#### Sample records for two-dimensional brownian dynamics

1. Performance Estimation for Two-Dimensional Brownian Rotary Ratchet Systems

Science.gov (United States)

Tutu, Hiroki; Horita, Takehiko; Ouchi, Katsuya

2015-04-01

Within the context of the Brownian ratchet model, a molecular rotary system that can perform unidirectional rotations induced by linearly polarized ac fields and produce positive work under loads was studied. The model is based on the Langevin equation for a particle in a two-dimensional (2D) three-tooth ratchet potential of threefold symmetry. The performance of the system is characterized by the coercive torque, i.e., the strength of the load competing with the torque induced by the ac driving field, and the energy efficiency in force conversion from the driving field to the torque. We propose a master equation for coarse-grained states, which takes into account the boundary motion between states, and develop a kinetic description to estimate the mean angular momentum (MAM) and powers relevant to the energy balance equation. The framework of analysis incorporates several 2D characteristics and is applicable to a wide class of models of smooth 2D ratchet potential. We confirm that the obtained expressions for MAM, power, and efficiency of the model can enable us to predict qualitative behaviors. We also discuss the usefulness of the torque/power relationship for experimental analyses, and propose a characteristic for 2D ratchet systems.

2. Dynamics of film. [two dimensional continua theory

Science.gov (United States)

Zak, M.

1979-01-01

The general theory of films as two-dimensional continua are elaborated upon. As physical realizations of such a model this paper examines: inextensible films, elastic films, and nets. The suggested dynamic equations have enabled us to find out the characteristic speeds of wave propagation of the invariants of external and internal geometry and formulate the criteria of instability of their shape. Also included herein is a detailed account of the equation describing the film motions beyond the limits of the shape stability accompanied by the formation of wrinkles. The theory is illustrated by examples.

3. Brownian motion from molecular dynamics

CERN Document Server

Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun

2010-01-01

Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.

4. Probabilistic Universality in two-dimensional Dynamics

CERN Document Server

Lyubich, Mikhail

2011-01-01

In this paper we continue to explore infinitely renormalizable H\\'enon maps with small Jacobian. It was shown in [CLM] that contrary to the one-dimensional intuition, the Cantor attractor of such a map is non-rigid and the conjugacy with the one-dimensional Cantor attractor is at most 1/2-H\\"older. Another formulation of this phenomenon is that the scaling structure of the H\\'enon Cantor attractor differs from its one-dimensional counterpart. However, in this paper we prove that the weight assigned by the canonical invariant measure to these bad spots tends to zero on microscopic scales. This phenomenon is called {\\it Probabilistic Universality}. It implies, in particular, that the Hausdorff dimension of the canonical measure is universal. In this way, universality and rigidity phenomena of one-dimensional dynamics assume a probabilistic nature in the two-dimensional world.

5. Quantization of Two-Dimensional Gravity with Dynamical Torsion

CERN Document Server

Lavrov, P M

1999-01-01

We consider two-dimensional gravity with dynamical torsion in the Batalin - Vilkovisky and Batalin - Lavrov - Tyutin formalisms of gauge theories quantization as well as in the background field method.

6. Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy

NARCIS (Netherlands)

Jansen, Thomas L. C.; Knoester, Jasper

We review recent work on the waiting time dynamics of coherent two-dimensional infrared (2DIR) spectroscopy. This dynamics can reveal chemical and physical processes that take place on the femto- and picosecond time scale, which is faster than the time scale that may be probed by, for example,

7. Dynamical phase transitions in the two-dimensional ANNNI model

Energy Technology Data Exchange (ETDEWEB)

Barber, M.N.; Derrida, B.

1988-06-01

We study the phase diagram of the two-dimensional anisotropic next-nearest neighbor Ising (ANNNI) model by comparing the time evolution of two distinct spin configurations submitted to the same thermal noise. We clearly se several dynamical transitions between ferromagnetic, paramagnetic, antiphase, and floating phases. These dynamical transitions seem to occur rather close to the transition lines determined previously in the literature.

8. Spin dynamics in a two-dimensional quantum gas

DEFF Research Database (Denmark)

Pedersen, Poul Lindholm; Gajdacz, Miroslav; Deuretzbacher, Frank

2014-01-01

We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions with superimp......We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions...

9. Dislocation climb in two-dimensional discrete dislocation dynamics

NARCIS (Netherlands)

Davoudi, K.M.; Nicola, L.; Vlassak, J.J.

