leads to a significant improvement over the direct usage of standard semi- and quasi-classical dynamics.

  12. Approximate but accurate quantum dynamics from the Mori formalism: I. Nonequilibrium dynamics

    International Nuclear Information System (INIS)

    Montoya-Castillo, Andrés; Reichman, David R.

    2016-01-01

    We present a formalism that explicitly unifies the commonly used Nakajima-Zwanzig approach for reduced density matrix dynamics with the more versatile Mori theory in the context of nonequilibrium dynamics. Employing a Dyson-type expansion to circumvent the difficulty of projected dynamics, we obtain a self-consistent equation for the memory kernel which requires only knowledge of normally evolved auxiliary kernels. To illustrate the properties of the current approach, we focus on the spin-boson model and limit our attention to the use of a simple and inexpensive quasi-classical dynamics, given by the Ehrenfest method, for the calculation of the auxiliary kernels. For the first time, we provide a detailed analysis of the dependence of the properties of the memory kernels obtained via different projection operators, namely, the thermal (Redfield-type) and population based (NIBA-type) projection operators. We further elucidate the conditions that lead to short-lived memory kernels and the regions of parameter space to which this program is best suited. Via a thorough analysis of the different closures available for the auxiliary kernels and the convergence properties of the self-consistently extracted memory kernel, we identify the mechanisms whereby the current approach leads to a significant improvement over the direct usage of standard semi- and quasi-classical dynamics.

  13. An impurity solver for nonequilibrium dynamical mean field theory based on hierarchical quantum master equations

    Energy Technology Data Exchange (ETDEWEB)

    Haertle, Rainer [Institut fuer Theoretische Physik, Georg-August-Universitaet Goettingen, Goettingen (Germany); Millis, Andrew J. [Department of Physics, Columbia University, New York (United States)

    2016-07-01

    We present a new impurity solver for real-time and nonequilibrium dynamical mean field theory applications, based on the recently developed hierarchical quantum master equation approach. Our method employs a hybridization expansion of the time evolution operator, including an advanced, systematic truncation scheme. Convergence to exact results for not too low temperatures has been demonstrated by a direct comparison to quantum Monte Carlo simulations. The approach is time-local, which gives us access to slow dynamics such as, e.g., in the presence of magnetic fields or exchange interactions and to nonequilibrium steady states. Here, we present first results of this new scheme for the description of strongly correlated materials in the framework of dynamical mean field theory, including benchmark and new results for the Hubbard and periodic Anderson model.

  14. The new physics of non-equilibrium condensates: insights from classical dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Eastham, P R [Theory of Condensed Matter, Cavendish Laboratory, Cambridge CB3 0HE (United Kingdom)

    2007-07-25

    We discuss the dynamics of classical Dicke-type models, aiming to clarify the mechanisms by which coherent states could develop in potentially non-equilibrium systems such as semiconductor microcavities. We present simulations of an undamped model which show spontaneous coherent states with persistent oscillations in the magnitude of the order parameter. These states are generalizations of superradiant ringing to the case of inhomogeneous broadening. They correspond to the persistent gap oscillations proposed in fermionic atomic condensates, and arise from a variety of initial conditions. We show that introducing randomness into the couplings can suppress the oscillations, leading to a limiting dynamics with a time-independent order parameter. This demonstrates that non-equilibrium generalizations of polariton condensates can be created even without dissipation. We explain the dynamical origins of the coherence in terms of instabilities of the normal state, and consider how it can additionally develop through scattering and dissipation.

  15. The new physics of non-equilibrium condensates: insights from classical dynamics

    International Nuclear Information System (INIS)

    Eastham, P R

    2007-01-01

    We discuss the dynamics of classical Dicke-type models, aiming to clarify the mechanisms by which coherent states could develop in potentially non-equilibrium systems such as semiconductor microcavities. We present simulations of an undamped model which show spontaneous coherent states with persistent oscillations in the magnitude of the order parameter. These states are generalizations of superradiant ringing to the case of inhomogeneous broadening. They correspond to the persistent gap oscillations proposed in fermionic atomic condensates, and arise from a variety of initial conditions. We show that introducing randomness into the couplings can suppress the oscillations, leading to a limiting dynamics with a time-independent order parameter. This demonstrates that non-equilibrium generalizations of polariton condensates can be created even without dissipation. We explain the dynamical origins of the coherence in terms of instabilities of the normal state, and consider how it can additionally develop through scattering and dissipation

  16. Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems

    International Nuclear Information System (INIS)

    Wu, Wei; Wang, Jin

    2014-01-01

    We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic and thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series

  17. Memory Effects and Nonequilibrium Correlations in the Dynamics of Open Quantum Systems

    Science.gov (United States)

    Morozov, V. G.

    2018-01-01

    We propose a systematic approach to the dynamics of open quantum systems in the framework of Zubarev's nonequilibrium statistical operator method. The approach is based on the relation between ensemble means of the Hubbard operators and the matrix elements of the reduced statistical operator of an open quantum system. This key relation allows deriving master equations for open systems following a scheme conceptually identical to the scheme used to derive kinetic equations for distribution functions. The advantage of the proposed formalism is that some relevant dynamical correlations between an open system and its environment can be taken into account. To illustrate the method, we derive a non-Markovian master equation containing the contribution of nonequilibrium correlations associated with energy conservation.

  18. Dynamical Cooper pairing in non-equilibrium electron-phonon systems

    Energy Technology Data Exchange (ETDEWEB)

    Knap, Michael [Technical University of Munich (Germany); Harvard University (United States); Babadi, Mehrtash; Refael, Gil [Caltech (United States); Martin, Ivar [Argonne National Laboratory (United States); Demler, Eugene [Harvard University (United States)

    2016-07-01

    Ultrafast laser pulses have been used to manipulate complex quantum materials and to induce dynamical phase transitions. One of the most striking examples is the transient enhancement of superconductivity in several classes of materials upon irradiating them with high intensity pulses of terahertz light. Motivated by these experiments we analyze the Cooper pairing instabilities in non-equilibrium electron-phonon systems. We demonstrate that the light induced non-equilibrium state of phonons results in a simultaneous increase of the superconducting coupling constant and the electron scattering. We analyze the competition between these effects and show that in a broad range of parameters the dynamic enhancement of Cooper pair formation dominates over the increase in the scattering rate. This opens the possibility of transient light induced superconductivity at temperatures that are considerably higher than the equilibrium transition temperatures. Our results pave new pathways for engineering high-temperature light-induced superconducting states.

  19. Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.; Kincaid, J.M.

    1985-01-01

    A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo time correlation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau

  20. Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.; Kincaid, J.M.

    1986-01-01

    A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure, which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo timecorrelation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau

  1. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-01-01

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition

  2. Nonequilibrium and Nonlinear Dynamics in Geomaterials I : The Low Strain Regime

    OpenAIRE

    Pasqualini, Donatella; Heitmann, Katrin; TenCate, James A.; Habib, Salman; Higdon, David; Johnson, Paul A.

    2006-01-01

    Members of a wide class of geomaterials are known to display complex and fascinating nonlinear and nonequilibrium dynamical behaviors over a wide range of bulk strains, down to surprisingly low values, e.g., 10^{-7}. In this paper we investigate two sandstones, Berea and Fontainebleau, and characterize their behavior under the influence of very small external forces via carefully controlled resonant bar experiments. By reducing environmental effects due to temperature and humidity variations,...

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

    Science.gov (United States)

    Echinaka, Yuki; Ozeki, Yukiyasu

    2016-10-01

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

  4. Matrix product algorithm for stochastic dynamics on networks applied to nonequilibrium Glauber dynamics

    Science.gov (United States)

    Barthel, Thomas; De Bacco, Caterina; Franz, Silvio

    2018-01-01

    We introduce and apply an efficient method for the precise simulation of stochastic dynamical processes on locally treelike graphs. Networks with cycles are treated in the framework of the cavity method. Such models correspond, for example, to spin-glass systems, Boolean networks, neural networks, or other technological, biological, and social networks. Building upon ideas from quantum many-body theory, our approach is based on a matrix product approximation of the so-called edge messages—conditional probabilities of vertex variable trajectories. Computation costs and accuracy can be tuned by controlling the matrix dimensions of the matrix product edge messages (MPEM) in truncations. In contrast to Monte Carlo simulations, the algorithm has a better error scaling and works for both single instances as well as the thermodynamic limit. We employ it to examine prototypical nonequilibrium Glauber dynamics in the kinetic Ising model. Because of the absence of cancellation effects, observables with small expectation values can be evaluated accurately, allowing for the study of decay processes and temporal correlations.

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

    International Nuclear Information System (INIS)

    Altaner, Bernhard

    2017-01-01

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

  6. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  7. Dynamical TAP equations for non-equilibrium Ising spin glasses

    DEFF Research Database (Denmark)

    Roudi, Yasser; Hertz, John

    2011-01-01

    We derive and study dynamical TAP equations for Ising spin glasses obeying both synchronous and asynchronous dynamics using a generating functional approach. The system can have an asymmetric coupling matrix, and the external fields can be time-dependent. In the synchronously updated model, the TAP...... equations take the form of self consistent equations for magnetizations at time t+1, given the magnetizations at time t. In the asynchronously updated model, the TAP equations determine the time derivatives of the magnetizations at each time, again via self consistent equations, given the current values...... of the magnetizations. Numerical simulations suggest that the TAP equations become exact for large systems....

  8. Broken detailed balance and non-equilibrium dynamics in living systems: a review

    Science.gov (United States)

    Gnesotto, F. S.; Mura, F.; Gladrow, J.; Broedersz, C. P.

    2018-06-01

    Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

  9. Broken detailed balance and non-equilibrium dynamics in living systems: a review.

    Science.gov (United States)

    Gnesotto, F S; Mura, F; Gladrow, J; Broedersz, C P

    2018-03-05

    Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

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

    Science.gov (United States)

    Altaner, Bernhard

    2017-11-01

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

  11. Dynamics of unstable sound waves in a non-equilibrium medium at the nonlinear stage

    Science.gov (United States)

    Khrapov, Sergey; Khoperskov, Alexander

    2018-03-01

    A new dispersion equation is obtained for a non-equilibrium medium with an exponential relaxation model of a vibrationally excited gas. We have researched the dependencies of the pump source and the heat removal on the medium thermodynamic parameters. The boundaries of sound waves stability regions in a non-equilibrium gas have been determined. The nonlinear stage of sound waves instability development in a vibrationally excited gas has been investigated within CSPH-TVD and MUSCL numerical schemes using parallel technologies OpenMP-CUDA. We have obtained a good agreement of numerical simulation results with the linear perturbations dynamics at the initial stage of the sound waves growth caused by instability. At the nonlinear stage, the sound waves amplitude reaches the maximum value that leads to the formation of shock waves system.

  12. Shear Viscosity of Benzene, Toluene, and p-Xylene by Non-equilibrium Molecular Dynamics Simulations

    International Nuclear Information System (INIS)

    Lee, Song Hi

    2004-01-01

    Green and Kubo showed that the phenomenological coefficients describing many transport processes and time dependent phenomena in general could be written as integrals over a certain type of function called a time correlation function. The Green-Kubo formulas are the formal expressions for hydrodynamic field variables and some of the thermodynamic properties in terms of the microscopic variables of an N-particle system. The identification of microscopic expressions for macroscopic variables is made by a process of comparison of the conservation equations of hydrodynamics with the microscopic equations of change for conserved densities. The importance of these formulas is three-fold: they provide an obvious method for calculating transport coefficients using computer simulation, a convenient starting point for constructing analytic theories for non-equilibrium processes, and an essential information for designing non-equilibrium molecular dynamics (NEMD) algorithm.

  13. Nonequilibrium dynamic critical scaling of the quantum Ising chain.

    Science.gov (United States)

    Kolodrubetz, Michael; Clark, Bryan K; Huse, David A

    2012-07-06

    We solve for the time-dependent finite-size scaling functions of the one-dimensional transverse-field Ising chain during a linear-in-time ramp of the field through the quantum critical point. We then simulate Mott-insulating bosons in a tilted potential, an experimentally studied system in the same equilibrium universality class, and demonstrate that universality holds for the dynamics as well. We find qualitatively athermal features of the scaling functions, such as negative spin correlations, and we show that they should be robustly observable within present cold atom experiments.

  14. A Local Probe for Universal Non-equilibrium Dynamics

    Science.gov (United States)

    2015-06-01

    shown are polarizing beam splitters . About 700µW are superimposed with a reference laser on a glass plate and coupled into an optical fiber to detect...A Local Probe for Universal Non -equilibrium Dynamics We report on the results obtained across a nine-month ARO-sponsored project, whose purpose was...to implement a local probe for a gas of ultracold atoms. We used a phase plate with a spiral phase gradient to create a hollow-core laser beam . This

  15. Atom transistor from the point of view of nonequilibrium dynamics

    International Nuclear Information System (INIS)

    Zhang, Z; Dunjko, V; Olshanii, M

    2015-01-01

    We analyze the atom field-effect transistor scheme (Stickney et al 2007 Phys. Rev. A 75 013608) using the standard tools of quantum and classical nonequlilibrium dynamics. We first study the correspondence between the quantum and the mean-field descriptions of this system by computing, both ab initio and by using their mean-field analogs, the deviations from the Eigenstate Thermalization Hypothesis, quantum fluctuations, and the density of states. We find that, as far as the quantities that interest us, the mean-field model can serve as a semi-classical emulator of the quantum system. Then, using the mean-field model, we interpret the point of maximal output signal in our transistor as the onset of ergodicity—the point where the system becomes, in principle, able to attain the thermal values of the former integrals of motion, albeit not being fully thermalized yet. (paper)

  16. Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems.

    Science.gov (United States)

    Wu, Wei; Wang, Jin

    2013-09-28

    We established a potential and flux field landscape theory to quantify the global stability and dynamics of general spatially dependent non-equilibrium deterministic and stochastic systems. We extended our potential and flux landscape theory for spatially independent non-equilibrium stochastic systems described by Fokker-Planck equations to spatially dependent stochastic systems governed by general functional Fokker-Planck equations as well as functional Kramers-Moyal equations derived from master equations. Our general theory is applied to reaction-diffusion systems. For equilibrium spatially dependent systems with detailed balance, the potential field landscape alone, defined in terms of the steady state probability distribution functional, determines the global stability and dynamics of the system. The global stability of the system is closely related to the topography of the potential field landscape in terms of the basins of attraction and barrier heights in the field configuration state space. The effective driving force of the system is generated by the functional gradient of the potential field alone. For non-equilibrium spatially dependent systems, the curl probability flux field is indispensable in breaking detailed balance and creating non-equilibrium condition for the system. A complete characterization of the non-equilibrium dynamics of the spatially dependent system requires both the potential field and the curl probability flux field. While the non-equilibrium potential field landscape attracts the system down along the functional gradient similar to an electron moving in an electric field, the non-equilibrium flux field drives the system in a curly way similar to an electron moving in a magnetic field. In the small fluctuation limit, the intrinsic potential field as the small fluctuation limit of the potential field for spatially dependent non-equilibrium systems, which is closely related to the steady state probability distribution functional, is

  17. Non-equilibrium dynamics due to moving deflagration front at RDX/HTPB interface

    Science.gov (United States)

    Chaudhuri, Santanu; Joshi, Kaushik; Lacevic, Naida

    Reactive dissipative particle dynamics (DPD-RX), a promising tool in characterizing the sensitivity and performance of heterogeneous solid propellants like polymer bonded explosives (PSXs), requires further testing for non-equilibrium dynamics. It is important to understand detailed atomistic chemistry for developing coarse grain reactive models needed for the DPD-RX. In order to obtain insights into combustion chemistry of RDX/HTPB binder, we used reactive molecular dynamics (RMD) to obtain energy up-pumping and reaction mechanisms at RDX/HTPB interface when exposed to a self-sustaining deflagration front. Hot spots are ignited near and away from the heterogeneous interface using the thermal pulse. The results show that the hot spot near interface significantly delays the transition from ignition to deflagration. We will present the mechanical response and the combustion chemistry of HTPB when the propagating deflagration front hits the polymer binder. We will discuss our efforts to incorporate this RMD based chemistry into the DPD-RX which will enable us to perform such non-equilibrium dynamics simulations on large-length scale with microstructural heterogeneities. Funding from DTRA Grant Number HDTRA1-15-1-0034 is acknowledged.

  18. A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics

    Science.gov (United States)

    Kretchmer, Joshua S.; Chan, Garnet Kin-Lic

    2018-02-01

    We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

  19. Vectorization of a Monte Carlo simulation scheme for nonequilibrium gas dynamics

    Science.gov (United States)

    Boyd, Iain D.

    1991-01-01

    Significant improvement has been obtained in the numerical performance of a Monte Carlo scheme for the analysis of nonequilibrium gas dynamics through an implementation of the algorithm which takes advantage of vector hardware, as presently demonstrated through application to three different problems. These are (1) a 1D standing-shock wave; (2) the flow of an expanding gas through an axisymmetric nozzle; and (3) the hypersonic flow of Ar gas over a 3D wedge. Problem (3) is illustrative of the greatly increased number of molecules which the simulation may involve, thanks to improved algorithm performance.

  20. Mathematical theory of nonequilibrium steady states on the frontier of probability and dynamical systems

    CERN Document Server

    Jiang, Da-Quan; Qian, Min-Ping

    2004-01-01

    This volume provides a systematic mathematical exposition of the conceptual problems of nonequilibrium statistical physics, such as entropy production, irreversibility, and ordered phenomena. Markov chains, diffusion processes, and hyperbolic dynamical systems are used as mathematical models of physical systems. A measure-theoretic definition of entropy production rate and its formulae in various cases are given. It vanishes if and only if the stationary system is reversible and in equilibrium. Moreover, in the cases of Markov chains and diffusion processes on manifolds, it can be expressed in terms of circulations on directed cycles. Regarding entropy production fluctuations, the Gallavotti-Cohen fluctuation theorem is rigorously proved.

  1. Non-equilibrium QCD of high-energy multi-gluon dynamics

    International Nuclear Information System (INIS)

    Geiger, K.

    1996-01-01

    A non-equilibrium QCD description of multiparticle dynamics in space-time is of both fundamental and phenomenological interest. Here the authors discusses an attempt to derive from first principles, a real-time formalism to study the dynamical interplay of quantum and statistical-kinetic properties of non-equilibrium multi-parton systems produced in high-energy QCD processes. The ultimate goal (from which one is still far away) is to have a practically applicable description of the space-time evolution of a general initial system of gluons and quarks, characterized by some large energy or momentum scale, that expands, diffuses and dissipates according to the self- and mutual-interactions, and eventually converts dynamically into final state hadrons. For example, the evolution of parton showers in the mechanism of parton-hadron conversion in high-energy hadronic collisions, or, the description of formation, evolution and freezeout of a quark-gluon plasma, in ultra-relativistic heavy-ion collisions

  2. Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

    Science.gov (United States)

    Min, Wei; Xie, X. Sunney; Bagchi, Biman

    2009-08-01

    Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

  3. Nonequilibrium Langevin dynamics: A demonstration study of shear flow fluctuations in a simple fluid

    Science.gov (United States)

    Belousov, Roman; Cohen, E. G. D.; Rondoni, Lamberto

    2017-08-01

    The present paper is based on a recent success of the second-order stochastic fluctuation theory in describing time autocorrelations of equilibrium and nonequilibrium physical systems. In particular, it was shown to yield values of the related deterministic parameters of the Langevin equation for a Couette flow in a microscopic molecular dynamics model of a simple fluid. In this paper we find all the remaining constants of the stochastic dynamics, which then is simulated numerically and compared directly with the original physical system. By using these data, we study in detail the accuracy and precision of a second-order Langevin model for nonequilibrium physical systems theoretically and computationally. We find an intriguing relation between an applied external force and cumulants of the resulting flow fluctuations. This is characterized by a linear dependence of an athermal cumulant ratio, an apposite quantity introduced here. In addition, we discuss how the order of a given Langevin dynamics can be raised systematically by introducing colored noise.

  4. Quantum thermodynamics from the nonequilibrium dynamics of open systems: Energy, heat capacity, and the third law.

    Science.gov (United States)

    Hsiang, J-T; Chou, C H; Subaşı, Y; Hu, B L

    2018-01-01

    In a series of papers, we intend to take the perspective of open quantum systems and examine from their nonequilibrium dynamics the conditions when the physical quantities, their relations, and the laws of thermodynamics become well defined and viable for quantum many-body systems. We first describe how an open-system nonequilibrium dynamics (ONEq) approach is different from the closed combined system +  environment in a global thermal state (CGTs) setup. Only after the open system equilibrates will it be amenable to conventional thermodynamics descriptions, thus quantum thermodynamics (QTD) comes at the end rather than assumed in the beginning. The linkage between the two comes from the reduced density matrix of ONEq in that stage having the same form as that of the system in the CGTs. We see the open-system approach having the advantage of dealing with nonequilibrium processes as many experiments in the near future will call for. Because it spells out the conditions of QTD's existence, it can also aid us in addressing the basic issues in quantum thermodynamics from first principles in a systematic way. We then study one broad class of open quantum systems where the full nonequilibrium dynamics can be solved exactly, that of the quantum Brownian motion of N strongly coupled harmonic oscillators, interacting strongly with a scalar-field environment. In this paper, we focus on the internal energy, heat capacity, and the third law. We show for this class of physical models, amongst other findings, the extensive property of the internal energy, the positivity of the heat capacity, and the validity of the third law from the perspective of the behavior of the heat capacity toward zero temperature. These conclusions obtained from exact solutions and quantitative analysis clearly disprove claims of negative specific heat in such systems and dispel allegations that in such systems the validity of the third law of thermodynamics relies on quantum entanglement. They are

  5. Phenomena at the QCD phase transition in nonequilibrium chiral fluid dynamics (NχFD)

    Energy Technology Data Exchange (ETDEWEB)

    Nahrgang, Marlene [Duke University, Department of Physics, Durham, NC (United States); Herold, Christoph [Suranaree University of Technology, School of Physics, Nakhon Ratchasima (Thailand)

    2016-08-15

    Heavy-ion collisions performed in the beam energy range accessible by the NICA collider facility are expected to produce systems of extreme net-baryon densities and can thus reach yet unexplored regions of the QCD phase diagram. Here, one expects the phase transition between the plasma of deconfined quarks and gluons and the hadronic matter to be of first order. A discovery of the first-order phase transition would as well prove the existence of the QCD critical point, a landmark in the phase diagram. In order to understand possible signals of the first-order phase transition in heavy-ion collision experiments it is very important to develop dynamical models of the phase transition. Here, we discuss the opportunities of studying dynamical effects at the QCD first-order phase transition within our model of nonequilibrium chiral fluid dynamics. (orig.)

  6. Critical dynamics a field theory approach to equilibrium and non-equilibrium scaling behavior

    CERN Document Server

    Täuber, Uwe C

    2014-01-01

    Introducing a unified framework for describing and understanding complex interacting systems common in physics, chemistry, biology, ecology, and the social sciences, this comprehensive overview of dynamic critical phenomena covers the description of systems at thermal equilibrium, quantum systems, and non-equilibrium systems. Powerful mathematical techniques for dealing with complex dynamic systems are carefully introduced, including field-theoretic tools and the perturbative dynamical renormalization group approach, rapidly building up a mathematical toolbox of relevant skills. Heuristic and qualitative arguments outlining the essential theory behind each type of system are introduced at the start of each chapter, alongside real-world numerical and experimental data, firmly linking new mathematical techniques to their practical applications. Each chapter is supported by carefully tailored problems for solution, and comprehensive suggestions for further reading, making this an excellent introduction to critic...

  7. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

    Science.gov (United States)

    Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

    2017-07-11

    Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

  8. Error suppression and error correction in adiabatic quantum computation: non-equilibrium dynamics

    International Nuclear Information System (INIS)

    Sarovar, Mohan; Young, Kevin C

    2013-01-01

    While adiabatic quantum computing (AQC) has some robustness to noise and decoherence, it is widely believed that encoding, error suppression and error correction will be required to scale AQC to large problem sizes. Previous works have established at least two different techniques for error suppression in AQC. In this paper we derive a model for describing the dynamics of encoded AQC and show that previous constructions for error suppression can be unified with this dynamical model. In addition, the model clarifies the mechanisms of error suppression and allows the identification of its weaknesses. In the second half of the paper, we utilize our description of non-equilibrium dynamics in encoded AQC to construct methods for error correction in AQC by cooling local degrees of freedom (qubits). While this is shown to be possible in principle, we also identify the key challenge to this approach: the requirement of high-weight Hamiltonians. Finally, we use our dynamical model to perform a simplified thermal stability analysis of concatenated-stabilizer-code encoded many-body systems for AQC or quantum memories. This work is a companion paper to ‘Error suppression and error correction in adiabatic quantum computation: techniques and challenges (2013 Phys. Rev. X 3 041013)’, which provides a quantum information perspective on the techniques and limitations of error suppression and correction in AQC. In this paper we couch the same results within a dynamical framework, which allows for a detailed analysis of the non-equilibrium dynamics of error suppression and correction in encoded AQC. (paper)

  9. Preface: Special issue featuring papers from the International Conference on Nonequilibrium Carrier Dynamics in Semiconductors

    Science.gov (United States)

    Reggiani, L.; Bordone, P.; Brunetti, R.

    2004-02-01

    The International Conference on Nonequilibrium Carrier Dynamics in Semiconductors (HCIS-13) celebrates 30 years since it first took place in Modena. Nonequilibrium dynamics of charge carriers, pioneered by the hot-electron concept, is an important issue for understanding electro-optic transport properties in semiconductor materials and structures. In these 30 years several topics have matured, and new ones have emerged thus fertilizing the field with a variety of physical problems and new ideas. The history of the conference is summarized in the opening paper `30 years of HCIS'. The future of the conference seems secure considering the continued lively interest of the participants. The conference addressed eleven major topics which constitute the backbone of the proceedings and are summarized as follows: carrier transport in low dimensional and nanostructure systems, nonequilibrium carriers in superlattices and devices, small devices and related phenomena, carrier dynamics and fluctuations, carrier quantum dynamics, coherent/incoherent carrier dynamics of optical excitations and ultra-fast optical phenomena, nonlinear optical effects, transport in organic matter, semiconductor-based spintronics, coherent dynamics in solid state systems for quantum processing and communication, novel materials and devices. Nanometric space scale and femtosecond time scale represent the ultimate domains of theoretical, experimental and practical interest. Traditional fields such as bulk properties, quantum transport, fluctuations and chaotic phenomena, etc, have received thorough and continuous attention. Emerging fields from previous conferences, such as quantum processing and communication, have been better assessed. New fields, such as spintronics and electron transport in organic matter, have appeared for the first time. One plenary talk, 11 invited talks, 230 submitted abstracts covering all these topics constituted a single-session conference. Following scientific selection

  10. Nonequilibrium molecular dynamics simulation of coupling between nanoparticles and base-fluid in a nanofluid

    International Nuclear Information System (INIS)

    Kang, Hongbo; Zhang, Yuwen; Yang, Mo; Li, Ling

    2012-01-01

    The intent of this study is to examine nonequilibrium heat transfer in a copper–argon nanofluid by molecular dynamics simulation. Two different methods, the physical definition method and the curve fitting method, are introduced to calculate the coupling factor between nanoparticles and base fluid. The results show that the coupling factors obtained by these two methods are consistent. The coupling factor is proportional to the volume fraction of the nanoparticle and inversely proportional to nanoparticle diameter. In the temperature range of 90–200 K, the coupling factor is not affected by temperature. The nanoparticle aggregation results in a decrease of the coupling factor. -- Highlights: ► Nonequilibrium heat transfer in a copper–argon nanofluid is investigated by molecular dynamics simulation. ► The coupling factor is proportion to the volume fraction of the nanoparticle and inverse proportion to nanoparticle diameter. ► In the temperature range of 90–200 K, there is no temperature effect on the coupling factor. ► The nanoparticle aggregation results in a decrease of the coupling factor.

  11. Non-equilibrium solid-to-plasma transition dynamics using XANES diagnostic

    Energy Technology Data Exchange (ETDEWEB)

    Dorchies, F., E-mail: dorchies@celia.u-bordeaux1.fr [Univ. Bordeaux, CNRS, CEA, CELIA (Centre Lasers Intenses et Applications), UMR 5107, F-33400 Talence (France); Recoules, V. [CEA-DAM-DIF, F-91297 Arpajon (France)

    2016-10-31

    The advent of femtosecond lasers has shed new light on non-equilibrium high energy density physics. The ultrafast energy absorption by electrons and the finite rate of their energy transfer to the lattice creates non-equilibrium states of matter, triggering a new class of non-thermal processes from the ambient solid up to extreme conditions of temperature and pressure, referred as the warm dense matter regime. The dynamical interplay between electron and atomic structures is the key issue that drives the ultrafast phase transitions dynamics. Bond weakening or bond hardening are predicted, but strongly depends on the material considered. Many studies have been conducted but this physics is still poorly understood. The experimental tools used up-to-now have provided an incomplete insight. Pure optical techniques measure only indirectly atomic motion through changes in the dielectric function whereas X-ray or electron diffraction only probes the average long-range order. This review is dedicated to recent developments in time-resolved X-ray absorption near-edge spectroscopy, which is expected to give a more complete picture by probing simultaneously the modifications of the near-continuum electron and local atomic structures. Results are reported for three different types of metals (simple, transition and noble metals) in which a confrontation has been carried out between measurements and ab initio simulations.

  12. Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.

    Science.gov (United States)

    O'Meara, Brian C; Smith, Stacey D; Armbruster, W Scott; Harder, Lawrence D; Hardy, Christopher R; Hileman, Lena C; Hufford, Larry; Litt, Amy; Magallón, Susana; Smith, Stephen A; Stevens, Peter F; Fenster, Charles B; Diggle, Pamela K

    2016-05-11

    Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years. © 2016 The Author(s).

  13. Non-equilibrium dynamics of single polymer adsorption to solid surfaces

    International Nuclear Information System (INIS)

    Panja, Debabrata; Barkema, Gerard T; Kolomeisky, Anatoly B

    2009-01-01

    The adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption of a single polymer of length N to a planar solid surface in the absence of hydrodynamic interactions. We find that for weak adsorption energies the adsorption timescales ∼N (1+2ν)/(1+ν) , where ν is the Flory exponent for the polymer. We argue that in this regime the single chain adsorption is closely related to a field-driven polymer translocation through narrow pores. Surprisingly, for high adsorption energies the adsorption time becomes longer, as it scales as ∼N 1+ν , which is explained by strong stretching of the unadsorbed part of the polymer close to the adsorbing surface. These two dynamic regimes are separated by an energy scale that is characterized by non-equilibrium contributions during the adsorption process. (fast track communication)

  14. Live Imaging of Calcium Dynamics during Axon Degeneration Reveals Two Functionally Distinct Phases of Calcium Influx

    Science.gov (United States)

    Yamagishi, Yuya; Tessier-Lavigne, Marc

    2015-01-01

    Calcium is a key regulator of axon degeneration caused by trauma and disease, but its specific spatial and temporal dynamics in injured axons remain unclear. To clarify the function of calcium in axon degeneration, we observed calcium dynamics in single injured neurons in live zebrafish larvae and tested the temporal requirement for calcium in zebrafish neurons and cultured mouse DRG neurons. Using laser axotomy to induce Wallerian degeneration (WD) in zebrafish peripheral sensory axons, we monitored calcium dynamics from injury to fragmentation, revealing two stereotyped phases of axonal calcium influx. First, axotomy triggered a transient local calcium wave originating at the injury site. This initial calcium wave only disrupted mitochondria near the injury site and was not altered by expression of the protective WD slow (WldS) protein. Inducing multiple waves with additional axotomies did not change the kinetics of degeneration. In contrast, a second phase of calcium influx occurring minutes before fragmentation spread as a wave throughout the axon, entered mitochondria, and was abolished by WldS expression. In live zebrafish, chelating calcium after the first wave, but before the second wave, delayed the progress of fragmentation. In cultured DRG neurons, chelating calcium early in the process of WD did not alter degeneration, but chelating calcium late in WD delayed fragmentation. We propose that a terminal calcium wave is a key instructive component of the axon degeneration program. SIGNIFICANCE STATEMENT Axon degeneration resulting from trauma or neurodegenerative disease can cause devastating deficits in neural function. Understanding the molecular and cellular events that execute axon degeneration is essential for developing treatments to address these conditions. Calcium is known to contribute to axon degeneration, but its temporal requirements in this process have been unclear. Live calcium imaging in severed zebrafish neurons and temporally controlled

  15. Non-equilibrium coherence dynamics in one-dimensional Bose gases

    DEFF Research Database (Denmark)

    Hofferberth, S.; Lesanovsky, Igor; Fischer, B.

    2007-01-01

    Low-dimensional systems provide beautiful examples of many-body quantum physics. For one-dimensional (1D) systems, the Luttinger liquid approach provides insight into universal properties. Much is known of the equilibrium state, both in the weakly and strongly interacting regimes. However......, the coherence factor is observed to approach a non-zero equilibrium value, as predicted by a Bogoliubov approach. This coupled-system decay to finite coherence is the matter wave equivalent of phase-locking two lasers by injection. The non-equilibrium dynamics of superfluids has an important role in a wide...... range of physical systems, such as superconductors, quantum Hall systems, superfluid helium and spin systems. Our experiments studying coherence dynamics show that 1D Bose gases are ideally suited for investigating this class of phenomena....

  16. Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon.

    Science.gov (United States)

    Jia, Chen; Qian, Minping; Jiang, Daquan

    2014-08-01

    A number of biological systems can be modelled by Markov chains. Recently, there has been an increasing concern about when biological systems modelled by Markov chains will perform a dynamic phenomenon called overshoot. In this study, the authors found that the steady-state behaviour of the system will have a great effect on the occurrence of overshoot. They showed that overshoot in general cannot occur in systems that will finally approach an equilibrium steady state. They further classified overshoot into two types, named as simple overshoot and oscillating overshoot. They showed that except for extreme cases, oscillating overshoot will occur if the system is far from equilibrium. All these results clearly show that overshoot is a non-equilibrium dynamic phenomenon with energy consumption. In addition, the main result in this study is validated with real experimental data.

  17. Nonequilibrium Spin Dynamics in a Trapped Fermi Gas with Effective Spin-Orbit Interactions

    International Nuclear Information System (INIS)

    Stanescu, Tudor D.; Zhang Chuanwei; Galitski, Victor

    2007-01-01

    We consider a trapped atomic system in the presence of spatially varying laser fields. The laser-atom interaction generates a pseudospin degree of freedom (referred to simply as spin) and leads to an effective spin-orbit coupling for the fermions in the trap. Reflections of the fermions from the trap boundaries provide a physical mechanism for effective momentum relaxation and nontrivial spin dynamics due to the emergent spin-orbit coupling. We explicitly consider evolution of an initially spin-polarized Fermi gas in a two-dimensional harmonic trap and derive nonequilibrium behavior of the spin polarization. It shows periodic echoes with a frequency equal to the harmonic trapping frequency. Perturbations, such as an asymmetry of the trap, lead to the suppression of the spin echo amplitudes. We discuss a possible experimental setup to observe spin dynamics and provide numerical estimates of relevant parameters

  18. 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.

  19. Nonequilibrium entropies

    International Nuclear Information System (INIS)

    Maes, Christian

    2012-01-01

    In contrast to the quite unique entropy concept useful for systems in (local) thermodynamic equilibrium, there is a variety of quite distinct nonequilibrium entropies, reflecting different physical points. We disentangle these entropies as they relate to heat, fluctuations, response, time asymmetry, variational principles, monotonicity, volume contraction or statistical forces. However, not all of those extensions yield state quantities as understood thermodynamically. At the end we sketch how aspects of dynamical activity can take over for obtaining an extended Clausius relation.

  20. Non-equilibrium coherence dynamics in one-dimensional Bose gases.

    Science.gov (United States)

    Hofferberth, S; Lesanovsky, I; Fischer, B; Schumm, T; Schmiedmayer, J

    2007-09-20

    Low-dimensional systems provide beautiful examples of many-body quantum physics. For one-dimensional (1D) systems, the Luttinger liquid approach provides insight into universal properties. Much is known of the equilibrium state, both in the weakly and strongly interacting regimes. However, it remains a challenge to probe the dynamics by which this equilibrium state is reached. Here we present a direct experimental study of the coherence dynamics in both isolated and coupled degenerate 1D Bose gases. Dynamic splitting is used to create two 1D systems in a phase coherent state. The time evolution of the coherence is revealed through local phase shifts of the subsequently observed interference patterns. Completely isolated 1D Bose gases are observed to exhibit universal sub-exponential coherence decay, in excellent agreement with recent predictions. For two coupled 1D Bose gases, the coherence factor is observed to approach a non-zero equilibrium value, as predicted by a Bogoliubov approach. This coupled-system decay to finite coherence is the matter wave equivalent of phase-locking two lasers by injection. The non-equilibrium dynamics of superfluids has an important role in a wide range of physical systems, such as superconductors, quantum Hall systems, superfluid helium and spin systems. Our experiments studying coherence dynamics show that 1D Bose gases are ideally suited for investigating this class of phenomena.

  1. Ultrafast dynamics of laser-pulse excited semiconductors: non-Markovian quantum kinetic equations with nonequilibrium correlations

    Directory of Open Access Journals (Sweden)

    V.V.Ignatyuk

    2004-01-01

    Full Text Available Non-Markovian kinetic equations in the second Born approximation are derived for a two-zone semiconductor excited by a short laser pulse. Both collision dynamics and running nonequilibrium correlations are taken into consideration. The energy balance and relaxation of the system to equilibrium are discussed. Results of numerical solution of the kinetic equations for carriers and phonons are presented.

  2. NON-EQUILIBRIUM MOLECULAR DYNAMICS USED TO OBTAIN SORET COEFFICIENTS OF BINARY HYDROCARBON MIXTURES

    Directory of Open Access Journals (Sweden)

    F. A. Furtado

    2015-09-01

    Full Text Available AbstractThe Boundary Driven Non-Equilibrium Molecular Dynamics (BD-NEMD method is employed to evaluate Soret coefficients of binary mixtures. Using a n-decane/n-pentane mixture at 298 K, we study several parameters and conditions of the simulation procedure such as system size, time step size, frequency of perturbation, and the undesired warming up of the system during the simulation. The Soret coefficients obtained here deviated around 20% when comparing with experimental data and with simulated results from the literature. We showed that fluctuations in composition gradients and the consequent deviations of the Soret coefficient may be due to characteristic fluctuations of the composition gradient. Best results were obtained with the smallest time steps and without using a thermostat, which shows that there is room for improvement and/or development of new BD-NEMD algorithms.

  3. Impact of early stage non-equilibrium dynamics on photon production in relativistic heavy ion collisions

    International Nuclear Information System (INIS)

    Oliva, L; Plumari, S; Scardina, F; Greco, V; Ruggieri, M

    2017-01-01

    In this study we discuss our results on the spectrum of photons emitted from the quark-gluon plasma produced in heavy ion collisions at RHIC energies. Simulating the space-time evolution of the fireball by solving the relativistic Boltzmann transport equation and including two-particle scattering processes with photon emission allows us to make a first step in the description of thermal photons from the QGP as well as of those produced in the pre-equilibrium stage. Indeed, we consider not only a standard Glauber initial condition but also a model in which quarks and gluons are produced in the very early stage through the Schwinger mechanism by the decay of an initial color-electric field. In the latter approach relativistic kinetic equations are coupled in a self-consistent way to field equations. We aim at spotting the impact of early stage non-equilibrium dynamics on the photon production. (paper)

  4. 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.

  5. Mode coupling theory for nonequilibrium glassy dynamics of thermal self-propelled particles.

    Science.gov (United States)

    Feng, Mengkai; Hou, Zhonghuai

    2017-06-28

    We present a mode coupling theory study for the relaxation and glassy dynamics of a system of strongly interacting self-propelled particles, wherein the self-propulsion force is described by Ornstein-Uhlenbeck colored noise and thermal noises are included. Our starting point is an effective Smoluchowski equation governing the distribution function of particle positions, from which we derive a memory function equation for the time dependence of density fluctuations in nonequilibrium steady states. With the basic assumption of the absence of macroscopic currents and standard mode coupling approximation, we can obtain expressions for the irreducible memory function and other relevant dynamic terms, wherein the nonequilibrium character of the active system is manifested through an averaged diffusion coefficient D[combining macron] and a nontrivial structural function S 2 (q) with q being the magnitude of wave vector q. D[combining macron] and S 2 (q) enter the frequency term and the vertex term for the memory function, and thus influence both the short time and the long time dynamics of the system. With these equations obtained, we study the glassy dynamics of this thermal self-propelled particle system by investigating the Debye-Waller factor f q and relaxation time τ α as functions of the persistence time τ p of self-propulsion, the single particle effective temperature T eff as well as the number density ρ. Consequently, we find the critical density ρ c for given τ p shifts to larger values with increasing magnitude of propulsion force or effective temperature, in good accordance with previously reported simulation work. In addition, the theory facilitates us to study the critical effective temperature T for fixed ρ as well as its dependence on τ p . We find that T increases with τ p and in the limit τ p → 0, it approaches the value for a simple passive Brownian system as expected. Our theory also well recovers the results for passive systems and can be

  6. Nonequilibrium dynamics of moving mirrors in quantum fields: Influence functional and the Langevin equation

    International Nuclear Information System (INIS)

    Wu, C.-H.; Lee, D.-S.

    2005-01-01

    We employ the Schwinger-Keldysh formalism to study the nonequilibrium dynamics of the mirror with perfect reflection moving in a quantum field. In the case where the mirror undergoes the small displacement, the coarse-grained effective action is obtained by integrating out the quantum field with the method of influence functional. The semiclassical Langevin equation is derived, and is found to involve two levels of backreaction effects on the dynamics of mirrors: radiation reaction induced by the motion of the mirror and backreaction dissipation arising from fluctuations in quantum field via a fluctuation-dissipation relation. Although the corresponding theorem of fluctuation and dissipation for the case with the small mirror's displacement is of model independence, the study from the first principles derivation shows that the theorem is also independent of the regulators introduced to deal with short-distance divergences from the quantum field. Thus, when the method of regularization is introduced to compute the dissipation and fluctuation effects, this theorem must be fulfilled as the results are obtained by taking the short-distance limit in the end of calculations. The backreaction effects from vacuum fluctuations on moving mirrors are found to be hardly detected while those effects from thermal fluctuations may be detectable

  7. Coupled forward-backward trajectory approach for nonequilibrium electron-ion dynamics

    Science.gov (United States)

    Sato, Shunsuke A.; Kelly, Aaron; Rubio, Angel

    2018-04-01

    We introduce a simple ansatz for the wave function of a many-body system based on coupled forward and backward propagating semiclassical trajectories. This method is primarily aimed at, but not limited to, treating nonequilibrium dynamics in electron-phonon systems. The time evolution of the system is obtained from the Euler-Lagrange variational principle, and we show that this ansatz yields Ehrenfest mean-field theory in the limit that the forward and backward trajectories are orthogonal, and in the limit that they coalesce. We investigate accuracy and performance of this method by simulating electronic relaxation in the spin-boson model and the Holstein model. Although this method involves only pairs of semiclassical trajectories, it shows a substantial improvement over mean-field theory, capturing quantum coherence of nuclear dynamics as well as electron-nuclear correlations. This improvement is particularly evident in nonadiabatic systems, where the accuracy of this coupled trajectory method extends well beyond the perturbative electron-phonon coupling regime. This approach thus provides an attractive route forward to the ab initio description of relaxation processes, such as thermalization, in condensed phase systems.

  8. Parallel Stochastic discrete event simulation of calcium dynamics in neuron.

    Science.gov (United States)

    Ishlam Patoary, Mohammad Nazrul; Tropper, Carl; McDougal, Robert A; Zhongwei, Lin; Lytton, William W

    2017-09-26

    The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.

  9. Mathematical investigation of IP3-dependent calcium dynamics in astrocytes.

    Science.gov (United States)

    Handy, Gregory; Taheri, Marsa; White, John A; Borisyuk, Alla

    2017-06-01

    We study evoked calcium dynamics in astrocytes, a major cell type in the mammalian brain. Experimental evidence has shown that such dynamics are highly variable between different trials, cells, and cell subcompartments. Here we present a qualitative analysis of a recent mathematical model of astrocyte calcium responses. We show how the major response types are generated in the model as a result of the underlying bifurcation structure. By varying key channel parameters, mimicking blockers used by experimentalists, we manipulate this underlying bifurcation structure and predict how the distributions of responses can change. We find that store-operated calcium channels, plasma membrane bound channels with little activity during calcium transients, have a surprisingly strong effect, underscoring the importance of considering these channels in both experiments and mathematical settings. Variation in the maximum flow in different calcium channels is also shown to determine the range of stable oscillations, as well as set the range of frequencies of the oscillations. Further, by conducting a randomized search through the parameter space and recording the resulting calcium responses, we create a database that can be used by experimentalists to help estimate the underlying channel distribution of their cells.

  10. Nonequilibrium dynamical renormalization group: Dynamical crossover from weak to infinite randomness in the transverse-field Ising chain

    Science.gov (United States)

    Heyl, Markus; Vojta, Matthias

    2015-09-01

    In this work we formulate the nonequilibrium dynamical renormalization group (ndRG). The ndRG represents a general renormalization-group scheme for the analytical description of the real-time dynamics of complex quantum many-body systems. In particular, the ndRG incorporates time as an additional scale which turns out to be important for the description of the long-time dynamics. It can be applied to both translational-invariant and disordered systems. As a concrete application, we study the real-time dynamics after a quench between two quantum critical points of different universality classes. We achieve this by switching on weak disorder in a one-dimensional transverse-field Ising model initially prepared at its clean quantum critical point. By comparing to numerically exact simulations for large systems, we show that the ndRG is capable of analytically capturing the full crossover from weak to infinite randomness. We analytically study signatures of localization in both real space and Fock space.

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

    Science.gov (United States)

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

    2016-02-01

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

  12. Colored thermal noise driven dynamical system in the presence and absence of non-equilibrium constraint: time dependence of information entropy flux and entropy production

    International Nuclear Information System (INIS)

    Goswami, Gurupada; Mukherjee, Biswajit; Bag, Bidhan Chandra

    2005-01-01

    We have studied the relaxation of non-Markovian and thermodynamically closed system both in the absence and presence of non-equilibrium constraint in terms of the information entropy flux and entropy production based on the Fokker-Planck and the entropy balance equations. Our calculation shows how the relaxation time depends on noise correlation time. It also considers how the non-equilibrium constraint is affected by system parameters such as noise correlation time, strength of dissipation and frequency of dynamical system. The interplay of non-equilibrium constraint, frictional memory kernel, noise correlation time and frequency of dynamical system reveals the extremum nature of the entropy production

  13. Colored thermal noise driven dynamical system in the presence and absence of non-equilibrium constraint: time dependence of information entropy flux and entropy production

    Science.gov (United States)

    Goswami, Gurupada; Mukherjee, Biswajit; Bag, Bidhan Chandra

    2005-06-01

    We have studied the relaxation of non-Markovian and thermodynamically closed system both in the absence and presence of non-equilibrium constraint in terms of the information entropy flux and entropy production based on the Fokker-Planck and the entropy balance equations. Our calculation shows how the relaxation time depends on noise correlation time. It also considers how the non-equilibrium constraint is affected by system parameters such as noise correlation time, strength of dissipation and frequency of dynamical system. The interplay of non-equilibrium constraint, frictional memory kernel, noise correlation time and frequency of dynamical system reveals the extremum nature of the entropy production.

  14. NON-EQUILIBRIUM CHEMISTRY OF DYNAMICALLY EVOLVING PRESTELLAR CORES. II. IONIZATION AND MAGNETIC FIELD

    International Nuclear Information System (INIS)

    Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.

    2012-01-01

    We study the effect that non-equilibrium chemistry in dynamical models of collapsing molecular cloud cores has on measurements of the magnetic field in these cores, the degree of ionization, and the mean molecular weight of ions. We find that OH and CN, usually used in Zeeman observations of the line-of-sight magnetic field, have an abundance that decreases toward the center of the core much faster than the density increases. As a result, Zeeman observations tend to sample the outer layers of the core and consistently underestimate the core magnetic field. The degree of ionization follows a complicated dependence on the number density at central densities up to 10 5 cm –3 for magnetic models and 10 6 cm –3 in non-magnetic models. At higher central densities, the scaling approaches a power law with a slope of –0.6 and a normalization which depends on the cosmic-ray ionization rate ζ and the temperature T as (ζT) 1/2 . The mean molecular weight of ions is systematically lower than the usually assumed value of 20-30, and, at high densities, approaches a value of 3 due to the asymptotic dominance of the H + 3 ion. This significantly lower value implies that ambipolar diffusion operates faster.

  15. 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.

  16. Nonequilibrium dynamics of spin-boson models from phase-space methods

    Science.gov (United States)

    Piñeiro Orioli, Asier; Safavi-Naini, Arghavan; Wall, Michael L.; Rey, Ana Maria

    2017-09-01

    An accurate description of the nonequilibrium dynamics of systems with coupled spin and bosonic degrees of freedom remains theoretically challenging, especially for large system sizes and in higher than one dimension. Phase-space methods such as the truncated Wigner approximation (TWA) have the advantage of being easily scalable and applicable to arbitrary dimensions. In this work we adapt the TWA to generic spin-boson models by making use of recently developed algorithms for discrete phase spaces [J. Schachenmayer, A. Pikovski, and A. M. Rey, Phys. Rev. X 5, 011022 (2015), 10.1103/PhysRevX.5.011022]. Furthermore we go beyond the standard TWA approximation by applying a scheme based on the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy of equations to our coupled spin-boson model. This allows us, in principle, to study how systematically adding higher-order corrections improves the convergence of the method. To test various levels of approximation we study an exactly solvable spin-boson model, which is particularly relevant for trapped-ion arrays. Using TWA and its BBGKY extension we accurately reproduce the time evolution of a number of one- and two-point correlation functions in several dimensions and for an arbitrary number of bosonic modes.

  17. Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands.

    Science.gov (United States)

    Valente, Luis M; Phillimore, Albert B; Etienne, Rampal S

    2015-08-01

    Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms. © 2015 The Authors Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  18. Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

    Science.gov (United States)

    Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

    2014-04-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  19. Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

    International Nuclear Information System (INIS)

    Philip, B.; Wang, Z.; Berrill, M.A.; Birke, M.; Pernice, M.

    2014-01-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton–Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence

  20. Viscosity of nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation.

    Science.gov (United States)

    Eslami, Hossein; Müller-Plathe, Florian

    2010-01-14

    Our new simulation scheme in isosurface-isothermal-isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Müller-Plathe, F. J. Chem. Phys. 2008, 129, 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a substantial slip at the surfaces, with the slip length depending on the shear rate and on the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation box depends on the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate.

  1. Dynamics of nonequilibrium conductivity of dielectrics with polaration properties controlled by in ection

    International Nuclear Information System (INIS)

    Arkhipov, V.I.; Rudenko, A.I.

    1979-01-01

    The effect of changes of radiation stimulation permittivity on nonequilibrium conductivity of dielectrics and high-resistance conductors in a radiation field has been studied theoretically. The plane-parallel sample under the constant voltage has been irradiated by penetrating radiation. The uniform radiation caused the transfer the current carriers from traps to the conduction band. The dependence of permittivity on charged traps concentration is shown to lead to negative nonequilibrium conductivity of high-resistance materials

  2. 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

  3. An Optimization Principle for Deriving Nonequilibrium Statistical Models of Hamiltonian Dynamics

    Science.gov (United States)

    Turkington, Bruce

    2013-08-01

    A general method for deriving closed reduced models of Hamiltonian dynamical systems is developed using techniques from optimization and statistical estimation. Given a vector of resolved variables, selected to describe the macroscopic state of the system, a family of quasi-equilibrium probability densities on phase space corresponding to the resolved variables is employed as a statistical model, and the evolution of the mean resolved vector is estimated by optimizing over paths of these densities. Specifically, a cost function is constructed to quantify the lack-of-fit to the microscopic dynamics of any feasible path of densities from the statistical model; it is an ensemble-averaged, weighted, squared-norm of the residual that results from submitting the path of densities to the Liouville equation. The path that minimizes the time integral of the cost function determines the best-fit evolution of the mean resolved vector. The closed reduced equations satisfied by the optimal path are derived by Hamilton-Jacobi theory. When expressed in terms of the macroscopic variables, these equations have the generic structure of governing equations for nonequilibrium thermodynamics. In particular, the value function for the optimization principle coincides with the dissipation potential that defines the relation between thermodynamic forces and fluxes. The adjustable closure parameters in the best-fit reduced equations depend explicitly on the arbitrary weights that enter into the lack-of-fit cost function. Two particular model reductions are outlined to illustrate the general method. In each example the set of weights in the optimization principle contracts into a single effective closure parameter.

  4. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

    Science.gov (United States)

    Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

    2018-01-01

    Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

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

    International Nuclear Information System (INIS)

    Medina-Noyola, M; RamIrez-Gonzalez, Pedro

    2009-01-01

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

  6. The non-equilibrium statistical mechanics of a simple geophysical fluid dynamics model

    Science.gov (United States)

    Verkley, Wim; Severijns, Camiel

    2014-05-01

    Lorenz [1] has devised a dynamical system that has proved to be very useful as a benchmark system in geophysical fluid dynamics. The system in its simplest form consists of a periodic array of variables that can be associated with an atmospheric field on a latitude circle. The system is driven by a constant forcing, is damped by linear friction and has a simple advection term that causes the model to behave chaotically if the forcing is large enough. Our aim is to predict the statistics of Lorenz' model on the basis of a given average value of its total energy - obtained from a numerical integration - and the assumption of statistical stationarity. Our method is the principle of maximum entropy [2] which in this case reads: the information entropy of the system's probability density function shall be maximal under the constraints of normalization, a given value of the average total energy and statistical stationarity. Statistical stationarity is incorporated approximately by using `stationarity constraints', i.e., by requiring that the average first and possibly higher-order time-derivatives of the energy are zero in the maximization of entropy. The analysis [3] reveals that, if the first stationarity constraint is used, the resulting probability density function rather accurately reproduces the statistics of the individual variables. If the second stationarity constraint is used as well, the correlations between the variables are also reproduced quite adequately. The method can be generalized straightforwardly and holds the promise of a viable non-equilibrium statistical mechanics of the forced-dissipative systems of geophysical fluid dynamics. [1] E.N. Lorenz, 1996: Predictability - A problem partly solved, in Proc. Seminar on Predictability (ECMWF, Reading, Berkshire, UK), Vol. 1, pp. 1-18. [2] E.T. Jaynes, 2003: Probability Theory - The Logic of Science (Cambridge University Press, Cambridge). [3] W.T.M. Verkley and C.A. Severijns, 2014: The maximum entropy

  7. Estimating the biophysical properties of neurons with intracellular calcium dynamics.

    Science.gov (United States)

    Ye, Jingxin; Rozdeba, Paul J; Morone, Uriel I; Daou, Arij; Abarbanel, Henry D I

    2014-06-01

    We investigate the dynamics of a conductance-based neuron model coupled to a model of intracellular calcium uptake and release by the endoplasmic reticulum. The intracellular calcium dynamics occur on a time scale that is orders of magnitude slower than voltage spiking behavior. Coupling these mechanisms sets the stage for the appearance of chaotic dynamics, which we observe within certain ranges of model parameter values. We then explore the question of whether one can, using observed voltage data alone, estimate the states and parameters of the voltage plus calcium (V+Ca) dynamics model. We find the answer is negative. Indeed, we show that voltage plus another observed quantity must be known to allow the estimation to be accurate. We show that observing both the voltage time course V(t) and the intracellular Ca time course will permit accurate estimation, and from the estimated model state, accurate prediction after observations are completed. This sets the stage for how one will be able to use a more detailed model of V+Ca dynamics in neuron activity in the analysis of experimental data on individual neurons as well as functional networks in which the nodes (neurons) have these biophysical properties.

  8. Thermodynamic versus non-equilibrium stability of palmitic acid monolayers in calcium-enriched sea spray aerosol proxy systems.

    Science.gov (United States)

    Wellen Rudd, Bethany A; Vidalis, Andrew S; Allen, Heather C

    2018-04-16

    Of the major cations in seawater (Na+, Mg2+, Ca2+, K+), Ca2+ is found to be the most enriched in fine sea spray aerosols (SSA). In this work, we investigate the binding of Ca2+ to the carboxylic acid headgroup of palmitic acid (PA), a marine-abundant fatty acid, and the impact such binding has on the stability of PA monolayers in both equilibrium and non-equilibrium systems. A range of Ca2+ conditions from 10 μM to 300 mM was utilized to represent the relative concentration of Ca2+ in high and low relative humidity aerosol environments. The CO2- stretching modes of PA detected by surface-sensitive infrared reflection-absorption spectroscopy (IRRAS) reveal ionic binding motifs of the Ca2+ ion to the carboxylate group with varying degrees of hydration. Surface tensiometry was used to determine the thermodynamic equilibrium spreading pressure (ESP) of PA on the various aqueous CaCl2 subphases. Up to concentrations of 1 mM Ca2+, each system reached equilibrium, and Ca2+:PA surface complexation gave rise to a lower energy state revealed by elevated surface pressures relative to water. We show that PA films are not thermodynamically stable at marine aerosol-relevant Ca2+ concentrations ([Ca2+] ≥ 10 mM). IRRAS and vibrational sum frequency generation (VSFG) spectroscopy were used to investigate the surface presence of PA on high concentration Ca2+ aqueous subphases. Non-equilibrium relaxation (NER) experiments were also conducted and monitored by Brewster angle microscopy (BAM) to determine the effect of the Ca2+ ions on PA stability. At high surface pressures, the relaxation mechanisms of PA varied among the systems and were dependent on Ca2+ concentration.

  9. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  10. Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-01

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  11. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

    Science.gov (United States)

    Sivak, David A; Chodera, John D; Crooks, Gavin E

    2014-06-19

    When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.

  12. Nonequilibrium self-energy functional theory. Accessing the real-time dynamics of strongly correlated fermionic lattice systems

    Energy Technology Data Exchange (ETDEWEB)

    Hofmann, Felix

    2016-07-05

    The self-energy functional theory (SFT) is extended to the nonequilibrium case and applied to the real-time dynamics of strongly correlated lattice-fermions. Exploiting the basic structure of the well established equilibrium theory the entire formalism is reformulated in the language of Keldysh-Matsubara Green's functions. To this end, a functional of general nonequilibrium self-energies is constructed which is stationary at the physical point where it moreover yields the physical grand potential of the initial thermal state. Nonperturbative approximations to the full self-energy can be constructed by reducing the original lattice problem to smaller reference systems and varying the functional on the space of the respective trial self-energies, which are parametrized by the reference system's one-particle parameters. Approximations constructed in this way can be shown to respect the macroscopic conservation laws related to the underlying symmetries of the original lattice model. Assuming thermal equilibrium, the original SFT is recovered from the extended formalism. However, in the general case, the nonequilibrium variational principle comprises functional derivatives off the physical parameter space. These can be carried out analytically to derive inherently causal conditional equations for the optimal physical parameters of the reference system and a computationally realizable propagation scheme is set up. As a benchmark for the numerical implementation the variational cluster approach is applied to the dynamics of a dimerized Hubbard model after fast ramps of its hopping parameters. Finally, the time-evolution of a homogeneous Hubbard model after sudden quenches and ramps of the interaction parameter is studied by means of a dynamical impurity approximation with a single bath site. Sharply separated by a critical interaction at which fast relaxation to a thermal final state is observed, two differing response regimes can be distinguished, where the

  13. Nonequilibrium Phenomena in Plasmas

    CERN Document Server

    Sharma, A Surjalal

    2005-01-01

    The complexity of plasmas arises mainly from their inherent nonlinearity and far from equilibrium nature. The nonequilibrium behavior of plasmas is evident in the natural settings, for example, in the Earth's magnetosphere. Similarly, laboratory plasmas such as fusion bottles also have their fair share of complex behavior. Nonequilibrium phenomena are intimately connected with statistical dynamics and form one of the growing research areas in modern nonlinear physics. These studies encompass the ideas of self-organization, phase transition, critical phenomena, self-organized criticality and turbulence. This book presents studies of complexity in the context of nonequilibrium phenomena using theory, modeling, simulations, and experiments, both in the laboratory and in nature.

  14. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-01-01

    The dynamic properties of liquid B 2 O 3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B 2 O 3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  15. Non-equilibrium reversible dynamics of work production in four-spin system in a magnetic field

    Directory of Open Access Journals (Sweden)

    E.A. Ivanchenko

    2011-06-01

    Full Text Available A closed system of the equations for the local Bloch vectors and spin correlation functions is obtained by decomplexification of the Liouville-von Neumann equation for 4 magnetic particles with the exchange interaction that takes place in an arbitrary time-dependent external magnetic field. The analytical and numerical analysis of the quantum thermodynamic variables is carried out depending on separable mixed initial state and the magnetic field modulation. Under unitary evolution, non-equilibrium reversible dynamics of power production in the finite environment is investigated.

  16. Temperature control in molecular dynamic simulations of non-equilibrium processes

    International Nuclear Information System (INIS)

    Toton, Dawid; Lorenz, Christian D; Rompotis, Nikolaos; Martsinovich, Natalia; Kantorovich, Lev

    2010-01-01

    Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF 2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO 2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic

  17. Quantum theory for the dynamic structure factor in correlated two-component systems in nonequilibrium: Application to x-ray scattering

    Science.gov (United States)

    Vorberger, J.; Chapman, D. A.

    2018-01-01

    We present a quantum theory for the dynamic structure factors in nonequilibrium, correlated, two-component systems such as plasmas or warm dense matter. The polarization function, which is needed as the input for the calculation of the structure factors, is calculated in nonequilibrium based on a perturbation expansion in the interaction strength. To make our theory applicable for x-ray scattering, a generalized Chihara decomposition for the total electron structure factor in nonequilibrium is derived. Examples are given and the influence of correlations and exchange on the structure and the x-ray-scattering spectrum are discussed for a model nonequilibrium distribution, as often encountered during laser heating of materials, as well as for two-temperature systems.

  18. Quantum theory for the dynamic structure factor in correlated two-component systems in nonequilibrium: Application to x-ray scattering.

    Science.gov (United States)

    Vorberger, J; Chapman, D A

    2018-01-01

    We present a quantum theory for the dynamic structure factors in nonequilibrium, correlated, two-component systems such as plasmas or warm dense matter. The polarization function, which is needed as the input for the calculation of the structure factors, is calculated in nonequilibrium based on a perturbation expansion in the interaction strength. To make our theory applicable for x-ray scattering, a generalized Chihara decomposition for the total electron structure factor in nonequilibrium is derived. Examples are given and the influence of correlations and exchange on the structure and the x-ray-scattering spectrum are discussed for a model nonequilibrium distribution, as often encountered during laser heating of materials, as well as for two-temperature systems.

  19. A mathematical model of T lymphocyte calcium dynamics derived from single transmembrane protein properties

    Directory of Open Access Journals (Sweden)

    Christine Dorothee Schmeitz

    2013-09-01

    Full Text Available Fate decision processes of T lymphocytes are crucial for health and disease. Whether a T lymphocyte is activated, divides, gets anergic or initiates apoptosis depends on extracellular triggers and intracellular signalling. Free cytosolic calcium dynamics plays an important role in this context. The relative contributions of store-derived calcium entry and calcium entry from extracellular space to T lymphocyte activation are still a matter of debate. Here we develop a quantitative mathematical model of T lymphocyte calcium dynamics in order to establish a tool which allows to disentangle cause-effect relationships between ion fluxes and observed calcium time courses. The model is based on single transmembrane protein characteristics which have been determined in independent experiments. This reduces the number of unknown parameters in the model to a minimum and ensures the predictive power of the model. Simulation results are subsequently used for an analysis of whole cell calcium dynamics measured under various experimental conditions. The model accounts for a variety of these conditions, which supports the suitability of the modelling approach. The simulation results suggest a model in which calcium dynamics dominantly relies on the opening of channels in calcium stores while calcium entry through calcium-release activated channels (CRAC is more associated with the maintenance of the T lymphocyte calcium levels and prevents the cell from calcium depletion. Our findings indicate that CRAC guarantees a long-term stable calcium level which is required for cell survival and sustained calcium enhancement.

  20. What Can Reinforcement Learning Teach Us About Non-Equilibrium Quantum Dynamics

    Science.gov (United States)

    Bukov, Marin; Day, Alexandre; Sels, Dries; Weinberg, Phillip; Polkovnikov, Anatoli; Mehta, Pankaj

    Equilibrium thermodynamics and statistical physics are the building blocks of modern science and technology. Yet, our understanding of thermodynamic processes away from equilibrium is largely missing. In this talk, I will reveal the potential of what artificial intelligence can teach us about the complex behaviour of non-equilibrium systems. Specifically, I will discuss the problem of finding optimal drive protocols to prepare a desired target state in quantum mechanical systems by applying ideas from Reinforcement Learning [one can think of Reinforcement Learning as the study of how an agent (e.g. a robot) can learn and perfect a given policy through interactions with an environment.]. The driving protocols learnt by our agent suggest that the non-equilibrium world features possibilities easily defying intuition based on equilibrium physics.

  1. Dynamics and non-equilibrium steady state in a system of coupled harmonic oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Ghesquière, Anne, E-mail: Anne.Ghesquiere@nithep.ac.za; Sinayskiy, Ilya, E-mail: sinayskiy@ukzn.ac.za; Petruccione, Francesco, E-mail: petruccione@ukzn.ac.za

    2013-10-15

    A system of two coupled oscillators, each of them coupled to an independent reservoir, is analysed. The analytical solution of the non-rotating wave master equation is obtained in the high-temperature and weak coupling limits. No thermal entanglement is found in the high-temperature limit. In the weak coupling limit the system converges to an entangled non-equilibrium steady state. A critical temperature for the appearance of quantum correlations is found.

  2. The dynamics of a non-equilibrium bubble near bio-materials

    International Nuclear Information System (INIS)

    Ohl, S W; Klaseboer, E; Khoo, B C

    2009-01-01

    In many medical treatments oscillating (non-equilibrium) bubbles appear. They can be the result of high-intensity-focused ultrasound, laser treatments or shock wave lithotripsy for example. The physics of such oscillating bubbles is often not very well understood. This is especially so if the bubbles are oscillating near (soft) bio-materials. It is well known that bubbles oscillating near (hard) materials have a tendency to form a high speed jet directed towards the material during the collapse phase of the bubble. It is equally well studied that bubbles near a free interface (air) tend to collapse with a jet directed away from this interface. If the interface is neither 'free' nor 'hard', such as often occurs in bio-materials, the resulting flow physics can be very complex. Yet, in many bio-applications, it is crucial to know in which direction the jet will go (if there is a jet at all). Some applications require a jet towards the tissue, for example to destroy it. For other applications, damage due to impacting jets is to be prevented at all cost. This paper tries to address some of the physics involved in these treatments by using a numerical method, the boundary element method (BEM), to study the dynamics of such bubbles near several bio-materials. In the present work, the behaviour of a bubble placed in a water-like medium near various bio-materials (modelled as elastic fluids) is investigated. It is found that its behaviour depends on the material properties (Young's modulus, Poisson ratio and density) of the bio-material. For soft bio-materials (fat, skin, brain and muscle), the bubble tends to split into smaller bubbles. In certain cases, the resulting bubbles develop opposing jets. For hard bio-materials (cornea, cartilage and bone), the bubble collapses towards the interface with high speed jets (between 100 and about 250 m s -1 ). A summary graph is provided identifying the combined effects of the dimensionless elasticity (κ) and density ratio (α) of

  3. Dynamic scaling for the growth of non-equilibrium fluctuations during thermophoretic diffusion in microgravity.

    Science.gov (United States)

    Cerbino, Roberto; Sun, Yifei; Donev, Aleksandar; Vailati, Alberto

    2015-09-30

    Diffusion processes are widespread in biological and chemical systems, where they play a fundamental role in the exchange of substances at the cellular level and in determining the rate of chemical reactions. Recently, the classical picture that portrays diffusion as random uncorrelated motion of molecules has been revised, when it was shown that giant non-equilibrium fluctuations develop during diffusion processes. Under microgravity conditions and at steady-state, non-equilibrium fluctuations exhibit scale invariance and their size is only limited by the boundaries of the system. In this work, we investigate the onset of non-equilibrium concentration fluctuations induced by thermophoretic diffusion in microgravity, a regime not accessible to analytical calculations but of great relevance for the understanding of several natural and technological processes. A combination of state of the art simulations and experiments allows us to attain a fully quantitative description of the development of fluctuations during transient diffusion in microgravity. Both experiments and simulations show that during the onset the fluctuations exhibit scale invariance at large wave vectors. In a broader range of wave vectors simulations predict a spinodal-like growth of fluctuations, where the amplitude and length-scale of the dominant mode are determined by the thickness of the diffuse layer.

  4. Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

    Science.gov (United States)

    Man, Viet Hoang; Li, Mai Suan; Derreumaux, Philippe; Nguyen, Phuong H.

    2018-03-01

    The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasound-induced blood-brain-barrier experiments is discussed in some detail.

  5. Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging.

    Science.gov (United States)

    Patel, Tapan P; Man, Karen; Firestein, Bonnie L; Meaney, David F

    2015-03-30

    Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s-1000+neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking. Here we introduce FluoroSNNAP, Fluorescence Single Neuron and Network Analysis Package. FluoroSNNAP is an open-source, interactive software developed in MATLAB for automated quantification of numerous biologically relevant features of both the calcium dynamics of single-cells and network activity patterns. FluoroSNNAP integrates and improves upon existing tools for spike detection, synchronization analysis, and inference of functional connectivity, making it most useful to experimentalists with little or no programming knowledge. We apply FluoroSNNAP to characterize the activity patterns of neuronal microcircuits undergoing developmental maturation in vitro. Separately, we highlight the utility of single-cell analysis for phenotyping a mixed population of neurons expressing a human mutant variant of the microtubule associated protein tau and wild-type tau. We show the performance of semi-automated cell segmentation using spatiotemporal independent component analysis and significant improvement in detecting calcium transients using a template-based algorithm in comparison to peak-based or wavelet-based detection methods. Our software further enables automated analysis of microcircuits, which is an improvement over existing methods. We expect the dissemination of this software will facilitate a comprehensive analysis of neuronal networks, promoting the rapid interrogation of circuits in health and disease. Copyright © 2015. Published by Elsevier B.V.

  6. Calcium

    Science.gov (United States)

    ... You can get decent amounts of calcium from baked beans, navy beans, white beans, and others. Canned fish. You're in luck if you like sardines and canned salmon with bones. Almond milk. Working Calcium Into Your ...

  7. Dynamical Quantum Phase Transitions in Spin Chains with Long-Range Interactions: Merging Different Concepts of Nonequilibrium Criticality

    Science.gov (United States)

    Žunkovič, Bojan; Heyl, Markus; Knap, Michael; Silva, Alessandro

    2018-03-01

    We theoretically study the dynamics of a transverse-field Ising chain with power-law decaying interactions characterized by an exponent α , which can be experimentally realized in ion traps. We focus on two classes of emergent dynamical critical phenomena following a quantum quench from a ferromagnetic initial state: The first one manifests in the time-averaged order parameter, which vanishes at a critical transverse field. We argue that such a transition occurs only for long-range interactions α ≤2 . The second class corresponds to the emergence of time-periodic singularities in the return probability to the ground-state manifold which is obtained for all values of α and agrees with the order parameter transition for α ≤2 . We characterize how the two classes of nonequilibrium criticality correspond to each other and give a physical interpretation based on the symmetry of the time-evolved quantum states.

  8. Nanosecond electric pulses modulate skeletal muscle calcium dynamics and contraction

    Science.gov (United States)

    Valdez, Chris; Jirjis, Michael B.; Roth, Caleb C.; Barnes, Ronald A.; Ibey, Bennett L.

    2017-02-01

    Irreversible electroporation therapy is utilized to remove cancerous tissues thru the delivery of rapid (250Hz) and high voltage (V) (1,500V/cm) electric pulses across microsecond durations. Clinical research demonstrated that bipolar (BP) high voltage microsecond pulses opposed to monophasic waveforms relieve muscle contraction during electroporation treatment. Our group along with others discovered that nanosecond electric pulses (nsEP) can activate second messenger cascades, induce cytoskeletal rearrangement, and depending on the nsEP duration and frequency, initiate apoptotic pathways. Of high interest across in vivo and in vitro applications, is how nsEP affects muscle physiology, and if nuances exist in comparison to longer duration electroporation applications. To this end, we exposed mature skeletal muscle cells to monopolar (MP) and BP nsEP stimulation across a wide range of electric field amplitudes (1-20 kV/cm). From live confocal microscopy, we simultaneously monitored intracellular calcium dynamics along with nsEP-induced muscle movement on a single cell level. In addition, we also evaluated membrane permeability with Yo-PRO-1 and Propidium Iodide (PI) across various nsEP parameters. The results from our findings suggest that skeletal muscle calcium dynamics, and nsEP-induced contraction exhibit exclusive responses to both MP and BP nsEP exposure. Overall the results suggest in vivo nsEP application may elicit unique physiology and field applications compared to longer pulse duration electroporation.

  9. Unifying treatment of nonequilibrium and unstable dynamics of cold bosonic atom system with time-dependent order parameter in Thermo Field Dynamics

    International Nuclear Information System (INIS)

    Nakamura, Y.; Yamanaka, Y.

    2011-01-01

    Research highlights: → Cold atoms with time-dependent condensate in nonequilibrium Thermo Field Dynamics. → Coupled equations which describe the temporal evolution of the system are derived. → They are not the naive assemblages of presumable equations, but the self-consistently ones. → Valid even for systems with Landau or dynamical instability, and describing decays. → Transport equation has new collision term that is important in Landau instability. - Abstract: The coupled equations which describe the temporal evolution of the Bose-Einstein condensed system are derived in the framework of nonequilibrium Thermo Field Dynamics. The key element is that they are not the naive assemblages of assumed equations, but are the self-consistent ones derived by appropriate renormalization conditions. While the order parameter is time-dependent, an explicit quasiparticle picture is constructed by a time-dependent expansion. Our formulation is valid even for the system with a unstable condensate, and describes the condensate decay caused by the Landau instability as well as by the dynamical one.

  10. Blume-Capel ferromagnet driven by propagating and standing magnetic field wave: Dynamical modes and nonequilibrium phase transition

    Energy Technology Data Exchange (ETDEWEB)

    Acharyya, Muktish, E-mail: muktish.physics@presiuniv.ac.in; Halder, Ajay, E-mail: ajay.rs@presiuniv.ac.in

    2017-03-15

    The dynamical responses of Blume-Capel (S=1) ferromagnet to the plane propagating (with fixed frequency and wavelength) and standing magnetic field waves are studied separately in two dimensions by extensive Monte Carlo simulation. Depending on the values of temperature, amplitude of the propagating magnetic field and the strength of anisotropy, two different dynamical phases are observed. For a fixed value of anisotropy and the amplitude of the propagating magnetic field, the system undergoes a dynamical phase transition from a driven spin wave propagating phase to a pinned or spin frozen state as the system is cooled down. The time averaged magnetisation over a full cycle of the propagating magnetic field plays the role of the dynamic order parameter. A comprehensive phase diagram is plotted in the plane formed by the amplitude of the propagating wave and the temperature of the system. It is found that the phase boundary shrinks inward as the anisotropy increases. The phase boundary, in the plane described by the strength of the anisotropy and temperature, is also drawn. This phase boundary was observed to shrink inward as the field amplitude increases. - Highlights: • The Blume-Capel ferromagnet in propagating and standing magnetic wave. • Monte Carlo single spin flip Metropolis algorithm is employed. • The dynamical modes are observed. • The nonequilibrium phase transitions are studied. • The phase boundaries are drawn.

  11. Kapitza thermal conductance at the interface between Lennard-Jones crystals using non-equilibrium molecular dynamics simulations

    International Nuclear Information System (INIS)

    Merabia, Samy; Termentzidis, Konstantinos

    2012-01-01

    We characterize the thermal Kapitza conductance between Lennard-Jones solids using non-equilibrium molecular dynamics simulations. We consider a series of perfect interfaces between mass-mismatched solids. We show that both the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) fail to predict the interfacial conductance even for large acoustic mismatched solids. This poor agreement may be explained by the use of equilibrium distributions of phonons in the expression of the conductance. On the other hand, we show that an extension of AMM taking into account the out-of-equilibrium phonon distribution on both sides of the interface leads to a good agreement with the simulation results, even for interfaces between almost similar materials. This opens the way to understand interfacial heat transport across real semi-conductors and dielectrics.

  12. Estuarine Facies Model Revisited: Conceptual Model of Estuarine Sediment Dynamics During Non-Equilibrium Conditions

    Science.gov (United States)

    Elliott, E. A.; Rodriguez, A. B.; McKee, B. A.

    2017-12-01

    Traditional models of estuarine systems show deposition occurs primarily within the central basin. There, accommodation space is high within the deep central valley, which is below regional wave base and where current energy is presumed to reach a relative minimum, promoting direct deposition of cohesive sediment and minimizing erosion. However, these models often reflect long-term (decadal-millennial) timescales, where accumulation rates are in relative equilibrium with the rate of relative sea-level rise, and lack the resolution to capture shorter term changes in sediment deposition and erosion within the central estuary. This work presents a conceptual model for estuarine sedimentation during non-equilibrium conditions, where high-energy inputs to the system reach a relative maximum in the central basin, resulting in temporary deposition and/or remobilization over sub-annual to annual timescales. As an example, we present a case study of Core Sound, NC, a lagoonal estuarine system where the regional base-level has been reached, and sediment deposition, resuspension and bypassing is largely a result of non-equilibrium, high-energy events. Utilizing a 465 cm-long sediment core from a mini-basin located between Core Sound and the continental shelf, a 40-year sub-annual chronology was developed for the system, with sediment accumulation rates (SAR) interpolated to a monthly basis over the 40-year record. This study links erosional processes in the estuary directly with sediment flux to the continental shelf, taking advantage of the highly efficient sediment trapping capability of the mini-basin. The SAR record indicates high variation in the estuarine sediment supply, with peaks in the SAR record at a recurrence interval of 1 year (+/- 0.25). This record has been compared to historical storm influence for the area. Through this multi-decadal record, sediment flushing events occur at a much more frequent interval than previously thought (i.e. annual rather than

  13. Open problems in non-equilibrium physics

    International Nuclear Information System (INIS)

    Kusnezov, D.

    1997-01-01

    The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions

  14. Open problems in non-equilibrium physics

    Energy Technology Data Exchange (ETDEWEB)

    Kusnezov, D.

    1997-09-22

    The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions.

  15. Non-equilibrium magnetic colloidal dispersions at liquid-air interfaces: dynamic patterns, magnetic order and self-assembled swimmers

    International Nuclear Information System (INIS)

    Snezhko, Alexey

    2011-01-01

    Colloidal dispersions of interacting particles subjected to an external periodic forcing often develop nontrivial self-assembled patterns and complex collective behavior. A fundamental issue is how collective ordering in such non-equilibrium systems arises from the dynamics of discrete interacting components. In addition, from a practical viewpoint, by working in regimes far from equilibrium new self-organized structures which are generally not available through equilibrium thermodynamics can be created. In this review spontaneous self-assembly phenomena in magnetic colloidal dispersions suspended at liquid-air interfaces and driven out of equilibrium by an alternating magnetic field are presented. Experiments reveal a new type of nontrivially ordered self-assembled structures emerging in such systems in a certain range of excitation parameters. These dynamic structures emerge as a result of the competition between magnetic and hydrodynamic forces and have complex unconventional magnetic ordering. Nontrivial self-induced hydrodynamic fields accompany each out-of-equilibrium pattern. Spontaneous symmetry breaking of the self-induced surface flows leading to a formation of self-propelled microstructures has been discovered. Some features of the self-localized structures can be understood in the framework of the amplitude equation (Ginzburg-Landau type equation) for parametric waves coupled to the conservation law equation describing the evolution of the magnetic particle density and the Navier-Stokes equation for hydrodynamic flows. To understand the fundamental microscopic mechanisms governing self-assembly processes in magnetic colloidal dispersions at liquid-air interfaces a first-principle model for a non-equilibrium self-assembly is presented. The latter model allows us to capture in detail the entire process of out-of-equilibrium self-assembly in the system and reproduces most of the observed phenomenology. (topical review)

  16. Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

    Science.gov (United States)

    Futera, Zdenek; English, Niall J.

    2017-07-01

    The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

  17. 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.

  18. Local versus global interactions in nonequilibrium transitions: A model of social dynamics

    Science.gov (United States)

    González-Avella, J. C.; Eguíluz, V. M.; Cosenza, M. G.; Klemm, K.; Herrera, J. L.; San Miguel, M.

    2006-04-01

    A nonequilibrium system of locally interacting elements in a lattice with an absorbing order-disorder phase transition is studied under the effect of additional interacting fields. These fields are shown to produce interesting effects in the collective behavior of this system. Both for autonomous and external fields, disorder grows in the system when the probability of the elements to interact with the field is increased. There exists a threshold value of this probability beyond which the system is always disordered. The domain of parameters of the ordered regime is larger for nonuniform local fields than for spatially uniform fields. However, the zero field limit is discontinous. In the limit of vanishingly small probability of interaction with the field, autonomous or external fields are able to order a system that would fall in a disordered phase under local interactions of the elements alone. We consider different types of fields which are interpreted as forms of mass media acting on a social system in the context of Axelrod’s model for cultural dissemination.

  19. Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi, E-mail: cbaig@unist.ac.kr [Department of Chemical Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798 (Korea, Republic of)

    2016-07-15

    We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chain structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.

  20. Non-equilibrium dynamics of disordered systems: understanding the broad continuum of relevant time scales via a strong-disorder RG in configuration space

    International Nuclear Information System (INIS)

    Monthus, Cecile; Garel, Thomas

    2008-01-01

    We show that an appropriate description of the non-equilibrium dynamics of disordered systems is obtained through a strong disorder renormalization procedure in configuration space that we define for any master equation with transitions rates W(C→C') between configurations. The idea is to eliminate iteratively the configuration with the highest exit rate W out (C)+Σ C' W(C→C') to obtain renormalized transition rates between the remaining configurations. The multiplicative structure of the new generated transition rates suggests that for a very broad class of disordered systems, the distribution of renormalized exit barriers defined as B out (C)≡-ln W out (C) will become broader and broader upon iteration, so that the strong disorder renormalization procedure should become asymptotically exact at large time scales. We have checked numerically this scenario for the non-equilibrium dynamics of a directed polymer in a two-dimensional random medium

  1. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    Energy Technology Data Exchange (ETDEWEB)

    Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  2. Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations.

    Science.gov (United States)

    Kundu, Mainak; He, Ting-Fang; Lu, Yangyi; Wang, Lijuan; Zhong, Dongping

    2018-05-03

    Short-range electron transfer (ET) in proteins is an ultrafast process on the similar timescales as local protein-solvent fluctuations thus the two dynamics are coupled. Here, we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with eleven mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical timescales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.

  3. Nonequilibrium structure and dynamics in a microscopic model of thin-film active gels

    NARCIS (Netherlands)

    Head, D.A.; Briels, Willem J.; Gompper, G.

    2014-01-01

    In the presence of adenosine triphosphate, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modeling can help to quantify the relationship between individual

  4. Mapping momentum-dependent electron-phonon coupling and nonequilibrium phonon dynamics with ultrafast electron diffuse scattering

    Science.gov (United States)

    Stern, Mark J.; René de Cotret, Laurent P.; Otto, Martin R.; Chatelain, Robert P.; Boisvert, Jean-Philippe; Sutton, Mark; Siwick, Bradley J.

    2018-04-01

    Despite their fundamental role in determining material properties, detailed momentum-dependent information on the strength of electron-phonon and phonon-phonon coupling (EPC and PPC, respectively) across the entire Brillouin zone has remained elusive. Here we demonstrate that ultrafast electron diffuse scattering (UEDS) directly provides such information. By exploiting symmetry-based selection rules and time resolution, scattering from different phonon branches can be distinguished even without energy resolution. Using graphite as a model system, we show that UEDS patterns map the relative EPC and PPC strength through their profound sensitivity to photoinduced changes in phonon populations. We measure strong EPC to the K -point TO phonon of A1' symmetry (K -A1' ) and along the entire TO branch between Γ -K , not only to the Γ -E2 g phonon. We also determine that the subsequent phonon relaxation of these strongly coupled optical phonons involve three stages: decay via several identifiable channels to TA and LA phonons (1 -2 ps), intraband thermalization of the non-equilibrium TA/LA phonon populations (30 -40 ps) and interband relaxation of the TA/LA modes (115 ps). Combining UEDS with ultrafast angle-resolved photoelectron spectroscopy will yield a complete picture of the dynamics within and between electron and phonon subsystems, helping to unravel complex phases in which the intertwined nature of these systems has a strong influence on emergent properties.

  5. Equivalence of the equilibrium and the nonequilibrium molecular dynamics methods for thermal conductivity calculations: From bulk to nanowire silicon

    Science.gov (United States)

    Dong, Haikuan; Fan, Zheyong; Shi, Libin; Harju, Ari; Ala-Nissila, Tapio

    2018-03-01

    Molecular dynamics (MD) simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either using the Green-Kubo formula in equilibrium MD (EMD) simulations or using Fourier's law in nonequilibrium MD (NEMD) simulations. These two methods have not been systematically compared for materials with different dimensions and inconsistencies between them have been occasionally reported in the literature. Here we give an in-depth comparison of them in terms of heat transport in three allotropes of Si: three-dimensional bulk silicon, two-dimensional silicene, and quasi-one-dimensional silicon nanowire. By multiplying the correlation time in the Green-Kubo formula with an appropriate effective group velocity, we can express the running thermal conductivity in the EMD method as a function of an effective length and directly compare it to the length-dependent thermal conductivity in the NEMD method. We find that the two methods quantitatively agree with each other for all the systems studied, firmly establishing their equivalence in computing thermal conductivity.

  6. Entropy production and nonequilibrium stationarity in quantum dynamical systems. Physical meaning of van Hove limit

    International Nuclear Information System (INIS)

    Ojima, Izumi

    1989-01-01

    With aid of the so-called dilation method, a concise formula is obtained for the entropy production in the algebraic formulation of quantum dynamical systems. In this framework, the initial ergodic state of an external force system plays a pivotal role in generating dissipativity as a conditional expectation. The physical meaning of van Hove limit is clarified through the scale-changing transformation to control transitions between microscopic and macroscopic levels. It plays a crucial role in realizing the macroscopic stationary in the presence of microscopic fluctuations as well as in the transition from non-Markovian (groupoid) dynamics to Markovian dissipative processes of state changes. The extension of the formalism to cases with spatial and internal inhomogeneity is indicated in the light of the groupoid dynamical systems and noncommutative integration theory

  7. Nonequilibrium dynamics of polariton entanglement in a cluster of coupled traps

    Energy Technology Data Exchange (ETDEWEB)

    Quiroga, L [Departamento de Fisica, Universidad de Los Andes, A.A.4976, Bogota D.C. (Colombia); Tejedor, C, E-mail: lquiroga@uniandes.edu.c [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, Cantoblanco, E-28049, Madrid (Spain)

    2009-05-01

    We study in detail the generation and relaxation of quantum coherences (entanglement) in a system of coupled polariton traps. By exploiting a Lie algebraic based super-operator technique we provide an analytical exact solution for the Markovian dissipative dynamics (Master equation) of such system which is valid for arbitrary cluster size, polariton-polariton interaction strength, temperature and initial state. Based on the exact solution of the Master equation at T = OK, we discuss how dissipation affects the quantum entanglement dynamics of coupled polariton systems.

  8. Dynamics of multiphase systems with complex microstructure. I. Development of the governing equations through nonequilibrium thermodynamics

    NARCIS (Netherlands)

    Sagis, L.M.C.; Öttinger, H.C.

    2013-01-01

    In this paper we present a general model for the dynamic behavior of multiphase systems in which the bulk phases and interfaces have a complex microstructure (for example, immiscible polymer blends with added compatibilizers, or polymer stabilized emulsions with thickening agents dispersed in the

  9. Discrete-State Stochastic Models of Calcium-Regulated Calcium Influx and Subspace Dynamics Are Not Well-Approximated by ODEs That Neglect Concentration Fluctuations

    Science.gov (United States)

    Weinberg, Seth H.; Smith, Gregory D.

    2012-01-01

    Cardiac myocyte calcium signaling is often modeled using deterministic ordinary differential equations (ODEs) and mass-action kinetics. However, spatially restricted “domains” associated with calcium influx are small enough (e.g., 10−17 liters) that local signaling may involve 1–100 calcium ions. Is it appropriate to model the dynamics of subspace calcium using deterministic ODEs or, alternatively, do we require stochastic descriptions that account for the fundamentally discrete nature of these local calcium signals? To address this question, we constructed a minimal Markov model of a calcium-regulated calcium channel and associated subspace. We compared the expected value of fluctuating subspace calcium concentration (a result that accounts for the small subspace volume) with the corresponding deterministic model (an approximation that assumes large system size). When subspace calcium did not regulate calcium influx, the deterministic and stochastic descriptions agreed. However, when calcium binding altered channel activity in the model, the continuous deterministic description often deviated significantly from the discrete stochastic model, unless the subspace volume is unrealistically large and/or the kinetics of the calcium binding are sufficiently fast. This principle was also demonstrated using a physiologically realistic model of calmodulin regulation of L-type calcium channels introduced by Yue and coworkers. PMID:23509597

  10. Many-body Tunneling and Nonequilibrium Dynamics of Doublons in Strongly Correlated Quantum Dots.

    Science.gov (United States)

    Hou, WenJie; Wang, YuanDong; Wei, JianHua; Zhu, ZhenGang; Yan, YiJing

    2017-05-30

    Quantum tunneling dominates coherent transport at low temperatures in many systems of great interest. In this work we report a many-body tunneling (MBT), by nonperturbatively solving the Anderson multi-impurity model, and identify it a fundamental tunneling process on top of the well-acknowledged sequential tunneling and cotunneling. We show that the MBT involves the dynamics of doublons in strongly correlated systems. Proportional to the numbers of dynamical doublons, the MBT can dominate the off-resonant transport in the strongly correlated regime. A T 3/2 -dependence of the MBT current on temperature is uncovered and can be identified as a fingerprint of the MBT in experiments. We also prove that the MBT can support the coherent long-range tunneling of doublons, which is well consistent with recent experiments on ultracold atoms. As a fundamental physical process, the MBT is expected to play important roles in general quantum systems.

  11. Nonequilibrium carrier dynamics in self-assembled InGaAs quantum dots

    International Nuclear Information System (INIS)

    Wesseli, M.; Ruppert, C.; Trumm, S.; Betz, M.; Krenner, H.J.; Finley, J.J.

    2006-01-01

    Carrier dynamics in InGaAs/GaAs quantum dots is analyzed with highly sensitive femtosecond transmission spectroscopy. In a first step, measurements on a large ensemble of nanoislands reveal the dynamical electronic filling of quantum dots from the surrounding wetting layer. Most interestingly, we find a spin-preserving phonon mediated scattering into fully localized states within a few picoseconds. Then, individual artificial atoms are isolated with metallic shadow masks. For the first time, a single self-assembled quantum dot is addressed in an ultrafast transmission experiment. We find bleaching signals in the order of 10 -5 that arise from individual interband transitions of one quantum dot. As a result, we have developed an ultrafast optical tool for both manipulation and read-out of a single self-assembled quantum dot. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  12. Dynamical Monte Carlo investigation of spin reversals and nonequilibrium magnetization of single-molecule magnets

    OpenAIRE

    Liu, Gui-Bin; Liu, Bang-Gui

    2010-01-01

    In this paper, we combine thermal effects with Landau-Zener (LZ) quantum tunneling effects in a dynamical Monte Carlo (DMC) framework to produce satisfactory magnetization curves of single-molecule magnet (SMM) systems. We use the giant spin approximation for SMM spins and consider regular lattices of SMMs with magnetic dipolar interactions (MDI). We calculate spin reversal probabilities from thermal-activated barrier hurdling, direct LZ tunneling, and thermal-assisted LZ tunnelings in the pr...

  13. Characterization of conformational dynamics of bistable RNA by equilibrium and non-equilibrium NMR.

    Science.gov (United States)

    Fürtig, Boris; Reining, Anke; Sochor, Florian; Oberhauser, Eva Marie; Heckel, Alexander; Schwalbe, Harald

    2014-12-19

    Unlike proteins, a given RNA sequence can adopt more than a single conformation. The two (or more) conformations are long-lived and have similar stabilities, but interconvert only slowly. Such bi- or multistability is often linked to the biological functions of the RNA. This unit describes how nuclear magnetic resonance (NMR) spectroscopy can be used to characterize the conformational dynamics of bistable RNAs. Copyright © 2014 John Wiley & Sons, Inc.

  14. Diversity and Stability in Food Webs : Impacts of Non-Equilibrium Dynamics, Topology and Variation

    OpenAIRE

    Groll, Fanny

    2016-01-01

    With progressive climate change, the preservation of biodiversity is becoming increasingly important. Only if the gene pool is large enough and requirements of species are diverse, there will be species that can adapt to the changing circumstances. To maintain biodiversity, we must understand the consequences of the various strategies. Mathematical models of population dynamics could provide prognoses. However, a model that would reproduce and explain the mechanisms behind the diversity of sp...

  15. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  16. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

    Science.gov (United States)

    Nandi, Prithwish K.; Futera, Zdenek; English, Niall J.

    2016-11-01

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ˜220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

  17. Finite-Temperature Non-equilibrium Quasicontinuum Method based on Langevin Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Marian, J; Venturini, G; Hansen, B; Knap, J; Ortiz, M; Campbell, G

    2009-05-08

    The concurrent bridging of molecular dynamics and continuum thermodynamics presents a number of challenges, mostly associated with energy transmission and changes in the constitutive description of a material across domain boundaries. In this paper, we propose a framework for simulating coarse dynamic systems in the canonical ensemble using the Quasicontinuum method (QC). The equations of motion are expressed in reduced QC coordinates and are strictly derived from dissipative Lagrangian mechanics. The derivation naturally leads to a classical Langevin implementation where the timescale is governed by vibrations emanating from the finest length scale occurring in the computational cell. The equations of motion are integrated explicitly via Newmark's ({beta} = 0; {gamma} = 1/2) method, leading to a robust numerical behavior and energy conservation. In its current form, the method only allows for wave propagations supported by the less compliant of the two meshes across a heterogeneous boundary, which requires the use of overdamped dynamics to avoid spurious heating due to reflected vibrations. We have applied the method to two independent crystallographic systems characterized by different interatomic potentials (Al and Ta) and have measured thermal expansion in order to quantify the vibrational entropy loss due to homogenization. We rationalize the results in terms of system size, mesh coarseness, and nodal cluster diameter within the framework of the quasiharmonic approximation. For Al, we find that the entropy loss introduced by mesh coarsening varies linearly with the element size, and that volumetric effects are not critical in driving the anharmonic behavior of the simulated systems. In Ta, the anomalies of the interatomic potential employed result in negative and zero thermal expansion at low and high temperatures, respectively.

  18. Nonequilibrium Dynamics in a Quasi-Two-Dimensional Electron Plasma after Ultrafast Intersubband Excitation

    International Nuclear Information System (INIS)

    Lutgen, S.; Kaindl, R.A.; Woerner, M.; Elsaesser, T.; Hase, A.; Kuenzel, H.; Gulia, M.; Meglio, D.; Lugli, P.