2012-01-01

In this paper, dislocation climb is incorporated in a two-dimensional discrete dislocation dynamics model. Calculations are carried out for polycrystalline thin films, passivated on one or both surfaces. Climb allows dislocations to escape from dislocation pile-ups and reduces the strain-hardening r

10. Dynamics of vortex interactions in two-dimensional flows

DEFF Research Database (Denmark)

Juul Rasmussen, J.; Nielsen, A.H.; Naulin, V.

2002-01-01

a critical value, a(c). Using the Weiss-field, a(c) is estimated for vortex patches. Introducing an effective radius for vortices with distributed vorticity, we find that 3.3 a(c) ...The dynamics and interaction of like-signed vortex structures in two dimensional flows are investigated by means of direct numerical solutions of the two-dimensional Navier-Stokes equations. Two vortices with distributed vorticity merge when their distance relative to their radius, d/R-0l. is below...

11. Tracking dynamics of two-dimensional continuous attractor neural networks

Science.gov (United States)

Fung, C. C. Alan; Wong, K. Y. Michael; Wu, Si

2009-12-01

We introduce an analytically solvable model of two-dimensional continuous attractor neural networks (CANNs). The synaptic input and the neuronal response form Gaussian bumps in the absence of external stimuli, and enable the network to track external stimuli by its translational displacement in the two-dimensional space. Basis functions of the two-dimensional quantum harmonic oscillator in polar coordinates are introduced to describe the distortion modes of the Gaussian bump. The perturbative method is applied to analyze its dynamics. Testing the method by considering the network behavior when the external stimulus abruptly changes its position, we obtain results of the reaction time and the amplitudes of various distortion modes, with excellent agreement with simulation results.

12. Enstrophy inertial range dynamics in generalized two-dimensional turbulence

Science.gov (United States)

Iwayama, Takahiro; Watanabe, Takeshi

2016-07-01

We show that the transition to a k-1 spectrum in the enstrophy inertial range of generalized two-dimensional turbulence can be derived analytically using the eddy damped quasinormal Markovianized (EDQNM) closure. The governing equation for the generalized two-dimensional fluid system includes a nonlinear term with a real parameter α . This parameter controls the relationship between the stream function and generalized vorticity and the nonlocality of the dynamics. An asymptotic analysis accounting for the overwhelming dominance of nonlocal triads allows the k-1 spectrum to be derived based upon a scaling analysis. We thereby provide a detailed analytical explanation for the scaling transition that occurs in the enstrophy inertial range at α =2 in terms of the spectral dynamics of the EDQNM closure, which extends and enhances the usual phenomenological explanations.

13. Complex dynamical invariants for two-dimensional complex potentials

J S Virdi; F Chand; C N Kumar; S C Mishra

2012-08-01

Complex dynamical invariants are searched out for two-dimensional complex potentials using rationalization method within the framework of an extended complex phase space characterized by $x = x_{1} + ip_{3}. y = x_{2} + ip_{4}, p_{x} = p_{1} + ix_{3}, p_{y} = p_{2} + ix_{4}$. It is found that the cubic oscillator and shifted harmonic oscillator admit quadratic complex invariants. THe obtained invariants may be useful for studying non-Hermitian Hamiltonian systems.

14. From Molecular Dynamics to Brownian Dynamics

CERN Document Server

2014-01-01

Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

15. Dynamical matrix of two-dimensional electron crystals

Science.gov (United States)

Côté, R.; Lemonde, M.-A.; Doiron, C. B.; Ettouhami, A. M.

2008-03-01

In a quantizing magnetic field, the two-dimensional electron gas has a rich phase diagram with broken translational symmetry phases such as Wigner, bubble, and stripe crystals. In this paper, we derive a method to obtain the dynamical matrix of these crystals from a calculation of the density response function performed in the generalized random-phase approximation (GRPA). We discuss the validity of our method by comparing the dynamical matrix calculated from the GRPA with that obtained from standard elasticity theory with the elastic coefficients obtained from a calculation of the deformation energy of the crystal.

16. Dynamic Multiscaling in Two-dimensional Fluid Turbulence

CERN Document Server

Ray, Samriddhi Sankar; Perlekar, Prasad; Pandit, Rahul

2011-01-01

We obtain, by extensive direct numerical simulations, time-dependent and equal-time structure functions for the vorticity, in both quasi-Lagrangian and Eulerian frames, for the direct-cascade regime in two-dimensional fluid turbulence with air-drag-induced friction. We show that different ways of extracting time scales from these time-dependent structure functions lead to different dynamic-multiscaling exponents, which are related to equal-time multiscaling exponents by different classes of bridge relations; for a representative value of the friction we verify that, given our error bars, these bridge relations hold.

17. A Direct Two-Dimensional Pressure Formulation in Molecular Dynamics

CERN Document Server

YD, Sumith

2016-01-01

Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.

18. Brownian motion on random dynamical landscapes

Science.gov (United States)

Suñé Simon, Marc; Sancho, José María; Lindenberg, Katja

2016-03-01

We present a study of overdamped Brownian particles moving on a random landscape of dynamic and deformable obstacles (spatio-temporal disorder). The obstacles move randomly, assemble, and dissociate following their own dynamics. This landscape may account for a soft matter or liquid environment in which large obstacles, such as macromolecules and organelles in the cytoplasm of a living cell, or colloids or polymers in a liquid, move slowly leading to crowding effects. This representation also constitutes a novel approach to the macroscopic dynamics exhibited by active matter media. We present numerical results on the transport and diffusion properties of Brownian particles under this disorder biased by a constant external force. The landscape dynamics are characterized by a Gaussian spatio-temporal correlation, with fixed time and spatial scales, and controlled obstacle concentrations.

19. Oscillation of Two-Dimensional Neutral Delay Dynamic Systems

Directory of Open Access Journals (Sweden)

Xinli Zhang

2013-01-01

Full Text Available We consider a class of nonlinear two-dimensional dynamic systems of the neutral type (x(t-a(tx(τ1(tΔ=p(tf1(y(t, yΔ(t=-q(tf2(x(τ2(t. We obtain sufficient conditions for all solutions of the system to be oscillatory. Our oscillation results when a(t=0 improve the oscillation results for dynamic systems on time scales that have been established by Fu and Lin (2010, since our results do not restrict to the case where f(u=u. Also, as a special case when =ℝ, our results do not require an to be a positive real sequence. Some examples are given to illustrate the main results.

20. Molecular-dynamics simulation of two-dimensional thermophoresis

Science.gov (United States)

Paredes; Idler; Hasmy; Castells; Botet

2000-11-01

A numerical technique is presented for the thermal force exerted on a solid particle by a gaseous medium between two flat plates at different temperatures, in the free molecular or transition flow. This is a two-dimensional molecular-dynamics simulation of hard disks in a inhomogeneous thermal environment. All steady-state features exhibited by the compressible hard-disk gas are shown to be consistent with the expected behaviors. Moreover the thermal force experienced by a large solid disk is investigated, and compared to the analytical case of cylinders moving perpendicularly to the constant temperature gradient for an infinite Knudsen number and in an infinite medium. We show precise examples of how this technique can be used simply to investigate more difficult practical problems, in particluar the influence of nonlinear gradients for large applied differences of temperature, of proximity of the walls, and of smaller Knudsen numbers.

1. Two-dimensional Numerical Modeling Research on Continent Subduction Dynamics

Institute of Scientific and Technical Information of China (English)

WANG Zhimin; XU Bei; ZHOU Yaoqi; XU Hehua; HUANG Shaoying

2004-01-01

Continent subduction is one of the hot research problems in geoscience. New models presented here have been set up and two-dimensional numerical modeling research on the possibility of continental subduction has been made with the finite element software, ANSYS, based on documentary evidence and reasonable assumptions that the subduction of oceanic crust has occurred, the subduction of continental crust can take place and the process can be simplified to a discontinuous plane strain theory model. The modeling results show that it is completely possible for continental crust to be subducted to a depth of 120 km under certain circumstances and conditions. At the same time, the simulations of continental subduction under a single dynamical factor have also been made, including the pull force of the subducted oceanic lithosphere, the drag force connected with mantle convection and the push force of the mid-ocean ridge. These experiments show that the drag force connected with mantle convection is critical for continent subduction.

2. The Dynamics of Water in Porous Two-Dimensional Crystals.

Science.gov (United States)

Strong, Steven E; Eaves, Joel D

2017-01-12

Porous two-dimensional crystals offer many promises for water desalination applications. For computer simulation to play a predictive role in this area, however, one needs to have reliable methods for simulating an atomistic system with hydrodynamic currents and interpretative tools to relate microscopic interactions to emergent macroscopic dynamical quantities, such as friction, slip length, and permeability. In this article, we use Gaussian dynamics, a nonequilibrium molecular dynamics method that provides microscopic insights into the interactions that control the flows of both simple liquids and liquid water through atomically small channels. In simulations of aqueous transport, we mimic the effect of changing the membrane chemical composition by adjusting the attractive strength of the van der Waals interactions between the membrane atoms and water. We find that the wetting contact angle, a common measure of a membrane's hydrophobicity, does not predict the permeability of a membrane. Instead, the hydrophobic effect is subtle, with both static and dynamic effects that can both help and hinder water transport through these materials. The competition between the static and dynamical hydrophobicity balances an atomic membrane's tendency to wet against hydrodynamic friction, and determines an optimal contact angle for water passage through nonpolar membranes. To a reasonable approximation, the optimal contact angle depends only on the aspect ratio of the pore. We also find that water molecules pass through the most hydrophobic membranes in a punctuated series of bursts that are separated by long pauses. A continuous-time Markov model of these data provides evidence of a molecular analogue to the clogging transition, a phenomenon observed in driven granular flows.