    1996-01-01

    The dynamics of electrons in GaInAs/AlInAs quantum wells is studied after excitation from the n=1 to the n=2 conduction subband. Femtosecond pump-probe experiments demonstrate for the first time athermal distributions of n=1 electrons on a surprisingly long time scale of 2ps. Thermalization involves intersubband scattering of excited electrons via optical phonon emission with a time constant of 1ps and intrasubband Coulomb and phonon scattering. Ensemble Monte Carlo simulations show that the slow electron equilibration results from Pauli blocking and screening of carrier-carrier scattering. copyright 1996 The American Physical Society

  19. Non-equilibrium trajectory dynamics and the kinematics of gliding in a flying snake

    International Nuclear Information System (INIS)

    Socha, John J; Jafari, Farid; Miklasz, Kevin; Vlachos, Pavlos P

    2010-01-01

    Given sufficient space, it is possible for gliding animals to reach an equilibrium state with no net forces acting on the body. In contrast, every gliding trajectory must begin with a non-steady component, and the relative importance of this phase is not well understood. Of any terrestrial animal glider, snakes exhibit the greatest active movements, which may affect their trajectory dynamics. Our primary aim was to determine the characteristics of snake gliding during the transition to equilibrium, quantifying changes in velocity, acceleration, and body orientation in the late phase of a glide sequence. We launched 'flying' snakes (Chrysopelea paradisi) from a 15 m tower and recorded the mid-to-end portion of trajectories with four videocameras to reconstruct the snake's body position with mm to cm accuracy. Additionally, we developed a simple analytical model of gliding assuming only steady-state forces of lift, drag and weight acting on the body and used it to explore effects of wing loading, lift-to-drag ratio, and initial velocity on trajectory dynamics. Despite the vertical space provided to transition to steady-state gliding, snakes did not exhibit equilibrium gliding and in fact displayed a net positive acceleration in the vertical axis, an effect also predicted by the analytical model.

  20. Non-equilibrium trajectory dynamics and the kinematics of gliding in a flying snake

    Energy Technology Data Exchange (ETDEWEB)

    Socha, John J; Jafari, Farid [Engineering Science and Mechanics, Virginia Tech, Blacksburg, VA 24061 (United States); Miklasz, Kevin [Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950 (United States); Vlachos, Pavlos P, E-mail: jjsocha@vt.ed [Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24061 (United States)

    2010-12-15

    Given sufficient space, it is possible for gliding animals to reach an equilibrium state with no net forces acting on the body. In contrast, every gliding trajectory must begin with a non-steady component, and the relative importance of this phase is not well understood. Of any terrestrial animal glider, snakes exhibit the greatest active movements, which may affect their trajectory dynamics. Our primary aim was to determine the characteristics of snake gliding during the transition to equilibrium, quantifying changes in velocity, acceleration, and body orientation in the late phase of a glide sequence. We launched 'flying' snakes (Chrysopelea paradisi) from a 15 m tower and recorded the mid-to-end portion of trajectories with four videocameras to reconstruct the snake's body position with mm to cm accuracy. Additionally, we developed a simple analytical model of gliding assuming only steady-state forces of lift, drag and weight acting on the body and used it to explore effects of wing loading, lift-to-drag ratio, and initial velocity on trajectory dynamics. Despite the vertical space provided to transition to steady-state gliding, snakes did not exhibit equilibrium gliding and in fact displayed a net positive acceleration in the vertical axis, an effect also predicted by the analytical model.

  1. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    Science.gov (United States)

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  2. Consequences of Molecular-Scale Non-Equilibrium Activity on the Dynamics and Mechanics of Self-Assembled Actin-Based Structures and Materials

    Science.gov (United States)

    Marshall Mccall, Patrick

    Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non-equilibrium

  3. Non-equilibrium steady states: maximization of the Shannon entropy associated with the distribution of dynamical trajectories in the presence of constraints

    International Nuclear Information System (INIS)

    Monthus, Cécile

    2011-01-01

    Filyokov and Karpov (1967 Inzh.-Fiz. Zh. 13 624) have proposed a theory of non-equilibrium steady states in direct analogy with the theory of equilibrium states: the principle is to maximize the Shannon entropy associated with the probability distribution of dynamical trajectories in the presence of constraints, including the macroscopic current of interest, via the method of Lagrange multipliers. This maximization leads directly to the generalized Gibbs distribution for the probability distribution of dynamical trajectories, and to some fluctuation relation of the integrated current. The simplest stochastic dynamics where these ideas can be applied are discrete-time Markov chains, defined by transition probabilities W i→j between configurations i and j: instead of choosing the dynamical rules W i→j a priori, one determines the transition probabilities and the associate stationary state that maximize the entropy of dynamical trajectories with the other physical constraints that one wishes to impose. We give a self-contained and unified presentation of this type of approach, both for discrete-time Markov chains and for continuous-time master equations. The obtained results are in full agreement with the Bayesian approach introduced by Evans (2004 Phys. Rev. Lett. 92 150601) under the name 'Non-equilibrium Counterpart to detailed balance', and with the 'invariant quantities' derived by Baule and Evans (2008 Phys. Rev. Lett. 101 240601), but provide a slightly different perspective via the formulation in terms of an eigenvalue problem

  4. Non-equilibrium fluctuation-induced interactions

    International Nuclear Information System (INIS)

    Dean, David S

    2012-01-01

    We discuss non-equilibrium aspects of fluctuation-induced interactions. While the equilibrium behavior of such interactions has been extensively studied and is relatively well understood, the study of these interactions out of equilibrium is relatively new. We discuss recent results on the non-equilibrium behavior of systems whose dynamics is of the dissipative stochastic type and identify a number of outstanding problems concerning non-equilibrium fluctuation-induced interactions.

  5. Dynamical Monte Carlo investigation of spin reversal and nonequilibrium magnetization of single-molecule magnets

    Science.gov (United States)

    Liu, Gui-Bin; Liu, Bang-Gui

    2010-10-01

    In this paper, we combine thermal effects with Landau-Zener (LZ) quantum tunneling effects in a dynamical Monte Carlo (DMC) framework to produce satisfactory magnetization curves of single-molecule magnet (SMM) systems. We use the giant spin approximation for SMM spins and consider regular lattices of SMMs with magnetic dipolar interactions (MDIs). We calculate spin-reversal probabilities from thermal-activated barrier hurdling, direct LZ tunneling, and thermal-assisted LZ tunnelings in the presence of sweeping magnetic fields. We do systematical DMC simulations for Mn12 systems with various temperatures and sweeping rates. Our simulations produce clear step structures in low-temperature magnetization curves, and our results show that the thermally activated barrier hurdling becomes dominating at high temperature near 3 K and the thermal-assisted tunnelings play important roles at intermediate temperature. These are consistent with corresponding experimental results on good Mn12 samples (with less disorders) in the presence of little misalignments between the easy axis and applied magnetic fields, and therefore our magnetization curves are satisfactory. Furthermore, our DMC results show that the MDI, with the thermal effects, have important effects on the LZ tunneling processes, but both the MDI and the LZ tunneling give place to the thermal-activated barrier hurdling effect in determining the magnetization curves when the temperature is near 3 K. This DMC approach can be applicable to other SMM systems and could be used to study other properties of SMM systems.

  6. Calcium dynamics of cortical astrocytic networks in vivo.

    Directory of Open Access Journals (Sweden)

    Hajime Hirase

    2004-04-01

    Full Text Available Large and long-lasting cytosolic calcium surges in astrocytes have been described in cultured cells and acute slice preparations. The mechanisms that give rise to these calcium events have been extensively studied in vitro. However, their existence and functions in the intact brain are unknown. We have topically applied Fluo-4 AM on the cerebral cortex of anesthetized rats, and imaged cytosolic calcium fluctuation in astrocyte populations of superficial cortical layers in vivo, using two-photon laser scanning microscopy. Spontaneous [Ca(2+](i events in individual astrocytes were similar to those observed in vitro. Coordination of [Ca(2+](i events among astrocytes was indicated by the broad cross-correlograms. Increased neuronal discharge was associated with increased astrocytic [Ca(2+](i activity in individual cells and a robust coordination of [Ca(2+](i signals in neighboring astrocytes. These findings indicate potential neuron-glia communication in the intact brain.

  7. Multiscale modeling and nested simulations of three-dimensional ionospheric plasmas: Rayleigh–Taylor turbulence and nonequilibrium layer dynamics at fine scales

    International Nuclear Information System (INIS)

    Mahalov, Alex

    2014-01-01

    Multiscale modeling and high resolution three-dimensional simulations of nonequilibrium ionospheric dynamics are major frontiers in the field of space sciences. The latest developments in fast computational algorithms and novel numerical methods have advanced reliable forecasting of ionospheric environments at fine scales. These new capabilities include improved physics-based predictive modeling, nesting and implicit relaxation techniques that are designed to integrate models of disparate scales. A range of scales, from mesoscale to ionospheric microscale, are included in a 3D modeling framework. Analyses and simulations of primary and secondary Rayleigh–Taylor instabilities in the equatorial spread F (ESF), the response of the plasma density to the neutral turbulent dynamics, and wave breaking in the lower region of the ionosphere and nonequilibrium layer dynamics at fine scales are presented for coupled systems (ions, electrons and neutral winds), thus enabling studies of mesoscale/microscale dynamics for a range of altitudes that encompass the ionospheric E and F layers. We examine the organizing mixing patterns for plasma flows, which occur due to polarized gravity wave excitations in the neutral field, using Lagrangian coherent structures (LCS). LCS objectively depict the flow topology and the extracted scintillation-producing irregularities that indicate a generation of ionospheric density gradients, due to the accumulation of plasma. The scintillation effects in propagation, through strongly inhomogeneous ionospheric media, are induced by trapping electromagnetic (EM) waves in parabolic cavities, which are created by the refractive index gradients along the propagation paths. (paper)

  8. Modeling motoneuron firing properties: dependency on size and calcium dynamics

    NARCIS (Netherlands)

    van der Heyden, M. J.; Hilgevoord, A. A.; Bour, L. J.; Ongerboer de Visser, B. W.

    1994-01-01

    The origin of functional differences between motoneurons of varying size was investigated by employing a one-compartmental motoneuron model containing a slow K+ conductance dependent on the intracellular calcium concentration. The size of the cell was included as an explicit parameter. Simulations

  9. Non-equilibrium phase transitions

    CERN Document Server

    Henkel, Malte; Lübeck, Sven

    2009-01-01

    This book describes two main classes of non-equilibrium phase-transitions: (a) static and dynamics of transitions into an absorbing state, and (b) dynamical scaling in far-from-equilibrium relaxation behaviour and ageing. The first volume begins with an introductory chapter which recalls the main concepts of phase-transitions, set for the convenience of the reader in an equilibrium context. The extension to non-equilibrium systems is made by using directed percolation as the main paradigm of absorbing phase transitions and in view of the richness of the known results an entire chapter is devoted to it, including a discussion of recent experimental results. Scaling theories and a large set of both numerical and analytical methods for the study of non-equilibrium phase transitions are thoroughly discussed. The techniques used for directed percolation are then extended to other universality classes and many important results on model parameters are provided for easy reference.

  10. Instabilities and nonequilibrium structures

    International Nuclear Information System (INIS)

    Tirapegui, E.; Villarroel, D.

    1987-01-01

    Physical systems can be studied both near to and far from equilibrium where instabilities appear. The behaviour in these two regions is reviewed in this book, from both the theoretical and application points of view. The influence of noise in these situations is an essential feature which cannot be ignored. It is therefore discussed using phenomenological and theoretical approaches for the numerous problems which still remain in the field. This volume should appeal to mathematicians and physicists interested in the areas of instability, bifurcation theory, dynamical systems, pattern formation, nonequilibrium structures and statistical mechanics. (Auth.)

  11. A Compact Synchronous Cellular Model of Nonlinear Calcium Dynamics: Simulation and FPGA Synthesis Results.

    Science.gov (United States)

    Soleimani, Hamid; Drakakis, Emmanuel M

    2017-06-01

    Recent studies have demonstrated that calcium is a widespread intracellular ion that controls a wide range of temporal dynamics in the mammalian body. The simulation and validation of such studies using experimental data would benefit from a fast large scale simulation and modelling tool. This paper presents a compact and fully reconfigurable cellular calcium model capable of mimicking Hopf bifurcation phenomenon and various nonlinear responses of the biological calcium dynamics. The proposed cellular model is synthesized on a digital platform for a single unit and a network model. Hardware synthesis, physical implementation on FPGA, and theoretical analysis confirm that the proposed cellular model can mimic the biological calcium behaviors with considerably low hardware overhead. The approach has the potential to speed up large-scale simulations of slow intracellular dynamics by sharing more cellular units in real-time. To this end, various networks constructed by pipelining 10 k to 40 k cellular calcium units are compared with an equivalent simulation run on a standard PC workstation. Results show that the cellular hardware model is, on average, 83 times faster than the CPU version.

  12. Non-equilibrium quantum dynamics of ultra-cold atomic mixtures: the multi-layer multi-configuration time-dependent Hartree method for bosons

    International Nuclear Information System (INIS)

    Krönke, Sven; Cao, Lushuai; Schmelcher, Peter; Vendrell, Oriol

    2013-01-01

    We develop and apply the multi-layer multi-configuration time-dependent Hartree method for bosons, which represents an ab initio method for investigating the non-equilibrium quantum dynamics of multi-species bosonic systems. Its multi-layer feature allows for tailoring the wave function ansatz to describe intra- and inter-species correlations accurately and efficiently. To demonstrate the beneficial scaling and efficiency of the method, we explored the correlated tunneling dynamics of two species with repulsive intra- and inter-species interactions, to which a third species with vanishing intra-species interaction was weakly coupled. The population imbalances of the first two species can feature a temporal equilibration and their time evolution significantly depends on the coupling to the third species. Bosons of the first and second species exhibit a bunching tendency, whose strength can be influenced by their coupling to the third species. (paper)

  13. Dynamical patterns of calcium signaling in a functional model of neuron-astrocyte networks

    DEFF Research Database (Denmark)

    Postnov, D.E.; Koreshkov, R.N.; Brazhe, N.A.

    2009-01-01

    We propose a functional mathematical model for neuron-astrocyte networks. The model incorporates elements of the tripartite synapse and the spatial branching structure of coupled astrocytes. We consider glutamate-induced calcium signaling as a specific mode of excitability and transmission...... in astrocytic-neuronal networks. We reproduce local and global dynamical patterns observed experimentally....

  14. Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces.

    Science.gov (United States)

    Spezia, Riccardo; Martínez-Nuñez, Emilio; Vazquez, Saulo; Hase, William L

    2017-04-28

    In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).

  15. Nonequilibrium dynamics of a mixed spin-1/2 and spin-3/2 Ising ferrimagnetic system with a time dependent oscillating magnetic field source

    Energy Technology Data Exchange (ETDEWEB)

    Vatansever, Erol [Dokuz Eylül University, Graduate School of Natural and Applied Sciences, TR-35160 Izmir (Turkey); Polat, Hamza, E-mail: hamza.polat@deu.edu.tr [Department of Physics, Dokuz Eylül University, TR-35160 Izmir (Turkey)

    2015-10-15

    Nonequilibrium phase transition properties of a mixed Ising ferrimagnetic model consisting of spin-1/2 and spin-3/2 on a square lattice under the existence of a time dependent oscillating magnetic field have been investigated by making use of Monte Carlo simulations with a single-spin flip Metropolis algorithm. A complete picture of dynamic phase boundary and magnetization profiles have been illustrated and the conditions of a dynamic compensation behavior have been discussed in detail. According to our simulation results, the considered system does not point out a dynamic compensation behavior, when it only includes the nearest-neighbor interaction, single-ion anisotropy and an oscillating magnetic field source. As the next-nearest-neighbor interaction between the spins-1/2 takes into account and exceeds a characteristic value which sensitively depends upon values of single-ion anisotropy and only of amplitude of external magnetic field, a dynamic compensation behavior occurs in the system. Finally, it is reported that it has not been found any evidence of dynamically first-order phase transition between dynamically ordered and disordered phases, which conflicts with the recently published molecular field investigation, for a wide range of selected system parameters. - Highlights: • Spin-1/2 and spin-3/2 Ising ferrimagnetic model is examined. • The system is exposed to time-dependent magnetic field. • Kinetic Monte Carlo simulation technique is used. • Any evidence of first-order phase transition has not been found.

  16. Molecular dynamics study of the solvation of calcium carbonate in water.

    Science.gov (United States)

    Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

    2007-10-25

    We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

  17. A mathematical model of calcium dynamics in HSY cells.

    Directory of Open Access Journals (Sweden)

    Jung Min Han

    2017-02-01

    Full Text Available Saliva is an essential part of activities such as speaking, masticating and swallowing. Enzymes in salivary fluid protect teeth and gums from infectious diseases, and also initiate the digestion process. Intracellular calcium (Ca2+ plays a critical role in saliva secretion and regulation. Experimental measurements of Ca2+ and inositol trisphosphate (IP3 concentrations in HSY cells, a human salivary duct cell line, show that when the cells are stimulated with adenosine triphosphate (ATP or carbachol (CCh, they exhibit coupled oscillations with Ca2+ spike peaks preceding IP3 spike peaks. Based on these data, we construct a mathematical model of coupled Ca2+ and IP3 oscillations in HSY cells and perform model simulations of three different experimental settings to forecast Ca2+ responses. The model predicts that when Ca2+ influx from the extracellular space is removed, oscillations gradually slow down until they stop. The model simulation of applying a pulse of IP3 predicts that photolysis of caged IP3 causes a transient increase in the frequency of the Ca2+ oscillations. Lastly, when Ca2+-dependent activation of PLC is inhibited, we see an increase in the oscillation frequency and a decrease in the amplitude. These model predictions are confirmed by experimental data. We conclude that, although concentrations of Ca2+ and IP3 oscillate, Ca2+ oscillations in HSY cells are the result of modulation of the IP3 receptor by intracellular Ca2+, and that the period is modulated by the accompanying IP3 oscillations.

  18. Computer simulation of nonequilibrium processes

    International Nuclear Information System (INIS)

    Wallace, D.C.

    1985-07-01

    The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed

  19. 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.

  20. Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

    Science.gov (United States)

    Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

    2010-05-07

    Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

  1. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  2. Application of ultra-small-angle X-ray scattering / X-ray photon correlation spectroscopy to relate equilibrium or non-equilibrium dynamics to microstructure

    Science.gov (United States)

    Allen, Andrew; Zhang, Fan; Levine, Lyle; Ilavsky, Jan

    2013-03-01

    Ultra-small-angle X-ray scattering (USAXS) can probe microstructures over the nanometer-to-micrometer scale range. Through use of a small instrument entrance slit, X-ray photon correlation spectroscopy (XPCS) exploits the partial coherence of an X-ray synchrotron undulator beam to provide unprecedented sensitivity to the dynamics of microstructural change. In USAXS/XPCS studies, the dynamics of local structures in a scale range of 100 nm to 1000 nm can be related to an overall hierarchical microstructure extending from 1 nm to more than 1000 nm. Using a point-detection scintillator mode, the equilibrium dynamics at ambient temperature of small particles (which move more slowly than nanoparticles) in aqueous suspension have been quantified directly for the first time. Using a USAXS-XPCS scanning mode for non-equilibrium dynamics incipient processes within dental composites have been elucidated, prior to effects becoming detectable using any other technique. Use of the Advanced Photon Source, an Office of Science User Facility operated for the United States Department of Energy (U.S. DOE) Office of Science by Argonne National Laboratory, was supported by the U.S. DOE under Contract No. DE-AC02-06CH11357.

  3. The influence of pore-water advection, benthic photosynthesis, and respiration on calcium carbonate dynamics in reef sands

    NARCIS (Netherlands)

    Rao, A.M.F.; Polerecky, L.; Ionescu, D.; Meysman, F.J.R.; de-Beer, D.

    2012-01-01

    To investigate diel calcium carbonate (CaCO3) dynamics in permeable coral reef sands, we measured pore-water profiles and fluxes of oxygen (O2), nutrients, pH, calcium (Ca2+), and alkalinity (TA) across the sediment-water interface in sands of different permeability

  4. Non-equilibrium Economics

    Directory of Open Access Journals (Sweden)

    Katalin Martinás

    2007-02-01

    Full Text Available A microeconomic, agent based framework to dynamic economics is formulated in a materialist approach. An axiomatic foundation of a non-equilibrium microeconomics is outlined. Economic activity is modelled as transformation and transport of commodities (materials owned by the agents. Rate of transformations (production intensity, and the rate of transport (trade are defined by the agents. Economic decision rules are derived from the observed economic behaviour. The non-linear equations are solved numerically for a model economy. Numerical solutions for simple model economies suggest that the some of the results of general equilibrium economics are consequences only of the equilibrium hypothesis. We show that perfect competition of selfish agents does not guarantee the stability of economic equilibrium, but cooperativity is needed, too.

  5. Nonequilibrium statistical mechanics ensemble method

    CERN Document Server

    Eu, Byung Chan

    1998-01-01

    In this monograph, nonequilibrium statistical mechanics is developed by means of ensemble methods on the basis of the Boltzmann equation, the generic Boltzmann equations for classical and quantum dilute gases, and a generalised Boltzmann equation for dense simple fluids The theories are developed in forms parallel with the equilibrium Gibbs ensemble theory in a way fully consistent with the laws of thermodynamics The generalised hydrodynamics equations are the integral part of the theory and describe the evolution of macroscopic processes in accordance with the laws of thermodynamics of systems far removed from equilibrium Audience This book will be of interest to researchers in the fields of statistical mechanics, condensed matter physics, gas dynamics, fluid dynamics, rheology, irreversible thermodynamics and nonequilibrium phenomena

  6. Structural dynamics of the cell nucleus: basis for morphology modulation of nuclear calcium signaling and gene transcription.

    Science.gov (United States)

    Queisser, Gillian; Wiegert, Simon; Bading, Hilmar

    2011-01-01

    Neuronal morphology plays an essential role in signal processing in the brain. Individual neurons can undergo use-dependent changes in their shape and connectivity, which affects how intracellular processes are regulated and how signals are transferred from one cell to another in a neuronal network. Calcium is one of the most important intracellular second messengers regulating cellular morphologies and functions. In neurons, intracellular calcium levels are controlled by ion channels in the plasma membrane such as NMDA receptors (NMDARs), voltage-gated calcium channels (VGCCs) and certain α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) as well as by calcium exchange pathways between the cytosol and internal calcium stores including the endoplasmic reticulum and mitochondria. Synaptic activity and the subsequent opening of ligand and/or voltage-gated calcium channels can initiate cytosolic calcium transients which propagate towards the cell soma and enter the nucleus via its nuclear pore complexes (NPCs) embedded in the nuclear envelope. We recently described the discovery that in hippocampal neurons the morphology of the nucleus affects the calcium dynamics within the nucleus. Here we propose that nuclear infoldings determine whether a nucleus functions as an integrator or detector of oscillating calcium signals. We outline possible ties between nuclear mophology and transcriptional activity and discuss the importance of extending the approach to whole cell calcium signal modeling in order to understand synapse-to-nucleus communication in healthy and dysfunctional neurons.

  7. Inference of neuronal network spike dynamics and topology from calcium imaging data

    Directory of Open Access Journals (Sweden)

    Henry eLütcke

    2013-12-01

    Full Text Available Two-photon calcium imaging enables functional analysis of neuronal circuits by inferring action potential (AP occurrence ('spike trains' from cellular fluorescence signals. It remains unclear how experimental parameters such as signal-to-noise ratio (SNR and acquisition rate affect spike inference and whether additional information about network structure can be extracted. Here we present a simulation framework for quantitatively assessing how well spike dynamics and network topology can be inferred from noisy calcium imaging data. For simulated AP-evoked calcium transients in neocortical pyramidal cells, we analyzed the quality of spike inference as a function of SNR and data acquisition rate using a recently introduced peeling algorithm. Given experimentally attainable values of SNR and acquisition rate, neural spike trains could be reconstructed accurately and with up to millisecond precision. We then applied statistical neuronal network models to explore how remaining uncertainties in spike inference affect estimates of network connectivity and topological features of network organization. We define the experimental conditions suitable for inferring whether the network has a scale-free structure and determine how well hub neurons can be identified. Our findings provide a benchmark for future calcium imaging studies that aim to reliably infer neuronal network properties.

  8. Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

    Science.gov (United States)

    Alavizargar, Azadeh; Berti, Claudio; Ejtehadi, Mohammad Reza; Furini, Simone

    2018-04-26

    Calcium release-activated calcium (CRAC) channels open upon depletion of Ca 2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca 2+ over Na + . The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

  9. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    Science.gov (United States)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  10. Dynamic transition on the seizure-like neuronal activity by astrocytic calcium channel block

    International Nuclear Information System (INIS)

    Li, Jiajia; Wang, Rong; Du, Mengmeng; Tang, Jun; Wu, Ying

    2016-01-01

    The involvement of astrocytes in neuronal firing dynamics is becoming increasingly evident. In this study, we used a classical hippocampal tripartite synapse model consisting of soma-dendrite coupled neuron models and a Hodgkin–Huxley-like astrocyte model, to investigate the seizure-like firing in the somatic neuron induced by the over-expressed neuronal N-methyl-d-aspartate (NMDA) receptors. Based on this model, we further investigated the effect of the astrocytic channel block on the neuronal firing through a bifurcation analysis. Results show that blocking inositol-1,4,5-triphosphate(IP3)-dependent calcium channel in astrocytes efficiently suppresses the astrocytic calcium oscillation, which in turn suppresses the seizure-like firing in the neuron.

  11. Nonequilibrium Statistical Operator Method and Generalized Kinetic Equations

    Science.gov (United States)

    Kuzemsky, A. L.

    2018-01-01

    We consider some principal problems of nonequilibrium statistical thermodynamics in the framework of the Zubarev nonequilibrium statistical operator approach. We present a brief comparative analysis of some approaches to describing irreversible processes based on the concept of nonequilibrium Gibbs ensembles and their applicability to describing nonequilibrium processes. We discuss the derivation of generalized kinetic equations for a system in a heat bath. We obtain and analyze a damped Schrödinger-type equation for a dynamical system in a heat bath. We study the dynamical behavior of a particle in a medium taking the dissipation effects into account. We consider the scattering problem for neutrons in a nonequilibrium medium and derive a generalized Van Hove formula. We show that the nonequilibrium statistical operator method is an effective, convenient tool for describing irreversible processes in condensed matter.

  12. Exploration of bulk and interface behavior of gas molecules and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid using equilibrium and nonequilibrium molecular dynamics simulation and quantum chemical calculation.

    Science.gov (United States)

    Yang, Quan; Achenie, Luke E K

    2018-04-18

    Ionic liquids (ILs) show brilliant performance in separating gas impurities, but few researchers have performed an in-depth exploration of the bulk and interface behavior of penetrants and ILs thoroughly. In this research, we have performed a study on both molecular dynamics (MD) simulation and quantum chemical (QC) calculation to explore the transport of acetylene and ethylene in the bulk and interface regions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]-[BF4]). The diffusivity, solubility and permeability of gas molecules in the bulk were researched with MD simulation first. The subdiffusion behavior of gas molecules is induced by coupling between the motion of gas molecules and the ions, and the relaxation processes of the ions after the disturbance caused by gas molecules. Then, QC calculation was performed to explore the optical geometry of ions, ion pairs and complexes of ions and penetrants, and interaction potential for pairs and complexes. Finally, nonequilibrium MD simulation was performed to explore the interface structure and properties of the IL-gas system and gas molecule behavior in the interface region. The research results may be used in the design of IL separation media.

  13. Nonideal plasmas as non-equilibrium media

    International Nuclear Information System (INIS)

    Morozov, I V; Norman, G E; Valuev, A A; Valuev, I A

    2003-01-01

    Various aspects of the collective behaviour of non-equilibrium nonideal plasmas are studied. The relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics (MD) method for two-component non-degenerate strongly non-equilibrium plasmas. The initial non-exponential stage, its duration and the subsequent exponential stage of the relaxation process are studied for a wide range of ion charge, nonideality parameter and ion mass. A simulation model of the nonideal plasma excited by an electron beam is proposed. An approach is developed to calculate the dynamic structure factor in non-stationary conditions. Instability increment is obtained from MD simulations

  14. Anisotropic nonequilibrium hydrodynamic attractor

    Science.gov (United States)

    Strickland, Michael; Noronha, Jorge; Denicol, Gabriel S.

    2018-02-01

    We determine the dynamical attractors associated with anisotropic hydrodynamics (aHydro) and the DNMR equations for a 0 +1 d conformal system using kinetic theory in the relaxation time approximation. We compare our results to the nonequilibrium attractor obtained from the exact solution of the 0 +1 d conformal Boltzmann equation, the Navier-Stokes theory, and the second-order Mueller-Israel-Stewart theory. We demonstrate that the aHydro attractor equation resums an infinite number of terms in the inverse Reynolds number. The resulting resummed aHydro attractor possesses a positive longitudinal-to-transverse pressure ratio and is virtually indistinguishable from the exact attractor. This suggests that an optimized hydrodynamic treatment of kinetic theory involves a resummation not only in gradients (Knudsen number) but also in the inverse Reynolds number. We also demonstrate that the DNMR result provides a better approximation of the exact kinetic theory attractor than the Mueller-Israel-Stewart theory. Finally, we introduce a new method for obtaining approximate aHydro equations which relies solely on an expansion in the inverse Reynolds number. We then carry this expansion out to the third order, and compare these third-order results to the exact kinetic theory solution.

  15. Nonequilibrium Dynamics of Anisotropic Large Spins in the Kondo Regime: Time-Dependent Numerical Renormalization Group Analysis

    Science.gov (United States)

    Roosen, David; Wegewijs, Maarten R.; Hofstetter, Walter

    2008-02-01

    We investigate the time-dependent Kondo effect in a single-molecule magnet (SMM) strongly coupled to metallic electrodes. Describing the SMM by a Kondo model with large spin S>1/2, we analyze the underscreening of the local moment and the effect of anisotropy terms on the relaxation dynamics of the magnetization. Underscreening by single-channel Kondo processes leads to a logarithmically slow relaxation, while finite uniaxial anisotropy causes a saturation of the SMM’s magnetization. Additional transverse anisotropy terms induce quantum spin tunneling and a pseudospin-1/2 Kondo effect sensitive to the spin parity.

  16. Nonequilibrium lattice-driven dynamics of stripes in nickelates using time-resolved x-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Lee, W.S.; Kung, Y.F.; Moritz, B.; Coslovich, G.; Kaindl, R.A.; Chuang, Y.D.; Moore, R.G.; Lu, D.H.; Kirchmann, P.S.; Robinson, J.S.; Minitti, M.P.; Dakovski, G.; Schlotter, W.F.; Turner, J.J.; Gerber, S.; Sasagawa, T.; Hussain, Z.; Shen, Z.X.; Devereaux, T.P.

    2017-03-13

    We investigate the lattice coupling to the spin and charge orders in the striped nickelate, La 1.75 Sr 0.25 NiO 4 , using time-resolved resonant x-ray scattering. Lattice-driven dynamics of both spin and charge orders are observed when the pump photon energy is tuned to that of an E u bond- stretching phonon. We present a likely scenario for the behavior of the spin and charge order parameters and its implications using a Ginzburg-Landau theory.

  17. Nonequilibrium quantum field theories

    International Nuclear Information System (INIS)

    Niemi, A.J.

    1988-01-01

    Combining the Feynman-Vernon influence functional formalism with the real-time formulation of finite-temperature quantum field theories we present a general approach to relativistic quantum field theories out of thermal equilibrium. We clarify the physical meaning of the additional fields encountered in the real-time formulation of quantum statistics and outline diagrammatic rules for perturbative nonequilibrium computations. We derive a generalization of Boltzmann's equation which gives a complete characterization of relativistic nonequilibrium phenomena. (orig.)

  18. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    Science.gov (United States)

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  19. Non-equilibrium lattice dynamics of one-dimensional In chains on Si(111 upon ultrafast optical excitation

    Directory of Open Access Journals (Sweden)

    T. Frigge

    2018-03-01

    Full Text Available The photoinduced structural dynamics of the atomic wire system on the Si(111-In surface has been studied by ultrafast electron diffraction in reflection geometry. Upon intense fs-laser excitation, this system can be driven in around 1 ps from the insulating (8×2 reconstructed low temperature phase to a metastable metallic (4×1 reconstructed high temperature phase. Subsequent to the structural transition, the surface heats up on a 6 times slower timescale as determined from a transient Debye-Waller analysis of the diffraction spots. From a comparison with the structural response of the high temperature (4×1 phase, we conclude that electron-phonon coupling is responsible for the slow energy transfer from the excited electron system to the lattice. The significant difference in timescales is evidence that the photoinduced structural transition is non-thermally driven.

  20. Time-dependent view of an isotope effect in electron-nuclear nonequilibrium dynamics with applications to N2.

    Science.gov (United States)

    Ajay, Jayanth S; Komarova, Ksenia G; Remacle, Francoise; Levine, R D

    2018-05-21

    Isotopic fractionation in the photodissociation of N 2 could explain the considerable variation in the 14 N/ 15 N ratio in different regions of our galaxy. We previously proposed that such an isotope effect is due to coupling of photoexcited bound valence and Rydberg electronic states in the frequency range where there is strong state mixing. We here identify features of the role of the mass in the dynamics through a time-dependent quantum-mechanical simulation. The photoexcitation of N 2 is by an ultrashort pulse so that the process has a sharply defined origin in time and so that we can monitor the isolated molecule dynamics in time. An ultrafast pulse is necessarily broad in frequency and spans several excited electronic states. Each excited molecule is therefore not in a given electronic state but in a superposition state. A short time after excitation, there is a fairly sharp onset of a mass-dependent large population transfer when wave packets on two different electronic states in the same molecule overlap. This coherent overlap of the wave packets on different electronic states in the region of strong coupling allows an effective transfer of population that is very mass dependent. The extent of the transfer depends on the product of the populations on the two different electronic states and on their relative phase. It is as if two molecules collide but the process occurs within one molecule, a molecule that is simultaneously in both states. An analytical toy model recovers the (strong) mass and energy dependence.

  1. Multilayer network representation of membrane potential and cytosolic calcium concentration dynamics in beta cells

    International Nuclear Information System (INIS)

    Gosak, Marko; Dolenšek, Jurij; Markovič, Rene; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž

    2015-01-01

    Highlights: • Physiological processes within and among pancreatic beta cells are very complex. • We analyze the simultaneous recordings of membrane potential and calcium dynamics. • We represent the interaction patterns among beta cells as a multilayer network. • The nature of the intracellular dynamics is found to rely on the network structure. - Abstract: Modern theory of networks has been recognized as a very successful methodological concept for the description and analysis of complex systems. However, some complex systems are more complex than others. For instance, several real-life systems are constituted by interdependent subsystems and their elements are subjected to different types of interactions that can also change with time. Recently, the multilayer network formalism has been proposed as a general theoretical framework for the description and analysis of such multi-dimensional complex systems and is acquiring more and more prominence in terms of a new research direction. In the present study, we use this methodology for the description of functional connectivity patterns and signal propagation between pancreatic beta cells in an islet of Langerhans at the levels of membrane potential (MP) and cytosolic calcium concentration ([Ca"2"+]_c) dynamics to study the extent of overlap in the two networks and to clarify whether time lags between the two signals in individual cells are in any way dependent on the role these cells play in the functional networks. The two corresponding network layers are constructed on the basis of signal directions and pairwise correlations, whereas the interlayer connections represent the time lag between both measured signals. Our results confirm our previous finding that both MP and [Ca"2"+]_c change spread across an islet in the form of a depolarization and a [Ca"2"+]_c wave, respectively. Both types of waves follow nearly the same path and the networks in both layers have a similar but not entirely the same structure

  2. Evolution and non-equilibrium physics

    DEFF Research Database (Denmark)

    Becker, Nikolaj; Sibani, Paolo

    2014-01-01

    We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of the Tangled Nature Model (TNM) of biological evolution...

  3. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy.

    Directory of Open Access Journals (Sweden)

    Alex Costa

    Full Text Available Selective Plane Illumination Microscopy (SPIM is an imaging technique particularly suited for long term in-vivo analysis of transparent specimens, able to visualize small organs or entire organisms, at cellular and eventually even subcellular resolution. Here we report the application of SPIM in Calcium imaging based on Förster Resonance Energy Transfer (FRET. Transgenic Arabidopsis plants expressing the genetically encoded-FRET-based Ca(2+ probe Cameleon, in the cytosol or nucleus, were used to demonstrate that SPIM enables ratiometric fluorescence imaging at high spatial and temporal resolution, both at tissue and single cell level. The SPIM-FRET technique enabled us to follow nuclear and cytosolic Ca(2+ dynamics in Arabidopsis root tip cells, deep inside the organ, in response to different stimuli. A relevant physiological phenomenon, namely Ca(2+ signal percolation, predicted in previous studies, has been directly visualized.

  4. Novel effect of interplay of internal and external noise on the dynamics of calcium oscillations

    International Nuclear Information System (INIS)

    Li Hongying; Ma Juan

    2010-01-01

    Graphical abstract: When the external noise is small (D ≤ 0.8), R goes through a maximum at an optimal system size V, indicating the occurring of internal-noise stochastic resonance (INSR), and the curves become higher with the increases of D, which shows that INSR can be enhanced by the external noise in a certain range of external noise intensity ((D ≤ 0.8). If D > 0.8, R monotonically increases and the peak disappears. When D increases further, the R curve becomes lower. Research highlights: → External noise coherence resonance (ENCR) can be suppressed by internal noise. → Internal noise stochastic resonance (INSR) can be enhanced by external noise. → When INSR occurs, the optimal system size can be regulated by the external noise. - Abstract: Using a mesoscopic stochastic model, the effect of interplay of external and internal noise on the dynamics of calcium oscillations was studied. When the system was tuned near a Hopf bifurcation point and driven by external noise or internal noise only, the existence of external noise coherence resonance (ENCR) or internal-noise stochastic resonance (INSR) was found, respectively. When both of the noises were considered, it was found that ENCR could be suppressed by internal noise, while INSR could be enhanced by external noise in a certain range of external noise intensity. It was also interesting to note that the optimal system size can be regulated by the external noise when the INSR occurs. The cell system may adapt to adjust the optimal size according to the external noise, indicating some kind of self-tuning mechanism involved in stochastic calcium dynamics.

  5. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD{sub 3}CN treated with a parallel multi-state EVB model

    Energy Technology Data Exchange (ETDEWEB)

    Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational

  6. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.

    Science.gov (United States)

    Glowacki, David R; Orr-Ewing, Andrew J; Harvey, Jeremy N

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol(-1) localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral

  7. Influence of dose reduction and iterative reconstruction on CT calcium scores : a multi-manufacturer dynamic phantom study

    NARCIS (Netherlands)

    van der Werf, N R; Willemink, M J; Willems, T P; Greuter, M J W; Leiner, T

    To evaluate the influence of dose reduction in combination with iterative reconstruction (IR) on coronary calcium scores (CCS) in a dynamic phantom on state-of-the-art CT systems from different manufacturers. Calcified inserts in an anthropomorphic chest phantom were translated at 20 mm/s

  8. Nonequilibrium electron transport through quantum dots in the Kondo regime

    DEFF Research Database (Denmark)

    Wölfle, Peter; Paaske, Jens; Rosch, Achim

    2005-01-01

    Electron transport at large bias voltage through quantum dots in the Kondo regime is described within the perturbative renormalization group extended to nonequilibrium. The conductance, local magnetization, dynamical spin susceptibility and local spectral function are calculated. We show how...

  9. Some recent developments in non-equilibrium statistical physics

    Indian Academy of Sciences (India)

    : ... This canonical prescription is the starting point for studying a system in ... abilistic approach to non-equilibrium dynamics by treating the case of Markovian ..... equation in this network between the incoming flux and the outgoing flux at each.

  10. Multi-modal in vivo imaging of brain blood oxygenation, blood flow and neural calcium dynamics during acute seizures

    Science.gov (United States)

    Ringuette, Dene; Jeffrey, Melanie A.; Carlen, Peter L.; Levi, Ofer

    2016-03-01

    Dysfunction of the vascular endothelium has been implicated in the development of epilepsy. To better understand the relation between vascular function and seizure and provide a foundation for interpreting results from functional imaging in chronic disease models, we investigate the relationship between intracellular calcium dynamics and local cerebral blood flow and blood oxygen saturation during acute seizure-like events and pharmacological seizure rescue. To probe the relation between the aforementioned physiological markers in an acute model of epilepsy in rats, we integrated three different optical modalities together with electrophysiological recordings: Laser speckle contrast imaging (LSCI) was used to study changes in flow speeds, Intrinsic optical signal imaging (IOSI) was used to monitor changes in oxygenated, de-oxygenated, and total hemoglobin concentration, and Calcium-sensitive dye imaging was used to monitor intracellular calcium dynamics. We designed a dedicated cortical flow chamber to remove superficial blood and dye resulting from the injection procedure, which reduced spurious artifacts. The near infrared light used for IOSI and LSCI was delivered via a light pipe integrated with the flow chamber to minimize the effect of fluid surface movement on illumination stability. Calcium-sensitive dye was injected via a glass electrode used for recording the local field potential. Our system allowed us to observe and correlate increases in intracellular calcium, blood flow and blood volume during seizure-like events and provide a quantitative analysis of neurovascular coupling changes associated with seizure rescue via injection of an anti-convulsive agent.

  11. Nonequilibrium statistical physics

    CERN Document Server

    Röpke, Gerd

    2013-01-01

    Authored by one of the top theoretical physicists in Germany, and a well-known authority in the field, this is the only coherent presentation of the subject suitable for masters and PhD students, as well as postdocs in physics and related disciplines.Starting from a general discussion of the nonequilibrium state, different standard approaches such as master equations, and kinetic and linear response theory, are derived after special assumptions. This allows for an insight into the problems of nonequilibrium physics, a discussion of the limits, and suggestions for improvements. Applications

  12. Functional connectivity structure of cortical calcium dynamics in anesthetized and awake mice.

    Science.gov (United States)

    Wright, Patrick W; Brier, Lindsey M; Bauer, Adam Q; Baxter, Grant A; Kraft, Andrew W; Reisman, Matthew D; Bice, Annie R; Snyder, Abraham Z; Lee, Jin-Moo; Culver, Joseph P

    2017-01-01

    The interplay between hemodynamic-based markers of cortical activity (e.g. fMRI and optical intrinsic signal imaging), which are an indirect and relatively slow report of neural activity, and underlying synaptic electrical and metabolic activity through neurovascular coupling is a topic of ongoing research and debate. As application of resting state functional connectivity measures is extended further into topics such as brain development, aging and disease, the importance of understanding the fundamental physiological basis for functional connectivity will grow. Here we extend functional connectivity analysis from hemodynamic- to calcium-based imaging. Transgenic mice (n = 7) expressing a fluorescent calcium indicator (GCaMP6) driven by the Thy1 promoter in glutamatergic neurons were imaged transcranially in both anesthetized (using ketamine/xylazine) and awake states. Sequential LED illumination (λ = 454, 523, 595, 640nm) enabled concurrent imaging of both GCaMP6 fluorescence emission (corrected for hemoglobin absorption) and hemodynamics. Functional connectivity network maps were constructed for infraslow (0.009-0.08Hz), intermediate (0.08-0.4Hz), and high (0.4-4.0Hz) frequency bands. At infraslow and intermediate frequencies, commonly used in BOLD fMRI and fcOIS studies of functional connectivity and implicated in neurovascular coupling mechanisms, GCaMP6 and HbO2 functional connectivity structures were in high agreement, both qualitatively and also quantitatively through a measure of spatial similarity. The spontaneous dynamics of both contrasts had the highest correlation when the GCaMP6 signal was delayed with a ~0.6-1.5s temporal offset. Within the higher-frequency delta band, sensitive to slow wave sleep oscillations in non-REM sleep and anesthesia, we evaluate the speed with which the connectivity analysis stabilized and found that the functional connectivity maps captured putative network structure within time window lengths as short as 30 seconds

  13. Small angle neutron scattering (SANS) under non-equilibrium conditions

    International Nuclear Information System (INIS)

    Oberthur, R.C.

    1984-01-01

    The use of small angle neutron scattering (SANS) for the study of systems under non-equilibrium conditions is illustrated by three types of experiments in the field of polymer research: - the relaxation of a system from an initial non-equilibrium state towards equilibrium, - the cyclic or repetitive installation of a series of non-equilibrium states in a system, - the steady non-equilibrium state maintained by a constant dissipation of energy within the system. Characteristic times obtained in these experiments with SANS are compared with the times obtained from quasi-elastic neutron and light scattering, which yield information about the equilibrium dynamics of the system. The limits of SANS applied to non-equilibrium systems for the measurement of relaxation times at different length scales are shown and compared to the limits of quasielastic neutron and light scattering

  14. Nonequilibrium thermodynamics of nucleation

    NARCIS (Netherlands)

    Schweizer, M.; Sagis, L.M.C.

    2014-01-01

    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a

  15. Non-equilibrium phase transition

    International Nuclear Information System (INIS)

    Mottola, E.; Cooper, F.M.; Bishop, A.R.; Habib, S.; Kluger, Y.; Jensen, N.G.

    1998-01-01

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Non-equilibrium phase transitions play a central role in a very broad range of scientific areas, ranging from nuclear, particle, and astrophysics to condensed matter physics and the material and biological sciences. The aim of this project was to explore the path to a deeper and more fundamental understanding of the common physical principles underlying the complex real time dynamics of phase transitions. The main emphasis was on the development of general theoretical tools to deal with non-equilibrium processes, and of numerical methods robust enough to capture the time-evolving structures that occur in actual experimental situations. Specific applications to Laboratory multidivisional efforts in relativistic heavy-ion physics (transition to a new phase of nuclear matter consisting of a quark-gluon plasma) and layered high-temperature superconductors (critical currents and flux flow at the National High Magnetic Field Laboratory) were undertaken

  16. Control of local intracellular calcium concentration with dynamic-clamp controlled 2-photon uncaging.

    Directory of Open Access Journals (Sweden)

    Erwin Idoux

    Full Text Available The variations of the intracellular concentration of calcium ion ([Ca(2+](i are at the heart of intracellular signaling, and their imaging is therefore of enormous interest. However, passive [Ca(2+](i imaging provides no control over these variations, meaning that a full exploration of the functional consequences of [Ca(2+](i changes is difficult to attain. The tools designed so far to modify [Ca(2+](i, even qualitatively, suffer drawbacks that undermine their widespread use. Here, we describe an electro-optical technique to quantitatively set [Ca(2+](i, in real time and with sub-cellular resolution, using two-photon Ca(2+ uncaging and dynamic-clamp. We experimentally demonstrate, on neurons from acute olfactory bulb slices of Long Evans rats, various capabilities of this technique previously difficult to achieve, such as the independent control of the membrane potential and [Ca(2+](i variations, the functional knocking-in of user-defined virtual voltage-dependent Ca(2+ channels, and the standardization of [Ca(2+](i patterns across different cells. Our goal is to lay the groundwork for this technique and establish it as a new and versatile tool for the study of cell signaling.

  17. Investigation of calcium-dependent activity and conformational dynamics of zebra fish 12-lipoxygenase.

    Science.gov (United States)

    Mittal, Monica; Hasan, Mahmudul; Balagunaseelan, Navisraj; Fauland, Alexander; Wheelock, Craig; Rådmark, Olof; Haeggström, Jesper Z; Rinaldo-Matthis, Agnes

    2017-08-01

    A 12-lipoxygenase in zebra fish (zf12-LOX) was found to be required for normal embryonic development and LOXs are of great interest for targeted drug designing. In this study, we investigate the structural-functional aspects of zf12-LOX in response to calcium. A soluble version of zf12-LOX was created by mutagenesis. Based on multiple sequence alignment, we mutated the putative calcium-responsive amino acids in N-PLAT domain of soluble zf12-LOX. Using a series of biophysical methods, we ascertained the oligomeric state, stability, structural integrity and conformational changes of zf12-LOX in response to calcium. We also compared the biophysical properties of soluble zf12-LOX with the mutant in the absence and presence of calcium. Here we provide a detailed characterization of soluble zf12-LOX and the mutant. Both proteins exist as compact monomers in solution, however the enzyme activity of soluble zf12-LOX is significantly increased in presence of calcium. We find that the stimulatory effect of calcium on zf12-LOX is related to a change in protein structure as observed by SAXS, adopting an open-state. In contrast, enzyme with a mutated calcium regulatory site has reduced activity-response to calcium and restricted large re-modeling, suggesting that it retains a closed-state in response to calcium. Taken together, our study suggests that Ca 2+ -dependent regulation is associated with different domain conformation(s) that might change the accessibility to substrate-binding site in response to calcium. The study can be broadly implicated in better understanding the mode(s) of action of LOXs, and the enzymes regulated by calcium in general. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Statistical thermodynamics of nonequilibrium processes

    CERN Document Server

    Keizer, Joel

    1987-01-01

    The structure of the theory ofthermodynamics has changed enormously since its inception in the middle of the nineteenth century. Shortly after Thomson and Clausius enunciated their versions of the Second Law, Clausius, Maxwell, and Boltzmann began actively pursuing the molecular basis of thermo­ dynamics, work that culminated in the Boltzmann equation and the theory of transport processes in dilute gases. Much later, Onsager undertook the elucidation of the symmetry oftransport coefficients and, thereby, established himself as the father of the theory of nonequilibrium thermodynamics. Com­ bining the statistical ideas of Gibbs and Langevin with the phenomenological transport equations, Onsager and others went on to develop a consistent statistical theory of irreversible processes. The power of that theory is in its ability to relate measurable quantities, such as transport coefficients and thermodynamic derivatives, to the results of experimental measurements. As powerful as that theory is, it is linear and...