3. Two dimensional electron spin resonance: Structure and dynamics of biomolecules

Science.gov (United States)

Saxena, Sunil; Freed, Jack H.

1998-03-01

The potential of two dimensional (2D) electron spin resonance (ESR) for measuring the structural properties and slow dynamics of labeled biomolecules will be presented. Specifically, it will be shown how the recently developed method of double quantum (DQ) 2D ESR (S. Saxena and J. H. Freed, J. Chem. Phys. 107), 1317, (1997) can be used to measure large interelectron distances in bilabeled peptides. The need for DQ ESR spectroscopy, as well as the challenges and advantages of this method will be discussed. The elucidation of the slow reorientational dynamics of this peptide (S. Saxena and J. H. Freed, J. Phys. Chem. A, 101) 7998 (1997) in a glassy medium using COSY and 2D ELDOR ESR spectroscopy will be demonstrated. The contributions to the homogeneous relaxation time, T_2, from the overall and/or internal rotations of the nitroxide can be distinguished from the COSY spectrum. The growth of spectral diffusion cross-peaks^2 with mixing time in the 2D ELDOR spectra can be used to directly determine a correlation time from the experiment which can be related to the rotational correlation time.

4. Sufficient Controllability Condition for Affine Systems with Two-Dimensional Control and Two-Dimensional Zero Dynamics

Directory of Open Access Journals (Sweden)

D. A. Fetisov

2015-01-01

Full Text Available The controllability conditions are well known if we speak about linear stationary systems: a linear stationary system is controllable if and only if the dimension of the state vector is equal to the rank of the controllability matrix. The concept of the controllability matrix is extended to affine systems, but relations between affine systems controllability and properties of this matrix are more complicated. Various controllability conditions are set for affine systems, but they deal as usual either with systems of some special form or with controllability in some small neighborhood of the concerned point. An affine system is known to be controllable if the system is equivalent to a system of a canonical form, which is defined and regular in the whole space of states. In this case, the system is said to be feedback linearizable in the space of states. However there are examples, which illustrate that a system can be controllable even if it is not feedback linearizable in any open subset in the space of states. In this article we deal with such systems.Affine systems with two-dimensional control are considered. The system in question is assumed to be equivalent to a system of a quasicanonical form with two-dimensional zero dynamics which is defined and regular in the whole space of states. Therefore the controllability of the original system is equivalent to the controllability of the received system of a quasicanonical form. In this article the sufficient condition for an available solution of the terminal problem is proven for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. The condition is valid in the case of an arbitrary time interval and arbitrary initial and finite states of the system. Therefore the controllability condition is set for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. An example is given which illustrates how the proved

5. Measured Two-Dimensional Ice-Wedge Polygon Thermal Dynamics

Science.gov (United States)

Cable, William; Romanovsky, Vladimir; Busey, Robert

2016-04-01

necessarily found in areas of higher MAGT. Active layer thickness does not appear to be correlated to mean annual air temperature but rather is a function of summer air temperature or thawing degree-days. While the refreezing of the active layer initiated at nearly the same time for all locations and polygons, we find differences in the proportion of top-down versus bottom-up freezing and the length of time required to complete the refreezing process. Examination of the daily temperature dynamics using interpolated two-dimensional temperature fields reveal that during the summer, the predominate temperature gradient is vertical while the isotherms tend to follow the topography. However, as the active layer begins to refreeze and snow accumulates, the thermal regime diverges. The fall shows an increased temperature gradient horizontally with landscape positions containing higher soil moisture and/or snow depth (low centers and troughs) cooling more slowly than the adjacent ground (rims and high centers). This two-dimensional effect is greatest as the active layer refreezes and persists until mid-winter, by which time the temperature gradients are again mostly vertical and the isotherms follow the topography. Our findings demonstrate the complexity and two-dimensionality of the temperature dynamics in these landscapes.

6. Dynamics of Brownian motors in deformable medium

Science.gov (United States)

Woulaché, Rosalie Laure; Kepnang Pebeu, Fabrice Maxime; Kofané, Timoléon C.

2016-10-01

The directed transport in a one-dimensional overdamped, Brownian motor subjected to a travelling wave potential with variable shape and exposed to an external bias is studied numerically. We focus our attention on the class of Remoissenet-Peyrard parametrized on-site potentials with slight modification, whose shape can be varied as a function of a parameter s, recovering the sine-Gordon shape as the special case. We demonstrate that in the presence of the travelling wave potential the observed dynamical properties of the Brownian motor which crucially depends on the travelling wave speed, the intensity of the noise and the external load is significantly influenced also by the geometry of the system. In particular, we notice that systems with sharp wells and broad barriers favour the transport under the influence of an applied load. The efficiency of transport of Brownian motors in deformable systems remains equal to 1 (in the absence of an applied load) up to a critical value of the travelling wave speed greater than that of the pure sine-Gordon shape.

7. Dynamic Properties of Two-Dimensional Polydisperse Granular Gases

Institute of Scientific and Technical Information of China (English)

2007-01-01

We propose a two-dimensional model of polydisperse granular mixtures with a power-law size distribution in the presence of stochastic driving. A fractal dimension D is introduced as a measurement of the inhomogeneity of the size distribution of particles. We define the global and partial granular temperatures of the multi-component mixture. By direct simulation Monte Carlo, we investigate how the inhomogeneity of the size distribution influences the dynamic properties of the mixture, focusing on the granular temperature, dissipated energy, velocity distribution, spatial clusterization, and collision time. We get the following results: a single granular temperature does not characterize a multi-component mixture and each species attains its own "granular temperature"; The velocity deviation from Gaussian distribution becomes more and more pronounced and the partial density of the assembly is more inhomogeneous with the increasing value of the fractal dimension D; The global granular temperature decreases and average dissipated energy per particle increases as the value of D augments.

8. Waiting time dynamics in two-dimensional infrared spectroscopy.

Science.gov (United States)

Jansen, Thomas L C; Knoester, Jasper

2009-09-15

We review recent work on the waiting time dynamics of coherent two-dimensional infrared (2DIR) spectroscopy. This dynamics can reveal chemical and physical processes that take place on the femto- and picosecond time scale, which is faster than the time scale that may be probed by, for example, nuclear magnetic resonance spectroscopy. A large number of chemically relevant processes take place on this time scale. Such processes range from forming and breaking hydrogen bonds and proton transfer to solvent exchange and vibrational population transfer. In typical 2DIR spectra, multiple processes contribute to the waiting time dynamics and the spectra are often congested. This makes the spectra challenging to interpret, and the aid of theoretical models and simulations is often needed. To be useful, such models need to account for all dynamical processes in the sample simultaneously. The numerical integration of the Schrodinger equation (NISE) method has proven to allow for a very general treatment of the dynamical processes. It accounts for both the motional narrowing resulting from solvent-induced frequency fluctuations and population transfer between coupled vibrations. At the same time, frequency shifts arising from chemical-exchange reactions and changes of the transition dipoles because of either non-Condon effects or molecular reorientation are included in the treatment. This method therefore allows for the disentanglement of all of these processes. The NISE method has thus far been successfully applied to study chemical-exchange processes. It was demonstrated that 2DIR is not only sensitive to reaction kinetics but also to the more detailed reaction dynamics. NISE has also been applied to the study of population transfer within the amide I band (CO stretch) and between the amide I and amide II bands (CN stretch and NH bend) in polypeptides. From the amide I studies, it was found that the population transfer can be used to enhance cross-peaks that act as

9. Topological defects in two-dimensional crystals

OpenAIRE

Chen, Yong; Qi, Wei-Kai

2008-01-01

By using topological current theory, we study the inner topological structure of the topological defects in two-dimensional (2D) crystal. We find that there are two elementary point defects topological current in two-dimensional crystal, one for dislocations and the other for disclinations. The topological quantization and evolution of topological defects in two-dimensional crystals are discussed. Finally, We compare our theory with Brownian-dynamics simulations in 2D Yukawa systems.

10. Chaotic dynamics for two-dimensional tent maps

Science.gov (United States)

Pumariño, Antonio; Ángel Rodríguez, José; Carles Tatjer, Joan; Vigil, Enrique

2015-02-01

For a two-dimensional extension of the classical one-dimensional family of tent maps, we prove the existence of an open set of parameters for which the respective transformation presents a strange attractor with two positive Lyapounov exponents. Moreover, periodic orbits are dense on this attractor and the attractor supports a unique ergodic invariant probability measure.