  19. Complex temporal and spatial patterns in nonequilibrium processes

    International Nuclear Information System (INIS)

    Swinney, H.L.

    1992-01-01

    We have used dynamical systems methods to study and characterize bifurcations and pattern formation in a variety of nonequilibrium systems. In this paper we describe our work on dynamical systems, chemical oscillations and chaos, chemical spatial patterns, instabilities in fluid dynamics, electrodeposition clusters, the ballast resistor, and crack propagation

  20. Impact of sarcoplasmic reticulum calcium release on calcium dynamics and action potential morphology in human atrial myocytes: a computational study.

    Directory of Open Access Journals (Sweden)

    Jussi T Koivumäki

    Full Text Available Electrophysiological studies of the human heart face the fundamental challenge that experimental data can be acquired only from patients with underlying heart disease. Regarding human atria, there exist sizable gaps in the understanding of the functional role of cellular Ca²+ dynamics, which differ crucially from that of ventricular cells, in the modulation of excitation-contraction coupling. Accordingly, the objective of this study was to develop a mathematical model of the human atrial myocyte that, in addition to the sarcolemmal (SL ion currents, accounts for the heterogeneity of intracellular Ca²+ dynamics emerging from a structurally detailed sarcoplasmic reticulum (SR. Based on the simulation results, our model convincingly reproduces the principal characteristics of Ca²+ dynamics: 1 the biphasic increment during the upstroke of the Ca²+ transient resulting from the delay between the peripheral and central SR Ca²+ release, and 2 the relative contribution of SL Ca²+ current and SR Ca²+ release to the Ca²+ transient. In line with experimental findings, the model also replicates the strong impact of intracellular Ca²+ dynamics on the shape of the action potential. The simulation results suggest that the peripheral SR Ca²+ release sites define the interface between Ca²+ and AP, whereas the central release sites are important for the fire-diffuse-fire propagation of Ca²+ diffusion. Furthermore, our analysis predicts that the modulation of the action potential duration due to increasing heart rate is largely mediated by changes in the intracellular Na+ concentration. Finally, the results indicate that the SR Ca²+ release is a strong modulator of AP duration and, consequently, myocyte refractoriness/excitability. We conclude that the developed model is robust and reproduces many fundamental aspects of the tight coupling between SL ion currents and intracellular Ca²+ signaling. Thus, the model provides a useful framework for future

  1. Time Dependent Hartree Fock Equation: Gateway to Nonequilibrium Plasmas

    International Nuclear Information System (INIS)

    Dufty, James W.

    2007-01-01

    This is the Final Technical Report for DE-FG02-2ER54677 award 'Time Dependent Hartree Fock Equation - Gateway to Nonequilibrium Plasmas'. Research has focused on the nonequilibrium dynamics of electrons in the presence of ions, both via basic quantum theory and via semi-classical molecular dynamics (MD) simulation. In addition, fundamental notions of dissipative dynamics have been explored for models of grains and dust, and for scalar fields (temperature) in turbulent edge plasmas. The specific topics addressed were Quantum Kinetic Theory for Metallic Clusters, Semi-classical MD Simulation of Plasmas , and Effects of Dissipative Dynamics.

  2. Comparative aspects of calcium dynamics in calcified tissues in the goldfish Carassius auratus

    International Nuclear Information System (INIS)

    Ichii, Taro; Mugiya, Yasuo

    1983-01-01

    The comparative nature of calcium physiology in bone, scales and otoliths was studied in young goldfish, Carassius auratus. Net calcium uptake by the fish was estimated to be 143 μg/g body weight/day. Of that, 79 % was distributed in bone, 13 % in scales, 3.5 % in otoliths and 4.5 % in soft tissues. Scales showed the highest incorporation of 45 Ca per mg-tissue weight after 1 or 2 days in 45 Ca-containing water; bone came second and otoliths last. However, 35 days after transfer to non-radioactive water, the order of descending radioactivity had changed to otoliths, bone and scales, reflecting different rates of calcium turnover. In bone, prelabeled 45 Ca activity increased for the first 2 days after transfer and then decreased gradually (biological half-life, Tsub(0.5) = 94 days). In otoliths, prelabeled radioactivity consistently increased for 35 days. Scales showed two phases of calcium turnover. They lost about 33 % of their prelabeled radioactivity during the first 7 days (Tsub(0.5) = 10.5 days) in non-radioactive water, but thereafter the rate of decrease slowed down greatly (Tsub(0.5) = 210 days). These two phases of calcium turnover were found in the osseous layer (including calcium crystals in the fibrillary plate) of scales, indicating the presence of physiologically labile as well as stable forms of calcium in the layer. (author)

  3. Comparative aspects of calcium dynamics in calcified tissues in the goldfish Carassius auratus

    Energy Technology Data Exchange (ETDEWEB)

    Ichii, Taro; Mugiya, Yasuo (Hokkaido Univ., Hakodate (Japan). Faculty of Fisheries)

    1983-07-01

    The comparative nature of calcium physiology in bone, scales and otoliths was studied in young goldfish, Carassius auratus. Net calcium uptake by the fish was estimated to be 143 ..mu..g/g body weight/day. Of that, 79 % was distributed in bone, 13 % in scales, 3.5 % in otoliths and 4.5 % in soft tissues. Scales showed the highest incorporation of /sup 45/Ca per mg-tissue weight after 1 or 2 days in /sup 45/Ca-containing water; bone came second and otoliths last. However, 35 days after transfer to non-radioactive water, the order of descending radioactivity had changed to otoliths, bone and scales, reflecting different rates of calcium turnover. In bone, prelabeled /sup 45/Ca activity increased for the first 2 days after transfer and then decreased gradually (biological half-life, Tsub(0.5) = 94 days). In otoliths, prelabeled radioactivity consistently increased for 35 days. Scales showed two phases of calcium turnover. They lost about 33 % of their prelabeled radioactivity during the first 7 days (Tsub(0.5) = 10.5 days) in non-radioactive water, but thereafter the rate of decrease slowed down greatly (Tsub(0.5) = 210 days). These two phases of calcium turnover were found in the osseous layer (including calcium crystals in the fibrillary plate) of scales, indicating the presence of physiologically labile as well as stable forms of calcium in the layer.

  4. Statistical mechanics of nonequilibrium liquids

    CERN Document Server

    Evans, Denis J; Craig, D P; McWeeny, R

    1990-01-01

    Statistical Mechanics of Nonequilibrium Liquids deals with theoretical rheology. The book discusses nonlinear response of systems and outlines the statistical mechanical theory. In discussing the framework of nonequilibrium statistical mechanics, the book explains the derivation of a nonequilibrium analogue of the Gibbsian basis for equilibrium statistical mechanics. The book reviews the linear irreversible thermodynamics, the Liouville equation, and the Irving-Kirkwood procedure. The text then explains the Green-Kubo relations used in linear transport coefficients, the linear response theory,

  5. Glucose-stimulated calcium dynamics in islets of Langerhans in acute mouse pancreas tissue slices.

    Directory of Open Access Journals (Sweden)

    Andraž Stožer

    Full Text Available In endocrine cells within islets of Langerhans calcium ions couple cell stimulation to hormone secretion. Since the advent of modern fluorimetry, numerous in vitro studies employing primarily isolated mouse islets have investigated the effects of various secretagogues on cytoplasmic calcium, predominantly in insulin-secreting beta cells. Due to technical limitations, insights of these studies are inherently limited to a rather small subpopulation of outermost cells. The results also seem to depend on various factors, like culture conditions and duration, and are not always easily reconcilable with findings in vivo. The main controversies regard the types of calcium oscillations, presence of calcium waves, and the level of synchronized activity. Here, we set out to combine the in situ acute mouse pancreas tissue slice preparation with noninvasive fluorescent calcium labeling and subsequent confocal laser scanning microscopy to shed new light on the existing controversies utilizing an innovative approach enabling the characterization of responses in many cells from all layers of islets. Our experiments reproducibly showed stable fast calcium oscillations on a sustained plateau rather than slow oscillations as the predominant type of response in acute tissue slices, and that calcium waves are the mechanistic substrate for synchronization of oscillations. We also found indirect evidence that even a large amplitude calcium signal was not sufficient and that metabolic activation was necessary to ensure cell synchronization upon stimulation with glucose. Our novel method helped resolve existing controversies and showed the potential to help answer important physiological questions, making it one of the methods of choice for the foreseeable future.

  6. Visualizing presynaptic calcium dynamics and vesicle fusion with a single genetically encoded reporter at individual synapses

    Directory of Open Access Journals (Sweden)

    Rachel E Jackson

    2016-07-01

    Full Text Available Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post-hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses.

  7. Nonequilibrium effects in Isoscaling

    International Nuclear Information System (INIS)

    Dorso, C. O.; Lopez, J. A.

    2007-01-01

    In this work we study within a simple model different properties of the system that allow us to understand the properties of the isoscaling observable. We first show that isoscaling is a general property of fragmenting systems. We show this by using a simple generalized percolation model. We show that the usual isoscaling property can be obtained in the case of bond percolation in bichromatic lattices with any regular topology. In this case the probabilities of each color (isospin) are independent. We then explore the effect of introducing 'non-equilibrium' effects

  8. Non-equilibrium thermodynamics

    CERN Document Server

    De Groot, Sybren Ruurds

    1984-01-01

    The study of thermodynamics is especially timely today, as its concepts are being applied to problems in biology, biochemistry, electrochemistry, and engineering. This book treats irreversible processes and phenomena - non-equilibrium thermodynamics.S. R. de Groot and P. Mazur, Professors of Theoretical Physics, present a comprehensive and insightful survey of the foundations of the field, providing the only complete discussion of the fluctuating linear theory of irreversible thermodynamics. The application covers a wide range of topics: the theory of diffusion and heat conduction, fluid dyn

  9. Investigation on non-equilibrium performance of composite adsorbent for resorption refrigeration

    International Nuclear Information System (INIS)

    Jiang, L.; Wang, L.W.; Zhou, Z.S.; Zhu, F.Q.; Wang, R.Z.

    2016-01-01

    Highlights: • Performance of resorption refrigeration is analyzed based on non-equilibrium reaction process. • The porous matrix improves the heat and mass performance of composite adsorbent. • The actual desorption process has the significant hysteresis phenomenon. • The highest energy efficiency of Manganese and Calcium chloride working pair is 0.272. - Abstract: The aims of this paper is to indicate that the non-equilibrium adsorption testing results is more suitable for prediction of real refrigeration performance than equilibrium data. Therefore, a test unit is constructed to test the non-equilibrium performance of different composite adsorbents. The adsorption and desorption quantity are measured and calculated by smart differential pressure transmitter. The non-equilibrium adsorption performances of working pair of Manganese chloride–ammonia, Calcium chloride–ammonia and Ammonium chloride–ammonia are investigated respectively. Results show that hysteresis phenomena happens obviously in non-equilibrium desorption process, which is related with dual variables rather than single variable. Based on the testing results, resorption refrigeration performance is analyzed, in which Manganese chloride is used as high temperature salt (HTS), and Calcium chloride, Ammonium chloride are selected as low temperature salt (LTS) for comparison. Results show that the highest COP and SCP for resorption refrigeration are about 0.272 and 45.6 W/kg, respectively. Performance of Manganese chloride–Calcium chloride and Manganese chloride–Ammonium chloride working pairs are much lower when compared with theoretical data.

  10. Differential impacts of calcium and aluminum treatments on sugar maple and American beech growth dynamics

    Science.gov (United States)

    Joshua M. Halman; Paul G. Schaberg; Gary J. Hawley; Christopher F. Hansen; Timothy J. Fahey

    2015-01-01

    Acid deposition induced losses of calcium (Ca) from northeastern forests have had negative effects on forest health for decades, including the mobilization of potentially phytotoxic aluminum (Al) from soils. To evaluate the impact of changes in Ca and Al availability on sugar maple (Acer saccharum Marsh.) and American beech (Fagus...

  11. Deterministic thermostats, theories of nonequilibrium systems and parallels with the ergodic condition

    International Nuclear Information System (INIS)

    Jepps, Owen G; Rondoni, Lamberto

    2010-01-01

    Deterministic 'thermostats' are mathematical tools used to model nonequilibrium steady states of fluids. The resulting dynamical systems correctly represent the transport properties of these fluids and are easily simulated on modern computers. More recently, the connection between such thermostats and entropy production has been exploited in the development of nonequilibrium fluid theories. The purpose and limitations of deterministic thermostats are discussed in the context of irreversible thermodynamics and the development of theories of nonequilibrium phenomena. We draw parallels between the development of such nonequilibrium theories and the development of notions of ergodicity in equilibrium theories. (topical review)

  12. Definition of Nonequilibrium Entropy of General Systems

    OpenAIRE

    Mei, Xiaochun

    1999-01-01

    The definition of nonequilibrium entropy is provided for the general nonequilibrium processes by connecting thermodynamics with statistical physics, and the principle of entropy increment in the nonequilibrium processes is also proved in the paper. The result shows that the definition of nonequilibrium entropy is not unique.

  13. Intracellular Calcium Dynamics and Autonomic Stimulation in Atrial Fibrillation: Mechanisms and Implications

    Directory of Open Access Journals (Sweden)

    Chung-Chuan Chou, MD

    2008-01-01

    Full Text Available While atrial fibrillation is characterized by the co-existence of multiple activation waves within the atria, rapid activations in the pulmonary veins play an important role for the initiation and maintenance of atrial fibrillation. In addition to reentry, non-reentrant mechanisms resulting from abnormal intracellular calcium handling and intracellular calcium overload can also be responsible for these rapid activations in the pulmonary veins. Meanwhile, alterations of autonomic tone, involving both the sympathetic and parasympathetic nervous system, have been implicated in initiating paroxysmal atrial fibrillation. But the effectiveness of autonomic modulation as an adjunctive therapeutic strategy to catheter ablation of atrial fibrillation has been inconsistent. The interactions between the autonomic nervous system and atrial fibrillation are more complex than currently understood and further mechanistic and clinical studies are warranted.

  14. Impaired osteoblast function in osteoporosis: comparison between calcium balance and dynamic histomorphometry.

    OpenAIRE

    Arlot, M; Edouard, C; Meunier, P J; Neer, R M; Reeve, J

    1984-01-01

    Osteoblast function was investigated in 27 patients with idiopathic osteoporosis. Transiliac bone biopsy specimens were taken after double labelling with tetracycline, and metabolic calcium balance was studied almost simultaneously. Many of the patients showed poor double labelling of their otherwise unremarkable trabecular osteoid, suggesting impaired formation of bone at many of these surfaces. This phenomenon was not accompanied by increased width of osteoid seams (as seen in osteomalacia)...

  15. Impaired osteoblast function in osteoporosis: comparison between calcium balance and dynamic histomorphometry.

    Science.gov (United States)

    Arlot, M; Edouard, C; Meunier, P J; Neer, R M; Reeve, J

    1984-09-01

    Osteoblast function was investigated in 27 patients with idiopathic osteoporosis. Transiliac bone biopsy specimens were taken after double labelling with tetracycline, and metabolic calcium balance was studied almost simultaneously. Many of the patients showed poor double labelling of their otherwise unremarkable trabecular osteoid, suggesting impaired formation of bone at many of these surfaces. This phenomenon was not accompanied by increased width of osteoid seams (as seen in osteomalacia), indicating that formation of the matrix and its mineralisation were in equilibrium. For the first time, highly significant positive correlations (p less than 0.01) were found between indices of bone formation, determined by labelling with tetracycline, and calcium balance. Thus some patients with osteoporosis who are rapidly losing bone have low rates of formation of trabecular bone both by individual osteoblasts and in relation to available bone surfaces. As histological indices of bone resorption also independently correlated strongly and inversely (p less than 0.01) with calcium balance the rate of initiation of new basic multicellular units by osteoclastic resorption of trabecular surfaces (or the depth of resorption at these surfaces) also appears to be an important determinant of mineral balance. The mechanisms that regulate the effective life span of mature osteoblasts require further investigation, particularly as some promising treatments that can increase trabecular bone volume in osteoporosis, such as parathyroid peptide hPTH (1-34) and sodium fluoride, must work through a reversal of osteoblastic depression.

  16. Nonequilibrium fermion production in quantum field theory

    International Nuclear Information System (INIS)

    Pruschke, Jens

    2010-01-01

    The creation of matter in the early universe or in relativistic heavy-ion collisions is inevitable connected to nonequilibrium physics. One of the key challenges is the explanation of the corresponding thermalization process following nonequilibrium instabilities. The role of fermionic quantum fields in such scenarios is discussed in the literature by using approximations of field theories which neglect important quantum corrections. This thesis goes beyond such approximations. A quantum field theory where scalar bosons interact with Dirac fermions via a Yukawa coupling is analyzed in the 2PI effective action formalism. The chosen approximation allows for a correct description of the dynamics including nonequilibrium instabilities. In particular, fermion-boson loop corrections allow to study the interaction of fermions with large boson fluctuations. The applied initial conditions generate nonequilibrium instabilities like parametric resonance or spinodal instabilities. The equations of motion for correlation functions are solved numerically and major characteristics of the fermion dynamics are described by analytical solutions. New mechanisms for the production of fermions are found. Simulations in the case of spinodal instability show that unstable boson fluctuations induce exponentially growing fermion modes with approximately the same growth rate. If the unstable regime lasts long enough a thermalization of the infrared part of the fermion occupation number occurs on time scales much shorter than the time scale on which bosonic quantum fields thermalize. Fermions acquire an excess of occupation in the ultraviolet regime compared to a Fermi-Dirac statistic characterized by a power-law with exponent two. The fermion production mechanism via parametric resonance is found to be most efficient after the instability ends. Quantum corrections then provide a very efficient particle creation mechanism which is interpreted as an amplification of decay processes. The ratio

  17. Universality in Nonequilibrium Lattice Systems Theoretical Foundations

    CERN Document Server

    Ódor, Géza

    2008-01-01

    Universal scaling behavior is an attractive feature in statistical physics because a wide range of models can be classified purely in terms of their collective behavior due to a diverging correlation length. This book provides a comprehensive overview of dynamical universality classes occurring in nonequilibrium systems defined on regular lattices. The factors determining these diverse universality classes have yet to be fully understood, but the book attempts to summarize our present knowledge, taking them into account systematically.The book helps the reader to navigate in the zoo of basic m

  18. Nonequilibrium fermion production in quantum field theory

    Energy Technology Data Exchange (ETDEWEB)

    Pruschke, Jens

    2010-06-16

    The creation of matter in the early universe or in relativistic heavy-ion collisions is inevitable connected to nonequilibrium physics. One of the key challenges is the explanation of the corresponding thermalization process following nonequilibrium instabilities. The role of fermionic quantum fields in such scenarios is discussed in the literature by using approximations of field theories which neglect important quantum corrections. This thesis goes beyond such approximations. A quantum field theory where scalar bosons interact with Dirac fermions via a Yukawa coupling is analyzed in the 2PI effective action formalism. The chosen approximation allows for a correct description of the dynamics including nonequilibrium instabilities. In particular, fermion-boson loop corrections allow to study the interaction of fermions with large boson fluctuations. The applied initial conditions generate nonequilibrium instabilities like parametric resonance or spinodal instabilities. The equations of motion for correlation functions are solved numerically and major characteristics of the fermion dynamics are described by analytical solutions. New mechanisms for the production of fermions are found. Simulations in the case of spinodal instability show that unstable boson fluctuations induce exponentially growing fermion modes with approximately the same growth rate. If the unstable regime lasts long enough a thermalization of the infrared part of the fermion occupation number occurs on time scales much shorter than the time scale on which bosonic quantum fields thermalize. Fermions acquire an excess of occupation in the ultraviolet regime compared to a Fermi-Dirac statistic characterized by a power-law with exponent two. The fermion production mechanism via parametric resonance is found to be most efficient after the instability ends. Quantum corrections then provide a very efficient particle creation mechanism which is interpreted as an amplification of decay processes. The ratio

  19. Origins of scaling relations in nonequilibrium growth

    International Nuclear Information System (INIS)

    Escudero, Carlos; Korutcheva, Elka

    2012-01-01

    Scaling and hyperscaling laws provide exact relations among critical exponents describing the behavior of a system at criticality. For nonequilibrium growth models with a conserved drift, there exist few of them. One such relation is α + z = 4, found to be inexact in a renormalization group calculation for several classical models in this field. Herein, we focus on the two-dimensional case and show that it is possible to construct conserved surface growth equations for which the relation α + z = 4 is exact in the renormalization group sense. We explain the presence of this scaling law in terms of the existence of geometric principles dominating the dynamics. (paper)

  20. Dynamic measurement of the calcium buffering properties of the sarcoplasmic reticulum in mouse skeletal muscle.

    Science.gov (United States)

    Manno, Carlo; Sztretye, Monika; Figueroa, Lourdes; Allen, Paul D; Ríos, Eduardo

    2013-01-15

    The buffering power, B, of the sarcoplasmic reticulum (SR), ratio of the changes in total and free [Ca(2+)], was determined in fast-twitch mouse muscle cells subjected to depleting membrane depolarization. Changes in total SR [Ca(2+)] were measured integrating Ca(2+) release flux, determined with a cytosolic [Ca(2+)] monitor. Free [Ca(2+)](SR) was measured using the cameleon D4cpv-Casq1. In 34 wild-type (WT) cells average B during the depolarization (ON phase) was 157 (SEM 26), implying that of 157 ions released, 156 were bound inside the SR. B was significantly greater when BAPTA, which increases release flux, was present in the cytosol. B was greater early in the pulse - when flux was greatest - than at its end, and greater in the ON than in the OFF. In 29 Casq1-null cells, B was 40 (3.6). The difference suggests that 75% of the releasable calcium is normally bound to calsequestrin. In the nulls the difference in B between ON and OFF was less than in the WT but still significant. This difference and the associated decay in B during the ON were not artifacts of a slow SR monitor, as they were also found in the WT when [Ca(2+)](SR) was tracked with the fast dye fluo-5N. The calcium buffering power, binding capacity and non-linear binding properties of the SR measured here could be accounted for by calsequestrin at the concentration present in mammalian muscle, provided that its properties were substantially different from those found in solution. Its affinity should be higher, or K(D) lower than the conventionally accepted 1 mm; its cooperativity (n in a Hill fit) should be higher and the stoichiometry of binding should be at the higher end of the values derived in solution. The reduction in B during release might reflect changes in calsequestrin conformation upon calcium loss.

  1. Dynamic and Mechanical Properties of Calcium Borophosphate Glasses in Relation to Structure and Topology

    DEFF Research Database (Denmark)

    Hermansen, Christian; Yue, Yuanzheng

    Calcium borophosphate glasses and glass ceramics are of interest as bone-replacement implants as they can bond to bone through an apatite layer, and dissolve in vitro at a rate comparable to the growth rate of natural bone. We investigate the pseudo-binary join between CaO•P2O5 and CaO•2B2O3...... the crystallization behavior of this glass series. The compositional variation of these properties is analyzed using the Phillips-Thorpe rigidity percolation paradigm and the temperature dependent constraint theory. This analysis gives insight into the link between properties and composition in borophosphate glasses....

  2. [The dynamics of calcium distribution in stigma and style of lettuce (Lactuca sativa L.) before and after pollination].

    Science.gov (United States)

    Qiu, Yi Lan; Liu, Ru Shi; Xie, Chao Tian; Yang, Yan Hong; Gu, Li; Tian, Hui Qiao

    2005-08-01

    Potassium antimonite was used to deposit calcium in the stigma and style of lettuce (Lactuca sativa L.) before and after pollination. The stigma of lettuce is two splits. Abundant calcium granules are displayed in the wall of papillae on the receptive surface of stigma before and after pollination, which may facilitate pollen germination. However, a few calcium granules in the wall of epidermis cell on no-receptive surface. Calcium distribution in style presents a gradient in transmitting tissue and parenchyma cells from the top to the base of the style before pollination. After pollination, calcium in transmitting tissue distinctly increased and its gradient distribution became more evident. Pollen tubes grow in the intercellular gaps of transmitting tissue. When pollen tubes grew into transmitting tissue, calcium granules in parenchyma around transmitting tissue decreased, suggesting a calcium movement was controlled by pollen tubes. The calcium gradient distribution also appeared in the trachea of vascular bundle of style. In general, calcium in style displays a feature of time-special distribution: transmitting tissue doesn't need much more calcium that is only stored in the parenchyma before pollination. However, calcium in parenchyma cells may be transported to transmitting tissue and make the latter contain more calcium to form an evident calcium gradient and meet the requirement of pollen tubes directionally growing after pollination. This is the second sample of calcium gradient existing in style, which was found by using potassium antimonite method.

  3. Spatiotemporal dynamics of rhythmic spinal interneurons measured with two-photon calcium imaging and coherence analysis.

    Science.gov (United States)

    Kwan, Alex C; Dietz, Shelby B; Zhong, Guisheng; Harris-Warrick, Ronald M; Webb, Watt W

    2010-12-01

    In rhythmic neural circuits, a neuron often fires action potentials with a constant phase to the rhythm, a timing relationship that can be functionally significant. To characterize these phase preferences in a large-scale, cell type-specific manner, we adapted multitaper coherence analysis for two-photon calcium imaging. Analysis of simulated data showed that coherence is a simple and robust measure of rhythmicity for calcium imaging data. When applied to the neonatal mouse hindlimb spinal locomotor network, the phase relationships between peak activity of >1,000 ventral spinal interneurons and motor output were characterized. Most interneurons showed rhythmic activity that was coherent and in phase with the ipsilateral motor output during fictive locomotion. The phase distributions of two genetically identified classes of interneurons were distinct from the ensemble population and from each other. There was no obvious spatial clustering of interneurons with similar phase preferences. Together, these results suggest that cell type, not neighboring neuron activity, is a better indicator of an interneuron's response during fictive locomotion. The ability to measure the phase preferences of many neurons with cell type and spatial information should be widely applicable for studying other rhythmic neural circuits.

  4. 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)

  5. Fluctuation theorems and orbital magnetism in nonequilibrium state

    Indian Academy of Sciences (India)

    We study Langevin dynamics of a driven charged particle in the presence as well as in the absence of magnetic field. We discuss the validity of various work fluctuation theorems using different model potentials and external drives. We also show that one can generate an orbital magnetic moment in a nonequilibrium state ...

  6. Forces and energy dissipation in inhomogeneous non-equilibrium superconductors

    International Nuclear Information System (INIS)

    Poluehktov, Yu.M.; Slezov, V.V.

    1987-01-01

    The phenomenological theory of volume forces and dissipation processes in inhomogeneous non-equilibrium superconductors near temperature transition from the normal to superconducting state is constructed. The approach is based on application of dynamic equations of superconductivity formulated on the basis of the Lagrangian formalism. These equations are generalized the Ginzburg-Landau theory in the nonstationary non-equilibrium case for ''foul'' superconductors. The value estimations of volume forces arising in inhomogeneities during relaxation of an order parameter and when the electrical field is penetrated into the superconductor, are given

  7. Experimental approaches for studying non-equilibrium atmospheric plasma jets

    Energy Technology Data Exchange (ETDEWEB)

    Shashurin, A., E-mail: ashashur@purdue.edu [School of Aeronautics & Astronautics, Purdue University, West Lafayette, Indiana 47907 (United States); Keidar, M. [Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, District of Columbia 20052 (United States)

    2015-12-15

    This work reviews recent research efforts undertaken in the area non-equilibrium atmospheric plasma jets with special focus on experimental approaches. Physics of small non-equilibrium atmospheric plasma jets operating in kHz frequency range at powers around few Watts will be analyzed, including mechanism of breakdown, process of ionization front propagation, electrical coupling of the ionization front with the discharge electrodes, distributions of excited and ionized species, discharge current spreading, transient dynamics of various plasma parameters, etc. Experimental diagnostic approaches utilized in the field will be considered, including Rayleigh microwave scattering, Thomson laser scattering, electrostatic streamer scatterers, optical emission spectroscopy, fast photographing, etc.

  8. Modeling, Measurements, and Fundamental Database Development for Nonequilibrium Hypersonic Aerothermodynamics

    Science.gov (United States)

    Bose, Deepak

    2012-01-01

    The design of entry vehicles requires predictions of aerothermal environment during the hypersonic phase of their flight trajectories. These predictions are made using computational fluid dynamics (CFD) codes that often rely on physics and chemistry models of nonequilibrium processes. The primary processes of interest are gas phase chemistry, internal energy relaxation, electronic excitation, nonequilibrium emission and absorption of radiation, and gas-surface interaction leading to surface recession and catalytic recombination. NASAs Hypersonics Project is advancing the state-of-the-art in modeling of nonequilibrium phenomena by making detailed spectroscopic measurements in shock tube and arcjets, using ab-initio quantum mechanical techniques develop fundamental chemistry and spectroscopic databases, making fundamental measurements of finite-rate gas surface interactions, implementing of detailed mechanisms in the state-of-the-art CFD codes, The development of new models is based on validation with relevant experiments. We will present the latest developments and a roadmap for the technical areas mentioned above

  9. Nonequilibrium thermodynamics and fluctuation relations for small systems

    International Nuclear Information System (INIS)

    Cao Liang; Ke Pu; Qiao Li-Yan; Zheng Zhi-Gang

    2014-01-01

    In this review, we give a retrospect of the recent progress in nonequilibrium statistical mechanics and thermodynamics in small dynamical systems. For systems with only a few number of particles, fluctuations and nonlinearity become significant and contribute to the nonequilibrium behaviors of the systems, hence the statistical properties and thermodynamics should be carefully studied. We review recent developments of this topic by starting from the Gallavotti—Cohen fluctuation theorem, and then to the Evans—Searles transient fluctuation theorem, Jarzynski free-energy equality, and the Crooks fluctuation relation. We also investigate the nonequilibrium free energy theorem for trajectories involving changes of the heat bath temperature and propose a generalized free-energy relation. It should be noticed that the non-Markovian property of the heat bath may lead to the violation of the free-energy relation. (topical review - statistical physics and complex systems)

  10. Spatiotemporal Wave Patterns: Information Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mikhail Rabinovich; Lev Tsimring

    2006-01-20

    Pattern formation has traditionally been studied in non-equilibrium physics from the viewpoint of describing the basic structures and their interactions. While this is still an important area of research, the emphasis in the last few years has shifted towards analysis of specific properties of patterns in various complex media. For example, diverse and unexpected phenomena occur in neuro-like media that are characterized by highly non-trivial local dynamics. We carried out an active research program on analysis of spatio-temporal patterns in various physical systems (convection, oscillating fluid layer, soap film), as well as in neuro-like media, with an emphasis on informational aspects of the dynamics. Nonlinear nonequilibrium media and their discrete analogs have a unique ability to represent, memorize, and process the information contained in spatio-temporal patterns. Recent neurophysiological experiments demonstrated a certain universality of spatio-temporal representation of information by neural ensembles. Information processing is also revealed in the spatio-temporal dynamics of cellular patterns in nonequilibrium media. It is extremely important for many applications to study the informational aspects of these dynamics, including the origins and mechanisms of information generation, propagation and storage. Some of our results are: the discovery of self-organization of periodically oscillatory patterns in chaotic heterogeneous media; the analysis of the propagation of the information along a chaotic media as function of the entropy of the signal; the analysis of wave propagation in discrete non-equilibrium media with autocatalytic properties, which simulates the calcium dynamics in cellular membranes. Based on biological experiments we suggest the mechanism by which the spatial sensory information is transferred into the spatio-temporal code in the neural media. We also found a new mechanism of self-pinning in cellular structures and the related phenomenon

  11. Probing in space and time the nuclear motion driven by nonequilibrium electronic dynamics in ultrafast pumped N.sub.2./sub.

    Czech Academy of Sciences Publication Activity Database

    Ajay, J.; Šmydke, Jan; Remacle, F.; Levine, R.D.

    2016-01-01

    Roč. 120, č. 19 (2016), s. 3335-3342 ISSN 1089-5639 Institutional support: RVO:68378271 Keywords : molecular dynamics * dissociation * excitation * ions Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.847, year: 2016

  12. Nonequilibrium work relation in a macroscopic system

    International Nuclear Information System (INIS)

    Sughiyama, Yuki; Ohzeki, Masayuki

    2013-01-01

    We reconsider a well-known relationship between the fluctuation theorem and the second law of thermodynamics by evaluating stochastic evolution of the density field (probability measure valued process). In order to establish a bridge between microscopic and macroscopic behaviors, we must take the thermodynamic limit of a stochastic dynamical system following the standard procedure in statistical mechanics. The thermodynamic path characterizing a dynamical behavior in the macroscopic scale can be formulated as an infimum of the action functional for the stochastic evolution of the density field. In our formulation, the second law of thermodynamics can be derived only by symmetry of the action functional without recourse to the Jarzynski equality. Our formulation leads to a nontrivial nonequilibrium work relation for metastable (quasi-stationary) states, which are peculiar in the macroscopic system. We propose a prescription for computing the free energy for metastable states based on the resultant work relation. (paper)

  13. Stochastic approach to equilibrium and nonequilibrium thermodynamics.

    Science.gov (United States)

    Tomé, Tânia; de Oliveira, Mário J

    2015-04-01

    We develop the stochastic approach to thermodynamics based on stochastic dynamics, which can be discrete (master equation) and continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of entropy itself and the second the definition of entropy production rate, which is non-negative and vanishes in thermodynamic equilibrium. Based on these assumptions, we study interacting systems with many degrees of freedom in equilibrium or out of thermodynamic equilibrium and how the macroscopic laws are derived from the stochastic dynamics. These studies include the quasiequilibrium processes; the convexity of the equilibrium surface; the monotonic time behavior of thermodynamic potentials, including entropy; the bilinear form of the entropy production rate; the Onsager coefficients and reciprocal relations; and the nonequilibrium steady states of chemical reactions.

  14. Nonequilibrium 2-hydroxyoctadecanoic acid monolayers: effect of electrolytes.

    Science.gov (United States)

    Lendrum, Conrad D; Ingham, Bridget; Lin, Binhua; Meron, Mati; Toney, Michael F; McGrath, Kathryn M

    2011-04-19

    2-Hydroxyacids display complex monolayer phase behavior due to the additional hydrogen bonding afforded by the presence of the second hydroxy group. The placement of this group at the position α to the carboxylic acid functionality also introduces the possibility of chelation, a utility important in crystallization including biomineralization. Biomineralization, like many biological processes, is inherently a nonequilibrium process. The nonequilibrium monolayer phase behavior of 2-hydroxyoctadecanoic acid was investigated on each of pure water, calcium chloride, sodium bicarbonate and calcium carbonate crystallizing subphases as a precursor study to a model calcium carbonate biomineralizing system, each at a pH of ∼6. The role of the bicarbonate co-ion in manipulating the monolayer structure was determined by comparison with monolayer phase behavior on a sodium chloride subphase. Monolayer phase behavior was probed using surface pressure/area isotherms, surface potential, Brewster angle microscopy, and synchrotron-based grazing incidence X-ray diffraction and X-ray reflectivity. Complex phase behavior was observed for all but the sodium chloride subphase with hydrogen bonding, electrostatic and steric effects defining the symmetry of the monolayer. On a pure water subphase hydrogen bonding dominates with three phases coexisting at low pressures. Introduction of calcium ions into the aqueous subphase ensures strong cation binding to the surfactant head groups through chelation. The monolayer becomes very unstable in the presence of bicarbonate ions within the subphase due to short-range hydrogen bonding interactions between the monolayer and bicarbonate ions facilitated by the sodium cation enhancing surfactant solubility. The combined effects of electrostatics and hydrogen bonding are observed on the calcium carbonate crystallizing subphase. © 2011 American Chemical Society

  15. Calcium supplements

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007477.htm Calcium supplements To use the sharing features on this page, please enable JavaScript. WHO SHOULD TAKE CALCIUM SUPPLEMENTS? Calcium is an important mineral for the ...

  16. Non-equilibrium supramolecular polymerization.

    Science.gov (United States)

    Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J; de Greef, Tom F A; Hermans, Thomas M

    2017-09-18

    Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term "non-equilibrium self-assembly" by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization.

  17. Nonequilibrium free diffusion in seed leachate

    Science.gov (United States)

    Ortiz G., Luis; Riquelme P., Pablo; Guzmán, R.

    2013-11-01

    In this work, we use a Schlieren-like Near Field Scattering (SNFS) setup to study nonequilibrium free diffusion behavior of a colloidal solution obtained from seeds leachate. The main objective is to compare the temporal behavior of the diffusion coefficient of seed leachate with an electric conductivity based vigor test. SNFS sizing measurements, based on Mie theory, were carried out to ensure its reliability and sensitivity. Then, we performed a typical nonequilibrium free diffusion experiment of a glycerol-water mixture. In this way, we confirmed that SNFS setup is sensitive to giant concentration fluctuations of nanocolloidal solutions. The results obtained in this stage reproduce properly the data reported elsewhere in literature. Moreover, seed leachate diffuse, in water, in a similar way that glycerol does. In both cases we used the same method (dynamic structure factor) to determine thermo-physical properties. We show that time evolution of diffusion coefficient of Lupinus Albus leachate exhibits three defined regimes as electric conductivity measurements. The results also exhibit a correspondence between the behavior of the diffusion coefficient and electric conductivity values of the two regions in the temporal range studied. Finally, we discuss biological processes involved in germination that could modulate this dependence, and the role played by the electrolytic nature of solutes.

  18. Phase transition universality classes of classical, nonequilibrium systems

    CERN Document Server

    Ódor, G

    2004-01-01

    In the first chapter I summarize the most important critical exponents and relations used in this work. In the second chapter I briefly address the question of scaling behavior at first order phase transitions.In chapter three I review dynamical extensions of basic static classes, show the effect of mixing dynamics and percolation behavior. The main body of this work is given in chapter four where genuine, dynamical universality classes specific to nonequilibrium systems are introduced. In chapter five I continue overviewing such nonequilibrium classes but in coupled, multi-component systems. Most of known transitions in low dimensional systems are between active and absorbing states of reaction-diffusion type systems, but I briefly introduce related classes that appear in interface growth models in chapter six. Some of them are related to critical behavior of coupled, multi-component systems. Finally in chapter seven I summarize families of absorbing state system classes, mean-field classes and the most freq...

  19. Effects of Applying Lime and CalciumMontmorillonite on Nitrification Dynamics in Acidic Soil

    Directory of Open Access Journals (Sweden)

    WANG Mei

    2017-01-01

    Full Text Available Soil acidification is known as a natural and slow process along with clay mineral weathering. In recent years however, with inten sive soil utilization in agriculture, soil acidification has increased dramatically and nitrification of ammonium nitrogen fertilizer is one of the main contributors to soil acidification. Lime application is the traditional practice to improve acidic soils but it often makes the soil acidic a gain leading to soil compaction in most cases. Montmorillonite is the main clay mineral component of alkaline or neutral soils, more so it is known to undergo further weathering processes during soil acidification. The laboratory-based incubations were used in this study, and nitri fication was measured while kinetic curves were fitted to check the effects of decreasing soil acidity by lime(Ca-OHand montmorillonite (Ca-Mon nitrification of the acidic soil. The results showed that significant nitrification was observed both in Ca-OH and Ca-M treatments, and the nitrification process was fitted in the first-order kinetic model, NNO3=N0+Np(1-exp(-k1t(P-1·d-1was significantly higher than that of Ca-M treatment(2.381 mg·kg-1·d-1. The potential nitrifi cation rate(Vpwere 6.42, 8.58 mg N·kg-1·d-1 at pH 5.7 and 6.2 respectively, and the average nitrification rate(Vaof Ca-OH treatment were 2.71, 3.88 mg N·kg-1·d-1 respectively, which were significantly greater than those of Ca-M treatment(Vp were 3.40, 4.56 mg N·kg-1·d-1 and Va were 2.36, 3.04 mg N·kg-1·d-1 at pH 5.7 and 6.2 respectively. Therefore the net nitrification rate, potential nitrification rate(Vp and average nitrification rate(Vaof Ca-OH treatment were significantly higher than that of Ca-M treatment, suggesting that the possibili ty and degree of soil reacidification by using lime to improve acidic soil is greater than using calcium montmorillonite. This study will provide a new reference for the improvement of acid soils.

  20. Nonlinear dynamics of non-equilibrium holes in p-type modulation-doped GaInNAs/GaAs quantum wells

    Directory of Open Access Journals (Sweden)

    Amann Andreas

    2011-01-01

    Full Text Available Abstract Nonlinear charge transport parallel to the layers of p-modulation-doped GaInNAs/GaAs quantum wells (QWs is studied both theoretically and experimentally. Experimental results show that at low temperature, T = 13 K, the presence of an applied electric field of about 6 kV/cm leads to the heating of the high mobility holes in the GaInNAs QWs, and their real-space transfer (RST into the low-mobility GaAs barriers. This results in a negative differential mobility and self-generated oscillatory instabilities in the RST regime. We developed an analytical model based upon the coupled nonlinear dynamics of the real-space hole transfer and of the interface potential barrier controlled by space-charge in the doped GaAs layer. Our simulation results predict dc bias-dependent self-generated current oscillations with frequencies in the high microwave range.

  1. Oleuropein-Enriched Olive Leaf Extract Affects Calcium Dynamics and Impairs Viability of Malignant Mesothelioma Cells

    Directory of Open Access Journals (Sweden)

    Carla Marchetti

    2015-01-01

    Full Text Available Malignant mesothelioma is a poor prognosis cancer in urgent need of alternative therapies. Oleuropein, the major phenolic of olive tree (Olea europaea L., is believed to have therapeutic potentials for various diseases, including tumors. We obtained an oleuropein-enriched fraction, consisting of 60% w/w oleuropein, from olive leaves, and assessed its effects on intracellular Ca2+ and cell viability in mesothelioma cells. Effects of the oleuropein-enriched fraction on Ca2+ dynamics and cell viability were studied in the REN mesothelioma cell line, using fura-2 microspectrofluorimetry and MTT assay, respectively. Fura-2-loaded cells, transiently exposed to the oleuropein-enriched fraction, showed dose-dependent transient elevations of cytosolic Ca2+ concentration (Ca2+i. Application of standard oleuropein and hydroxytyrosol, and of the inhibitor of low-voltage T-type Ca2+ channels NNC-55-0396, suggested that the effect is mainly due to oleuropein acting through its hydroxytyrosol moiety on T-type Ca2+ channels. The oleuropein-enriched fraction and standard oleuropein displayed a significant antiproliferative effect, as measured on REN cells by MTT cell viability assay, with IC50 of 22 μg/mL oleuropein. Data suggest that our oleuropein-enriched fraction from olive leaf extract could have pharmacological application in malignant mesothelioma anticancer therapy, possibly by targeting T-type Ca2+ channels and thereby dysregulating intracellular Ca2+ dynamics.

  2. Introduction to nonequilibrium statistical mechanics with quantum field theory

    International Nuclear Information System (INIS)

    Kita, Takafumi

    2010-01-01

    quantum field theory, including fluctuations. We also discuss a derivation of the quantum transport equations for electrons in electromagnetic fields based on the gauge-invariant Wigner transformation so that the Lorentz force is reproduced naturally. As for (3), the Gibbs entropy of equilibrium statistical mechanics suffers from the flaw that it does not evolve in time. We show here that a microscopic expression of nonequilibrium dynamical entropy can be derived from the quantum transport equations so as to be compatible with the law of increase in entropy as well as equilibrium statistical mechanics. (author)

  3. TRPC1, STIM1, and ORAI influence signal-regulated intracellular and endoplasmic reticulum calcium dynamics in human myometrial cells.

    Science.gov (United States)

    Murtazina, Dilyara A; Chung, Daesuk; Ulloa, Aida; Bryan, Emily; Galan, Henry L; Sanborn, Barbara M

    2011-08-01

    To explore the relationship between signal-stimulated increases in intracellular calcium ([Ca(2+)](i)) and depletion and refilling of the endoplasmic reticulum (ER) Ca(2+) stores ([Ca(2+)](L)) in human myometrial cells, we measured simultaneous changes in [Ca(2+)](i) and [Ca(2+)](L) using Fura-2 and Mag-fluo-4, respectively, in PHM1-41 immortalized and primary cells derived from pregnant myometrium and in primary cells derived from nonpregnant tissue. Signal- and extracellular Ca(2+)-dependent increases in [Ca(2+)](i) (SRCE) and ER refilling stimulated by oxytocin and cyclopiazonic acid were not inhibited by voltage-operated channel blocker nifedipine or mibefradil, inhibition of Na(+)/Ca(2+) exchange with KB-R7943, or zero extracellular Na(+) in PHM1-41 cells. Gadolinium-inhibited oxytocin- and cyclopiazonic acid-induced SRCE and slowed ER store refilling. TRPC1 mRNA knockdown specifically inhibited oxytocin-stimulated SRCE but had no statistically significant effect on ER store refilling and no effect on either parameter following cyclopiazonic acid treatment. Dominant negative STIMΔERM expression attenuated oxytocin- and thapsigargin-stimulated SRCE. Both STIM1 and ORAI1-ORAI3 mRNA knockdowns significantly attenuated oxytocin- and cyclopiazonic acid-stimulated SRCE. The data also suggest that reduction in STIM1 or ORAI1-ORAI3 mRNA can impede the rate of ER store refilling following removal of SERCA inhibition. These data provide evidence for both distinct and overlapping influences of TRPC1, STIM1, and ORAI1-ORAI3 on SRCE and ER store refilling in human myometrial cells that may contribute to the regulation of myometrial Ca(2+) dynamics. These findings have important implications for understanding the control of myometrial Ca(2+) dynamics in relation to myometrial contractile function.

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

    Science.gov (United States)

    Grossman, B.; Cinnella, P.

    1990-01-01

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

  5. An integrated model of cardiac mitochondrial energy metabolism and calcium dynamics.

    Science.gov (United States)

    Cortassa, Sonia; Aon, Miguel A; Marbán, Eduardo; Winslow, Raimond L; O'Rourke, Brian

    2003-04-01

    We present an integrated thermokinetic model describing control of cardiac mitochondrial bioenergetics. The model describes the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and mitochondrial Ca(2+) handling. The kinetic component of the model includes effectors of the TCA cycle enzymes regulating production of NADH and FADH(2), which in turn are used by the electron transport chain to establish a proton motive force (Delta mu(H)), driving the F(1)F(0)-ATPase. In addition, mitochondrial matrix Ca(2+), determined by Ca(2+) uniporter and Na(+)/Ca(2+) exchanger activities, regulates activity of the TCA cycle enzymes isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase. The model is described by twelve ordinary differential equations for the time rate of change of mitochondrial membrane potential (Delta Psi(m)), and matrix concentrations of Ca(2+), NADH, ADP, and TCA cycle intermediates. The model is used to predict the response of mitochondria to changes in substrate delivery, metabolic inhibition, the rate of adenine nucleotide exchange, and Ca(2+). The model is able to reproduce, qualitatively and semiquantitatively, experimental data concerning mitochondrial bioenergetics, Ca(2+) dynamics, and respiratory control. Significant increases in oxygen consumption (V(O(2))), proton efflux, NADH, and ATP synthesis, in response to an increase in cytoplasmic Ca(2+), are obtained when the Ca(2+)-sensitive dehydrogenases are the main rate-controlling steps of respiratory flux. These responses diminished when control is shifted downstream (e.g., the respiratory chain or adenine nucleotide translocator). The time-dependent behavior of the model, under conditions simulating an increase in workload, closely reproduces experimentally observed mitochondrial NADH dynamics in heart trabeculae subjected to changes in pacing frequency. The steady-state and time-dependent behavior of the model support the hypothesis that mitochondrial matrix Ca(2+) plays an

  6. 15N NMR relaxation studies of calcium-loaded parvalbumin show tight dynamics compared to those of other EF-hand proteins

    DEFF Research Database (Denmark)

    Baldellon, C; Alattia, J R; Strub, M P

    1998-01-01

    Dynamics of the rat alpha-parvalbumin calcium-loaded form have been determined by measurement of 15N nuclear relaxation using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed using spectral density functions and the Lipari-Szabo formalism. The major dynamic features...... for the rat alpha-parvalbumin calcium-loaded form are (1) the extreme rigidity of the helix-loop-helix EF-hand motifs and the linker segment connecting them, (2) the N and C termini of the protein being restricted in their mobility, (3) a conformational exchange occurring at the kink of helix D, and (4...... properties which are conserved in the EF-hand domains from different members of this superfamily: (1) a tendency toward higher mobility of NH vectors at relative position 2 in the Ca2+-binding loop, (2) a restricted mobility for the other residues in the binding loop, and (3) an overall rigidity...