11. Brownian dynamics simulations of nanosheet solutions under shear.

Science.gov (United States)

Xu, Yueyi; Green, Micah J

2014-07-14

The flow-induced conformation dynamics of nanosheets are simulated using a Brownian Dynamics (BD) formulation applied to a bead-rod sheetlike molecular model. This is the first-ever use of BD to simulate flow-induced dynamics of two-dimensional structures. Using this framework, we simulate dilute suspensions of coarse-grained nanosheets and compute conformation dynamics for simple shear flow. The data show power law scaling relationships between nanosheet parameters (such as bending moduli and molecular weight) and the resulting intrinsic viscosity and conformation. For nonzero bending moduli, an effective dimension of 2.77 at equilibrium is calculated from the scaling relationship between radius of gyration and molecular weight. We also find that intrinsic viscosity varies with molecular weight with an exponent of 2.12 ± 0.23; this dependence is significantly larger than those found for linear polymers. Weak shear thinning is observed at high Weissenberg number (Wi). This simulation method provides a computational basis for developing manufacturing processes for nanosheet-derived materials by relating flow forces and nanosheet parameters to the resulting material morphology.

12. Confinement and dynamical regulation in two-dimensional convective turbulence

DEFF Research Database (Denmark)

Bian, N.H.; Garcia, O.E.

2003-01-01

In this work the nature of confinement improvement implied by the self-consistent generation of mean flows in two-dimensional convective turbulence is studied. The confinement variations are linked to two distinct regulation mechanisms which are also shown to be at the origin of low-frequency bur......In this work the nature of confinement improvement implied by the self-consistent generation of mean flows in two-dimensional convective turbulence is studied. The confinement variations are linked to two distinct regulation mechanisms which are also shown to be at the origin of low......-frequency bursting in the fluctuation level and the convective heat flux integral, both resulting in a state of large-scale intermittency. The first one involves the control of convective transport by sheared mean flows. This regulation relies on the conservative transfer of kinetic energy from tilted fluctuations...... to the mean component of the flow. Bursting can also result from the quasi-linear modification of the linear instability drive which is the mean pressure gradient. For each bursting process the relevant zero-dimensional model equations are given. These are finally coupled in a minimal model of convection...

13. Rotational Brownian Dynamics simulations of clathrin cage formation

Energy Technology Data Exchange (ETDEWEB)

Ilie, Ioana M.; Briels, Wim J. [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Otter, Wouter K. den, E-mail: w.k.denotter@utwente.nl [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

2014-08-14

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

14. Rotational Brownian dynamics simulations of clathrin cage formation.

Science.gov (United States)

Ilie, Ioana M; den Otter, Wouter K; Briels, Wim J

2014-08-14

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

15. Fluid dynamics of two-dimensional pollination in Ruppia maritima

Science.gov (United States)

Musunuri, Naga; Bunker, Daniel; Pell, Susan; Pell, Fischer; Singh, Pushpendra

2016-11-01

The aim of this work is to understand the physics underlying the mechanisms of two-dimensional aquatic pollen dispersal, known as hydrophily. We observed two mechanisms by which the pollen released from male inflorescences of Ruppia maritima is adsorbed on a water surface: (i) inflorescences rise above the surface and after they mature their pollen mass falls onto the surface as clumps and disperses on the surface; (ii) inflorescences remain below the surface and produce air bubbles which carry their pollen mass to the surface where it disperses. In both cases dispersed pollen masses combined under the action of capillary forces to form pollen rafts. This increases the probability of pollination since the capillary force on a pollen raft towards a stigma is much larger than on a single pollen grain. The presence of a trace amount of surfactant can disrupt the pollination process so that the pollen is not transported or captured on the water surface. National Science Foundation.

16. Stochastic description of quantum Brownian dynamics

Science.gov (United States)

Yan, Yun-An; Shao, Jiushu

2016-08-01

Classical Brownian motion has well been investigated since the pioneering work of Einstein, which inspired mathematicians to lay the theoretical foundation of stochastic processes. A stochastic formulation for quantum dynamics of dissipative systems described by the system-plus-bath model has been developed and found many applications in chemical dynamics, spectroscopy, quantum transport, and other fields. This article provides a tutorial review of the stochastic formulation for quantum dissipative dynamics. The key idea is to decouple the interaction between the system and the bath by virtue of the Hubbard-Stratonovich transformation or Itô calculus so that the system and the bath are not directly entangled during evolution, rather they are correlated due to the complex white noises introduced. The influence of the bath on the system is thereby defined by an induced stochastic field, which leads to the stochastic Liouville equation for the system. The exact reduced density matrix can be calculated as the stochastic average in the presence of bath-induced fields. In general, the plain implementation of the stochastic formulation is only useful for short-time dynamics, but not efficient for long-time dynamics as the statistical errors go very fast. For linear and other specific systems, the stochastic Liouville equation is a good starting point to derive the master equation. For general systems with decomposable bath-induced processes, the hierarchical approach in the form of a set of deterministic equations of motion is derived based on the stochastic formulation and provides an effective means for simulating the dissipative dynamics. A combination of the stochastic simulation and the hierarchical approach is suggested to solve the zero-temperature dynamics of the spin-boson model. This scheme correctly describes the coherent-incoherent transition (Toulouse limit) at moderate dissipation and predicts a rate dynamics in the overdamped regime. Challenging problems

17. Quantum vortex dynamics in two-dimensional neutral superfluids

NARCIS (Netherlands)

Wang, C. -C J.; Duine, R.A.; MacDonald, A.H.

2010-01-01

We derive an effective action for the vortex-position degree of freedom in a superfluid by integrating out condensate phase- and density-fluctuation environmental modes. When the quantum dynamics of environmental fluctuations is neglected, we confirm the occurrence of the vortex Magnus force and

18. Coarse-graining two-dimensional turbulence via dynamical optimization

CERN Document Server

Turkington, Bruce; Thalabard, Simon

2015-01-01

A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosit...

19. Coarse-graining two-dimensional turbulence via dynamical optimization

Science.gov (United States)

Turkington, Bruce; Chen, Qian-Yong; Thalabard, Simon

2016-10-01

A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosity, modified nonlinear interactions between the low mode means, and a nonlinear coupling between the mean and variance of each low mode. The predictive skill of this optimal closure is validated quantitatively by comparing it against direct numerical simulations. These tests show that good agreement is achieved without adjusting any closure parameters.

20. Extrinsic curvature in two-dimensional causal dynamical triangulation

Science.gov (United States)

Glaser, Lisa; Sotiriou, Thomas P.; Weinfurtner, Silke

2016-09-01

Causal dynamical triangulation (CDT) is a nonperturbative quantization of general relativity. Hořava-Lifshitz gravity, on the other hand, modifies general relativity to allow for perturbative quantization. Past work has given rise to the speculation that Hořava-Lifshitz gravity might correspond to the continuum limit of CDT. In this paper we add another piece to this puzzle by applying the CDT quantization prescription directly to Hořava-Lifshitz gravity in two dimensions. We derive the continuum Hamiltonian, and we show that it matches exactly the Hamiltonian derived from canonically quantizing the Hořava-Lifshitz action. Unlike the standard CDT case, here the introduction of a foliated lattice does not impose further restriction on the configuration space and, as a result, lattice quantization does not leave any imprint on continuum physics as expected.

1. From generalized Langevin equations to Brownian dynamics and embedded Brownian dynamics

Science.gov (United States)

Ma, Lina; Li, Xiantao; Liu, Chun

2016-09-01

We present the reduction of generalized Langevin equations to a coordinate-only stochastic model, which in its exact form involves a forcing term with memory and a general Gaussian noise. It will be shown that a similar fluctuation-dissipation theorem still holds at this level. We study the approximation by the typical Brownian dynamics as a first approximation. Our numerical test indicates how the intrinsic frequency of the kernel function influences the accuracy of this approximation. In the case when such an approximate is inadequate, further approximations can be derived by embedding the nonlocal model into an extended dynamics without memory. By imposing noises in the auxiliary variables, we show how the second fluctuation-dissipation theorem is still exactly satisfied.

2. Weighted-ensemble Brownian dynamics simulation: sampling of rare events in nonequilibrium systems.

Science.gov (United States)

Kromer, Justus A; Schimansky-Geier, Lutz; Toral, Raul

2013-06-01

We provide an algorithm based on weighted-ensemble (WE) methods, to accurately sample systems at steady state. Applying our method to different one- and two-dimensional models, we succeed in calculating steady-state probabilities of order 10(-300) and reproduce the Arrhenius law for rates of order 10(-280). Special attention is payed to the simulation of nonpotential systems where no detailed balance assumption exists. For this large class of stochastic systems, the stationary probability distribution density is often unknown and cannot be used as preknowledge during the simulation. We compare the algorithm's efficiency with standard Brownian dynamics simulations and the original WE method.