  7. Nonequilibrium Thermodynamics of Driven Disordered Materials

    Science.gov (United States)

    Bouchbinder, Eran

    2011-03-01

    We present a nonequilibrium thermodynamic framework for describing the dynamics of driven disordered solids (noncrystalline solids near and below their glass temperature, soft glassy materials such as colloidal suspensions and heavily dislocated polycrystalline solids). A central idea in our approach is that the set of mechanically stable configurations, i.e. the part of the system that is described by inherent structures, evolves slowly as compared to thermal vibrations and is characterized by an effective disorder temperature. Our thermodynamics-motivated equations of motion for the flow of energy and entropy are supplemented by coarse-grained internal variables that carry information about the relevant microscopic physics. Applications of this framework to amorphous visco-plasticity (Shear-Transformation-Zone theory), glassy memory effects (the Kovacs effect) and dislocation-mediated polycrystalline plasticity will be briefly discussed.

  8. Nonequilibrium Chromosome Looping via Molecular Slip Links

    Science.gov (United States)

    Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

    2017-09-01

    We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

  9. Calcium absorption

    International Nuclear Information System (INIS)

    Carlmark, B.; Reizenstein, P.; Dudley, R.A.

    1976-01-01

    The methods most commonly used to measure the absorption and retention of orally administered calcium are reviewed. Nearly all make use of calcium radioisotopes. The magnitude of calcium absorption and retention depends upon the chemical form and amount of calcium administered, and the clinical and nutritional status of the subject; these influences are briefly surveyed. (author)

  10. Nonequilibrium mesoscopic transport: a genealogy

    International Nuclear Information System (INIS)

    Das, Mukunda P; Green, Frederick

    2012-01-01

    Models of nonequilibrium quantum transport underpin all modern electronic devices, from the largest scales to the smallest. Past simplifications such as coarse graining and bulk self-averaging served well to understand electronic materials. Such particular notions become inapplicable at mesoscopic dimensions, edging towards the truly quantum regime. Nevertheless a unifying thread continues to run through transport physics, animating the design of small-scale electronic technology: microscopic conservation and nonequilibrium dissipation. These fundamentals are inherent in quantum transport and gain even greater and more explicit experimental meaning in the passage to atomic-sized devices. We review their genesis, their theoretical context, and their governing role in the electronic response of meso- and nanoscopic systems. (topical review)

  11. Nonequilibrium quantum fluctuations of work.

    Science.gov (United States)

    Allahverdyan, A E

    2014-09-01

    The concept of work is basic for statistical thermodynamics. To gain a fuller understanding of work and its (quantum) features, it needs to be represented as an average of a fluctuating quantity. Here I focus on the work done between two moments of time for a thermally isolated quantum system driven by a time-dependent Hamiltonian. I formulate two natural conditions needed for the fluctuating work to be physically meaningful for a system that starts its evolution from a nonequilibrium state. The existing definitions do not satisfy these conditions due to issues that are traced back to noncommutativity. I propose a definition of fluctuating work that is free of previous drawbacks and that applies for a wide class of nonequilibrium initial states. It allows the deduction of a generalized work-fluctuation theorem that applies for an arbitrary (out-of-equilibrium) initial state.

  12. Nonequilibrium two-dimensional Ising model with stationary uphill diffusion

    Science.gov (United States)

    Colangeli, Matteo; Giardinà, Cristian; Giberti, Claudio; Vernia, Cecilia

    2018-03-01

    Usually, in a nonequilibrium setting, a current brings mass from the highest density regions to the lowest density ones. Although rare, the opposite phenomenon (known as "uphill diffusion") has also been observed in multicomponent systems, where it appears as an artificial effect of the interaction among components. We show here that uphill diffusion can be a substantial effect, i.e., it may occur even in single component systems as a consequence of some external work. To this aim we consider the two-dimensional ferromagnetic Ising model in contact with two reservoirs that fix, at the left and the right boundaries, magnetizations of the same magnitude but of opposite signs.We provide numerical evidence that a class of nonequilibrium steady states exists in which, by tuning the reservoir magnetizations, the current in the system changes from "downhill" to "uphill". Moreover, we also show that, in such nonequilibrium setup, the current vanishes when the reservoir magnetization attains a value approaching, in the large volume limit, the magnetization of the equilibrium dynamics, thus establishing a relation between equilibrium and nonequilibrium properties.

  13. Complex temporal and spatial patterns in nonequilibrium processes. Progress report, December 1, 1987--November 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Swinney, H.L.

    1992-10-01

    We have used dynamical systems methods to study and characterize bifurcations and pattern formation in a variety of nonequilibrium systems. In this paper we describe our work on dynamical systems, chemical oscillations and chaos, chemical spatial patterns, instabilities in fluid dynamics, electrodeposition clusters, the ballast resistor, and crack propagation.

  14. Subthreshold membrane potential oscillations in inferior olive neurons are dynamically regulated by P/Q- and T-type calcium channels: a study in mutant mice.

    Science.gov (United States)

    Choi, Soonwook; Yu, Eunah; Kim, Daesoo; Urbano, Francisco J; Makarenko, Vladimir; Shin, Hee-Sup; Llinás, Rodolfo R

    2010-08-15

    The role of P/Q- and T-type calcium channels in the rhythmic oscillatory behaviour of inferior olive (IO) neurons was investigated in mutant mice. Mice lacking either the CaV2.1 gene of the pore-forming alpha1A subunit for P/Q-type calcium channel, or the CaV3.1 gene of the pore-forming alpha1G subunit for T-type calcium channel were used. In vitro intracellular recording from IO neurons reveals that the amplitude and frequency of sinusoidal subthreshold oscillations (SSTOs) were reduced in the CaV2.1-/- mice. In the CaV3.1-/- mice, IO neurons also showed altered patterns of SSTOs and the probability of SSTO generation was significantly lower (15%, 5 of 34 neurons) than that of wild-type (78%, 31 of 40 neurons) or CaV2.1-/- mice (73%, 22 of 30 neurons). In addition, the low-threshold calcium spike and the sustained endogenous oscillation following rebound potentials were absent in IO neurons from CaV3.1-/- mice. Moreover, the phase-reset dynamics of oscillatory properties of single neurons and neuronal clusters in IO were remarkably altered in both CaV2.1-/- and CaV3.1-/- mice. These results suggest that both alpha1A P/Q- and alpha1G T-type calcium channels are required for the dynamic control of neuronal oscillations in the IO. These findings were supported by results from a mathematical IO neuronal model that incorporated T and P/Q channel kinetics.

  15. The behavior of matter under nonequilibrium conditions: Fundamental aspects and applications

    International Nuclear Information System (INIS)

    Prigogine, I.

    1989-10-01

    As in the previous period, our work has been concerned with the study of the properties of nonequilibrium systems and especially with the mechanism of self-organization. As is well-known, the study of self-organization began with the investigation of hydrodynamical or chemical instabilities studied from the point of view of macroscopic physics. The main outcome is that nonequilibrium generates spatial correlations of macroscopic physics. The main outcome is that nonequilibrium generates spatial correlations of macroscopic range whose characteristics length is an intrinsic property and whose amplitude is determined by nonequilibrium constraints. A survey of the macroscopic approach to nonequilibrium states is given in the paper ''Nonequilibrium States and Long Range Correlations in Chemical Dynamics,'' by G. Nicolis et al. However, over the last few years important progress has been made in the simulation of nonequilibrium situations using mainly molecular dynamics. It appears now that processes corresponding to self-organization as well as the appearance of long-range correlations can be obtained in this way starting from a program involving Newtonian dynamics (generally the laws of interaction correspond to hard spheres or hard disks). Examples of such types of studies leading to Benard instabilities, to chemical clocks, or to spatial structure formation are given in this report. As a result, we may now view self-organization as a direct expression of an appropriate microscopic dynamics. This is the reason why we have devoted much work to the study of large Poincare systems (LPS) involving continuous sets of resonances. These systems have been shown to lead, according to the constraints, either to equilibrium situations or to nonequilibrium states involving long range correlations. We discuss LPS in the frame of classical mechanics

  16. Optical orientation of the homogeneous non-equilibrium Bose-Einstein condensate of bright excitons (polaritons)

    OpenAIRE

    Korenev, V. L.

    2011-01-01

    A simple model, describing the dynamics of the non-equilibrium pseudospin of a homogeneous Bose-Einstein condensate of exciton polaritons, has been formulated. It explains the suppression of spin splitting of a non-equilibrium polariton condensate in an external magnetic field, the optical alignment, and the conversion of alignment into orientation of polaritons. It has been shown that inverse effects are possible, to wit, the spontaneous circular polarization and the enhancement of spin spli...

  17. Fluctuations When Driving Between Nonequilibrium Steady States

    Science.gov (United States)

    Riechers, Paul M.; Crutchfield, James P.

    2017-08-01

    Maintained by environmental fluxes, biological systems are thermodynamic processes that operate far from equilibrium without detailed-balanced dynamics. Yet, they often exhibit well defined nonequilibrium steady states (NESSs). More importantly, critical thermodynamic functionality arises directly from transitions among their NESSs, driven by environmental switching. Here, we identify the constraints on excess heat and dissipated work necessary to control a system that is kept far from equilibrium by background, uncontrolled "housekeeping" forces. We do this by extending the Crooks fluctuation theorem to transitions among NESSs, without invoking an unphysical dual dynamics. This and corresponding integral fluctuation theorems determine how much work must be expended when controlling systems maintained far from equilibrium. This generalizes thermodynamic feedback control theory, showing that Maxwellian Demons can leverage mesoscopic-state information to take advantage of the excess energetics in NESS transitions. We also generalize an approach recently used to determine the work dissipated when driving between functionally relevant configurations of an active energy-consuming complex system. Altogether, these results highlight universal thermodynamic laws that apply to the accessible degrees of freedom within the effective dynamic at any emergent level of hierarchical organization. By way of illustration, we analyze a voltage-gated sodium ion channel whose molecular conformational dynamics play a critical functional role in propagating action potentials in mammalian neuronal membranes.

  18. Plasma membrane calcium ATPase 4b inhibits nitric oxide generation through calcium-induced dynamic interaction with neuronal nitric oxide synthase.

    Science.gov (United States)

    Duan, Wenjuan; Zhou, Juefei; Li, Wei; Zhou, Teng; Chen, Qianqian; Yang, Fuyu; Wei, Taotao

    2013-04-01

    The activation and deactivation of Ca(2+)- and calmodulindependent neuronal nitric oxide synthase (nNOS) in the central nervous system must be tightly controlled to prevent excessive nitric oxide (NO) generation. Considering plasma membrane calcium ATPase (PMCA) is a key deactivator of nNOS, the present investigation aims to determine the key events involved in nNOS deactivation of by PMCA in living cells to maintain its cellular context. Using time-resolved Förster resonance energy transfer (FRET), we determined the occurrence of Ca(2+)-induced protein-protein interactions between plasma membrane calcium ATPase 4b (PMCA4b) and nNOS in living cells. PMCA activation significantly decreased the intracellular Ca(2+) concentrations ([Ca(2+)]i), which deactivates nNOS and slowdowns NO synthesis. Under the basal [Ca(2+)]i caused by PMCA activation, no protein-protein interactions were observed between PMCA4b and nNOS. Furthermore, both the PDZ domain of nNOS and the PDZ-binding motif of PMCA4b were essential for the protein-protein interaction. The involvement of lipid raft microdomains on the activity of PMCA4b and nNOS was also investigated. Unlike other PMCA isoforms, PMCA4 was relatively more concentrated in the raft fractions. Disruption of lipid rafts altered the intracellular localization of PMCA4b and affected the interaction between PMCA4b and nNOS, which suggest that the unique lipid raft distribution of PMCA4 may be responsible for its regulation of nNOS activity. In summary, lipid rafts may act as platforms for the PMCA4b regulation of nNOS activity and the transient tethering of nNOS to PMCA4b is responsible for rapid nNOS deactivation.

  19. On nonequilibrium many-body systems III: nonlinear transport theory

    International Nuclear Information System (INIS)

    Luzzi, R.; Vasconcellos, A.R.; Algarte, A.C.S.

    1986-01-01

    A nonlinear transport theory for many-body systems arbitrarily away from equilibrium, based on the nonequilibrium statistical operator (NSO) method, is presented. Nonlinear transport equations for a basis set of dynamical quantities are derived using two equivalent treatments that may be considered far reaching generalizations of the Hilbert-Chapman-Enskog method and Mori's generalized Langevin equations method. The first case is considered in some detail and the general characteristics of the theory are discussed. (Author) [pt

  20. Physical exercise in aging human skeletal muscle increases mitochondrial calcium uniporter expression levels and affects mitochondria dynamics.

    Science.gov (United States)

    Zampieri, Sandra; Mammucari, Cristina; Romanello, Vanina; Barberi, Laura; Pietrangelo, Laura; Fusella, Aurora; Mosole, Simone; Gherardi, Gaia; Höfer, Christian; Löfler, Stefan; Sarabon, Nejc; Cvecka, Jan; Krenn, Matthias; Carraro, Ugo; Kern, Helmut; Protasi, Feliciano; Musarò, Antonio; Sandri, Marco; Rizzuto, Rosario

    2016-12-01

    Age-related sarcopenia is characterized by a progressive loss of muscle mass with decline in specific force, having dramatic consequences on mobility and quality of life in seniors. The etiology of sarcopenia is multifactorial and underlying mechanisms are currently not fully elucidated. Physical exercise is known to have beneficial effects on muscle trophism and force production. Alterations of mitochondrial Ca 2+ homeostasis regulated by mitochondrial calcium uniporter (MCU) have been recently shown to affect muscle trophism in vivo in mice. To understand the relevance of MCU-dependent mitochondrial Ca 2+ uptake in aging and to investigate the effect of physical exercise on MCU expression and mitochondria dynamics, we analyzed skeletal muscle biopsies from 70-year-old subjects 9 weeks trained with either neuromuscular electrical stimulation (ES) or leg press. Here, we demonstrate that improved muscle function and structure induced by both trainings are linked to increased protein levels of MCU Ultrastructural analyses by electron microscopy showed remodeling of mitochondrial apparatus in ES-trained muscles that is consistent with an adaptation to physical exercise, a response likely mediated by an increased expression of mitochondrial fusion protein OPA1. Altogether these results indicate that the ES-dependent physiological effects on skeletal muscle size and force are associated with changes in mitochondrial-related proteins involved in Ca 2+ homeostasis and mitochondrial shape. These original findings in aging human skeletal muscle confirm the data obtained in mice and propose MCU and mitochondria-related proteins as potential pharmacological targets to counteract age-related muscle loss. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

  1. On microscopic stress nonequilibrium: Application to the magnetopause

    International Nuclear Information System (INIS)

    Wu, Z.J.

    1986-01-01

    The main purpose of this paper is to propose the concept of microscopic stress nonequilibrium (or simply micro-nonequilibrium) in plasma physics. This concept arises as a consequence of the insolubility of the steady-state Vlasov-Maxwell equations (or the kinetic-field equations in general) under certain conditions. In what follows: (1) A general stress equilibrium condition for tangential plasma discontinuities is derived from the Maxwell tensor and the plasma stress tensor. (2) An equivalent equilibrium condition, which takes the form of equations of motion of a ''fictitious particle'', is also derived from the above condition. (3) A general solution of the distribution functions is derived according to Jeans's theorem or Liouville's theorem for the solar wind particles in a tangential magnetopause. (4) This solution is applied to the equilibrium condition to investigate the equilibrium state of the tangential magnetopause. Both Parker's tail-region and Wu's dawn-side ''nonequilibria''are confirmed to be micro-nonequilibria because of the violation of the above equilibrium condition. (5) The effects of various factors in micro-nonequilibria are discussed. It is found that randomly trapped particles and inwards electric field in the magnetopause layer generally cannot relieve the dawn-side or tail-region micro-nonequilibria; and that a northward magnetic field in the solar wind generally can suppress the dawn-side nonequilibrium, while a southward field can jeopardize a dusk-side Vlasov equilibrium. (6) Discussion: The concept of ''micro-nonequilibrium'' may become of importance in basic plasma dynamics. It is also possible that the micro-nonequilibrium may play a fundamental role in solar wind particles entering the magnetopause and in magnetospheric substorms

  2. Absorption of calcium ions on oxidized graphene sheets and study its dynamic behavior by kinetic and isothermal models

    Directory of Open Access Journals (Sweden)

    Mahmoud Fathy

    2016-07-01

    Full Text Available Abstract Sorption of calcium ion from the hard underground water using novel oxidized graphene (GO sheets was studied in this paper. Physicochemical properties and microstructure of graphene sheets were investigated using Raman spectrometer, thermogravimetry analyzer, transmission electron microscope, scanning electron microscope. The kinetics adsorption of calcium on graphene oxide sheets was examined using Lagergren first and second orders. The results show that the Lagergren second-order was the best-fit model that suggests the conception process of calcium ion adsorption on the Go sheets. For isothermal studies, the Langmuir and Freundlich isotherm models were used at temperatures ranging between 283 and 313 K. Thermodynamic parameters resolved at 283, 298 and 313 K indicating that the GO adsorption was exothermic spontaneous process. Finally, the graphene sheets show high partiality toward calcium particles and it will be useful in softening and treatment of hard water.

  3. Overshooting Effects in Nonequilibrium Ordering Dynamics

    DEFF Research Database (Denmark)

    Gilhøj, Henriette; Jeppesen, Claus; Mouritsen, Ole G.

    1995-01-01

    Using Monte Carlo simulation on the simplest possible statistical mechanical model, the two-dimensional, nonconserved kinetic Ising model that undergoes an order-disorder transition, we show that the local order of the ordering domains, subsequent to a temperature quench, transiently overshoots...

  4. Inflation and non-equilibrium dynamics

    International Nuclear Information System (INIS)

    Pi, S.

    1989-01-01

    Herman Feshbach is a premier nuclear physicist. Although I do no research in his physics subfield, I have found it useful to apply methods developed in that area to early universe investigations that rely on a field-theoretic description for the time evolution of pure and/or mixed initial states. On the occasion of his seventieth birthday, I offer for his enjoyment this essay in which I describe how time-dependent Hartree--Fock methods and their generalizations to mixed states are used in attempts to establish various cosmological scenarios, in particular, inflation. copyright 1989 Academic Press, Inc

  5. Calcium - ionized

    Science.gov (United States)

    ... diuretics Thrombocytosis (high platelet count) Tumors Vitamin A excess Vitamin D excess Lower-than-normal levels may be due to: Hypoparathyroidism Malabsorption Osteomalacia Pancreatitis Renal failure Rickets Vitamin D deficiency Alternative Names Free calcium; Ionized calcium ...

  6. Calcium Carbonate

    Science.gov (United States)

    ... Calcium is needed by the body for healthy bones, muscles, nervous system, and heart. Calcium carbonate also ... to your pharmacist or contact your local garbage/recycling department to learn about take-back programs in ...

  7. Zubarev's Nonequilibrium Statistical Operator Method in the Generalized Statistics of Multiparticle Systems

    Science.gov (United States)

    Glushak, P. A.; Markiv, B. B.; Tokarchuk, M. V.

    2018-01-01

    We present a generalization of Zubarev's nonequilibrium statistical operator method based on the principle of maximum Renyi entropy. In the framework of this approach, we obtain transport equations for the basic set of parameters of the reduced description of nonequilibrium processes in a classical system of interacting particles using Liouville equations with fractional derivatives. For a classical systems of particles in a medium with a fractal structure, we obtain a non-Markovian diffusion equation with fractional spatial derivatives. For a concrete model of the frequency dependence of a memory function, we obtain generalized Kettano-type diffusion equation with the spatial and temporal fractality taken into account. We present a generalization of nonequilibrium thermofield dynamics in Zubarev's nonequilibrium statistical operator method in the framework of Renyi statistics.

  8. Non-equilibrium reactive flux: A unified framework for slow and fast reaction kinetics.

    Science.gov (United States)

    Bose, Amartya; Makri, Nancy

    2017-10-21

    The flux formulation of reaction rate theory is recast in terms of the expectation value of the reactive flux with an initial condition that corresponds to a non-equilibrium, factorized reactant density. In the common case of slow reactive processes, the non-equilibrium expression reaches the plateau regime only slightly slower than the equilibrium flux form. When the reactants are described by a single quantum state, as in the case of electron transfer reactions, the factorized reactant density describes the true initial condition of the reactive process. In such cases, the time integral of the non-equilibrium flux expression yields the reactant population as a function of time, allowing characterization of the dynamics in cases where there is no clear separation of time scales and thus a plateau regime cannot be identified. The non-equilibrium flux offers a unified approach to the kinetics of slow and fast chemical reactions and is ideally suited to mixed quantum-classical methods.

  9. Nonequilibrium theory of flame propagation

    International Nuclear Information System (INIS)

    Merzhanov, A.G.

    1995-01-01

    The nonequilibrium theory of flame propagation is considered as applied to the following three processes of wave propagation: the combustion waves of the second kind, the combustion waves with broad reaction zones, and the combustion waves with chemical stages. Kinetic and combustion wave parameters are presented for different in composition mixtures of boron and transition metals, such as Zr, Hf, Ti, Nb, Ta, Mo, as well as for the Ta-N, Zr-C-H, Nb-B-O systems to illustrate specific features of the above-mentioned processes [ru

  10. Force-dominated non-equilibrium oxidation kinetics of tantalum

    International Nuclear Information System (INIS)

    Kar, Prasenjit; Wang, Ke; Liang, Hong

    2008-01-01

    Using a combined electrochemical and mechanical manipulation technique, we compared the equilibrium and non-equilibrium oxidation processes and states of tantalum. Experimentally, a setup was developed with an electrochemical system attached to a sliding mechanical configuration capable of friction force measurement. The surface chemistry of a sliding surface, i.e., tantalum, was modified through the electrolyte. The mechanically applied force was fixed and the dynamics of the surface was monitored in situ through a force sensor. The formation of non-equilibrium oxidation states of tantalum was found in oxidation limiting environment of acetic acid. An oxidative environment of deionized water saturated with KCl was used as comparison. We proposed a modified Arrhenius-Eyring equation in which the mechanical factor was considered. We found that the mechanical energy induced the non-stable-state reactions leading to metastable oxidation states of tantalum. This equation can be used to predict mechanochemical reactions that are important in many industrial applications

  11. Crossover from equilibration to aging: Nonequilibrium theory versus simulations.

    Science.gov (United States)

    Mendoza-Méndez, P; Lázaro-Lázaro, E; Sánchez-Díaz, L E; Ramírez-González, P E; Pérez-Ángel, G; Medina-Noyola, M

    2017-08-01

    Understanding glasses and the glass transition requires comprehending the nature of the crossover from the ergodic (or equilibrium) regime, in which the stationary properties of the system have no history dependence, to the mysterious glass transition region, where the measured properties are nonstationary and depend on the protocol of preparation. In this work we use nonequilibrium molecular dynamics simulations to test the main features of the crossover predicted by the molecular version of the recently developed multicomponent nonequilibrium self-consistent generalized Langevin equation theory. According to this theory, the glass transition involves the abrupt passage from the ordinary pattern of full equilibration to the aging scenario characteristic of glass-forming liquids. The same theory explains that this abrupt transition will always be observed as a blurred crossover due to the unavoidable finiteness of the time window of any experimental observation. We find that within their finite waiting-time window, the simulations confirm the general trends predicted by the theory.

  12. Non-equilibrium statistical physics with application to disordered systems

    CERN Document Server

    Cáceres, Manuel Osvaldo

    2017-01-01

    This textbook is the result of the enhancement of several courses on non-equilibrium statistics, stochastic processes, stochastic differential equations, anomalous diffusion and disorder. The target audience includes students of physics, mathematics, biology, chemistry, and engineering at undergraduate and graduate level with a grasp of the basic elements of mathematics and physics of the fourth year of a typical undergraduate course. The little-known physical and mathematical concepts are described in sections and specific exercises throughout the text, as well as in appendices. Physical-mathematical motivation is the main driving force for the development of this text. It presents the academic topics of probability theory and stochastic processes as well as new educational aspects in the presentation of non-equilibrium statistical theory and stochastic differential equations.. In particular it discusses the problem of irreversibility in that context and the dynamics of Fokker-Planck. An introduction on fluc...

  13. Linear response in the nonequilibrium zero range process

    International Nuclear Information System (INIS)

    Maes, Christian; Salazar, Alberto

    2014-01-01

    We explore a number of explicit response formulæ around the boundary driven zero range process to changes in the exit and entrance rates. In such a nonequilibrium regime kinetic (and not only thermodynamic) aspects make a difference in the response. Apart from a number of formal approaches, we illustrate a general decomposition of the linear response into entropic and frenetic contributions, the latter being realized from changes in the dynamical activity at the boundaries. In particular in this way one obtains nonlinear modifications to the Green–Kubo relation. We end by bringing some general remarks about the situation where that nonequilibrium response remains given by the (equilibrium) Kubo formula such as for the density profile in the boundary driven Lorentz gas

  14. Black hole evaporation in a heat bath as a nonequilibrium process and its final fate

    International Nuclear Information System (INIS)

    Saida, Hiromi

    2007-01-01

    We consider a black hole in a heat bath, and the whole system which consists of the black hole and the heat bath is isolated from outside environments. When the black hole evaporates, the Hawking radiation causes an energy flow from the black hole to the heat bath. Therefore, since no energy flow arises in an equilibrium state, the thermodynamic state of the whole system is not in equilibrium. That is, in a region around the black hole, the matter field of Hawking radiation and that of heat bath should be in a nonequilibrium state due to the energy flow. Using a simple model which reflects the nonequilibrium nature of energy flow, we find the nonequilibrium effect on a black hole evaporation as follows: if the nonequilibrium region around a black hole is not so large, the evaporation time scale of a black hole in a heat bath becomes longer than that in an empty space (a situation without heat bath), because of the incoming energy flow from the heat bath to the black hole. However, if the nonequilibrium region around a black hole is sufficiently large, the evaporation time scale in a heat bath becomes shorter than that in an empty space, because a nonequilibrium effect of the temperature difference between the black hole and heat bath appears as a strong energy extraction from the black hole by the heat bath. Further, a specific nonequilibrium phenomenon is found: a quasi-equilibrium evaporation stage under the nonequilibrium effect proceeds abruptly to a quantum evaporation stage at a semi-classical level (at black hole radius R g > Planck length) within a very short time scale with a strong burst of energy. (Contrarily, when the nonequilibrium effect is not taken into account, a quasi-equilibrium stage proceeds smoothly to a quantum stage at R g < Planck length without so strong an energy burst.) That is, the nonequilibrium effect of energy flow tends to make a black hole evaporation process more dynamical and to accelerate that process. Finally, on the final fate

  15. On the fundamental equation of nonequilibrium statistical physics—Nonequilibrium entropy evolution equation and the formula for entropy production rate

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In this paper the author presents an overview on his own research works. More than ten years ago, we proposed a new fundamental equation of nonequilibrium statistical physics in place of the present Liouville equation. That is the stochastic velocity type’s Langevin equation in 6N dimensional phase space or its equivalent Liouville diffusion equation. This equation is time-reversed asymmetrical. It shows that the form of motion of particles in statistical thermodynamic systems has the drift-diffusion duality, and the law of motion of statistical thermodynamics is expressed by a superposition of both the law of dynamics and the stochastic velocity and possesses both determinism and probability. Hence it is different from the law of motion of particles in dynamical systems. The stochastic diffusion motion of the particles is the microscopic origin of macroscopic irreversibility. Starting from this fundamental equation the BBGKY diffusion equation hierarchy, the Boltzmann collision diffusion equation, the hydrodynamic equations such as the mass drift-diffusion equation, the Navier-Stokes equation and the thermal conductivity equation have been derived and presented here. What is more important, we first constructed a nonlinear evolution equation of nonequilibrium entropy density in 6N, 6 and 3 dimensional phase space, predicted the existence of entropy diffusion. This entropy evolution equation plays a leading role in nonequilibrium entropy theory, it reveals that the time rate of change of nonequilibrium entropy density originates together from its drift, diffusion and production in space. From this evolution equation, we presented a formula for entropy production rate (i.e. the law of entropy increase) in 6N and 6 dimensional phase space, proved that internal attractive force in nonequilibrium system can result in entropy decrease while internal repulsive force leads to another entropy increase, and derived a common expression for this entropy decrease rate or

  16. Nonequilibrium landscape theory of neural networks.

    Science.gov (United States)

    Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

    2013-11-05

    The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.

  17. Nonequilibrium landscape theory of neural networks

    Science.gov (United States)

    Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

    2013-01-01

    The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape–flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments. PMID:24145451

  18. Complex temporal and spatial patterns in nonequilibrium processes

    International Nuclear Information System (INIS)

    1992-01-01

    Dynamical systems methods have been used to study bifurcations and pattern formation in nonequilibrium systems. Accomplishments during this period include: information-theoretic methods for analyzing chaos, chemical reactors for studying sustained reaction-diffusion patterns, a reactor exploiting pattern formation to extract short- lived intermediate species, observation of bifurcation from periodic to quasiperiodic rotating chemical spiral patterns, observation of a Turing bifurcation (transition from uniform state to a stationary chemical pattern), method for extracting noise strength in ramped convection, self-similar fractal structure of Zn clusters in electrodeposition, and dynamical instability in crack propagation

  19. Functional Modeling of the Shift in Cellular Calcium Dynamics at the Onset of Synchronization in Smooth Muscle Cells

    DEFF Research Database (Denmark)

    Postnov, D E; Brings Jacobsen, J C; von Holstein-Rathlou, Niels-Henrik

    2011-01-01

    In the present paper we address the nature of synchronization properties found in populations of mesenteric artery smooth muscle cells. We present a minimal model of the onset of synchronization in the individual smooth muscle cell that is manifested as a transition from calcium waves to whole......-cell calcium oscillations. We discuss how different types of ion currents may influence both amplitude and frequency in the regime of whole-cell oscillations. The model may also explain the occurrence of mixed-mode oscillations and chaotic oscillations frequently observed in the experimental system....

  20. An oligogalacturonide-derived molecular probe demonstrates the dynamics of calcium-mediated pectin complexation in cell walls of tip-growing structures

    DEFF Research Database (Denmark)

    Mravec, Jozef; Kracun, Stjepan Kresimir; Rydahl, Maja Gro

    2017-01-01

    walls and in mediating cell-to-cell adhesion. Current immunological methods enable only steady-state detection of egg box formation in situ. Here we present a tool for efficient real-time visualisation of available sites for HG crosslinking within cell wall microdomains. Our approach is based on calcium-mediated...... thermodynamic model. Using defined carbohydrate microarrays, we show that the long OG probe binds exclusively to HG that has a very low degree of esterification and in the presence of divalent ions. We used this probe to study real-time dynamics of HG during elongation of Arabidopsis pollen tubes and root hairs...

  1. INTRODUCTION: Nonequilibrium Processes in Plasmas

    Science.gov (United States)

    Petrović, Zoran; Marić, Dragana; Malović, Gordana

    2009-07-01

    This book aims to give a cross section from a wide range of phenomena that, to different degrees, fall under the heading of non-equilibrium phenomenology. The selection is, of course, biased by the interests of the members of the scientific committee and of the FP6 Project 026328 IPB-CNP Reinforcing Experimental Centre for Non-equilibrium Studies with Application in Nano-technologies, Etching of Integrated Circuits and Environmental Research. Some of the papers included here are texts based on selected lectures presented at the Second International Workshop on Non-equilibrium Processes in Plasmas and Environmental Science. However, this volume is not just the proceedings of that conference as it contains a number of papers from authors that did not attend the conference. The goal was to put together a volume that would cover the interests of the project and support further work. It is published in the Institute of Physics journal Journal of Physics: Conference Series to ensure a wide accessibility of the articles. The texts presented here range from in-depth reviews of the current status and past achievements to progress reports of currently developed experimental devices and recently obtained still unpublished results. All papers have been refereed twice, first when speakers were selected based on their reputation and recently published results, and second after the paper was submitted both by the editorial board and individual assigned referees according to the standards of the conference and of the journal. Nevertheless, we still leave the responsibility (and honours) for the contents of the papers to the authors. The papers in this book are review articles that give a summary of the already published work or present the work in progress that will be published in full at a later date (or both). In the introduction to the first volume, in order to show how far reaching, ubiquitous and important non-equilibrium phenomena are, we claimed that ever since the early

  2. Nonequilibrium fluctuations in a resistor.

    Science.gov (United States)

    Garnier, N; Ciliberto, S

    2005-06-01

    In small systems where relevant energies are comparable to thermal agitation, fluctuations are of the order of average values. In systems in thermodynamical equilibrium, the variance of these fluctuations can be related to the dissipation constant in the system, exploiting the fluctuation-dissipation theorem. In nonequilibrium steady systems, fluctuations theorems (FT) additionally describe symmetry properties of the probability density functions (PDFs) of the fluctuations of injected and dissipated energies. We experimentally probe a model system: an electrical dipole driven out of equilibrium by a small constant current I, and show that FT are experimentally accessible and valid. Furthermore, we stress that FT can be used to measure the dissipated power P = R I2 in the system by just studying the PDFs' symmetries.

  3. Nonequilibrium thermodynamics of dilute polymer solutions in flow.

    Science.gov (United States)

    Latinwo, Folarin; Hsiao, Kai-Wen; Schroeder, Charles M

    2014-11-07

    Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

  4. A Computational Model Based on Multi-Regional Calcium Imaging Represents the Spatio-Temporal Dynamics in a Caenorhabditis elegans Sensory Neuron.

    Directory of Open Access Journals (Sweden)

    Masahiro Kuramochi

    Full Text Available Due to the huge number of neuronal cells in the brain and their complex circuit formation, computer simulation of neuronal activity is indispensable to understanding whole brain dynamics. Recently, various computational models have been developed based on whole-brain calcium imaging data. However, these analyses monitor only the activity of neuronal cell bodies and treat the cells as point unit. This point-neuron model is inexpensive in computational costs, but the model is unrealistically simplistic at representing intact neural activities in the brain. Here, we describe a novel three-unit Ordinary Differential Equation (ODE model based on the neuronal responses derived from a Caenorhabditis elegans salt-sensing neuron. We recorded calcium responses in three regions of the ASER neuron using a simple downstep of NaCl concentration. Our simple ODE model generated from a single recording can adequately reproduce and predict the temporal responses of each part of the neuron to various types of NaCl concentration changes. Our strategy which combines a simple recording data and an ODE mathematical model may be extended to realistically understand whole brain dynamics by computational simulation.

  5. Every day I'm rufflin': Calcium sensing and actin dynamics in the growth factor-independent membrane ruffling of professional phagocytes.

    Science.gov (United States)

    Schlam, Daniel; Canton, Johnathan

    2017-04-03

    Professional phagocytes continuously extend dynamic, actin-driven membrane protrusions. These protrusions, often referred to as membrane ruffles, serve a critical role in the essential phagocyte processes of macropinocytosis and phagocytosis. Small GTPases, such as RAC1/2, spatially and temporally regulate membrane ruffle formation. We have recently shown that extracellular calcium regulates the elaboration of membrane ruffles primarily through the synthesis of phosphatidic acid (PtdOH) at the plasma membrane. RAC1/2 guanine nucleotide exchange factors harbouring polybasic stretches are recruited by PtdOH to sites of ruffle formation. Here we discuss our findings and offer perspectives on how the regulation of dynamic actin structures at the plasma membrane by small GTPases is a critical component of phagocyte function.

  6. Non-equilibrium magnetic interactions in strongly correlated systems

    Energy Technology Data Exchange (ETDEWEB)

    Secchi, A., E-mail: a.secchi@science.ru.nl [Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen (Netherlands); Brener, S.; Lichtenstein, A.I. [Institut für Theoretische Physik, Universitat Hamburg, Jungiusstraße 9, D-20355 Hamburg (Germany); Katsnelson, M.I. [Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen (Netherlands)

    2013-06-15

    We formulate a low-energy theory for the magnetic interactions between electrons in the multi-band Hubbard model under non-equilibrium conditions determined by an external time-dependent electric field which simulates laser-induced spin dynamics. We derive expressions for dynamical exchange parameters in terms of non-equilibrium electronic Green functions and self-energies, which can be computed, e.g., with the methods of time-dependent dynamical mean-field theory. Moreover, we find that a correct description of the system requires, in addition to exchange, a new kind of magnetic interaction, that we name twist exchange, which formally resembles Dzyaloshinskii–Moriya coupling, but is not due to spin–orbit, and is actually due to an effective three-spin interaction. Our theory allows the evaluation of the related time-dependent parameters as well. -- Highlights: •We develop a theory for magnetism of strongly correlated systems out of equilibrium. •Our theory is suitable for laser-induced ultrafast magnetization dynamics. •We write time-dependent exchange parameters in terms of electronic Green functions. •We find a new magnetic interaction, a “twist exchange”. •We give general expressions for magnetic noise in itinerant-electron systems.

  7. Nonequilibrium emergent phenomena in organic molecular solids

    Energy Technology Data Exchange (ETDEWEB)

    Mitrano, Matteo

    2015-07-15

    The manipulation of matter with ultrashort laser pulses is a relevant research field from both a fundamental and an applied perspective, owing to the efficient coupling to the electronic degrees of freedom on femtosecond timescales and the ability to induce transient phases that cannot be realized in equilibrium scenarios. Strongly correlated materials are a natural environment for the observation of such novel and emergent out-of-equilibrium physics because small modifications to the electron-electron interactions can induce transitions between remarkably different macroscopic phases. One of the most effective means of modifying the effective electron-electron interactions is to perturb the crystal structure through pressure, strain or even light. However, it remains largely unexplored how perturbing the structural degrees of freedom affects the electron dynamics of the transiently driven states and how the interplay of correlations and electron-lattice interactions determine the intrinsic timescales of these nonequilibrium states. This thesis investigates how to control the light-induced nonequilibrium electronic properties in strongly correlated organics, that are highly tunable with moderate variations of external parameters, by perturbing their structural degrees of freedom, either via static pressures or vibrational excitation. We study the role of correlations in determining the relaxation rate of holes (holons) and double occupancies (doublons) in a solid state Mott insulator, the ET-F{sub 2}TCNQ, driven across a transient insulator-to-metal transition. By mapping holon-doublon lifetimes onto the ground-state electronic interactions, we found that the decay rate of the photoinjected quasiparticles depends on the degree of correlation between carriers and is affected by the presence of a competition between local recombination and delocalization of holon-doublon pairs. By optically controlling the effective correlations in organic molecular crystals through

  8. Nonequilibrium Distribution of the Microscopic Thermal Current in Steady Thermal Transport Systems

    KAUST Repository

    Yukawa, Satoshi; Ogushi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2010-01-01

    Nonequilibrium distribution of the microscopic thermal current is investigated by direct molecular dynamics simulations. The microscopic thermal current in this study is defined by a flow of kinetic energy carried by a single particle. Asymptotic parallel and antiparallel tails of the nonequilibrium distribution to an average thermal current are identical to ones of equilibrium distribution with different temperatures. These temperatures characterizing the tails are dependent on a characteristic length in which a memory of dynamics is completely erased by several particle collisions. This property of the tails of nonequilibrium distribution is confirmed in other thermal transport systems. In addition, statistical properties of a particle trapped by a harmonic potential in a steady thermal conducting state are also studied. This particle feels a finite force parallel to the average thermal current as a consequence of the skewness of the distribution of the current. This force is interpreted as the microscopic origin of thermophoresis.

  9. Nonequilibrium statistical mechanics of shear flow: invariant quantities and current relations

    International Nuclear Information System (INIS)

    Baule, A; Evans, R M L

    2010-01-01

    In modeling nonequilibrium systems one usually starts with a definition of the microscopic dynamics, e.g., in terms of transition rates, and then derives the resulting macroscopic behavior. We address the inverse question for a class of steady state systems, namely complex fluids under continuous shear flow: how does an externally imposed shear current affect the microscopic dynamics of the fluid? The answer can be formulated in the form of invariant quantities, exact relations for the transition rates in the nonequilibrium steady state, as discussed in a recent letter (Baule and Evans, 2008 Phys. Rev. Lett. 101 240601). Here, we present a more pedagogical account of the invariant quantities and the theory underlying them, known as the nonequilibrium counterpart to detailed balance (NCDB). Furthermore, we investigate the relationship between the transition rates and the shear current in the steady state. We show that a fluctuation relation of the Gallavotti–Cohen type holds for systems satisfying NCDB

  10. Nonequilibrium thermodynamics of interacting tunneling transport: variational grand potential, density functional formulation and nature of steady-state forces

    International Nuclear Information System (INIS)

    Hyldgaard, P

    2012-01-01

    The standard formulation of tunneling transport rests on an open-boundary modeling. There, conserving approximations to nonequilibrium Green function or quantum statistical mechanics provide consistent but computational costly approaches; alternatively, the use of density-dependent ballistic-transport calculations (e.g., Lang 1995 Phys. Rev. B 52 5335), here denoted ‘DBT’, provides computationally efficient (approximate) atomistic characterizations of the electron behavior but has until now lacked a formal justification. This paper presents an exact, variational nonequilibrium thermodynamic theory for fully interacting tunneling and provides a rigorous foundation for frozen-nuclei DBT calculations as a lowest-order approximation to an exact nonequilibrium thermodynamic density functional evaluation. The theory starts from the complete electron nonequilibrium quantum statistical mechanics and I identify the operator for the nonequilibrium Gibbs free energy which, generally, must be treated as an implicit solution of the fully interacting many-body dynamics. I demonstrate a minimal property of a functional for the nonequilibrium thermodynamic grand potential which thus uniquely identifies the solution as the exact nonequilibrium density matrix. I also show that the uniqueness-of-density proof from a closely related Lippmann-Schwinger collision density functional theory (Hyldgaard 2008 Phys. Rev. B 78 165109) makes it possible to express the variational nonequilibrium thermodynamic description as a single-particle formulation based on universal electron-density functionals; the full nonequilibrium single-particle formulation improves the DBT method, for example, by a more refined account of Gibbs free energy effects. I illustrate a formal evaluation of the zero-temperature thermodynamic grand potential value which I find is closely related to the variation in the scattering phase shifts and hence to Friedel density oscillations. This paper also discusses the

  11. Link prediction based on nonequilibrium cooperation effect

    Science.gov (United States)

    Li, Lanxi; Zhu, Xuzhen; Tian, Hui

    2018-04-01

    Link prediction in complex networks has become a common focus of many researchers. But most existing methods concentrate on neighbors, and rarely consider degree heterogeneity of two endpoints. Node degree represents the importance or status of endpoints. We describe the large-degree heterogeneity as the nonequilibrium between nodes. This nonequilibrium facilitates a stable cooperation between endpoints, so that two endpoints with large-degree heterogeneity tend to connect stably. We name such a phenomenon as the nonequilibrium cooperation effect. Therefore, this paper proposes a link prediction method based on the nonequilibrium cooperation effect to improve accuracy. Theoretical analysis will be processed in advance, and at the end, experiments will be performed in 12 real-world networks to compare the mainstream methods with our indices in the network through numerical analysis.

  12. Investigation of Non-Equilibrium Radiation for Earth Entry

    Science.gov (United States)

    Brandis, A. M.; Johnston, C. O.; Cruden, B. A.

    2016-01-01

    For Earth re-entry at velocities between 8 and 11.5 km/s, the accuracy of NASA's computational uid dynamic and radiative simulations of non-equilibrium shock layer radiation is assessed through comparisons with measurements. These measurements were obtained in the NASA Ames Research Center's Electric Arc Shock Tube (EAST) facility. The experiments were aimed at measuring the spatially and spectrally resolved radiance at relevant entry conditions for both an approximate Earth atmosphere (79% N2 : 21% O2 by mole) as well as a more accurate composition featuring the trace species Ar and CO2 (78.08% N2 : 20.95% O2 : 0.04% CO2 : 0.93% Ar by mole). The experiments were configured to target a wide range of conditions, of which shots from 8 to 11.5 km/s at 0.2 Torr (26.7 Pa) are examined in this paper. The non-equilibrium component was chosen to be the focus of this study as it can account for a significant percentage of the emitted radiation for Earth re-entry, and more importantly, non-equilibrium has traditionally been assigned a large uncertainty for vehicle design. The main goals of this study are to present the shock tube data in the form of a non-equilibrium metric, evaluate the level of agreement between the experiment and simulations, identify key discrepancies and to examine critical aspects of modeling non-equilibrium radiating flows. Radiance pro les integrated over discreet wavelength regions, ranging from the Vacuum Ultra Violet (VUV) through to the Near Infra-Red (NIR), were compared in order to maximize both the spectral coverage and the number of experiments that could be used in the analysis. A previously defined non-equilibrium metric has been used to allow comparisons with several shots and reveal trends in the data. Overall, LAURA/HARA is shown to under-predict EAST by as much as 40% and over-predict by as much as 12% depending on the shock speed. DPLR/NEQAIR is shown to under-predict EAST by as much as 50% and over-predict by as much as 20% depending

  13. Calcium waves.

    Science.gov (United States)

    Jaffe, Lionel F

    2008-04-12

    Waves through living systems are best characterized by their speeds at 20 degrees C. These speeds vary from those of calcium action potentials to those of ultraslow ones which move at 1-10 and/or 10-20 nm s(-1). All such waves are known or inferred to be calcium waves. The two classes of calcium waves which include ones with important morphogenetic effects are slow waves that move at 0.2-2 microm s(-1) and ultraslow ones. Both may be propagated by cycles in which the entry of calcium through the plasma membrane induces subsurface contraction. This contraction opens nearby stretch-sensitive calcium channels. Calcium entry through these channels propagates the calcium wave. Many slow waves are seen as waves of indentation. Some are considered to act via cellular peristalsis; for example, those which seem to drive the germ plasm to the vegetal pole of the Xenopus egg. Other good examples of morphogenetic slow waves are ones through fertilizing maize eggs, through developing barnacle eggs and through axolotl embryos during neural induction. Good examples of ultraslow morphogenetic waves are ones during inversion in developing Volvox embryos and across developing Drosophila eye discs. Morphogenetic waves may be best pursued by imaging their calcium with aequorins.

  14. Non-equilibrium dog-flea model

    Science.gov (United States)

    Ackerson, Bruce J.

    2017-11-01

    We develop the open dog-flea model to serve as a check of proposed non-equilibrium theories of statistical mechanics. The model is developed in detail. Then it is applied to four recent models for non-equilibrium statistical mechanics. Comparison of the dog-flea solution with these different models allows checking claims and giving a concrete example of the theoretical models.

  15. Plasma wave instabilities in nonequilibrium graphene

    DEFF Research Database (Denmark)

    Aryal, Chinta M.; Hu, Ben Yu-Kuang; Jauho, Antti-Pekka

    2016-01-01

    We study two-stream instabilities in a nonequilibrium system in which a stream of electrons is injected into doped graphene. As with equivalent nonequilibrium parabolic band systems, we find that the graphene systems can support unstable charge-density waves whose amplitudes grow with time. We...... of the injected electrons that maximizes the growth rate increases with increasing | q |. We compare the range and strength of the instability in graphene to that of two- and three-dimensional parabolic band systems....

  16. Quantum thermodynamics: a nonequilibrium Green's function approach.

    Science.gov (United States)

    Esposito, Massimiliano; Ochoa, Maicol A; Galperin, Michael

    2015-02-27

    We establish the foundations of a nonequilibrium theory of quantum thermodynamics for noninteracting open quantum systems strongly coupled to their reservoirs within the framework of the nonequilibrium Green's functions. The energy of the system and its coupling to the reservoirs are controlled by a slow external time-dependent force treated to first order beyond the quasistatic limit. We derive the four basic laws of thermodynamics and characterize reversible transformations. Stochastic thermodynamics is recovered in the weak coupling limit.

  17. NON-EQUILIBRIUM HELIUM IONIZATION IN AN MHD SIMULATION OF THE SOLAR ATMOSPHERE

    International Nuclear Information System (INIS)

    Golding, Thomas Peter; Carlsson, Mats; Leenaarts, Jorrit

    2016-01-01

    The ionization state of the gas in the dynamic solar chromosphere can depart strongly from the instantaneous statistical equilibrium commonly assumed in numerical modeling. We improve on earlier simulations of the solar atmosphere that only included non-equilibrium hydrogen ionization by performing a 2D radiation-magnetohydrodynamics simulation featuring non-equilibrium ionization of both hydrogen and helium. The simulation includes the effect of hydrogen Lyα and the EUV radiation from the corona on the ionization and heating of the atmosphere. Details on code implementation are given. We obtain helium ion fractions that are far from their equilibrium values. Comparison with models with local thermodynamic equilibrium (LTE) ionization shows that non-equilibrium helium ionization leads to higher temperatures in wavefronts and lower temperatures in the gas between shocks. Assuming LTE ionization results in a thermostat-like behavior with matter accumulating around the temperatures where the LTE ionization fractions change rapidly. Comparison of DEM curves computed from our models shows that non-equilibrium ionization leads to more radiating material in the temperature range 11–18 kK, compared to models with LTE helium ionization. We conclude that non-equilibrium helium ionization is important for the dynamics and thermal structure of the upper chromosphere and transition region. It might also help resolve the problem that intensities of chromospheric lines computed from current models are smaller than those observed

  18. Aerospace Applications of Non-Equilibrium Plasma

    Science.gov (United States)

    Blankson, Isaiah M.

    2016-01-01

    Nonequilibrium plasma/non-thermal plasma/cold plasmas are being used in a wide range of new applications in aeronautics, active flow control, heat transfer reduction, plasma-assisted ignition and combustion, noise suppression, and power generation. Industrial applications may be found in pollution control, materials surface treatment, and water purification. In order for these plasma processes to become practical, efficient means of ionization are necessary. A primary challenge for these applications is to create a desired non-equilibrium plasma in air by preventing the discharge from transitioning into an arc. Of particular interest is the impact on simulations and experimental data with and without detailed consideration of non-equilibrium effects, and the consequences of neglecting non-equilibrium. This presentation will provide an assessment of the presence and influence of non-equilibrium phenomena for various aerospace needs and applications. Specific examples to be considered will include the forward energy deposition of laser-induced non-equilibrium plasmoids for sonic boom mitigation, weakly ionized flows obtained from pulsed nanosecond discharges for an annular Hall type MHD generator duct for turbojet energy bypass, and fundamental mechanisms affecting the design and operation of novel plasma-assisted reactive systems in dielectric liquids (water purification, in-pipe modification of fuels, etc.).

  19. The non-equilibrium nature of culinary evolution

    Science.gov (United States)

    Kinouchi, Osame; Diez-Garcia, Rosa W.; Holanda, Adriano J.; Zambianchi, Pedro; Roque, Antonio C.

    2008-07-01

    Food is an essential part of civilization, with a scope that ranges from the biological to the economic and cultural levels. Here, we study the statistics of ingredients and recipes taken from Brazilian, British, French and Medieval cookery books. We find universal distributions with scale invariant behaviour. We propose a copy-mutate process to model culinary evolution that fits our empirical data very well. We find a cultural 'founder effect' produced by the non-equilibrium dynamics of the model. Both the invariant and idiosyncratic aspects of culture are accounted for by our model, which may have applications in other kinds of evolutionary processes.

  20. Neutron scattering on equilibrium and nonequilibrium phonons, excitons and polaritons

    International Nuclear Information System (INIS)

    Broude, V.L.; Sheka, E.F.

    1978-01-01

    A number of problems of solid-state physics representing interest for neutron spectroscopy of future is considered. The development of the neutron inelastic scattering spectroscopy (neutron spectroscopy of equilibrium phonons) is discussed with application to nuclear dynamics of crystals in the thermodynamic equilibrium. The results of high-flux neutron source experiments on molecular crystals are presented. The advantages of neutron inelastic scattering over optical spectroscopy are discussed. The spectroscopy of quasi-equilibrium and non-equilibrium quasi-particles is discussed. In particular, the neutron scattering on polaritons, excitons in thermal equilibrium and production of light-excitons are considered. The problem of the possibility of such experiments is elucidated

  1. Calcium Signaling in Taste Cells

    Science.gov (United States)

    Medler, Kathryn F.

    2014-01-01

    The sense of taste is a common ability shared by all organisms and is used to detect nutrients as well as potentially harmful compounds. Thus taste is critical to survival. Despite its importance, surprisingly little is known about the mechanisms generating and regulating responses to taste stimuli. All taste responses depend on calcium signals to generate appropriate responses which are relayed to the brain. Some taste cells have conventional synapses and rely on calcium influx through voltage-gated calcium channels. Other taste cells lack these synapses and depend on calcium release to formulate an output signal through a hemichannel. Beyond establishing these characteristics, few studies have focused on understanding how these calcium signals are formed. We identified multiple calcium clearance mechanisms that regulate calcium levels in taste cells as well as a calcium influx that contributes to maintaining appropriate calcium homeostasis in these cells. Multiple factors regulate the evoked taste signals with varying roles in different cell populations. Clearly, calcium signaling is a dynamic process in taste cells and is more complex than has previously been appreciated. PMID:25450977

  2. 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.

  3. Relevance of rangeland degradation in semiarid Northeastern South Africa to the nonequilibrium theory

    CSIR Research Space (South Africa)

    Wessels, Konrad J

    2007-04-01

    Full Text Available degraded areas which have been mapped by the National Land Cover (NLC) program. Much evidence suggests that long-term heavy grazing is the cause of this degradation. In order to test for the prevalence of nonequilibrium dynamics, we determined the relative...

  4. Travelling wave solutions for the Richards equation incorporating non-equilibrium effects in the capillarity pressure

    NARCIS (Netherlands)

    van Duijn, C. J.; Mitra, K.; Pop, I. S.

    2018-01-01

    The Richards equation is a mathematical model for unsaturated flow through porous media. This paper considers an extension of the Richards equation, where non-equilibrium effects like hysteresis and dynamic capillarity are incorporated in the relationship that relates the water pressure and the

  5. Modeling chromatographic columns. Non-equilibrium packed-bed adsorption with non-linear adsorption isotherms

    NARCIS (Netherlands)

    Özdural, A.R.; Alkan, A.; Kerkhof, P.J.A.M.

    2004-01-01

    In this work a new mathematical model, based on non-equilibrium conditions, describing the dynamic adsorption of proteins in columns packed with spherical adsorbent particles is used to study the performance of chromatographic systems. Simulations of frontal chromatography, including axial

  6. Non-equilibrium mean-field theories on scale-free networks

    International Nuclear Information System (INIS)

    Caccioli, Fabio; Dall'Asta, Luca

    2009-01-01

    Many non-equilibrium processes on scale-free networks present anomalous critical behavior that is not explained by standard mean-field theories. We propose a systematic method to derive stochastic equations for mean-field order parameters that implicitly account for the degree heterogeneity. The method is used to correctly predict the dynamical critical behavior of some binary spin models and reaction–diffusion processes. The validity of our non-equilibrium theory is further supported by showing its relation with the generalized Landau theory of equilibrium critical phenomena on networks

  7. Calcium Electroporation

    DEFF Research Database (Denmark)

    Frandsen, Stine Krog; Gibot, Laure; Madi, Moinecha

    2015-01-01

    BACKGROUND: Calcium electroporation describes the use of high voltage electric pulses to introduce supraphysiological calcium concentrations into cells. This promising method is currently in clinical trial as an anti-cancer treatment. One very important issue is the relation between tumor cell kill...... efficacy-and normal cell sensitivity. METHODS: Using a 3D spheroid cell culture model we have tested the effect of calcium electroporation and electrochemotherapy using bleomycin on three different human cancer cell lines: a colorectal adenocarcinoma (HT29), a bladder transitional cell carcinoma (SW780......), and a breast adenocarcinoma (MDA-MB231), as well as on primary normal human dermal fibroblasts (HDF-n). RESULTS: The results showed a clear reduction in spheroid size in all three cancer cell spheroids three days after treatment with respectively calcium electroporation (p

  8. Nonequilibrium self-organization in alloys under irradiation leading to the formation of nano composites

    CERN Document Server

    Enrique, R A; Averback, R S; Bellon, P

    2003-01-01

    Alloys under irradiation are continuously driven away from equilibrium: Every time an external particle interacts with the atoms in the solid, a perturbation very localized in space and time is produced. Under this external forcing, phase and microstructural evolution depends ultimately on the dynamical interaction between the external perturbation and the internal recovery kinetics of the alloy. We consider the nonequilibrium steady state of an immiscible binary alloy subject to mixing by heavy-ion irradiation. It has been found that the range of the forced atomic relocations taking place during collision cascades plays an important role on the final microstructure: when this range is large enough, it can lead to the spontaneous formation of compositional patterns at the nanometer scale. These results were rationalized in the framework of a continuum model solved by deriving a nonequilibrium thermodynamic potential. Here we derive the nonequilibrium structure factor by including the role of fluctuations. In ...

  9. Emergence of a fluctuation relation for heat in nonequilibrium Landauer processes

    Science.gov (United States)

    Taranto, Philip; Modi, Kavan; Pollock, Felix A.

    2018-05-01

    In a generalized framework for the Landauer erasure protocol, we study bounds on the heat dissipated in typical nonequilibrium quantum processes. In contrast to thermodynamic processes, quantum fluctuations are not suppressed in the nonequilibrium regime and cannot be ignored, making such processes difficult to understand and treat. Here we derive an emergent fluctuation relation that virtually guarantees the average heat produced to be dissipated into the reservoir either when the system or reservoir is large (or both) or when the temperature is high. The implication of our result is that for nonequilibrium processes, heat fluctuations away from its average value are suppressed independently of the underlying dynamics exponentially quickly in the dimension of the larger subsystem and linearly in the inverse temperature. We achieve these results by generalizing a concentration of measure relation for subsystem states to the case where the global state is mixed.

  10. Non-equilibrium scaling analysis of the Kondo model with voltage bias

    International Nuclear Information System (INIS)

    Fritsch, Peter; Kehrein, Stefan

    2009-01-01

    The quintessential description of Kondo physics in equilibrium is obtained within a scaling picture that shows the buildup of Kondo screening at low temperature. For the non-equilibrium Kondo model with a voltage bias, the key new feature are decoherence effects due to the current across the impurity. In the present paper, we show how one can develop a consistent framework for studying the non-equilibrium Kondo model within a scaling picture of infinitesimal unitary transformations (flow equations). Decoherence effects appear naturally in third order of the β-function and dominate the Hamiltonian flow for sufficiently large voltage bias. We work out the spin dynamics in non-equilibrium and compare it with finite temperature equilibrium results. In particular, we report on the behavior of the static spin susceptibility including leading logarithmic corrections and compare it with the celebrated equilibrium result as a function of temperature.

  11. Amplitude oscillations in a non-equilibrium polariton condensate

    Science.gov (United States)

    Brierley, Richard; Littlewood, Peter; Eastham, Paul

    2011-03-01

    Like cold atomic gases, semiconductor nanostructures provide new opportunities for exploring non-equilibrium quantum dynamics. In semiconductor microcavities the strong coupling between trapped photons and excitons produces new quasiparticles, polaritons, which can undergo Bose-Einstein condensation. Quantum quenches can be realised by rapidly creating cold exciton populations with a laser [Eastham and Phillips, PRB 79 165303 (2009)]. The mean field theory of non-equilibrium polariton condensates predicts oscillations in the condensate amplitude due to the excitation of a Higgs mode. These oscillations are the analogs of those predicted in quenched cold atomic gases and may occur in the polariton system after performing a quench or by direct excitation of the amplitude mode. We have studied the stability of these oscillations beyond mean field theory. We show that homogeneous amplitude oscillations are unstable to decay into lower energy phase modes at finite wavevectors, suggesting the onset of chaotic behaviour. The resulting hierarchy of decay processes can be understood by analogy to optical parametric oscillators in microcavities. Polariton systems thus provide an interesting opportunity to study the dynamics of Higgs-like modes in a solid state system.

  12. Non-Equilibrium Thermodynamics in Multiphase Flows

    CERN Document Server

    Mauri, Roberto

    2013-01-01

    Non-equilibrium thermodynamics is a general framework that allows the macroscopic description of irreversible processes. This book introduces non-equilibrium thermodynamics and its applications to the rheology of multiphase flows. The subject is relevant to graduate students in chemical and mechanical engineering, physics and material science. This book is divided into two parts. The first part presents the theory of non-equilibrium thermodynamics, reviewing its essential features and showing, when possible, some applications. The second part of this book deals with how the general theory can be applied to model multiphase flows and, in particular, how to determine their constitutive relations. Each chapter contains problems at the end, the solutions of which are given at the end of the book. No prior knowledge of statistical mechanics is required; the necessary prerequisites are elements of transport phenomena and on thermodynamics. “The style of the book is mathematical, but nonetheless it remains very re...

  13. Nonequilibrium statistical physics a modern perspective

    CERN Document Server

    Livi, Roberto

    2017-01-01

    Statistical mechanics has been proven to be successful at describing physical systems at thermodynamic equilibrium. Since most natural phenomena occur in nonequilibrium conditions, the present challenge is to find suitable physical approaches for such conditions: this book provides a pedagogical pathway that explores various perspectives. The use of clear language, and explanatory figures and diagrams to describe models, simulations and experimental findings makes the book a valuable resource for undergraduate and graduate students, and also for lecturers organizing teaching at varying levels of experience in the field. Written in three parts, it covers basic and traditional concepts of nonequilibrium physics, modern aspects concerning nonequilibrium phase transitions, and application-orientated topics from a modern perspective. A broad range of topics is covered, including Langevin equations, Levy processes, directed percolation, kinetic roughening and pattern formation.

  14. Nonequilibrium thermodynamics of restricted Boltzmann machines

    Science.gov (United States)

    Salazar, Domingos S. P.

    2017-08-01

    In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

  15. Nonequilibrium thermodynamics of restricted Boltzmann machines.

    Science.gov (United States)

    Salazar, Domingos S P

    2017-08-01

    In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

  16. How should we understand non-equilibrium many-body steady states?

    Science.gov (United States)

    Maghrebi, Mohammad; Gorshkov, Alexey

    : Many-body systems with both coherent dynamics and dissipation constitute a rich class of models which are nevertheless much less explored than their dissipationless counterparts. The advent of numerous experimental platforms that simulate such dynamics poses an immediate challenge to systematically understand and classify these models. In particular, nontrivial many-body states emerge as steady states under non-equilibrium dynamics. In this talk, I use a field-theoretic approach based on the Keldysh formalism to study nonequilibrium phases and phase transitions in such models. I show that an effective temperature generically emerges as a result of dissipation, and the universal behavior including the dynamics near the steady state is described by a thermodynamic universality class. In the end, I will also discuss possibilities that go beyond the paradigm of an effective thermodynamic behavior.

  17. Effect of changes in water salinity on ammonium, calcium, dissolved inorganic carbon and influence on water/sediment dynamics

    Science.gov (United States)

    López, P.

    2003-04-01

    The effect of a sudden increase in salinity from 10 to 37 in porewater concentration and the benthic fluxes of ammonium, calcium and dissolved inorganic carbon were studied in sediments of a small coastal lagoon, the Albufera d'Es Grau (Minorca Island, Spain). The temporal effects of the changes in salinity were examined over 17 days using a single diffusion-reaction model and a mass-balance approach. After the salinity change, NH 4+-flux to the water and Ca-flux toward sediments increased (NH 4+-flux: 5000-3000 μmol m -2 d -1 in seawater and 600/250 μmol m -2 d -1 in brackish water; Ca-flux: -40/-76 meq m -2 d -1 at S=37 and -13/-10 meq m -2 d -1 at S=10); however, later NH 4+-flux decreased in seawater, reaching values lower than in brackish water. In contrast, Ca-flux presented similar values in both conditions. The fluxes of dissolved inorganic carbon, which were constant at S=10 (55/45 mmol m -2 d -1), increased during the experiment at S=37 (from ˜30 mmol m -2 d -1 immediately after salinity increase to ˜60 mmol m -2 d -1 after 17 days). In brackish conditions, NH 4+ and Ca 2+ fluxes were consistent with a single diffusion-reaction model that assumes a zero-order reaction for NH 4+ production and a first-order reaction for Ca 2+ production. In seawater, this model explained the Ca-flux observed, but did not account for the high initial flux of NH 4+. The mass balance for 17 days indicated a higher retention of NH 4+ in porewater in the littoral station in seawater conditions (9.5 mmol m -2 at S=37 and 1.6 mmol m -2 at S=10) and a significant reduction in the water consumption at both sites (5 mmol m -2 at S=37; 35/23 mmol m -2 at S=10). In contrast, accumulation of dissolved inorganic carbon in porewater was lower in seawater incubations (-10/-1 meq m -2 at S=37; 50/90 meq m -2 at S=10) and was linked to a higher efflux of CO 2 to the atmosphere, because of calcium carbonate precipitation in water (675/500 meq m -2). These results indicate that increased

  18. Canonical operator formulation of nonequilibrium thermodynamics

    International Nuclear Information System (INIS)

    Mehrafarin, M.

    1992-09-01

    A novel formulation of nonequilibrium thermodynamics is proposed which emphasises the fundamental role played by the Boltzmann constant k in fluctuations. The equivalence of this and the stochastic formulation is demonstrated. The k → 0 limit of this theory yields the classical deterministic description of nonequilibrium thermodynamics. The new formulation possesses unique features which bear two important results namely the thermodynamic uncertainty principle and the quantisation of entropy production rate. Such a theory becomes indispensable whenever fluctuations play a significant role. (author). 7 refs

  19. On the excess energy of nonequilibrium plasma

    International Nuclear Information System (INIS)

    Timofeev, A. V.

    2012-01-01

    The energy that can be released in plasma due to the onset of instability (the excess plasma energy) is estimated. Three potentially unstable plasma states are considered, namely, plasma with an anisotropic Maxwellian velocity distribution of plasma particles, plasma with a two-beam velocity distribution, and an inhomogeneous plasma in a magnetic field with a local Maxwellian velocity distribution. The excess energy can serve as a measure of the degree to which plasma is nonequilibrium. In particular, this quantity can be used to compare plasmas in different nonequilibrium states.

  20. Characterization of nonequilibrium states of trapped Bose–Einstein condensates

    Science.gov (United States)

    Yukalov, V. I.; Novikov, A. N.; Bagnato, V. S.

    2018-06-01

    The generation of different nonequilibrium states in trapped Bose–Einstein condensates is studied by numerically solving the nonlinear Schrödinger equation. Inducing nonequilibrium states by shaking a trap creates the following states: weak nonequilibrium, the state of vortex germs, the state of vortex rings, the state of straight vortex lines, the state of deformed vortices, vortex turbulence, grain turbulence, and wave turbulence. A characterization of nonequilibrium states is advanced by introducing effective temperature, Fresnel number, and Mach number.

  1. Exactly solvable nonequilibrium Langevin relaxation of a trapped nanoparticle

    International Nuclear Information System (INIS)

    Salazar, Domingos S P; Lira, Sérgio A

    2016-01-01

    In this work, we study the nonequilibrium statistical properties of the relaxation dynamics of a nanoparticle trapped in a harmonic potential. We report an exact time-dependent analytical solution to the Langevin dynamics that arises from the stochastic differential equation of our system’s energy in the underdamped regime. By utilizing this stochastic thermodynamics approach, we are able to completely describe the heat exchange process between the nanoparticle and the surrounding environment. As an important consequence of our results, we observe the validity of the heat exchange fluctuation theorem in our setup, which holds for systems arbitrarily far from equilibrium conditions. By extending our results for the case of N noninterating nanoparticles, we perform analytical asymptotic limits and direct numerical simulations that corroborate our analytical predictions. (paper)

  2. Decay of non-equilibrium polariton condensate in semiconductors

    International Nuclear Information System (INIS)

    Beloussov, I.V.; Shvera, Y.M.

    1993-08-01

    Excitation dynamics of polariton quantum fluctuations arising in direct-gap semi-conductor as a result of parametric decay of non-equilibrium polariton condensate with non-zero wave vector is studied. The predominant mechanism of polariton scattering is supposed to be exciton-exciton interaction. Steady state which corresponds to the case of dynamic equilibrium between the polariton condensate and quantum fluctuations is obtained. Distribution functions of non-condensate polaritons are localized in the resonant regions, corresponding to two-particle excitation of polaritons from the condensate. The spectrum of elementary excitations in steady state coincides with usual polariton energy with the shift proportional to initial density of polariton condensate. (author). 25 refs

  3. Sampling rare events in nonequilibrium and nonstationary systems.

    Science.gov (United States)

    Berryman, Joshua T; Schilling, Tanja

    2010-12-28

    Although many computational methods for rare event sampling exist, this type of calculation is not usually practical for general nonequilibrium conditions, with macroscopically irreversible dynamics and away from both stationary and metastable states. A novel method for calculating the time-series of the probability of a rare event is presented which is designed for these conditions. The method is validated for the cases of the Glauber-Ising model under time-varying shear flow, the Kawasaki-Ising model after a quench into the region between nucleation dominated and spinodal decomposition dominated phase change dynamics, and the parallel open asymmetric exclusion process. The method requires a subdivision of the phase space of the system: it is benchmarked and found to scale well for increasingly fine subdivisions, meaning that it can be applied without detailed foreknowledge of the physically important reaction pathways.

  4. Nonequilibrium thermodynamic potentials for continuous-time Markov chains.

    Science.gov (United States)

    Verley, Gatien

    2016-01-01

    We connect the rare fluctuations of an equilibrium (EQ) process and the typical fluctuations of a nonequilibrium (NE) stationary process. In the framework of large deviation theory, this observation allows us to introduce NE thermodynamic potentials. For continuous-time Markov chains, we identify the relevant pairs of conjugated variables and propose two NE ensembles: one with fixed dynamics and fluctuating time-averaged variables, and another with fixed time-averaged variables, but a fluctuating dynamics. Accordingly, we show that NE processes are equivalent to conditioned EQ processes ensuring that NE potentials are Legendre dual. We find a variational principle satisfied by the NE potentials that reach their maximum in the NE stationary state and whose first derivatives produce the NE equations of state and second derivatives produce the NE Maxwell relations generalizing the Onsager reciprocity relations.

  5. Extra entropy production due to non-equilibrium phase transitions in relativistic heavy ion reactions

    International Nuclear Information System (INIS)

    Csernai, L.P.; Lukacs, B.

    1984-04-01

    In a fluid-dynamical model the extra entropy production is calculated which arises from a non-equilibrium phase transition from nuclear to quark matter. The dynamics of processes producing extra entropy are treated in linear approximation. It is shown that there is a considerable extra entropy production provided the transition is not too fast. In measuring the entropy at the break-up, an excess entropy might signalize the phase transition to a transient quark-gluon plasma. (D.Gy.)

  6. Platelet activating factor enhances synaptic vesicle exocytosis via PKC, elevated intracellular calcium, and modulation of synapsin 1 dynamics and phosphorylation

    Directory of Open Access Journals (Sweden)

    Jennetta W Hammond

    2016-01-01

    Full Text Available Platelet activating factor (PAF is an inflammatory phospholipid signaling molecule implicated in synaptic plasticity, learning and memory and neurotoxicity during neuroinflammation. However, little is known about the intracellular mechanisms mediating PAF’s physiological or pathological effects on synaptic facilitation. We show here that PAF receptors are localized at the synapse. Using fluorescent reporters of presynaptic activity we show that a non-hydrolysable analogue of PAF (cPAF enhances synaptic vesicle release from individual presynaptic boutons by increasing the size or release of the readily releasable pool and the exocytosis rate of the total recycling pool. cPAF also activates previously silent boutons resulting in vesicle release from a larger number of terminals. The underlying mechanism involves elevated calcium within presynaptic boutons and protein kinase C (PKC activation. Furthermore, cPAF increases synapsin I phosphorylation at sites 1 and 3, and increases dispersion of synapsin I from the presynaptic compartment during stimulation, freeing synaptic vesicles for subsequent release. These findings provide a conceptual framework for how PAF, regardless of its cellular origin, can modulate synapses during normal and pathologic synaptic activity.

  7. Advancing non-equilibrium ARPES experiments by a 9.3 eV coherent ultrafast photon source

    Energy Technology Data Exchange (ETDEWEB)

    Cilento, F., E-mail: federico.cilento@elettra.eu [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); C.N.R. – I.O.M., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Crepaldi, A. [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Manzoni, G.; Sterzi, A. [Universitá degli Studi di Trieste, Via A. Valerio 2, Trieste 34127 (Italy); Zacchigna, M. [C.N.R. – I.O.M., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Bugnon, Ph.; Berger, H. [Institute of Condensed Matter Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Parmigiani, F. [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Universitá degli Studi di Trieste, Via A. Valerio 2, Trieste 34127 (Italy); International Faculty, University of Köln, 50937 Köln (Germany)

    2016-02-15

    The quest for investigating the non-equilibrium dynamics of the band structure of strongly-correlated materials over their entire Brillouin zone is a primary objective. However, the actual ultrafast UV light sources are not suitable for addressing several critical questions in the field. Here we report on a novel light source generating sub-250 fs, 9.3 eV photon energy light pulses at 250 kHz repetition rate, obtained via third-harmonic generation in Xe of frequency-doubled 50 fs laser pulses at 1.55 eV. By reporting the measured band dispersion of a Cu(111) crystal and the non-equilibrium dynamics of the Bi{sub 2}Se{sub 3} topological insulator, we prove that this source is suitable for studying the non-equilibrium dynamics of the entire Fermi surface of several complex materials, with high signal statistics and limited space-charge effect.

  8. Nonequilibrium thermodynamics and energy efficiency in weight loss diets

    Directory of Open Access Journals (Sweden)

    Fine Eugene J

    2007-07-01

    effect on hormone levels controls fatty acid flux and oxidation, 2 the rate of lipolysis is a primary target of insulin, postprandial, and 3 chronic carbohydrate-restricted diets reduce the levels of plasma TAG in response to a single meal. In summary, we propose that, in isocaloric diets of different macronutrient composition, there is variable flux of stored TAG controlled by the kinetic effects of insulin and other hormones. Because the fatty acid-TAG cycle never comes to equilibrium, net gain or loss is possible. The greater weight loss on carbohydrate restricted diets, popularly referred to as metabolic advantage can thus be understood in terms of the principles of nonequilibrium thermodynamics and is a consequence of the dynamic nature of bioenergetics where it is important to consider kinetic as well as thermodynamic variables.

  9. Modeling the nonequilibrium effects in a nonquasi-equilibrium thermodynamic cycle based on steepest entropy ascent and an isothermal-isobaric ensemble

    International Nuclear Information System (INIS)

    Li, Guanchen; Spakovsky, Michael R. von

    2016-01-01

    Conventional first principle approaches for studying nonequilibrium or far-from-equilibrium processes depend on the mechanics of individual particles or quantum states. They also require many details of the mechanical features of a system to arrive at a macroscopic property. In contrast, thermodynamics provides an approach for determining macroscopic property values without going into these details, because the overall effect of particle dynamics results, for example, at stable equilibrium in an invariant pattern of the “Maxwellian distribution”, which in turn leads to macroscopic properties. However, such an approach is not generally applicable to a nonequilibrium process except in the near-equilibrium realm. To adequately address these drawbacks, steepest-entropy-ascent quantum thermodynamics (SEAQT) provides a first principle, thermodynamic-ensemble approach applicable to the entire nonequilibrium realm. Based on prior developments by the authors, this paper applies the SEAQT framework to modeling the nonquasi-equilibrium cycle, which a system with variable volume undergoes. Using the concept of hypoequilibrium state and nonequilibrium intensive properties, this framework provides a complete description of the nonequilibrium evolution in state of the system. Results presented here reveal how nonequilibrium effects influence the performance of the cycle. - Highlights: • First-principles nonequilibrium model of thermodynamic cycles. • Study of thermal efficiency losses due to nonequilibrium effects. • Study of systems undergoing nonquasi-equilibrium processes. • Study of the coupling of system relaxation and interaction with a reservoir.

  10. Quantum distribution function of nonequilibrium system

    International Nuclear Information System (INIS)

    Sogo, Kiyoshi; Fujimoto, Yasushi.

    1990-03-01

    A path integral representation is derived for the Wigner distribution function of a nonequilibrium system coupled with heat bath. Under appropriate conditions, the Wigner distribution function approaches an equilibrium distribution, which manifests shifting and broadening of spectral lines due to the interaction with heat bath. It is shown that the equilibrium distribution becomes the quantum canonical distribution in the vanishing coupling constant limit. (author)

  11. Nonequilibrium Molecular Energy Coupling and Conversion Mechanisms

    Science.gov (United States)

    2016-08-28

    resolved temperature measurements, by pure rotational picosecond broadband Coherent Anti-Stokes Raman Spectroscopy ( CARS ), and kinetic modeling...rotational ps CARS for thermometry measurements in highly transient nonequilibrium plasmas. Rotational-translational temperatures are measured for time...primarily on localized flow heating on sub-acoustic time scale, and for assessing feasibility of high-speed aerodynamic flow control by vibrational

  12. Non-equilibrium thermodynamics and physical kinetics

    CERN Document Server

    Bikkin, Halid

    2014-01-01

    This graduate textbook covers contemporary directions of non-equilibrium statistical mechanics as well as classical methods of kinetics. With one of the main propositions being to avoid terms such as "obviously" and "it is easy to show", this treatise is an easy-to-read introduction into this traditional, yet vibrant field.

  13. Introduction to the nonequilibrium functional renormalization group

    International Nuclear Information System (INIS)

    Berges, J.; Mesterházy, D.

    2012-01-01

    In these lectures we introduce the functional renormalization group out of equilibrium. While in thermal equilibrium typically a Euclidean formulation is adequate, nonequilibrium properties require real-time descriptions. For quantum systems specified by a given density matrix at initial time, a generating functional for real-time correlation functions can be written down using the Schwinger-Keldysh closed time path. This can be used to construct a nonequilibrium functional renormalization group along similar lines as for Euclidean field theories in thermal equilibrium. Important differences include the absence of a fluctuation-dissipation relation for general out-of-equilibrium situations. The nonequilibrium renormalization group takes on a particularly simple form at a fixed point, where the corresponding scale-invariant system becomes independent of the details of the initial density matrix. We discuss some basic examples, for which we derive a hierarchy of fixed point solutions with increasing complexity from vacuum and thermal equilibrium to nonequilibrium. The latter solutions are then associated to the phenomenon of turbulence in quantum field theory.

  14. Generators of nonequilibrium low-temperature plasma

    International Nuclear Information System (INIS)

    Dautov, G.Yu.

    1988-01-01

    Results are described of a study and of the characteristics of sources of a non-equilibrium gas-discharge plasma. The plasma generators considered include glow, high frequency, and arc discharge generators. Thermodynamic, ionic, and electronic processes occurring in the plasmas are evaluated

  15. Non-equilibrium modelling of distillation

    NARCIS (Netherlands)

    Wesselingh, JA; Darton, R

    1997-01-01

    There are nasty conceptual problems in the classical way of describing distillation columns via equilibrium stages, and efficiencies or HETP's. We can nowadays avoid these problems by simulating the behaviour of a complete column in one go using a non-equilibrium model. Such a model has phase

  16. Non-equilibrium condensation process in holographic superconductor with nonlinear electrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yunqi; Gong, Yungui [School of Physics, Huazhong University of Science and Technology,Wuhan, Hubei 430074 (China); Wang, Bin [IFSA Collaborative Innovation Center, Department of Physics and Astronomy, Shanghai Jiao Tong University,Shanghai 200240 (China)

    2016-02-17

    We study the non-equilibrium condensation process in a holographic superconductor with nonlinear corrections to the U(1) gauge field. We start with an asymptotic Anti-de-Sitter(AdS) black hole against a complex scalar perturbation at the initial time, and solve the dynamics of the gravitational systems in the bulk. When the black hole temperature T is smaller than a critical value T{sub c}, the scalar perturbation grows exponentially till saturation, the final state of spacetime approaches to a hairy black hole. In the bulk theory, we find the clue of the influence of nonlinear corrections in the gauge filed on the process of the scalar field condensation. We show that the bulk dynamics in the non-equilibrium process is completely consistent with the observations on the boundary order parameter. Furthermore we examine the time evolution of horizons in the bulk non-equilibrium transformation process from the bald AdS black hole to the AdS hairy hole. Both the evolution of apparent and event horizons show that the original AdS black hole configuration requires more time to finish the transformation to become a hairy black hole if there is nonlinear correction to the electromagnetic field. We generalize our non-equilibrium discussions to the holographic entanglement entropy and find that the holographic entanglement entropy can give us further understanding of the influence of the nonlinearity in the gauge field on the scalar condensation.

  17. Nonequilibrium Equation of State in Suspensions of Active Colloids

    Directory of Open Access Journals (Sweden)

    Félix Ginot

    2015-01-01

    Full Text Available Active colloids constitute a novel class of materials composed of colloidal-scale particles locally converting chemical energy into motility, mimicking micro-organisms. Evolving far from equilibrium, these systems display structural organizations and dynamical properties distinct from thermalized colloidal assemblies. Harvesting the potential of this new class of systems requires the development of a conceptual framework to describe these intrinsically nonequilibrium systems. We use sedimentation experiments to probe the nonequilibrium equation of state of a bidimensional assembly of active Janus microspheres and conduct computer simulations of a model of self-propelled hard disks. Self-propulsion profoundly affects the equation of state, but these changes can be rationalized using equilibrium concepts. We show that active colloids behave, in the dilute limit, as an ideal gas with an activity-dependent effective temperature. At finite density, increasing the activity is similar to increasing adhesion between equilibrium particles. We quantify this effective adhesion and obtain a unique scaling law relating activity and effective adhesion in both experiments and simulations. Our results provide a new and efficient way to understand the emergence of novel phases of matter in active colloidal suspensions.

  18. Phase separation in the nonequilibrium Verwey transition in magnetite

    Science.gov (United States)

    Randi, F.; Vergara, I.; Novelli, F.; Esposito, M.; Dell'Angela, M.; Brabers, V. A. M.; Metcalf, P.; Kukreja, R.; Dürr, H. A.; Fausti, D.; Grüninger, M.; Parmigiani, F.

    2016-02-01

    We present equilibrium and out-of-equilibrium studies of the Verwey transition in magnetite. In the equilibrium optical conductivity, we find a steplike change at the phase transition for photon energies below about 2 eV. The possibility of triggering a nonequilibrium transient metallic state in insulating magnetite by photo excitation was recently demonstrated by an x-ray study. Here we report a full characterization of the optical properties in the visible frequency range across the nonequilibrium phase transition. Our analysis of the spectral features is based on a detailed description of the equilibrium properties. The out-of-equilibrium optical data bear the initial electronic response associated to localized photoexcitation, the occurrence of phase separation, and the transition to a transient metallic phase for excitation density larger than a critical value. This allows us to identify the electronic nature of the transient state, to unveil the phase transition dynamics, and to study the consequences of phase separation on the reflectivity, suggesting a spectroscopic feature that may be generally linked to out-of-equilibrium phase separation.

  19. Non-equilibrium theory of arrested spinodal decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Olais-Govea, José Manuel; López-Flores, Leticia; Medina-Noyola, Magdaleno [Instituto de Física “Manuel Sandoval Vallarta,” Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, SLP (Mexico)

    2015-11-07

    The non-equilibrium self-consistent generalized Langevin equation theory of irreversible relaxation [P. E. Ramŕez-González and M. Medina-Noyola, Phys. Rev. E 82, 061503 (2010); 82, 061504 (2010)] is applied to the description of the non-equilibrium processes involved in the spinodal decomposition of suddenly and deeply quenched simple liquids. For model liquids with hard-sphere plus attractive (Yukawa or square well) pair potential, the theory predicts that the spinodal curve, besides being the threshold of the thermodynamic stability of homogeneous states, is also the borderline between the regions of ergodic and non-ergodic homogeneous states. It also predicts that the high-density liquid-glass transition line, whose high-temperature limit corresponds to the well-known hard-sphere glass transition, at lower temperature intersects the spinodal curve and continues inside the spinodal region as a glass-glass transition line. Within the region bounded from below by this low-temperature glass-glass transition and from above by the spinodal dynamic arrest line, we can recognize two distinct domains with qualitatively different temperature dependence of various physical properties. We interpret these two domains as corresponding to full gas-liquid phase separation conditions and to the formation of physical gels by arrested spinodal decomposition. The resulting theoretical scenario is consistent with the corresponding experimental observations in a specific colloidal model system.

  20. Get Enough Calcium

    Science.gov (United States)

    ... Calcium Print This Topic En español Get Enough Calcium Browse Sections The Basics Overview Foods and Vitamins ... women, don't get enough calcium. How much calcium do I need every day? Women: If you ...

  1. Calcium - urine

    Science.gov (United States)

    ... Female urinary tract Male urinary tract Calcium urine test References Bringhurst FR, Demay MB, Kronenberg HM. Hormones and disorders of mineral metabolism. In: Melmed S, Polonsky KS, Larsen PR, Kronenberg HM, eds. Williams Textbook of Endocrinology . 13th ed. Philadelphia, PA: Elsevier; ...

  2. Monte Carlo estimates of interfacial tension in the two-dimensional Ising model from non-equilibrium methods

    International Nuclear Information System (INIS)

    Híjar, Humberto; Sutmann, Godehard

    2008-01-01

    Non-equilibrium methods for estimating free energy differences are used in order to calculate the interfacial tension between domains with opposite magnetizations in two-dimensional Ising lattices. Non-equilibrium processes are driven by changing the boundary conditions for two opposite sides of the lattice from periodic to antiperiodic and vice versa. This mechanism, which promotes the appearance and disappearance of the interface, is studied by means of Monte Carlo simulations performed at different rates and using different algorithms, thus allowing for testing the applicability of non-equilibrium methods for processes driven far from or close to equilibrium. Interfaces in lattices with different widths and heights are studied and the interface tension as a function of these quantities is obtained. It is found that the estimates of the interfacial tension from non-equilibrium procedures are in good agreement with previous reports as well as with exact results. The efficiency of the different procedures used is analyzed and the dynamics of the interface under these perturbations is briefly discussed. A method for determining the efficiency of non-equilibrium methods as regards thermodynamic perturbation is also presented. It is found that for all cases studied, the Crooks non-equilibrium method for estimating free energy differences is the most efficient one

  3. Emergence of an enslaved phononic bandgap in a non-equilibrium pseudo-crystal

    Science.gov (United States)

    Bachelard, Nicolas; Ropp, Chad; Dubois, Marc; Zhao, Rongkuo; Wang, Yuan; Zhang, Xiang

    2017-08-01

    Material systems that reside far from thermodynamic equilibrium have the potential to exhibit dynamic properties and behaviours resembling those of living organisms. Here we realize a non-equilibrium material characterized by a bandgap whose edge is enslaved to the wavelength of an external coherent drive. The structure dynamically self-assembles into an unconventional pseudo-crystal geometry that equally distributes momentum across elements. The emergent bandgap is bestowed with lifelike properties, such as the ability to self-heal to perturbations and adapt to sudden changes in the drive. We derive an exact analytical solution for both the spatial organization and the bandgap features, revealing the mechanism for enslavement. This work presents a framework for conceiving lifelike non-equilibrium materials and emphasizes the potential for the dynamic imprinting of material properties through external degrees of freedom.

  4. Emergence of an enslaved phononic bandgap in a non-equilibrium pseudo-crystal.

    Science.gov (United States)

    Bachelard, Nicolas; Ropp, Chad; Dubois, Marc; Zhao, Rongkuo; Wang, Yuan; Zhang, Xiang

    2017-08-01

    Material systems that reside far from thermodynamic equilibrium have the potential to exhibit dynamic properties and behaviours resembling those of living organisms. Here we realize a non-equilibrium material characterized by a bandgap whose edge is enslaved to the wavelength of an external coherent drive. The structure dynamically self-assembles into an unconventional pseudo-crystal geometry that equally distributes momentum across elements. The emergent bandgap is bestowed with lifelike properties, such as the ability to self-heal to perturbations and adapt to sudden changes in the drive. We derive an exact analytical solution for both the spatial organization and the bandgap features, revealing the mechanism for enslavement. This work presents a framework for conceiving lifelike non-equilibrium materials and emphasizes the potential for the dynamic imprinting of material properties through external degrees of freedom.

  5. Complex temporal and spatial patterns in nonequilibrium systems: Progress report, December 1, 1987-November 30, 1988

    International Nuclear Information System (INIS)

    Swinney, H.L.

    1988-09-01

    Dynamical systems methods are being developed and used to characterize nonequilibrium processes and to address outstanding unresolved questions regarding bifurcations and chaos, especially in reaction-diffusion systems. An information-theoretic property, the mutual information, is being examined as a means for detecting and quantifying spatiotemporal chaos. A recent analysis has shown that information on dynamics deduced from noisy data can be used to reduce the noise in those data. These tools from dynamical systems and information theory are being applied to data obtained in laboratory experiments on homogeneous systems and on extended systems. A novel unstirred chemical reactor has been designed for studies of the development and evolution of chemical spatial patterns, and experiments with this reactor have yielded the first sustained chemical spatial patterns in a controlled laboratory environment. These laboratory experiments and numerical and analytic studies of models should provide general insights into spatiotemporal patterns in nonequilibrium systems. 14 refs

  6. Non-Equilibrium Liouville and Wigner Equations: Moment Methods and Long-Time Approximations

    Directory of Open Access Journals (Sweden)

    Ramon F. Álvarez-Estrada

    2014-03-01

    Full Text Available We treat the non-equilibrium evolution of an open one-particle statistical system, subject to a potential and to an external “heat bath” (hb with negligible dissipation. For the classical equilibrium Boltzmann distribution, Wc,eq, a non-equilibrium three-term hierarchy for moments fulfills Hermiticity, which allows one to justify an approximate long-time thermalization. That gives partial dynamical support to Boltzmann’s Wc,eq, out of the set of classical stationary distributions, Wc;st, also investigated here, for which neither Hermiticity nor that thermalization hold, in general. For closed classical many-particle systems without hb (by using Wc,eq, the long-time approximate thermalization for three-term hierarchies is justified and yields an approximate Lyapunov function and an arrow of time. The largest part of the work treats an open quantum one-particle system through the non-equilibrium Wigner function, W. Weq for a repulsive finite square well is reported. W’s (< 0 in various cases are assumed to be quasi-definite functionals regarding their dependences on momentum (q. That yields orthogonal polynomials, HQ,n(q, for Weq (and for stationary Wst, non-equilibrium moments, Wn, of W and hierarchies. For the first excited state of the harmonic oscillator, its stationary Wst is a quasi-definite functional, and the orthogonal polynomials and three-term hierarchy are studied. In general, the non-equilibrium quantum hierarchies (associated with Weq for the Wn’s are not three-term ones. As an illustration, we outline a non-equilibrium four-term hierarchy and its solution in terms of generalized operator continued fractions. Such structures also allow one to formulate long-time approximations, but make it more difficult to justify thermalization. For large thermal and de Broglie wavelengths, the dominant Weq and a non-equilibrium equation for W are reported: the non-equilibrium hierarchy could plausibly be a three-term one and possibly not

  7. Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride.

    Science.gov (United States)

    He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

    2018-06-14

    To understand the initial hydration processes of CaCl 2 , we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl 2 (H 2 O) n - (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl-Ca ion pair is investigated in CaCl 2 (H 2 O) n - anions, where the first Ca-Cl ionic bond required 4 water molecules, and both Ca-Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl 2 (H 2 O) n clusters, breaking of the first Ca-Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl 2 (H 2 O) n requires fewer water molecules than those for MgCl 2 (H 2 O) n . Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

  8. Presynaptic calcium signalling in cerebellar mossy fibres

    DEFF Research Database (Denmark)

    Thomsen, Louiza Bohn; Jörntell, Henrik; Midtgaard, Jens

    2010-01-01

    Whole-cell recordings were obtained from mossy fibre terminals in adult turtles in order to characterize the basic membrane properties. Calcium imaging of presynaptic calcium signals was carried out in order to analyse calcium dynamics and presynaptic GABA B inhibition. A tetrodotoxin (TTX......)-sensitive fast Na(+) spike faithfully followed repetitive depolarizing pulses with little change in spike duration or amplitude, while a strong outward rectification dominated responses to long-lasting depolarizations. High-threshold calcium spikes were uncovered following addition of potassium channel blockers....... Calcium imaging using Calcium-Green dextran revealed a stimulus-evoked all-or-none TTX-sensitive calcium signal in simple and complex rosettes. All compartments of a complex rosette were activated during electrical activation of the mossy fibre, while individual simple and complex rosettes along an axon...

  9. Calcium paradox and calcium entry blockers

    NARCIS (Netherlands)

    Ruigrok, T.J.C.; Slade, A.M.; Nayler, W.G.; Meijler, F.L.

    1984-01-01

    Reperfusion of isolated hearts with calcium-containing solution after a short period of calcium-free perfusion results in irreversible cell damage (calcium paradox). This phenomenon is characterized by an excessive influx of calcium into the cells, the rapid onset of myocardial contracture,

  10. Non-equilibrium dilepton production in hadronic transport approaches

    International Nuclear Information System (INIS)

    Staudenmaier, Jan; Weil, Janus; Petersen, Hannah

    2017-01-01

    In this work the non-equilibrium dilepton production from a hadronic transport approach (SMASH) is presented. The dilepton emission from the hadronic stage is of interest for current HADES results measured at GSI in the beam energy range from 1.25 - 3.5 GeV. Also at high collision energies (RHIC/LHC) the later dilute stages of the reaction are dominated by hadronic dynamics. The newly developed hadronic transport approach called SMASH (=Simulating Many Accelerated Strongly-interacting Hadrons) is introduced first. After explaining the basic interaction mechanisms, a comparison of elementary cross sections for pion production to experimental data is shown. The dilepton production within SMASH is explained in detail. The main contribution to the dilepton spectra in the low energy regime of GSI/FAIR/RHIC-BES originates from resonance decays. Results of the dilepton production with SMASH such as invariant mass spectra are shown. (paper)

  11. Nonequilibrium quark production in the expanding QCD plasma

    Science.gov (United States)

    Tanji, Naoto; Berges, Jürgen

    2018-02-01

    We perform real-time lattice simulations of nonequilibrium quark production in the longitudinally expanding QCD plasma. Starting from a highly occupied gluonic state with vacuum quark sector, we extract the time evolution of quark and gluon number densities per unit transverse area and rapidity. The total quark number shows after an initial rapid increase an almost linear growth with time. Remarkably, this growth rate appears to be consistent with a simple kinetic theory estimate involving only two-to-two scattering processes in small-angle approximation. This extends previous findings about the role of two-to-two scatterings for purely gluonic dynamics in accordance with the early stages of the bottom-up thermalization scenario.

  12. Diffusion of nonequilibrium quasi-particles in a cuprate superconductor

    International Nuclear Information System (INIS)

    Gedik, N.; Orenstein, J.; Liang, Ruixing; Bonn, D.A.; Hardy, W.N.

    2003-01-01

    We report a transport study of nonequilibrium quasi-particles in a high-transition-temperature cuprate superconductor using the transient grating technique. Low-intensity laser excitation (at a photon energy of 1.5 electron volts) was used to introduce a spatially periodic density of quasi-particles into a high-quality untwinned single crystal of YBa2Cu3O6.5. Probing the evolution of the initial density through space and time yielded the quasi-particle diffusion coefficient and the inelastic and elastic scattering rates. The technique reported here is potentially applicable to precision measurements of quasi-particle dynamics not only in cuprate superconductors but in other electronic systems as well

  13. Nonequilibrium statistical operator in hot-electron transport theory

    International Nuclear Information System (INIS)

    Xing, D.Y.; Liu, M.

    1991-09-01

    The Nonequilibrium Statistical Operator method developed by Zubarev is generalized and applied to the study of hot-electron transport in semiconductors. The steady-state balance equations for momentum and energy are derived to the lowest order in the electron-lattice coupling. We show that the derived balance equations are exactly the same as those obtained by Lei and Ting. This equivalence stems from the fact that to the linear order in the electron-lattice coupling, two statistical density matrices have identical effect when they are used to calculate the average value of a dynamical operator. The application to the steady-state and transient hot-electron transport in multivalley semiconductors is also discussed. (author). 28 refs, 1 fig

  14. Non-equilibrium synthesis of alloys using lasers

    International Nuclear Information System (INIS)

    Mazumder, J.; Choi, J.; Ribaudo, C.; Wang, A.; Kar, A.

    1993-01-01

    This paper discusses microstructure and properties of alloys, produced by laser alloying and cladding technique, for various applications. These include Fe-Cr-W-C alloys for wear resistance, Ni-Cr-Al-Hf alloys for high temperature oxidation resistance and Mg-Al alloys for corrosion resistance. Also a mathematical model will be presented for the prediction of the composition of the metastable phases produced by laser synthesis. Microstructure was characterized using various electron optical techniques such as Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Auger Electron Spectroscopy (AES) and Energy Dispersive X-Ray Analysis (EDAX). Wear properties were characterized by a line contact Block on Cylinder method. High temperature oxidation properties were characterized by using Perkin-Elmer Thermo-Gravimetric Analyzer (TGA) where dynamic weight change were monitored at 1,200 C. Corrosion properties were evaluated by a potentio-dynamic method using a computer controlled Potentiostat manufactured by EG ampersand G. A non-equilibrium M 6 C type carbide was found to be responsible for the improved wear resistance. Increased solid-solubility of Hf was found to be a major factor in improving the high temperature oxidation resistance of the Ni-Cr-Al-Hf alloys. Micro-Crystalline phases were observed in Mg-Al alloys. The rapid solidification was modeled using heat transfer in the liquid pool and the solid substrate and mass transfer in the liquid pool. Non-equilibrium partition coefficient was introduced through the boundary condition at the liquid-solid interface. A good correlation was observed between the prediction and the experimental data. 54 refs

  15. Nonequilibrium recombination after a curved shock wave

    Science.gov (United States)

    Wen, Chihyung; Hornung, Hans

    2010-02-01

    The effect of nonequilibrium recombination after a curved two-dimensional shock wave in a hypervelocity dissociating flow of an inviscid Lighthill-Freeman gas is considered. An analytical solution is obtained with the effective shock values derived by Hornung (1976) [5] and the assumption that the flow is ‘quasi-frozen’ after a thin dissociating layer near the shock. The solution gives the expression of dissociation fraction as a function of temperature on a streamline. A rule of thumb can then be provided to check the validity of binary scaling for experimental conditions and a tool to determine the limiting streamline that delineates the validity zone of binary scaling. The effects on the nonequilibrium chemical reaction of the large difference in free stream temperature between free-piston shock tunnel and equivalent flight conditions are discussed. Numerical examples are presented and the results are compared with solutions obtained with two-dimensional Euler equations using the code of Candler (1988) [10].

  16. Species Turnover through Time: Colonization and Extinction Dynamics across Metacommunities.

    Science.gov (United States)

    Nuvoloni, Felipe Micali; Feres, Reinaldo José Fazzio; Gilbert, Benjamin

    2016-06-01

    Island biogeography and metacommunity theory often use equilibrium assumptions to predict local diversity, yet nonequilibrium dynamics are common in nature. In nonequilibrium communities, local diversity fluctuates through time as the relative importance of colonization and extinction change. Here, we test the prevalence and causes of nonequilibrium dynamics in metacommunities of mites associated with rubber trees distributed over large spatial (>1,000 km) and temporal (>30-60 generations) scales in Brazil. We measured colonization and extinction rates to test species turnover and nonequilibrium dynamics over a growing season. Mite metacommunities exhibited nonequilibrium dynamics for most months of the year, and these dynamics tracked climatic conditions. Monthly shifts in temperature of more than 1°C resulted in nonequilibrium dynamics, as did mean temperatures outside of two critical ranges. Nonequilibrium dynamics were caused by a change in colonization with temperature change and changes in both colonization and extinction with absolute temperature. Species turnover showed different trends; high relative humidity increased both colonization and extinction rates, increasing turnover but not nonequilibrium dynamics. Our study illustrates that testing nonequilibrium dynamics can provide new insights into the drivers of colonization, extinction, and diversity fluctuations in metacommunities.

  17. Modelling non-equilibrium thermodynamic systems from the speed-gradient principle.

    Science.gov (United States)

    Khantuleva, Tatiana A; Shalymov, Dmitry S

    2017-03-06

    The application of the speed-gradient (SG) principle to the non-equilibrium distribution systems far away from thermodynamic equilibrium is investigated. The options for applying the SG principle to describe the non-equilibrium transport processes in real-world environments are discussed. Investigation of a non-equilibrium system's evolution at different scale levels via the SG principle allows for a fresh look at the thermodynamics problems associated with the behaviour of the system entropy. Generalized dynamic equations for finite and infinite number of constraints are proposed. It is shown that the stationary solution to the equations, resulting from the SG principle, entirely coincides with the locally equilibrium distribution function obtained by Zubarev. A new approach to describe time evolution of systems far from equilibrium is proposed based on application of the SG principle at the intermediate scale level of the system's internal structure. The problem of the high-rate shear flow of viscous fluid near the rigid plane plate is discussed. It is shown that the SG principle allows closed mathematical models of non-equilibrium processes to be constructed.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

  18. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

    Energy Technology Data Exchange (ETDEWEB)

    Nilmeier, J. P.; Crooks, G. E.; Minh, D. D. L.; Chodera, J. D.

    2011-10-24

    Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Here, we introduce a new class of moves based on nonequilibrium dynamics: candidate configurations are generated through a finite-time process in which a system is actively driven out of equilibrium, and accepted with criteria that preserve the equilibrium distribution. The acceptance rule is similar to the Metropolis acceptance probability, but related to the nonequilibrium work rather than the instantaneous energy difference. Our method is applicable to sampling from both a single thermodynamic state or a mixture of thermodynamic states, and allows both coordinates and thermodynamic parameters to be driven in nonequilibrium proposals. While generating finite-time switching trajectories incurs an additional cost, driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times. Using nonequilibrium driven processes vastly expands the repertoire of useful Monte Carlo proposals in simulations of dense solvated systems.

  19. Phase transitions, scaling and renormalisation in nonequilibrium systems

    International Nuclear Information System (INIS)

    Hanney, T.E.

    2002-01-01

    Nonequilibrium phase transitions and critical phenomena in simple lattice-based interacting particle models are considered. Specific models of interest are exclusion models in low dimensions, with particular reference to the asymmetric simple exclusion process (ASEP) which provides a testbed for many of the calculations. The aim of the thesis is to devise approximate scaling techniques for such models which account for fluctuations and which are more widely applicable than methods pursuing an exact solution. Scaling techniques which have been applied to models described by a linear equation of motion are extended to the case where the equation of motion is nonlinear. These methods capture the dynamic transition in the ASEP but fail to properly account for the nonlinearity in their predictions for the dynamic exponent, z. A new and widely applicable real space renormalisation group procedure is developed. It provides a direct and transparent scaling method to extract universal and non-universal properties of the steady state and dynamic critical behaviour in the boundary-driven ASEP in one dimension. In particular, we obtain a flow diagram for the problem from which we can interpret all the qualitative features of the (exactly known) steady state phase diagram and which predicts the exact value for the critical point. Further, the dynamic scaling is consistent with a crossover between diflusive behaviour near the zero current fixed point and z = 3/2 dynamics at the critical fixed point. Extensions to include disorder, to higher dimensions, and to other models are all possible using the method. Using the mapping between the Master equation and the Schroedinger equation in imaginary time, this scaling procedure is rephrased as a new blocking for quantum-spin systems. Existing methods of real space renormalisation for quantum-spin systems are applied to a variety of previously unconsidered exclusion models. In particular, it is shown how such techniques can be applied

  20. P2X7 receptor-mediated calcium dynamics in HEK293 cells: experimental characterization and modelling approach

    International Nuclear Information System (INIS)

    Di Garbo, A; Alloisio, S; Nobile, M

    2012-01-01

    The P2X7 receptor (P2X7R) induces ionotropic Ca 2+  signalling in different cell types. It plays an important role in the immune response and in the nervous system. Here, the mechanisms underlying intracellular Ca 2+  variations evoked by 3′-O-(4-benzoyl)benzoyl-ATP (BzATP), a potent agonist of the P2X7R, in transfected HEK293 cells, are investigated both experimentally and theoretically. We propose a minimal model of P2X7R that is capable of reproducing, qualitatively and quantitatively, the experimental data. This approach was also adopted for the P2X7R variant, which lacks the entire C-terminus tail (trP2X7R). Then we introduce a biophysical model describing the Ca 2+  dynamics in HEK293. Our model gives an account of the ionotropic Ca 2+  influx evoked by BzATP on the basis of the kinetics model of P2X7R. To explain the complex Ca 2+  responses evoked by BzATP, the model predicted that an impairment in Ca 2+  extrusion flux through the plasma membrane is a key factor for Ca 2+ homeostasis in HEK293 cells. (paper)

  1. P2X7 receptor-mediated calcium dynamics in HEK293 cells: experimental characterization and modelling approach

    Science.gov (United States)

    Di Garbo, A.; Alloisio, S.; Nobile, M.

    2012-04-01

    The P2X7 receptor (P2X7R) induces ionotropic Ca2 + signalling in different cell types. It plays an important role in the immune response and in the nervous system. Here, the mechanisms underlying intracellular Ca2 + variations evoked by 3‧-O-(4-benzoyl)benzoyl-ATP (BzATP), a potent agonist of the P2X7R, in transfected HEK293 cells, are investigated both experimentally and theoretically. We propose a minimal model of P2X7R that is capable of reproducing, qualitatively and quantitatively, the experimental data. This approach was also adopted for the P2X7R variant, which lacks the entire C-terminus tail (trP2X7R). Then we introduce a biophysical model describing the Ca2 + dynamics in HEK293. Our model gives an account of the ionotropic Ca2 + influx evoked by BzATP on the basis of the kinetics model of P2X7R. To explain the complex Ca2 + responses evoked by BzATP, the model predicted that an impairment in Ca2 + extrusion flux through the plasma membrane is a key factor for Ca2 + homeostasis in HEK293 cells.

  2. Lattice Boltzmann approach for complex nonequilibrium flows.

    Science.gov (United States)

    Montessori, A; Prestininzi, P; La Rocca, M; Succi, S

    2015-10-01

    We present a lattice Boltzmann realization of Grad's extended hydrodynamic approach to nonequilibrium flows. This is achieved by using higher-order isotropic lattices coupled with a higher-order regularization procedure. The method is assessed for flow across parallel plates and three-dimensional flows in porous media, showing excellent agreement of the mass flow with analytical and numerical solutions of the Boltzmann equation across the full range of Knudsen numbers, from the hydrodynamic regime to ballistic motion.

  3. Efficiency bounds for nonequilibrium heat engines

    International Nuclear Information System (INIS)

    Mehta, Pankaj; Polkovnikov, Anatoli

    2013-01-01

    We analyze the efficiency of thermal engines (either quantum or classical) working with a single heat reservoir like an atmosphere. The engine first gets an energy intake, which can be done in an arbitrary nonequilibrium way e.g. combustion of fuel. Then the engine performs the work and returns to the initial state. We distinguish two general classes of engines where the working body first equilibrates within itself and then performs the work (ergodic engine) or when it performs the work before equilibrating (non-ergodic engine). We show that in both cases the second law of thermodynamics limits their efficiency. For ergodic engines we find a rigorous upper bound for the efficiency, which is strictly smaller than the equivalent Carnot efficiency. I.e. the Carnot efficiency can be never achieved in single reservoir heat engines. For non-ergodic engines the efficiency can be higher and can exceed the equilibrium Carnot bound. By extending the fundamental thermodynamic relation to nonequilibrium processes, we find a rigorous thermodynamic bound for the efficiency of both ergodic and non-ergodic engines and show that it is given by the relative entropy of the nonequilibrium and initial equilibrium distributions. These results suggest a new general strategy for designing more efficient engines. We illustrate our ideas by using simple examples. -- Highlights: ► Derived efficiency bounds for heat engines working with a single reservoir. ► Analyzed both ergodic and non-ergodic engines. ► Showed that non-ergodic engines can be more efficient. ► Extended fundamental thermodynamic relation to arbitrary nonequilibrium processes

  4. Nonequilibrium Phase Transitions Associated with DNA Replication

    Science.gov (United States)

    2011-02-11

    polymerases) catalyzing the growth of a DNA primer strand (the nascent chain of nucleotides complementary to the template strand) based on the Watson ...the fraction (error rate) of monomers for which y, where y is the correct Watson - Crick complementary base of , can be obtained by ¼ X...Nonequilibrium Phase Transitions Associated with DNA Replication Hyung-June Woo* and Anders Wallqvist Biotechnology High Performance Computing

  5. RETRAN nonequilibrium two-phase flow model for operational transient analyses

    International Nuclear Information System (INIS)

    Paulsen, M.P.; Hughes, E.D.

    1982-01-01

    The field balance equations, flow-field models, and equation of state for a nonequilibrium two-phase flow model for RETRAN are given. The differential field balance model equations are: (1) conservation of mixture mass; (2) conservation of vapor mass; (3) balance of mixture momentum; (4) a dynamic-slip model for the velocity difference; and (5) conservation of mixture energy. The equation of state is formulated such that the liquid phase may be subcooled, saturated, or superheated. The vapor phase is constrained to be at the saturation state. The dynamic-slip model includes wall-to-phase and interphase momentum exchanges. A mechanistic vapor generation model is used to describe vapor production under bulk subcooling conditions. The speed of sound for the mixture under nonequilibrium conditions is obtained from the equation of state formulation. The steady-state and transient solution methods are described

  6. Amorphous ices explained in terms of nonequilibrium phase transitions in supercooled water

    Science.gov (United States)

    Limmer, David; Chandler, David

    2013-03-01

    We analyze the phase diagram of supercooled water out-of-equilibrium using concepts from space-time thermodynamics and the dynamic facilitation theory of the glass transition, together with molecular dynamics simulations. We find that when water is driven out-of-equilibrium, it can exist in multiple amorphous states. In contrast, we find that when water is at equilibrium, it can exist in only one liquid state. The amorphous non-equilibrium states are solids, distinguished from the liquid by their lack of mobility, and distinguished from each other by their different densities and local structure. This finding explains the experimentally observed polyamorphism of water as a class of nonequilibrium phenomena involving glasses of different densities. While the amorphous solids can be long lived, they are thermodynamically unstable. When allowed to relax to equilibrium, they crystallize with pathways that pass first through liquid state configurations and then to ordered ice.

  7. PREFACE: International Symposium on Non-Equilibrium Soft Matter 2010 International Symposium on Non-Equilibrium Soft Matter 2010

    Science.gov (United States)

    Kawakatsu, T.; Matsuyama, A.; Ohta, T.; Tanaka, H.; Tanaka, S.

    2011-07-01

    Soft matter is a rapidly growing interdisciplinary research field covering a range of subject areas including physics, chemistry, biology, mathematics and engineering. Some of the important universal features of these materials are their mesoscopic structures and their dynamics. Due to the existence of such large-scale structures, which nevertheless exhibit interactions of the order of the thermal energy, soft matter can readily be taken out of equilibrium by imposing a weak external field such as an electric field, a mechanical stress or a shear flow. The importance of the coexistence of microscopic molecular dynamics and the mesoscopic/macroscopic structures and flows requires us to develop hierarchical approaches to understand the nonlinear and nonequilibrium phenomena, which is one of the central issues of current soft matter research. This special section presents selected contributions from the 'International Symposium on Non-Equilibrium Soft Matter 2010' held from 17-20 August 2010 in Nara, Japan, which aimed to describe recent advances in soft matter research focusing especially on its nonequilibrium aspects. The topics discussed cover statics and dynamics of a wide variety of materials ranging from traditional soft matter like polymers, gels, emulsions, liquid crystals and colloids to biomaterials such as biopolymers and biomembranes. Among these studies, we highlighted the physics of biomembranes and vesicles, which has attracted great attention during the last decade; we organized a special session for this active field. The work presented in this issue deals with (1) structure formation in biomembranes and vesicles, (2) rheology of polymers and gels, (3) mesophases in block copolymers, (4) mesoscopic structures in liquid crystals and ionic liquids, and (5) nonequilibrium dynamics. This symposium was organized as part of a research project supported by the Grant-in-Aid for the priority area 'Soft Matter Physics' (2006-2010) from the Ministry of Education

  8. Modeling and Control of an Ornithopter for Non-Equilibrium Maneuvers

    OpenAIRE

    Rose, Cameron Jarrel

    2015-01-01

    Flapping-winged flight is very complex, and it is difficult to efficiently model the unsteady airflow and nonlinear dynamics for online control. While steady state flight is well understood, transitions between flight regimes are not readily modeled or controlled. Maneuverability in non-equilibrium flight, which birds and insects readily exhibit in nature, is necessary to operate in the types of cluttered environments that small-scale flapping-winged robots are best suited for. The advantages...

  9. Portfolio theory of optimal isometric force production: Variability predictions and nonequilibrium fluctuation dissipation theorem

    Science.gov (United States)

    Frank, T. D.; Patanarapeelert, K.; Beek, P. J.

    2008-05-01

    We derive a fundamental relationship between the mean and the variability of isometric force. The relationship arises from an optimal collection of active motor units such that the force variability assumes a minimum (optimal isometric force). The relationship is shown to be independent of the explicit motor unit properties and of the dynamical features of isometric force production. A constant coefficient of variation in the asymptotic regime and a nonequilibrium fluctuation-dissipation theorem for optimal isometric force are predicted.

  10. Portfolio theory of optimal isometric force production: Variability predictions and nonequilibrium fluctuation-dissipation theorem

    International Nuclear Information System (INIS)

    Frank, T.D.; Patanarapeelert, K.; Beek, P.J.

    2008-01-01

    We derive a fundamental relationship between the mean and the variability of isometric force. The relationship arises from an optimal collection of active motor units such that the force variability assumes a minimum (optimal isometric force). The relationship is shown to be independent of the explicit motor unit properties and of the dynamical features of isometric force production. A constant coefficient of variation in the asymptotic regime and a nonequilibrium fluctuation-dissipation theorem for optimal isometric force are predicted

  11. On nonequilibrium many-body systems. 1: The nonequilibrium statistical operator method

    International Nuclear Information System (INIS)

    Algarte, A.C.S.; Vasconcellos, A.R.; Luzzi, R.; Sampaio, A.J.C.

    1985-01-01

    The theoretical aspects involved in the treatment of many-body systems strongly departed from equilibrium are discussed. The nonequilibrium statistical operator (NSO) method is considered in detail. Using Jaynes' maximum entropy formalism complemented with an ad hoc hypothesis a nonequilibrium statistical operator is obtained. This approach introduces irreversibility from the outset and we recover statistical operators like those of Green-Mori and Zubarev as particular cases. The connection with Generalized Thermodynamics and the construction of nonlinear transport equations are briefly described. (Author) [pt

  12. Structural characterization of lipidic systems under nonequilibrium conditions

    DEFF Research Database (Denmark)

    Yaghmur, Anan; Rappolt, Michael

    2012-01-01

    This review covers recent studies on the characterization of the dynamics of lipidic nanostructures formed via self-assembly processes. The focus is placed on two main topics: First, an overview of advanced experimental small-angle X-ray scattering (SAXS) setups combined with various sample...... negatively charged vesicles with calcium ions, and in situ hydration-induced formation of inverted-type liquid-crystalline phases loaded with the local anesthetic bupivacaine are summarized. These in situ time-resolved experiments allow real-time monitoring of the dynamics of the structural changes...

  13. A nonequilibrium simulation method for calculating tracer diffusion coefficients of small solutes in n-alkane liquids and polymers

    NARCIS (Netherlands)

    van der Vegt, N.F.A.; Briels, Willem J.; Wessling, Matthias; Strathmann, H.

    1998-01-01

    The tracer diffusion coefficients of methane in n-alkane liquids of increasing chain length were calculated by measuring the friction from short time nonequilibrium molecular dynamics simulations. The frictional constant was calculated from the exponentially decaying distance between two methane

  14. Models of calcium signalling

    CERN Document Server

    Dupont, Geneviève; Kirk, Vivien; Sneyd, James

    2016-01-01

    This book discusses the ways in which mathematical, computational, and modelling methods can be used to help understand the dynamics of intracellular calcium. The concentration of free intracellular calcium is vital for controlling a wide range of cellular processes, and is thus of great physiological importance. However, because of the complex ways in which the calcium concentration varies, it is also of great mathematical interest.This book presents the general modelling theory as well as a large number of specific case examples, to show how mathematical modelling can interact with experimental approaches, in an interdisciplinary and multifaceted approach to the study of an important physiological control mechanism. Geneviève Dupont is FNRS Research Director at the Unit of Theoretical Chronobiology of the Université Libre de Bruxelles;Martin Falcke is head of the Mathematical Cell Physiology group at the Max Delbrück Center for Molecular Medicine, Berlin;Vivien Kirk is an Associate Professor in the Depar...

  15. Superoperator nonequilibrium Green's function theory of many-body systems; applications to charge transfer and transport in open junctions

    International Nuclear Information System (INIS)

    Harbola, U.; Mukamel, S.

    2008-01-01

    Nonequilibrium Green's functions provide a powerful tool for computing the dynamical response and particle exchange statistics of coupled quantum systems. We formulate the theory in terms of the density matrix in Liouville space and introduce superoperator algebra that greatly simplifies the derivation and the physical interpretation of all quantities. Expressions for various observables are derived directly in real time in terms of superoperator nonequilibrium Green's functions (SNGF), rather than the artificial time-loop required in Schwinger's Hilbert-space formulation. Applications for computing interaction energies, charge densities, average currents, current induced fluorescence, electroluminescence and current fluctuation (electron counting) statistics are discussed

  16. Calcium blood test

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003477.htm Calcium blood test To use the sharing features on this page, please enable JavaScript. The calcium blood test measures the level of calcium in the blood. ...

  17. Calcium source (image)

    Science.gov (United States)

    Getting enough calcium to keep bones from thinning throughout a person's life may be made more difficult if that person has ... as a tendency toward kidney stones, for avoiding calcium-rich food sources. Calcium deficiency also effects the ...

  18. Calcium Pyrophosphate Deposition (CPPD)

    Science.gov (United States)

    ... Patient / Caregiver Diseases & Conditions Calcium Pyrophosphate Deposition (CPPD) Calcium Pyrophosphate Deposition (CPPD) Fast Facts The risk of ... young people, too. Proper diagnosis depends on detecting calcium pyrophosphate crystals in the fluid of an affected ...

  19. Calcium carbonate overdose

    Science.gov (United States)

    Tums overdose; Calcium overdose ... Calcium carbonate can be dangerous in large amounts. ... Products that contain calcium carbonate are certain: Antacids (Tums, Chooz) Mineral supplements Hand lotions Vitamin and mineral supplements Other products may also contain ...

  20. Calcium and bones (image)

    Science.gov (United States)

    Calcium is one of the most important minerals for the growth, maintenance, and reproduction of the human ... body, are continually being re-formed and incorporate calcium into their structure. Calcium is essential for the ...

  1. Calcium hydroxide poisoning

    Science.gov (United States)

    Hydrate - calcium; Lime milk; Slaked lime ... Calcium hydroxide ... These products contain calcium hydroxide: Cement Limewater Many industrial solvents and cleaners (hundreds to thousands of construction products, flooring strippers, brick cleaners, cement ...

  2. Modeling Inflation Using a Non-Equilibrium Equation of Exchange

    Science.gov (United States)

    Chamberlain, Robert G.

    2013-01-01

    Inflation is a change in the prices of goods that takes place without changes in the actual values of those goods. The Equation of Exchange, formulated clearly in a seminal paper by Irving Fisher in 1911, establishes an equilibrium relationship between the price index P (also known as "inflation"), the economy's aggregate output Q (also known as "the real gross domestic product"), the amount of money available for spending M (also known as "the money supply"), and the rate at which money is reused V (also known as "the velocity of circulation of money"). This paper offers first a qualitative discussion of what can cause these factors to change and how those causes might be controlled, then develops a quantitative model of inflation based on a non-equilibrium version of the Equation of Exchange. Causal relationships are different from equations in that the effects of changes in the causal variables take time to play out-often significant amounts of time. In the model described here, wages track prices, but only after a distributed lag. Prices change whenever the money supply, aggregate output, or the velocity of circulation of money change, but only after a distributed lag. Similarly, the money supply depends on the supplies of domestic and foreign money, which depend on the monetary base and a variety of foreign transactions, respectively. The spreading of delays mitigates the shocks of sudden changes to important inputs, but the most important aspect of this model is that delays, which often have dramatic consequences in dynamic systems, are explicitly incorporated.macroeconomics, inflation, equation of exchange, non-equilibrium, Athena Project

  3. Renormalisation of Nonequilibrium Phonons Under Strong Perturbative Influences.

    Science.gov (United States)

    Mehta, Sushrut Madhukar

    Effects of strong perturbative influences, namely the presence of a narrow distribution of acoustic phonons, and the presence of an electron plasma, on the dynamics of nonequilibrium, near zone center, longitudinal optical phonons in GaP have been investigated in two separate experiments. The study of the effects of the interaction between the LO phonons and a heavily populated, narrow distribution of acoustic phonons lead to the observation of a new optically driven nonequilibrium phonon state. Time Resolved Coherent Antistokes Raman Scattering (TR-CARS), with picosecond resolution, was used to investigate the new mode. In order to achieve high occupation numbers in the acoustic branch, the picosecond laser pulses used were amplified up to 1.0 GW/cm^2 peak power per laser beam. An important characteristic property of the new state which differentiates it from the well known LO phonon state is the fact that rather than having the single decay rate observed under thermal equilibrium, the new state has two decay rates. Moreover, these two decay rates depend strongly on the distribution of the acoustic phonon occupation number. The coupling of the LO phonons with an electron plasma, on the other hand, was investigated by measurements of the shape of the Raman scattered line associated with the phonon-plasmon coupled mode. The plasma was generated by thermal excitation of carriers in doped samples. It was possible to study a large variety of plasma excitations by controlling the concentration of the dopant and the ambient temperature. A complete, self consistant model based on standard dielectric response theory is presented, and applied to the measurements of the phonon-plasmon coupled mode. It is possible to recover, via this model, the effective coupled mode damping rate, the plasma damping rate, and the plasma frequency as functions of ambient temperature, or the carrier concentration.

  4. Calcium in Urine Test

    Science.gov (United States)

    ... K. Brunner & Suddarth's Handbook of Laboratory and Diagnostic Tests. 2 nd Ed, Kindle. Philadelphia: Wolters Kluwer Health, Lippincott Williams & Wilkins; c2014. Calcium, Serum; Calcium and Phosphates, Urine; ...

  5. Transcellular transport of calcium

    Energy Technology Data Exchange (ETDEWEB)

    Terepka, A R; Coleman, J R; Armbrecht, H J; Gunter, T E

    1976-01-01

    Studies of two calcium transporting epithelia, embryonic chick chorioallantoic membrane and the small intestine of rat and chick, have strongly suggested that the transfer of calcium across a cell involves processes distinctly different from intracellular calcium ion regulation. In the proposed model, transcellular calcium transport is considered as a specialized process developed only by certain cells in those tissues charged with bulk transfer of calcium. The overall effect of the endocytotic mechanism is bulk calcium movement across a cell, protection of mitochondria from exposure to high concentrations of calcium, and the avoidance of wide and potentially toxic fluctuations in cytosol ionic calcium levels. (MFB)

  6. Simple models of equilibrium and nonequilibrium phenomena

    International Nuclear Information System (INIS)

    Lebowitz, J.L.

    1987-01-01

    This volume consists of two chapters of particular interest to researchers in the field of statistical mechanics. The first chapter is based on the premise that the best way to understand the qualitative properties that characterize many-body (i.e. macroscopic) systems is to study 'a number of the more significant model systems which, at least in principle are susceptible of complete analysis'. The second chapter deals exclusively with nonequilibrium phenomena. It reviews the theory of fluctuations in open systems to which they have made important contributions. Simple but interesting model examples are emphasised

  7. A Lagrangian formalism for nonequilibrium ensembles

    International Nuclear Information System (INIS)

    Sobouti, Y.

    1989-08-01

    It is suggested to formulate a nonequilibrium ensemble theory by maximizing a time-integrated entropy constrained by Liouville's equation. This leads to distribution functions of the form f = Z -1 exp(-g/kT), where g(p,q,t) is a solution of Liouville's equation. A further requirement that the entropy should be an additivie functional of the integrals of Liouville's equation, limits the choice of g to linear superpositions of the nonlinearly independent integrals of motion. Time-dependent and time-independent integrals may participate in this superposition. (author). 14 refs

  8. Edge Singularities and Quasilong-Range Order in Nonequilibrium Steady States

    Science.gov (United States)

    De Nardis, Jacopo; Panfil, Miłosz

    2018-05-01

    The singularities of the dynamical response function are one of the most remarkable effects in many-body interacting systems. However in one dimension these divergences only exist strictly at zero temperature, making their observation very difficult in most cold atomic experimental settings. Moreover the presence of a finite temperature destroys another feature of one-dimensional quantum liquids: the real space quasilong-range order in which the spatial correlation functions exhibit power-law decay. We consider a nonequilibrium protocol where two interacting Bose gases are prepared either at different temperatures or chemical potentials and then joined. We show that the nonequilibrium steady state emerging at large times around the junction displays edge singularities in the response function and quasilong-range order.

  9. Electrical Conductivity of Charged Particle Systems and Zubarev's Nonequilibrium Statistical Operator Method

    Science.gov (United States)

    Röpke, G.

    2018-01-01

    One of the fundamental problems in physics that are not yet rigorously solved is the statistical mechanics of nonequilibrium processes. An important contribution to describing irreversible behavior starting from reversible Hamiltonian dynamics was given by D. N. Zubarev, who invented the method of the nonequilibrium statistical operator. We discuss this approach, in particular, the extended von Neumann equation, and as an example consider the electrical conductivity of a system of charged particles. We consider the selection of the set of relevant observables. We show the relation between kinetic theory and linear response theory. Using thermodynamic Green's functions, we present a systematic treatment of correlation functions, but the convergence needs investigation. We compare different expressions for the conductivity and list open questions.

  10. Experimental signatures of a nonequilibrium phase transition governing the yielding of a soft glass.

    Science.gov (United States)

    Hima Nagamanasa, K; Gokhale, Shreyas; Sood, A K; Ganapathy, Rajesh

    2014-06-01

    We present direct experimental signatures of a nonequilibrium phase transition associated with the yield point of a prototypical soft solid-a binary colloidal glass. By simultaneously quantifying single-particle dynamics and bulk mechanical response, we identified the threshold for the onset of irreversibility with the yield strain. We extracted the relaxation time from the transient behavior of the loss modulus and found that it diverges in the vicinity of the yield strain. This critical slowing down is accompanied by a growing correlation length associated with the size of regions of high Debye-Waller factor, which are precursors to yield events in glasses. Our results affirm that the paradigm of nonequilibrium critical phenomena is instrumental in achieving a holistic understanding of yielding in soft solids.

  11. Numerical Simulation of Non-Equilibrium Two-Phase Wet Steam Flow through an Asymmetric Nozzle

    Directory of Open Access Journals (Sweden)

    Miah Md Ashraful Alam

    2017-11-01

    Full Text Available The present study reported of the numerical investigation of a high-speed wet steam flow through an asymmetric nozzle. The spontaneous non-equilibrium homogeneous condensation of wet steam was numerically modeled based on the classical nucleation theory and droplet growth rate equation combined with the field conservations within the computational fluid dynamics (CFD code of ANSYS Fluent 13.0. The equations describing droplet formations and interphase change were solved sequentially after solving the main flow conservation equations. The calculations were carried out assuming the flow two-dimensional, compressible, turbulent, and viscous. The SST k-ω model was used for modeling the turbulence within an unstructured mesh solver. The validation of numerical model was accomplished, and the results showed a good agreement between the numerical simulation and experimental data. The effect of spontaneous non-equilibrium condensation on the jet and shock structures was revealed, and the condensation shown a great influence on the jet structure.

  12. Specific heat, polarization and heat conduction in microwave heating systems: A nonequilibrium thermodynamic point of view

    International Nuclear Information System (INIS)

    Bergese, Paolo

    2006-01-01

    A microwave (MW) field can induce in a dielectric material an oscillatory polarization. By this mechanism part of the energy carried by the waves is converted into chaotic agitation, and the material heats up. MW heating is a nonequilibrium phenomenon, while conventional heating can generally be considered as quasi-static. Excess (or nonthermal) effects of MWs with respect to conventional heating lie in this difference. Macroscopically, MW heating can be described in the framework of linear nonequilibrium thermodynamics (NET). This approach indicates that in a dielectric material under MW heating the specific heat has a dynamic component linked to the variation of polarization with temperature, and that polarization and heat conduction are intertwined. In particular, linear NET provides a new phenomenological equation for heat conduction that is composed of the classic Fourier's law and an additional term due to polarization relaxation. This term quantitatively describes the excess effect of MWs on thermal conduction

  13. Numerical simulation of nonequilibrium flows by using the state-to-state approach in commercial software

    Science.gov (United States)

    Kunova, O. V.; Shoev, G. V.; Kudryavtsev, A. N.

    2017-01-01

    Nonequilibrium flows of a two-component oxygen mixture O2/O behind a shock wave are studied with due allowance for the state-to-state vibrational and chemical kinetics. The system of gas-dynamic equations is supplemented with kinetic equations including contributions of VT (TV)-exchange and dissociation processes. A method of the numerical solution of this system with the use of the ANSYS Fluent commercial software package is proposed, which is used in a combination with the authors' code that takes into account nonequilibrium kinetics. The computed results are compared with parameters obtained by solving the problem in the shock-fitting formulation. The vibrational temperature is compared with experimental data. The numerical tool proposed in the present paper is applied to study the flow around a cylinder.

  14. Non-equilibrium spectroscopy of high-Tc superconductors

    International Nuclear Information System (INIS)

    Krasnov, V M

    2009-01-01

    In superconductors, recombination of two non-equilibrium quasiparticles into a Cooper pair results in emission of excitation that mediates superconductivity. This is the basis of the proposed new type of 'non-equilibrium' spectroscopy of high T c superconductors, which may open a possibility for direct and unambiguous determination of the coupling mechanism of high T c superconductivity. In case of low T c superconductors, the feasibility of such the non-equilibrium spectroscopy was demonstrated in classical phonon generation-detection experiments almost four decades ago. Recently it was demonstrated that a similar technique can be used for high T c superconductors, using natural intrinsic Josephson junctions both for injection of non-equilibrium quasiparticles and for detection of the non-equilibrium radiation. Here I analyze theoretically non-equilibrium phenomena in intrinsic Josephson junctions. It is shown that extreme non-equilibrium state can be achieved at bias equal to integer number of the gap voltage, which can lead to laser-like emission from the stack. I argue that identification of the boson type, constituting this non-equilibrium radiation would unambiguously reveal the coupling mechanism of high Tc superconductors.

  15. Exploring Chemical and Thermal Non-equilibrium in Nitrogen Arcs

    International Nuclear Information System (INIS)

    Ghorui, S; Das, A K

    2012-01-01

    Plasma torches operating with nitrogen are of special importance as they can operate with usual tungsten based refractory electrodes and offer radical rich non-oxidizing high temperature environment for plasma chemistry. Strong gradients in temperature as well as species densities and huge convective fluxes lead to varying degrees of chemical non-equilibrium in associated regions. An axi-symmetric two-temperature chemical non-equilibrium model of a nitrogen plasma torch has been developed to understand the effects of thermal and chemical non-equilibrium in arcs. A 2-D finite volume CFD code in association with a non-equilibrium property routine enabled extraction of steady state self-consistent distributions of various plasma quantities inside the torch under various thermal and chemical non-equilibrium conditions. Chemical non-equilibrium has been incorporated through computation of diffusive and convective fluxes in each finite volume cell in every iteration and associating corresponding thermodynamic and transport properties through the scheme of 'chemical non-equilibrium parameter' introduced by Ghorui et. al. Recombination coefficient data from Nahar et. al. and radiation data from Krey and Morris have been used in the simulation. Results are presented for distributions of temperature, pressure, velocity, current density, electric potential, species densities and chemical non-equilibrium effects. Obtained results are compared with similar results under LTE.

  16. Phase transitions in nonequilibrium traffic theory

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, H.M.

    2000-02-01

    This paper uses the center difference scheme of Lax-Friedrichs to numerically solve a newly developed continuum traffic flow theory and the kinematic theory of Lighthill and Whitham, and Richards, and it studies the flow-concentration phase transitions in flow containing both shock and rarefaction waves. A homogeneous road with finite length was modeled by both theories. Numerical simulations show that both theories yield nearly identical results for two representative Riemann problems--one has a shock solution and the other a rarefaction wave solution. Their phase transition curves, however, are different: those derived from the new theory have two branches--one for acceleration flow and one for deceleration flow, whereas those derived from the LWR theory comprise a single curve--the equilibrium curve. The phase transition curves in the shock case agree well with certain experimental observations but disagree with others. This disagreement may be resolved by studying transitions among nonequilibrium states, which awaits further development of a more accurate finite difference approximation of the nonequilibrium theory.

  17. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  18. Enforcing conservation laws in nonequilibrium cluster perturbation theory

    Science.gov (United States)

    Gramsch, Christian; Potthoff, Michael

    2017-05-01

    Using the recently introduced time-local formulation of the nonequilibrium cluster perturbation theory (CPT), we construct a generalization of the approach such that macroscopic conservation laws are respected. This is achieved by exploiting the freedom for the choice of the starting point of the all-order perturbation theory in the intercluster hopping. The proposed conserving CPT is a self-consistent propagation scheme which respects the conservation of energy, particle number, and spin, which treats short-range correlations exactly up to the linear scale of the cluster, and which represents a mean-field-like approach on length scales beyond the cluster size. Using Green's functions, conservation laws are formulated as local constraints on the local spin-dependent particle and the doublon density. We consider them as conditional equations to self-consistently fix the time-dependent intracluster one-particle parameters. Thanks to the intrinsic causality of the CPT, this can be set up as a step-by-step time propagation scheme with a computational effort scaling linearly with the maximum propagation time and exponentially in the cluster size. As a proof of concept, we consider the dynamics of the two-dimensional, particle-hole-symmetric Hubbard model following a weak interaction quench by simply employing two-site clusters only. Conservation laws are satisfied by construction. We demonstrate that enforcing them has strong impact on the dynamics. While the doublon density is strongly oscillating within plain CPT, a monotonic relaxation is observed within the conserving CPT.

  19. Nonequilibrium localization and the interplay between disorder and interactions

    International Nuclear Information System (INIS)

    Mascarenhas, Eduardo; Bragança, Helena; Aguiar, M C O; França Santos, M; Drumond, R

    2016-01-01

    We study the nonequilibrium interplay between disorder and interactions in a closed quantum system. We base our analysis on the notion of dynamical state-space localization, calculated via the Loschmidt echo. Although real-space and state-space localization are independent concepts in general, we show that both perspectives may be directly connected through a specific choice of initial states, namely, maximally localized states (ML-states). We show numerically that in the noninteracting case the average echo is found to be monotonically increasing with increasing disorder; these results are in agreement with an analytical evaluation in the single particle case in which the echo is found to be inversely proportional to the localization length. We also show that for interacting systems, the length scale under which equilibration may occur is upper bounded and such bound is smaller the greater the average echo of ML-states. When disorder and interactions, both being localization mechanisms, are simultaneously at play the echo features a non-monotonic behaviour indicating a non-trivial interplay of the two processes. This interplay induces delocalization of the dynamics which is accompanied by delocalization in real-space. This non-monotonic behaviour is also present in the effective integrability which we show by evaluating the gap statistics. (paper)

  20. Nonequilibrium localization and the interplay between disorder and interactions.

    Science.gov (United States)

    Mascarenhas, Eduardo; Bragança, Helena; Drumond, R; Aguiar, M C O; França Santos, M

    2016-05-18

    We study the nonequilibrium interplay between disorder and interactions in a closed quantum system. We base our analysis on the notion of dynamical state-space localization, calculated via the Loschmidt echo. Although real-space and state-space localization are independent concepts in general, we show that both perspectives may be directly connected through a specific choice of initial states, namely, maximally localized states (ML-states). We show numerically that in the noninteracting case the average echo is found to be monotonically increasing with increasing disorder; these results are in agreement with an analytical evaluation in the single particle case in which the echo is found to be inversely proportional to the localization length. We also show that for interacting systems, the length scale under which equilibration may occur is upper bounded and such bound is smaller the greater the average echo of ML-states. When disorder and interactions, both being localization mechanisms, are simultaneously at play the echo features a non-monotonic behaviour indicating a non-trivial interplay of the two processes. This interplay induces delocalization of the dynamics which is accompanied by delocalization in real-space. This non-monotonic behaviour is also present in the effective integrability which we show by evaluating the gap statistics.

  1. Nonequilibrium forces between neutral atoms mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2010-01-01

    We study forces between two neutral atoms, modeled as three-dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center-of-mass motion of the atom, its internal degrees of freedom, and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first-principles, systematic, and unified description including the intrinsic and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces--London, van der Waals, and Casimir-Polder--between neutral atoms in the long-time limit. We also reproduce a recently reported force between atoms when the system is out of thermal equilibrium at late times. More noteworthy is the discovery of the existence of a type of (or identification of the source of some known) interatomic force which we call the ''entanglement force,'' originating from the quantum correlations of the internal degrees of freedom of entangled atoms.

  2. Complex temporal and spatial patterns in nonequilibrium processes. Final report, December 1, 1987--November 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    1992-12-31

    Dynamical systems methods have been used to study bifurcations and pattern formation in nonequilibrium systems. Accomplishments during this period include: information-theoretic methods for analyzing chaos, chemical reactors for studying sustained reaction-diffusion patterns, a reactor exploiting pattern formation to extract short- lived intermediate species, observation of bifurcation from periodic to quasiperiodic rotating chemical spiral patterns, observation of a Turing bifurcation (transition from uniform state to a stationary chemical pattern), method for extracting noise strength in ramped convection, self-similar fractal structure of Zn clusters in electrodeposition, and dynamical instability in crack propagation.

  3. Calcium sensing in exocytosis

    DEFF Research Database (Denmark)

    Gustavsson, Natalia; Wu, Bingbing; Han, Weiping

    2012-01-01

    an increase in intracellular calcium levels. Besides the triggering role, calcium signaling modulates the precise amount and kinetics of vesicle release. Thus, it is a central question to understand the molecular machineries responsible for calcium sensing in exocytosis. Here we provide an overview of our...... current understanding of calcium sensing in neurotransmitter release and hormone secretion....

  4. Calcium fluoride

    International Nuclear Information System (INIS)

    King, C.W.; Nestor, O.H.

    1989-01-01

    A new process for producing large, single, oriented crystals of calcium fluoride (CaF 2 ) has been developed which overcomes the limitations of current growing methods. This process has been reduced to practice and has yielded oriented crystals 17.5 x 17.5 x 5 cm 3 . Currently nearing completion is a system for producing 35 x 35 x 7.5 cm 3 single crystals. A scale up to one-meter-square is considered feasible. This crystal growing process makes possible the fabrication of very large CaF 2 windows. Suitability for very high power lasers, however, requires attention to properties beyond mere size. A process to generate higher purity growth stock (starting material) was also developed. The additional purification of the growth stock contributes to lower bulk absorption, the absence of color centers and increased radiation hardness. Also identified were several specific impurities which correlate with radiation hardness. A correlation was found between color centers induced by laser radiation and ionizing radiation. Other CaF 2 crystal properties such as tensile strength, absorption and laser damage thresholds were studied and are discussed

  5. 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.

  6. Dynamics of the phase transitions in the system of nonequilibrium charge carriers in quantum-dimensional Si{sub 1−x}Ge{sub x}/Si structures

    Energy Technology Data Exchange (ETDEWEB)

    Bagaev, V. S.; Krivobok, V. S., E-mail: krivobok@lebedev.ru; Nikolaev, S. N.; Onishchenko, E. E.; Pruchkina, A. A.; Aminev, D. F.; Skorikov, M. L. [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation); Lobanov, D. N.; Novikov, A. V. [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation)

    2013-11-15

    The dynamics of the phase transition from an electron-hole plasma to an exciton gas is studied during pulsed excitation of heterostructures with Si{sub 1−x}Ge{sub x}/Si quantum wells. The scenario of the phase transition is shown to depend radically on the germanium content in the Si{sub 1−x}Ge{sub x} layer. The electron-hole system decomposes into a rarefied exciton and a dense plasma phases for quantum wells with a germanium content x = 3.5% in the time range 100–500 ns after an excitation pulse. In this case, the electron-hole plasma existing in quantum wells has all signs of an electron-hole liquid. A qualitatively different picture of the phase transition is observed for quantum wells with x = 9.5%, where no separation into phases with different electronic spectra is detected. The carrier recombination in the electron-hole plasma leads a gradual weakening of screening and the appearance of exciton states. For a germanium content of 5–7%, the scenario of the phase transition is complex: 20–250 ns after an excitation pulse, the properties of the electron-hole system are described in terms of a homogeneous electron-hole plasma, whereas its separation into an electron-hole liquid and an exciton gas is detected after 350 ns. It is shown that, for the electron-hole liquid to exist in quantum wells with x = 5–7% Ge, the exciton gas should have a substantially higher density than in quantum wells with x = 3.5% Ge. This finding agrees with a decrease in the depth of the local minimum of the electron-hole plasma energy with increasing germanium concentration in the SiGe layer. An increase in the density of the exciton gas coexisting with the electron-hole liquid is shown to enhance the role of multiparticle states, which are likely to be represented by trions T{sup +} and biexcitons, in the exciton gas.

  7. Mice deficient in carbonic anhydrase type 8 exhibit motor dysfunctions and abnormal calcium dynamics in the somatic region of cerebellar granule cells.

    Science.gov (United States)

    Lamont, Matthew G; Weber, John T

    2015-06-01

    The waddles (wdl) mouse is characterized by a namesake "side-to-side" waddling gait due to a homozygous mutation of the Car8 gene. This mutation results in non-functional copies of the protein carbonic anhydrase type 8. Rota-rod testing was conducted to characterize the wdl mutations' effect on motor output. Results indicated that younger homozygotes outperformed their older cohorts, an effect not seen in previous studies. Heterozygotes, which were thought to be free of motor impairment, displayed motor learning deficiencies when compared with wild type performance. Acute cerebellar slices were then utilized for fluorescent calcium imaging experiments, which revealed significant alterations in cerebellar granule cell somatic calcium signaling when exposed to glutamate. The contribution of GABAergic signaling to these alterations was also verified using bath application of bicuculline. Changes in somatic calcium signals were found to be applicable to an in vivo scenario by comparing group responses to electrical stimulation of afferent mossy fiber projections. Finally, intracellular calcium store function was also found to be altered by the wdl mutation when slices were treated with thapsigargin. These findings, taken together with previous work on the wdl mouse, indicate a widespread disruption in cerebellar circuitry hampering proper neuronal communication. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. A Study of Phosphorus and Calcium Dynamics in an Integrated Rainbow Trout and Spinach (Nores variety Aquaponic System with Different Crop Densities

    Directory of Open Access Journals (Sweden)

    Stefan Mihai Petrea

    2014-10-01

    Full Text Available The goal of this study is to quantify both calcium and phosphorus budgets for an integrated rainbow trout – spinach (Nores variety aquaponic system, where three crops densities were used (BH1 –59 crops/m2, BH2 – 48 crops/m2 and BH3 – 39 crops/m2 and a control variant. Fish were fed with two types of feed (41% and 50% protein, using 3 different feeding regimes. Total calcium and total phosphorus retention rates for each of the three tested spinach biomass densities were individually determined by water chemical and plant biochemical analysis. Also, the concentration of those two macroelements was determined from fish meat and fish faeces.  Significant differences (p<0.05 were recorded between fish faeces total phosphorus content and between total calcium and total phosphorus retention rates for each of the three variants of tested crops densities (significant higher at BH1 compared to BH3, p < 0.05. It is recommended that lower densities to be used for a better crop absorption of both calcium and phosphorus or a lower hydraulic flow regime and a better light intensity to be applied in case of the used integrated aquaponic system.

  9. "Non-equilibrium" block copolymer micelles with glassy cores: a predictive approach based on theory of equilibrium micelles.

    Science.gov (United States)

    Nagarajan, Ramanathan

    2015-07-01

    Micelles generated in water from most amphiphilic block copolymers are widely recognized to be non-equilibrium structures. Typically, the micelles are prepared by a kinetic process, first allowing molecular scale dissolution of the block copolymer in a common solvent that likes both the blocks and then gradually replacing the common solvent by water to promote the hydrophobic blocks to aggregate and create the micelles. The non-equilibrium nature of the micelle originates from the fact that dynamic exchange between the block copolymer molecules in the micelle and the singly dispersed block copolymer molecules in water is suppressed, because of the glassy nature of the core forming polymer block and/or its very large hydrophobicity. Although most amphiphilic block copolymers generate such non-equilibrium micelles, no theoretical approach to a priori predict the micelle characteristics currently exists. In this work, we propose a predictive approach for non-equilibrium micelles with glassy cores by applying the equilibrium theory of micelles in two steps. In the first, we calculate the properties of micelles formed in the mixed solvent while true equilibrium prevails, until the micelle core becomes glassy. In the second step, we freeze the micelle aggregation number at this glassy state and calculate the corona dimension from the equilibrium theory of micelles. The condition when the micelle core becomes glassy is independently determined from a statistical thermodynamic treatment of diluent effect on polymer glass transition temperature. The predictions based on this "non-equilibrium" model compare reasonably well with experimental data for polystyrene-polyethylene oxide diblock copolymer, which is the most extensively studied system in the literature. In contrast, the application of the equilibrium model to describe such a system significantly overpredicts the micelle core and corona dimensions and the aggregation number. The non-equilibrium model suggests ways to

  10. Calcium dynamics in the healing of tooth extraction sockets in mice evaluated using 45Ca-autoradiography and Electron Probe Micro Analysis

    International Nuclear Information System (INIS)

    Tanaka, Takeo

    2006-01-01

    The calcium distribution in tooth extraction sockets of mice was examined using 45-Calcium autoradiography (ARG) and Electron Probe Micro Analysis (EPMA). Mice were divided into 8 groups (n=8) according to the number of days (1, 2, 3, 4, 5, 7, 10, 20 respectively) after extraction. Frozen sections were taken from mice on each experimental day after injection of 45-Calcium (RI). The process of formation of new bone was observed using ARG. An ultimate analysis was performed by EPMA. Histological analysis was performed with toluidine blue- and alizarin red S-staining. In toluidine blue-staining, an osteoblast was found along the socket wall at 4 days and non-calcified periodontal ligament was recognized until 5 days after extraction. In alizarin red S-staining, new bone was recognized separated from the socket wall at 4 days after extraction. 45 Ca-labeling was detected strongly in the periosteum of the mandible, the surface of cement and periodontal ligament in control animals. 45 Ca-labeling was moved from the bottom to the top of the tooth extraction socket during the period from 1 to 5 days after extraction, but in the periodontal ligament lower than in the granulation tissue. 45 Ca-labeling was detected in the socket at 7, 10 and 20 days. At 4 days, calcium phosphate was observed in the central portion of the socket using EPMA. 45 Ca-labeling showed deposition of calcium phosphate for alveolar bone and new bone. These results suggest that the granulation tissue may be involved in the initial calcification in the tooth extraction socket and lead to the formation of new bone in it. (author)

  11. Non-equilibrium effects in the plasmas

    International Nuclear Information System (INIS)

    Einfeld, D.

    1975-01-01

    Radial dependences of non-equilibrium effects of a He plasma were studied in a wall-stabilized short-time discharge. The electron density (nsub(e) = 2.5 x 10 22 m -3 ), the electron temperature and the equilibrium shift were determined by calculations of the continuum beam density and the beam densities of one He-I and one He-II line, respectively. In the discharge axis, the overpopulation factors of the ground state of He-I and He-II are about 75. As the distance to the axis increases, they increase for He-I and decrease for He-II. Except for the usual errors of measurement, the overpopulation factors found here correspond to those calculated from the balance equations (Drawin). (orig./AK) [de

  12. Non-equilibrium in flowing atmospheric plasmas

    International Nuclear Information System (INIS)

    Haas, J.C.M. de.

    1986-01-01

    This thesis deals with the fundamental aspects of two different plasmas applied in technological processes. The first one is the cesium seeded argon plasma in a closed cycle Magnetohydrodynamic (MHD) generator, the second is the thermal argon plasma in a cascade arc with an imposed flow. In Chapter 2 the influence of non-equilibrium on the mass and energy balances of a plasma is worked out. The general theory presented there can be applied to both the plasma in an MHD generator and to the cascade arc with imposed flow. Introductions to these plasmas are given in the Chapters 3 and 6 respectively. These chapters are both followed by two chapters which treat the theoretical and the experimental investigations. The results are summarized in Chapter 9. (Auth.)

  13. Landau superfluids as nonequilibrium stationary states

    International Nuclear Information System (INIS)

    Wreszinski, Walter F.

    2015-01-01

    We define a superfluid state to be a nonequilibrium stationary state (NESS), which, at zero temperature, satisfies certain metastability conditions, which physically express that there should be a sufficiently small energy-momentum transfer between the particles of the fluid and the surroundings (e.g., pipe). It is shown that two models, the Girardeau model and the Huang-Yang-Luttinger (HYL) model, describe superfluids in this sense and, moreover, that, in the case of the HYL model, the metastability condition is directly related to Nozières’ conjecture that, due to the repulsive interaction, the condensate does not suffer fragmentation into two (or more) parts, thereby assuring its quantum coherence. The models are rigorous examples of NESS in which the system is not finite, but rather a many-body system

  14. Non-equilibrium quantum heat machines

    Science.gov (United States)

    Alicki, Robert; Gelbwaser-Klimovsky, David

    2015-11-01

    Standard heat machines (engine, heat pump, refrigerator) are composed of a system (working fluid) coupled to at least two equilibrium baths at different temperatures and periodically driven by an external device (piston or rotor) sometimes called the work reservoir. The aim of this paper is to go beyond this scheme by considering environments which are stationary but cannot be decomposed into a few baths at thermal equilibrium. Such situations are important, for example in solar cells, chemical machines in biology, various realizations of laser cooling or nanoscopic machines driven by laser radiation. We classify non-equilibrium baths depending on their thermodynamic behavior and show that the efficiency of heat machines powered by them is limited by the generalized Carnot bound.

  15. Magnetic polarons in a nonequilibrium polariton condensate

    Science.gov (United States)

    Mietki, Paweł; Matuszewski, Michał

    2017-09-01

    We consider a condensate of exciton polaritons in a diluted magnetic semiconductor microcavity. Such a system may exhibit magnetic self-trapping in the case of sufficiently strong coupling between polaritons and magnetic ions embedded in the semiconductor. We investigate the effect of the nonequilibrium nature of exciton polaritons on the physics of the resulting self-trapped magnetic polarons. We find that multiple polarons can exist at the same time, and we derive a critical condition for self-trapping that is different from the one predicted previously in the equilibrium case. Using the Bogoliubov-de Gennes approximation, we calculate the excitation spectrum and provide a physical explanation in terms of the effective magnetic attraction between polaritons, mediated by the ion subsystem.

  16. Anomalous properties of hot dense nonequilibrium plasmas

    International Nuclear Information System (INIS)

    Ferrante, G; Zarcone, M; Uryupin, S A

    2005-01-01

    A concise overview of a number of anomalous properties of hot dense nonequilibrium plasmas is given. The possibility of quasistationary megagauss magnetic field generation due to Weibel instability is discussed for plasmas created in atom tunnel ionization. The collisionless absorption and reflection of a test electromagnetic wave normally impinging on the plasma with two-temperature bi-maxwellian electron velocity distribution function are studied. Due to the wave magnetic field influence on the electron kinetics in the skin layer the wave absorption and reflection significantly depend on the degree of the electron temperature anisotropy. The linearly polarized impinging wave during reflection transforms into an elliptically polarized one. The problem of transmission of an ultrashort laser pulse through a layer of dense plasma, formed as a result of ionization of a thin foil, is considered. It is shown that the strong photoelectron distribution anisotropy yields an anomalous penetration of the wave field through the foil

  17. Non-equilibrium quantum heat machines

    International Nuclear Information System (INIS)

    Alicki, Robert; Gelbwaser-Klimovsky, David

    2015-01-01

    Standard heat machines (engine, heat pump, refrigerator) are composed of a system (working fluid) coupled to at least two equilibrium baths at different temperatures and periodically driven by an external device (piston or rotor) sometimes called the work reservoir. The aim of this paper is to go beyond this scheme by considering environments which are stationary but cannot be decomposed into a few baths at thermal equilibrium. Such situations are important, for example in solar cells, chemical machines in biology, various realizations of laser cooling or nanoscopic machines driven by laser radiation. We classify non-equilibrium baths depending on their thermodynamic behavior and show that the efficiency of heat machines powered by them is limited by the generalized Carnot bound. (paper)

  18. MMS two-phase nonequilibrium pressurizer

    International Nuclear Information System (INIS)

    Oh, S.J.; Sursock, J.P.

    1987-01-01

    The pressurizer of a nuclear steam supply system establishes and maintains the nuclear plant primary loop pressure within the prescribed limit. It is a vertical cylindrical vessel which provides a water reserve and a steam surge chamber to accommodate coolant density changes during operation. To adjust the pressure to a desired value, electric heaters are provided in its lower section and the spray nozzles are provided in its upper section. Also, to protect against the buildup of the excess pressure, the pressurizer has two different types of relief valves, i.e., power operated relief valve and the safety relief valve. The pressurizer model implemented to the MMS is described in detail. In particular, the handling of the nonequilibrium condition, surgeline CCFL (Counter-current Flooding Limitation), and the level tracking model are described in detail. Next, the simulation of the Shippingport pressurizer load drop test is reported

  19. A nonequilibrium model for reactive contaminant transport through fractured porous media: Model development and semianalytical solution

    Science.gov (United States)

    Joshi, Nitin; Ojha, C. S. P.; Sharma, P. K.

    2012-10-01

    In this study a conceptual model that accounts for the effects of nonequilibrium contaminant transport in a fractured porous media is developed. Present model accounts for both physical and sorption nonequilibrium. Analytical solution was developed using the Laplace transform technique, which was then numerically inverted to obtain solute concentration in the fracture matrix system. The semianalytical solution developed here can incorporate both semi-infinite and finite fracture matrix extent. In addition, the model can account for flexible boundary conditions and nonzero initial condition in the fracture matrix system. The present semianalytical solution was validated against the existing analytical solutions for the fracture matrix system. In order to differentiate between various sorption/transport mechanism different cases of sorption and mass transfer were analyzed by comparing the breakthrough curves and temporal moments. It was found that significant differences in the signature of sorption and mass transfer exists. Applicability of the developed model was evaluated by simulating the published experimental data of Calcium and Strontium transport in a single fracture. The present model simulated the experimental data reasonably well in comparison to the model based on equilibrium sorption assumption in fracture matrix system, and multi rate mass transfer model.

  20. Non-equilibrium synergistic effects in atmospheric pressure plasmas.

    Science.gov (United States)

    Guo, Heng; Zhang, Xiao-Ning; Chen, Jian; Li, He-Ping; Ostrikov, Kostya Ken

    2018-03-19

    Non-equilibrium is one of the important features of an atmospheric gas discharge plasma. It involves complicated physical-chemical processes and plays a key role in various actual plasma processing. In this report, a novel complete non-equilibrium model is developed to reveal the non-equilibrium synergistic effects for the atmospheric-pressure low-temperature plasmas (AP-LTPs). It combines a thermal-chemical non-equilibrium fluid model for the quasi-neutral plasma region and a simplified sheath model for the electrode sheath region. The free-burning argon arc is selected as a model system because both the electrical-thermal-chemical equilibrium and non-equilibrium regions are involved simultaneously in this arc plasma system. The modeling results indicate for the first time that it is the strong and synergistic interactions among the mass, momentum and energy transfer processes that determine the self-consistent non-equilibrium characteristics of the AP-LTPs. An energy transfer process related to the non-uniform spatial distributions of the electron-to-heavy-particle temperature ratio has also been discovered for the first time. It has a significant influence for self-consistently predicting the transition region between the "hot" and "cold" equilibrium regions of an AP-LTP system. The modeling results would provide an instructive guidance for predicting and possibly controlling the non-equilibrium particle-energy transportation process in various AP-LTPs in future.

  1. Nanoscale hotspots due to nonequilibrium thermal transport

    International Nuclear Information System (INIS)

    Sinha, Sanjiv; Goodson, Kenneth E.

    2004-01-01

    Recent experimental and modeling efforts have been directed towards the issue of temperature localization and hotspot formation in the vicinity of nanoscale heat generating devices. The nonequilibrium transport conditions which develop around these nanoscale devices results in elevated temperatures near the heat source which can not be predicted by continuum diffusion theory. Efforts to determine the severity of this temperature localization phenomena in silicon devices near and above room temperature are of technological importance to the development of microelectronics and other nanotechnologies. In this work, we have developed a new modeling tool in order to explore the magnitude of the additional thermal resistance which forms around nanoscale hotspots from temperatures of 100-1000K. The models are based on a two fluid approximation in which thermal energy is transferred between ''stationary'' optical phonons and fast propagating acoustic phonon modes. The results of the model have shown excellent agreement with experimental results of localized hotspots in silicon at lower temperatures. The model predicts that the effect of added thermal resistance due to the nonequilibrium phonon distribution is greatest at lower temperatures, but is maintained out to temperatures of 1000K. The resistance predicted by the numerical code can be easily integrated with continuum models in order to predict the temperature distribution around nanoscale heat sources with improved accuracy. Additional research efforts also focused on the measurements of the thermal resistance of silicon thin films at higher temperatures, with a focus on polycrystalline silicon. This work was intended to provide much needed experimental data on the thermal transport properties for micro and nanoscale devices built with this material. Initial experiments have shown that the exposure of polycrystalline silicon to high temperatures may induce recrystallization and radically increase the thermal

  2. TIME DEPENDENT NONEQUILIBRIUM IONIZATION OF TRANSITION REGION LINES OBSERVED WITH IRIS

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Sykora, Juan; Pontieu, Bart De; Hansteen, Viggo H. [Lockheed Martin Solar and Astrophysics Laboratory, Palo Alto, CA 94304 (United States); Gudiksen, Boris, E-mail: j.m.sykora@astro.uio.no [Institute of Theoretical Astrophysics, University of Oslo, P.O. Box 1029 Blindern, NO-0315 Oslo (Norway)

    2016-01-20

    The properties of nonstatistical equilibrium ionization of silicon and oxygen ions are analyzed in this work. We focus on five solar targets (quiet Sun; coronal hole; plage; quiescent active region, AR; and flaring AR) as observed with the Interface Region Imaging Spectrograph (IRIS). IRIS is best suited for this work owing to the high cadence (up to 0.5 s), high spatial resolution (up to 0.″32), and high signal-to-noise ratios for O iv λ1401 and Si iv λ1402. We find that the observed intensity ratio between lines of three times ionized silicon and oxygen ions depends on their total intensity and that this correlation varies depending on the region observed (quiet Sun, coronal holes, plage, or active regions) and on the specific observational objects present (spicules, dynamic loops, jets, microflares, or umbra). In order to interpret the observations, we compare them with synthetic profiles taken from 2D self-consistent radiative MHD simulations of the solar atmosphere, where the statistical equilibrium or nonequilibrium treatment of silicon and oxygen is applied. These synthetic observations show vaguely similar correlations to those in the observations, i.e., between the intensity ratios and their intensities, but only in the nonequilibrium case do we find that (some of) the observations can be reproduced. We conclude that these lines are formed out of statistical equilibrium. We use our time-dependent nonequilibrium ionization simulations to describe the physical mechanisms behind these observed properties.

  3. Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics

    International Nuclear Information System (INIS)

    Ge Hao; Qian Min; Qian Hong

    2012-01-01

    The mathematical theory of nonequilibrium steady state (NESS) has a natural application in open biochemical systems which have sustained source(s) and sink(s) in terms of a difference in their chemical potentials. After a brief introduction in Section , in Part II of this review, we present the widely studied biochemical enzyme kinetics, the workhorse of biochemical dynamic modeling, in terms of the theory of NESS (Section ). We then show that several phenomena in enzyme kinetics, including a newly discovered activation–inhibition switching (Section ) and the well-known non-Michaelis–Menten-cooperativity (Section ) and kinetic proofreading (Section ), are all consequences of the NESS of driven biochemical systems with associated cycle fluxes. Section is focused on nonlinear and nonequilibrium systems of biochemical reactions. We use the phosphorylation–dephosphorylation cycle (PdPC), one of the most important biochemical signaling networks, as an example (Section ). It starts with a brief introduction of the Delbrück–Gillespie process approach to mesoscopic biochemical kinetics (Sections ). We shall discuss the zeroth-order ultrasensitivity of PdPC in terms of a new concept — the temporal cooperativity (Sections ), as well as PdPC with feedback which leads to biochemical nonlinear bistability (Section ). Also, both are nonequilibrium phenomena. PdPC with a nonlinear feedback is kinetically isomorphic to a self-regulating gene expression network, hence the theory of NESS discussed here could have wide applications to many other biochemical systems.

  4. Coherent anti-Stokes Raman scattering and spontaneous Raman scattering diagnostics of nonequilibrium plasmas and flows

    Science.gov (United States)

    Lempert, Walter R.; Adamovich, Igor V.

    2014-10-01

    The paper provides an overview of the use of coherent anti-Stokes Raman scattering (CARS) and spontaneous Raman scattering for diagnostics of low-temperature nonequilibrium plasmas and nonequilibrium high-enthalpy flows. A brief review of the theoretical background of CARS, four-wave mixing and Raman scattering, as well as a discussion of experimental techniques and data reduction, are included. The experimental results reviewed include measurements of vibrational level populations, rotational/translational temperature, electric fields in a quasi-steady-state and transient molecular plasmas and afterglow, in nonequilibrium expansion flows, and behind strong shock waves. Insight into the kinetics of vibrational energy transfer, energy thermalization mechanisms and dynamics of the pulse discharge development, provided by these experiments, is discussed. Availability of short pulse duration, high peak power lasers, as well as broadband dye lasers, makes possible the use of these diagnostics at relatively low pressures, potentially with a sub-nanosecond time resolution, as well as obtaining single laser shot, high signal-to-noise spectra at higher pressures. Possibilities for the development of single-shot 2D CARS imaging and spectroscopy, using picosecond and femtosecond lasers, as well as novel phase matching and detection techniques, are discussed.

  5. Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-01-01

    In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables--the medium, the quantum field, and the atom's internal degrees of freedom, in that order--to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom's internal degrees of freedom results in an equation of motion for the atom's center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom's motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.

  6. Mechanochemically driven nonequilibrium processes in MNH2-CaH2 systems (M = Li or Na)

    International Nuclear Information System (INIS)

    Dolotko, Oleksandr; Zhang Haiqiao; Li Sa; Jena, Puru; Pecharsky, Vitalij

    2010-01-01

    Mechanochemical transformations of lithium and sodium amides with calcium hydride have been investigated using gas volumetric analysis, X-ray powder diffraction, and residual gas analysis. The overall mechanochemical transformations are equimolar, and they proceed as the following solid state reaction: MNH 2 + CaH 2 → CaNH + MH + H 2 , where M = Li or Na. The transformation kinetics of the lithium containing system is markedly faster compared to the system with sodium. The difference in the rates of solid state transformations, and therefore, in hydrogen release kinetics can be explained by difference in mobility of lithium and sodium atoms. Total energies and enthalpies of formation for different reaction products during the dehydrogenation of CaH 2 -MNH 2 mixtures were calculated using density functional theory. Compared to thermochemical transformations, which proceed in accordance with thermodynamic equilibrium, reactions induced by mechanical energy drive the MNH 2 -CaH 2 systems to nonequilibrium configurations with different final products.

  7. Foundations of modelling of nonequilibrium low-temperature plasmas

    Science.gov (United States)

    Alves, L. L.; Bogaerts, A.; Guerra, V.; Turner, M. M.

    2018-02-01

    This work explains the need for plasma models, introduces arguments for choosing the type of model that better fits the purpose of each study, and presents the basics of the most common nonequilibrium low-temperature plasma models and the information available from each one, along with an extensive list of references for complementary in-depth reading. The paper presents the following models, organised according to the level of multi-dimensional description of the plasma: kinetic models, based on either a statistical particle-in-cell/Monte-Carlo approach or the solution to the Boltzmann equation (in the latter case, special focus is given to the description of the electron kinetics); multi-fluid models, based on the solution to the hydrodynamic equations; global (spatially-average) models, based on the solution to the particle and energy rate-balance equations for the main plasma species, usually including a very complete reaction chemistry; mesoscopic models for plasma-surface interaction, adopting either a deterministic approach or a stochastic dynamical Monte-Carlo approach. For each plasma model, the paper puts forward the physics context, introduces the fundamental equations, presents advantages and limitations, also from a numerical perspective, and illustrates its application with some examples. Whenever pertinent, the interconnection between models is also discussed, in view of multi-scale hybrid approaches.

  8. Manifest and Subtle Cyclic Behavior in Nonequilibrium Steady States

    International Nuclear Information System (INIS)

    Zia, R K P; Weiss, Jeffrey B; Mandal, Dibyendu; Fox-Kemper, Baylor

    2016-01-01

    Many interesting phenomena in nature are described by stochastic processes with irreversible dynamics. To model these phenomena, we focus on a master equation or a Fokker-Planck equation with rates which violate detailed balance. When the system settles in a stationary state, it will be a nonequilibrium steady state (NESS), with time independent probability distribution as well as persistent probability current loops. The observable consequences of the latter are explored. In particular, cyclic behavior of some form must be present: some are prominent and manifest, while others are more obscure and subtle. We present a theoretical framework to analyze such properties, introducing the notion of “probability angular momentum” and its distribution. Using several examples, we illustrate the manifest and subtle categories and how best to distinguish between them. These techniques can be applied to reveal the NESS nature of a wide range of systems in a large variety of areas. We illustrate with one application: variability of ocean heat content in our climate system. (paper)

  9. A calculational scheme for nonequilibrium quantum field system

    International Nuclear Information System (INIS)

    Yamanaka, Y.

    1991-01-01

    A new calculational scheme is presented for interacting nonequi-librium time dependent quantum field systems within the framework of thermo field dynamics (TFD), taking account of the fact that the thermal vacuum should go through many inequivalent state vector spaces. A para-meter parametrizing various state vector spaces has to be introduced and plays a role of new time-variable. Thus we have double-time TFD. The 2 requirements in this double-time TFD are imposed to establish a quasi-particle picture to get an attainable scheme of perturbative calculation : the existence of the spectral representation for the full propagator and the diagonalization of the quasi-particle Hamiltonian. The 1st condition turns out to amount to the existence of local-time tempera-ture. The 2nd condition leads to the master equation for the number density. This formalism is applied to high-energy heavy ion collision process. The very fundamental question is then how the thermodynamical properties such as heat and temperature appear in such an isolated system. This double-time TFD, suitable for isolated thermal systems of quantum fields, can handle the situation from the beginning of the process. (author). 24 refs.; 1 fig

  10. Examples of equilibrium and non-equilibrium behavior in evolutionary systems

    Science.gov (United States)

    Soulier, Arne

    With this thesis, we want to shed some light into the darkness of our understanding of simply defined statistical mechanics systems and the surprisingly complex dynamical behavior they exhibit. We will do so by presenting in turn one equilibrium and then one non-equilibrium system with evolutionary dynamics. In part 1, we will present the seceder-model, a newly developed system that cannot equilibrate. We will then study several properties of the system and obtain an idea of the richness of the dynamics of the seceder model, which is particular impressive given the minimal amount of modeling necessary in its setup. In part 2, we will present extensions to the directed polymer in random media problem on a hypercube and its connection to the Eigen model of evolution. Our main interest will be the influence of time-dependent and time-independent changes in the fitness landscape viewed by an evolving population. This part contains the equilibrium dynamics. The stochastic models and the topic of evolution and non-equilibrium in general will allow us to point out similarities to the various lines of thought in game theory.

  11. Non-equilibrium hydrogen ionization in 2D simulations of the solar atmosphere

    Science.gov (United States)

    Leenaarts, J.; Carlsson, M.; Hansteen, V.; Rutten, R. J.

    2007-10-01

    Context: The ionization of hydrogen in the solar chromosphere and transition region does not obey LTE or instantaneous statistical equilibrium because the timescale is long compared with important hydrodynamical timescales, especially of magneto-acoustic shocks. Since the pressure, temperature, and electron density depend sensitively on hydrogen ionization, numerical simulation of the solar atmosphere requires non-equilibrium treatment of all pertinent hydrogen transitions. The same holds for any diagnostic application employing hydrogen lines. Aims: To demonstrate the importance and to quantify the effects of non-equilibrium hydrogen ionization, both on the dynamical structure of the solar atmosphere and on hydrogen line formation, in particular Hα. Methods: We implement an algorithm to compute non-equilibrium hydrogen ionization and its coupling into the MHD equations within an existing radiation MHD code, and perform a two-dimensional simulation of the solar atmosphere from the convection zone to the corona. Results: Analysis of the simulation results and comparison to a companion simulation assuming LTE shows that: a) non-equilibrium computation delivers much smaller variations of the chromospheric hydrogen ionization than for LTE. The ionization is smaller within shocks but subsequently remains high in the cool intershock phases. As a result, the chromospheric temperature variations are much larger than for LTE because in non-equilibrium, hydrogen ionization is a less effective internal energy buffer. The actual shock temperatures are therefore higher and the intershock temperatures lower. b) The chromospheric populations of the hydrogen n = 2 level, which governs the opacity of Hα, are coupled to the ion populations. They are set by the high temperature in shocks and subsequently remain high in the cool intershock phases. c) The temperature structure and the hydrogen level populations differ much between the chromosphere above photospheric magnetic elements

  12. Voltage-gated calcium flux mediates Escherichia coli mechanosensation.

    Science.gov (United States)

    Bruni, Giancarlo N; Weekley, R Andrew; Dodd, Benjamin J T; Kralj, Joel M

    2017-08-29

    Electrically excitable cells harness voltage-coupled calcium influx to transmit intracellular signals, typically studied in neurons and cardiomyocytes. Despite intense study in higher organisms, investigations of voltage and calcium signaling in bacteria have lagged due to their small size and a lack of sensitive tools. Only recently were bacteria shown to modulate their membrane potential on the timescale of seconds, and little is known about the downstream effects from this modulation. In this paper, we report on the effects of electrophysiology in individual bacteria. A genetically encoded calcium sensor expressed in Escherichia coli revealed calcium transients in single cells. A fusion sensor that simultaneously reports voltage and calcium indicated that calcium influx is induced by voltage depolarizations, similar to metazoan action potentials. Cytoplasmic calcium levels and transients increased upon mechanical stimulation with a hydrogel, and single cells altered protein concentrations dependent on the mechanical environment. Blocking voltage and calcium flux altered mechanically induced changes in protein concentration, while inducing calcium flux reproduced these changes. Thus, voltage and calcium relay a bacterial sense of touch and alter cellular lifestyle. Although the calcium effectors remain unknown, these data open a host of new questions about E. coli , including the identity of the underlying molecular players, as well as other signals conveyed by voltage and calcium. These data also provide evidence that dynamic voltage and calcium exists as a signaling modality in the oldest domain of life, and therefore studying electrophysiology beyond canonical electrically excitable cells could yield exciting new findings.

  13. Rate of tunneling nonequilibrium quasiparticles in superconducting qubits

    International Nuclear Information System (INIS)

    Ansari, Mohammad H

    2015-01-01

    In superconducting qubits the lifetime of quantum states cannot be prolonged arbitrarily by decreasing temperature. At low temperature quasiparticles tunneling between the electromagnetic environment and superconducting islands takes the condensate state out of equilibrium due to charge imbalance. We obtain the tunneling rate from a phenomenological model of non-equilibrium, where nonequilibrium quasiparticle tunnelling stimulates a temperature-dependent chemical potential shift in the superconductor. As a result we obtain a non-monotonic behavior for relaxation rate as a function of temperature. Depending on the fabrication parameters for some qubits, the lowest tunneling rate of nonequilibrium quasiparticles can take place only near the onset temperature below which nonequilibrium quasiparticles dominate over equilibrium one. Our theory also indicates that such tunnelings can influence the probability of transitions in qubits through a coupling to the zero-point energy of phase fluctuations. (paper)

  14. Nonequilibrium constitutive models for RELAP5/MOD2

    International Nuclear Information System (INIS)

    Lin, J.C.; Trapp, J.A.; Riemke, R.A.; Ransom, V.H.

    1983-01-01

    RELAP5/MOD2 is a new version of RELAP5 containing improved modeling features that provide a generic pressurized-water transient simulation capability. In particular, the nonequilibrium modeling capability has been generalized to include conditions that occur in operational transients including repressurization and emergency-feed-water injection with loss-of-coolant accidents. The improvements include addition of a second energy equation to the hydrodynamic model, addition of nonequilibrium heat-transfer models, and the associated nonequilibrium vapor-generation models. The objective of this paper is to describe these models and to report the developmental assessment results obtained from similar of several separate effects experiments. The assessment shows that RELAP5 calculated results are in good agreement with data and the nonequilibrium phenomena are properly modeled

  15. Non-Equilibrium Thermodynamics of Self-Replicating Protocells

    DEFF Research Database (Denmark)

    Fellermann, Harold; Corominas-Murtra, Bernat; Hansen, Per Lyngs

    2018-01-01

    We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth...... and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non......-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology....

  16. Equilibrium and non-equilibrium phenomena in arcs and torches

    NARCIS (Netherlands)

    Mullen, van der J.J.A.M.

    2000-01-01

    A general treatment of non-equilibrium plasma aspects is obtained by relating transport fluxes to equilibrium restoring processes in so-called disturbed Bilateral Relations. The (non) equilibrium stage of a small microwave induced plasma serves as case study.

  17. Electrolytes: transport properties and non-equilibrium thermodynamics

    International Nuclear Information System (INIS)

    Miller, D.G.

    1980-12-01

    This paper presents a review on the application of non-equilibrium thermodynamics to transport in electrolyte solutions, and some recent experimental work and results for mutual diffusion in electrolyte solutions

  18. Foundations of atmospheric pressure non-equilibrium plasmas

    Science.gov (United States)

    Bruggeman, Peter J.; Iza, Felipe; Brandenburg, Ronny

    2017-12-01

    Non-equilibrium plasmas have been intensively studied over the past century in the context of material processing, environmental remediation, ozone generation, excimer lamps and plasma display panels. Research on atmospheric pressure non-equilibrium plasmas intensified over the last two decades leading to a large variety of plasma sources that have been developed for an extended application range including chemical conversion, medicine, chemical analysis and disinfection. The fundamental understanding of these discharges is emerging but there remain a lot of unexplained phenomena in these intrinsically complex plasmas. The properties of non-equilibrium plasmas at atmospheric pressure span over a huge range of electron densities as well as heavy particle and electron temperatures. This paper provides an overview of the key underlying processes that are important for the generation and stabilization of atmospheric pressure non-equilibrium plasmas. The unique physical and chemical properties of theses discharges are also summarized.

  19. Calcium and magnesium determination

    International Nuclear Information System (INIS)

    Bhattacharya, S.K.

    1982-01-01

    The roles of calcium and magnesium in human health and disease have been extensively studied. Calcium and magnesium have been determined in biological specimens by atomic absorption spectroscopy using stiochiometric nitrous oxide-acetylene flame

  20. Fenoprofen calcium overdose

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/002649.htm Fenoprofen calcium overdose To use the sharing features on this page, please enable JavaScript. Fenoprofen calcium is a type of medicine called a nonsteroidal ...

  1. Calcium channel blocker overdose

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/002580.htm Calcium-channel blocker overdose To use the sharing features on this page, please enable JavaScript. Calcium-channel blockers are a type of medicine used ...

  2. Dynamics of mesoscopic systems: Non-equilibrium Green's functions approach

    Czech Academy of Sciences Publication Activity Database

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

    2010-01-01

    Roč. 42, č. 3 (2010), s. 525-538 ISSN 1386-9477 R&D Projects: GA ČR GA202/08/0361 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z10100521 Keywords : mesoscopic systems * NGF * initial condition * correlations * Ward identities * transients Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.304, year: 2010

  3. Universal Nonequilibrium Signatures of Majorana Zero Modes in Quench Dynamics

    Directory of Open Access Journals (Sweden)

    R. Vasseur

    2014-10-01

    Full Text Available The quantum evolution that occurs after a metallic lead is suddenly connected to an electron system contains information about the excitation spectrum of the combined system. We exploit this type of “quantum quench” to probe the presence of Majorana fermions at the ends of a topological superconducting wire. We obtain an algebraically decaying overlap (Loschmidt echo L(t=|⟨ψ(0|ψ(t⟩|^{2}∼t^{-α} for large times after the quench, with a universal critical exponent α=1/4 that is found to be remarkably robust against details of the setup, such as interactions in the normal lead, the existence of additional lead channels, or the presence of bound levels between the lead and the superconductor. As in recent quantum-dot experiments, this exponent could be measured by optical absorption, offering a new signature of Majorana zero modes that is distinct from interferometry and tunneling spectroscopy.

  4. Nonequilibrium carrier dynamics in transition metal dichalcogenide semiconductors

    Science.gov (United States)

    Steinhoff, A.; Florian, M.; Rösner, M.; Lorke, M.; Wehling, T. O.; Gies, C.; Jahnke, F.

    2016-09-01

    When exploring new materials for their potential in (opto)electronic device applications, it is important to understand the role of various carrier interaction and scattering processes. In atomically thin transition metal dichalcogenide semiconductors, the Coulomb interaction is known to be much stronger than in quantum wells of conventional semiconductors like GaAs, as witnessed by the 50 times larger exciton binding energy. The question arises, whether this directly translates into equivalently faster carrier-carrier Coulomb scattering of excited carriers. Here we show that a combination of ab initio band-structure and many-body theory predicts Coulomb-mediated carrier relaxation on a sub-100 fs time scale for a wide range of excitation densities, which is less than an order of magnitude faster than in quantum wells.

  5. Density-functional method for nonequilibrium electron transport

    DEFF Research Database (Denmark)

    Brandbyge, Mads; Mozos, J.L.; Ordejon, P.

    2002-01-01

    the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme...... wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects....

  6. Calcium and Mitosis

    Science.gov (United States)

    Hepler, P.

    1983-01-01

    Although the mechanism of calcium regulation is not understood, there is evidence that calcium plays a role in mitosis. Experiments conducted show that: (1) the spindle apparatus contains a highly developed membrane system that has many characteristics of sarcoplasmic reticulum of muscle; (2) this membrane system contains calcium; and (3) there are ionic fluxes occurring during mitosis which can be seen by a variety of fluorescence probes. Whether the process of mitosis can be modulated by experimentally modulating calcium is discussed.

  7. Gas-kinetic unified algorithm for hypersonic flows covering various flow regimes solving Boltzmann model equation in nonequilibrium effect

    International Nuclear Information System (INIS)

    Li, Zhihui; Ma, Qiang; Wu, Junlin; Jiang, Xinyu; Zhang, Hanxin

    2014-01-01

    Based on the Gas-Kinetic Unified Algorithm (GKUA) directly solving the Boltzmann model equation, the effect of rotational non-equilibrium is investigated recurring to the kinetic Rykov model with relaxation property of rotational degrees of freedom. The spin movement of diatomic molecule is described by moment of inertia, and the conservation of total angle momentum is taken as a new Boltzmann collision invariant. The molecular velocity distribution function is integrated by the weight factor on the internal energy, and the closed system of two kinetic controlling equations is obtained with inelastic and elastic collisions. The optimization selection technique of discrete velocity ordinate points and numerical quadrature rules for macroscopic flow variables with dynamic updating evolvement are developed to simulate hypersonic flows, and the gas-kinetic numerical scheme is constructed to capture the time evolution of the discretized velocity distribution functions. The gas-kinetic boundary conditions in thermodynamic non-equilibrium and numerical procedures are studied and implemented by directly acting on the velocity distribution function, and then the unified algorithm of Boltzmann model equation involving non-equilibrium effect is presented for the whole range of flow regimes. The hypersonic flows involving non-equilibrium effect are numerically simulated including the inner flows of shock wave structures in nitrogen with different Mach numbers of 1.5-Ma-25, the planar ramp flow with the whole range of Knudsen numbers of 0.0009-Kn-10 and the three-dimensional re-entering flows around tine double-cone body

  8. Non-equilibrium phenomena in confined soft matter irreversible adsorption, physical aging and glass transition at the nanoscale

    CERN Document Server

    2015-01-01

    This book presents cutting-edge experimental and computational results and provides comprehensive coverage on the impact of non-equilibrium structure and dynamics on the properties of soft matter confined to the nanoscale. The book is organized into three main sections: ·         Equilibration and physical aging: by treating non-equilibrium phenomena with the formal methodology of statistical physics in bulk, the analysis of the kinetics of equilibration sheds new light on the physical origin of the non-equilibrium character of thin polymer films. Both the impact of sample preparation and that of interfacial interactions are analyzed using a large set of experiments. A historical overview of the investigation of the non-equilibrium character of thin polymer films is also presented. Furthermore, the discussion focuses on how interfaces and geometrical confinement perturb the pathways and kinetics of equilibrations of soft glasses (a process of tremendous technological interest). ·         Irr...

  9. Self-organization of dissipative and coherent vortex structures in non-equilibrium magnetized two-dimensional plasmas

    International Nuclear Information System (INIS)

    Bystrenko, O; Bystrenko, T

    2010-01-01

    The properties of non-equilibrium magnetized plasmas confined in planar geometry are studied on the basis of first-principle microscopic Langevin dynamics computer simulations. The non-equilibrium state of plasmas is maintained due to the recombination and generation of charges. The intrinsic microscopic structure of non-equilibrium steady-state magnetized plasmas, in particular the inter-particle correlations and self-organization of vortex structures, are examined. The simulations have been performed for a wide range of parameters including strong plasma coupling, high charge recombination and generation rates and intense magnetic field. As is shown in simulations, the non-equilibrium recombination and generation processes trigger the formation of ordered dissipative or coherent drift vortex states in 2D plasmas with distinctly spatially separated components, which are far from thermal equilibrium. This is evident from the unusual properties of binary distributions and behavior of the Coulomb energy of the system, which turn out to be quite different from the ones typical for the equilibrium state of plasmas under the same conditions.

  10. Role of non-equilibrium conformations on driven polymer translocation.

    Science.gov (United States)

    Katkar, H H; Muthukumar, M

    2018-01-14

    One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/N K , is longer than the relaxation time τ 0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations. We have studied the role of initial conformations of a polyelectrolyte chain (which were artificially generated with a flow field) on the kinetics of its translocation across a nanopore under the action of an externally applied transmembrane voltage V (in the absence of the initial flow field). Stretched (out-of-equilibrium) polyelectrolyte chain conformations are deliberately and systematically generated and used as initial conformations in translocation simulations. Independent simulations are performed to study the relaxation behavior of these stretched chains, and a comparison is made between the relaxation time scale and the mean translocation time (⟨τ⟩). For such artificially stretched initial states, ⟨τ⟩/N K polymers including single stranded DNA (ssDNA), double stranded DNA (dsDNA), and synthetic polymers. Even when these data are rescaled assuming a constant effective velocity of translocation, it is found that for flexible (ssDNA and synthetic) polymers with N K Kuhn segments, the condition ⟨τ⟩/N K polymers such as ssDNA, a crossover from quasi-equilibrium to non-equilibrium behavior would occur at N K ∼ O(1000).

  11. Achieving Radiation Tolerance through Non-Equilibrium Grain Boundary Structures.

    Science.gov (United States)

    Vetterick, Gregory A; Gruber, Jacob; Suri, Pranav K; Baldwin, Jon K; Kirk, Marquis A; Baldo, Pete; Wang, Yong Q; Misra, Amit; Tucker, Garritt J; Taheri, Mitra L

    2017-09-25

    Many methods used to produce nanocrystalline (NC) materials leave behind non-equilibrium grain boundaries (GBs) containing excess free volume and higher energy than their equilibrium counterparts with identical 5 degrees of freedom. Since non-equilibrium GBs have increased amounts of both strain and free volume, these boundaries may act as more efficient sinks for the excess interstitials and vacancies produced in a material under irradiation as compared to equilibrium GBs. The relative sink strengths of equilibrium and non-equilibrium GBs were explored by comparing the behavior of annealed (equilibrium) and as-deposited (non-equilibrium) NC iron films on irradiation. These results were coupled with atomistic simulations to better reveal the underlying processes occurring on timescales too short to capture using in situ TEM. After irradiation, NC iron with non-equilibrium GBs contains both a smaller number density of defect clusters and a smaller average defect cluster size. Simulations showed that excess free volume contribute to a decreased survival rate of point defects in cascades occurring adjacent to the GB and that these boundaries undergo less dramatic changes in structure upon irradiation. These results suggest that non-equilibrium GBs act as more efficient sinks for defects and could be utilized to create more radiation tolerant materials in future.

  12. Microcavity quantum-dot systems for non-equilibrium Bose-Einstein condensation

    International Nuclear Information System (INIS)

    Piper, I M; Ediger, M; Wilson, A M; Wu, Y; Phillips, R T; Eastham, P R; Hugues, M; Hopkinson, M

    2010-01-01

    We review the practical conditions required to achieve a non-equilibrium BEC driven by quantum dynamics in a system comprising a microcavity field mode and a distribution of localised two-level systems driven to a step-like population inversion profile. A candidate system based on eight 3.8nm layers of In 0.23 Ga 0.77 As in GaAs shows promising characteristics with regard to the total dipole strength which can be coupled to the field mode.

  13. Microcavity quantum-dot systems for non-equilibrium Bose-Einstein condensation

    Energy Technology Data Exchange (ETDEWEB)

    Piper, I M; Ediger, M; Wilson, A M; Wu, Y; Phillips, R T [Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Eastham, P R [School of Physics, Trinity College Dublin, Dublin 2 (Ireland); Hugues, M; Hopkinson, M, E-mail: imp24@cam.ac.u [Department of Electronic and Electrical Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD (United Kingdom)

    2010-09-01

    We review the practical conditions required to achieve a non-equilibrium BEC driven by quantum dynamics in a system comprising a microcavity field mode and a distribution of localised two-level systems driven to a step-like population inversion profile. A candidate system based on eight 3.8nm layers of In{sub 0.23}Ga{sub 0.77}As in GaAs shows promising characteristics with regard to the total dipole strength which can be coupled to the field mode.

  14. Calcium en cardioplegie

    NARCIS (Netherlands)

    Ruigrok, T.J.C.; Meijler, F.L.

    1985-01-01

    Coronary perfusion with a calcium-free solution, followed by reperfusion with a calcium containing solution, may result in acute myocardial cell death and in irreversible loss of the e1ectrical and mechanical activity of the heart. This phenomenon is known as the calcium paradox. A number of

  15. Development of a method based on inductively coupled plasma-dynamic reaction cell-mass spectrometry for the simultaneous determination of phosphorus, calcium and strontium in bone and dental tissue

    International Nuclear Information System (INIS)

    De Muynck, David; Vanhaecke, Frank

    2009-01-01

    A method, based on the use of a quadrupole-based inductively coupled plasma-mass spectrometry instrument equipped with a quadrupole-based collision/reaction cell (dynamic reaction cell, DRC), was developed for the simultaneous determination of phosphorus, calcium and strontium in bone and dental (enamel and dentine) tissue. The use of NH 3 , introduced at a gas flow rate of 0.8 mL min -1 in the dynamic reaction cell, combined with a rejection parameter q (RPq) setting of 0.65, allows interference-free determination of calcium via its low-abundant isotopes 42 Ca, 43 Ca and 44 Ca, and of strontium via its isotopes 86 Sr and 88 Sr that are freed from overlap due to the occurrence of ArCa + and/or Ca 2 + ions. Also the determination of phosphorus ( 31 P, mono-isotopic) was shown to be achievable using the same dynamic reaction cell operating conditions. The bone certified reference materials NIST SRM 1400 Bone Ash and NIST SRM 1486 Bone Meal were used for validation of the measurement protocol that was shown capable of providing accurate and reproducible results. Detection limits of P, Ca and Sr in dental tissue digests were established as 3 μg L -1 for P, 2 μg L -1 for Ca and 0.2 μg L -1 for Sr. This method can be used to simultaneously (i) evaluate the impact of diagenesis on the elemental and isotopic composition of buried skeletal tissue via its Ca/P ratio and (ii) determine its Sr concentration. The measurement protocol was demonstrated as fit-for-purpose by the analysis of a set of teeth of archaeological interest for their Ca/P ratio and Sr concentration.

  16. Path-space variational inference for non-equilibrium coarse-grained systems

    International Nuclear Information System (INIS)

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr

    2016-01-01

    In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

  17. Path-space variational inference for non-equilibrium coarse-grained systems

    Energy Technology Data Exchange (ETDEWEB)

    Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Katsoulakis, Markos, E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts at Amherst (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware (United States)

    2016-06-01

    In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

  18. Physical phenomena in a low-temperature non-equilibrium plasma and in MHD generators with non-equilibrium conductivity

    International Nuclear Information System (INIS)

    Velikhov, E.P.; Golubev, V.S.; Dykhne, A.M.

    1976-01-01

    The paper assesses the position in 1975 of theoretical and experimental work on the physics of a magnetohydrodynamic generator with non-equilibrium plasma conductivity. This research started at the beginning of the 1960s; as work on the properties of thermally non-equilibrium plasma in magnetic fields and also in MHD generator ducts progressed, a number of phenomena were discovered and investigated that had either been unknown in plasma physics or had remained uninvestigated until that time: ionization instability and ionization turbulence of plasma in a magnetic field, acoustic instability of a plasma with anisotropic conductivity, the non-equilibrium ionization wave and the energy balance of a non-equilibrium plasma. At the same time, it was discovered what physical requirements an MHD generator with non-equilibrium conductivity must satisfy to achieve high efficiency in converting the thermal or kinetic energy of the gas flow into electric energy. The experiments on MHD power generation with thermally non-equilibrium plasma carried out up to 1975 indicated that it should be possible to achieve conversion efficiencies of up to 20-30%. (author)

  19. The behavior of matter under nonequilibrium conditions: Fundamental aspects and applications in energy-oriented problems: Progress report for period September 1984--November 1987

    International Nuclear Information System (INIS)

    Prigogine, I.

    1987-01-01

    This report briefly discusses progress on the following topics: state selection dynamics; polymerization under nonequilibrium conditions; inhomogeneous fluctuations in hydrodynamics and in completely mixed reactors; homoclinic bifurcations and mixed-mode oscillations; intrinsic randomness and spontaneous symmetry breaking in explosive systems; and microscopic means of irreversibility

  20. Calcium absorption and achlorhydria

    International Nuclear Information System (INIS)

    Recker, R.R.

    1985-01-01

    Defective absorption of calcium has been thought to exist in patients with achlorhydria. The author compared absorption of calcium in its carbonate form with that in a pH-adjusted citrate form in a group of 11 fasting patients with achlorhydria and in 9 fasting normal subjects. Fractional calcium absorption was measured by a modified double-isotope procedure with 0.25 g of calcium used as the carrier. Mean calcium absorption (+/- S.D.) in the patients with achlorhydria was 0.452 +/- 0.125 for citrate and 0.042 +/- 0.021 for carbonate (P less than 0.0001). Fractional calcium absorption in the normal subjects was 0.243 +/- 0.049 for citrate and 0.225 +/- 0.108 for carbonate (not significant). Absorption of calcium from carbonate in patients with achlorhydria was significantly lower than in the normal subjects and was lower than absorption from citrate in either group; absorption from citrate in those with achlorhydria was significantly higher than in the normal subjects, as well as higher than absorption from carbonate in either group. Administration of calcium carbonate as part of a normal breakfast resulted in completely normal absorption in the achlorhydric subjects. These results indicate that calcium absorption from carbonate is impaired in achlorhydria under fasting conditions. Since achlorhydria is common in older persons, calcium carbonate may not be the ideal dietary supplement