3. Brownian Dynamics of charged particles in a constant magnetic field

CERN Document Server

Hou, L J; Piel, A; Shukla, P K

2009-01-01

Numerical algorithms are proposed for simulating the Brownian dynamics of charged particles in an external magnetic field, taking into account the Brownian motion of charged particles, damping effect and the effect of magnetic field self-consistently. Performance of these algorithms is tested in terms of their accuracy and long-time stability by using a three-dimensional Brownian oscillator model with constant magnetic field. Step-by-step recipes for implementing these algorithms are given in detail. It is expected that these algorithms can be directly used to study particle dynamics in various dispersed systems in the presence of a magnetic field, including polymer solutions, colloidal suspensions and, particularly complex (dusty) plasmas. The proposed algorithms can also be used as thermostat in the usual molecular dynamics simulation in the presence of magnetic field.

4. Construction of exact complex dynamical invariant of a two-dimensional classical system

Fakir Chand; S C Mishra

2006-12-01

We present the construction of exact complex dynamical invariant of a two-dimensional classical dynamical system on an extended complex space utilizing Lie algebraic approach. These invariants are expected to play a vital role in understanding the complex trajectories of both classical and quantum systems.

5. Lattice gas dynamics: application to driven vortices in two dimensional superconductors.

Science.gov (United States)

Gotcheva, Violeta; Wang, Albert T J; Teitel, S

2004-06-18

A continuous time Monte Carlo lattice gas dynamics is developed to model driven steady states of vortices in two dimensional superconducting networks. Dramatic differences are found when compared to a simpler Metropolis dynamics. Subtle finite size effects are found at low temperature, with a moving smectic that becomes unstable to an anisotropic liquid on sufficiently large length scales.

6. Brownian dynamics determine universality of charge transport in ionic liquids

Energy Technology Data Exchange (ETDEWEB)

Sangoro, Joshua R [ORNL; Iacob, Ciprian [University of Leipzig; Mierzwa, Michal [University of Silesia, Uniwersytecka, Katowice, Poland; Paluch, Marian [University of Silesia, Uniwersytecka, Katowice, Poland; Kremer, Friedrich [University of Leipzig

2012-01-01

Broadband dielectric spectroscopy is employed to investigate charge transport in a variety of glass-forming ionic liquids over wide frequency, temperature and pressure ranges. Using a combination of Einstein, Einstein-Smoluchowski, and Langevin relations, the observed universal scaling of charge transport in ionic liquids is traced back to the dominant role of Brownian dynamics.

7. Rotational Brownian Dynamics simulations of clathrin cage formation

NARCIS (Netherlands)

Ilie, I.M.; Otter, den W.K.; Briels, W.J.

2014-01-01

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assem

8. Rotational Brownian Dynamics simulations of clathrin cage formation

NARCIS (Netherlands)

Ilie, Ioana Mariuca; den Otter, Wouter K.; Briels, Willem J.

2014-01-01

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the

9. Brownian dynamics simulations with hard-body interactions: Spherical particles

CERN Document Server

Behringer, Hans; 10.1063/1.4761827

2012-01-01

A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian particle on a one-dimensional half-line. The motion of a Brownian particle is decomposed into a component that is affected by hard-body interactions and into components that are unaffected. The hard-body interactions are incorporated by replacing the affected component of motion by the evolution on a half-line. It is discussed under which circumstances this approach is justified. In particular, the algorithm is developed and formulated for systems with space-fixed obstacles and for systems comprising spherical particles. The validity and justification of the algorithm is investigated numerically by looking at exemplary model systems of soft matter, namely at colloids in flow fields and at protein interactions. Furthermore, a thorough discussion of properties of other heurist...

10. Coherent electron dynamics in a two-dimensional random system with mobility edges

NARCIS (Netherlands)

de Moura, F. A. B. F.; Lyra, M. L.; Dominguez-Adame, F.; Malyshev, V.A.

2007-01-01

We study numerically the dynamics of a one-electron wavepacket in a two-dimensional random lattice with long-range correlated diagonal disorder in the presence of a uniform electric field. The time-dependent Schrodinger equation is used for this purpose. We find that the wavepacket displays Bloch-li

11. Direct control of the small-scale energy balance in two-dimensional fluid dynamics

NARCIS (Netherlands)

Frank, Jason; Leimkuhler, Benedict; Myerscough, Keith W.

2015-01-01

We explore the direct modification of the pseudo-spectral truncation of two-dimensional, incompressible fluid dynamics to maintain a prescribed kinetic energy spectrum. The method provides a means of simulating fluid states with defined spectral properties, for the purpose of matching simulation sta

12. Simulation of Dynamics in Two-Dimensional Vortex Systems in Random Media

Institute of Scientific and Technical Information of China (English)

ZHANG Wei; SUN Li-Zhen; LUO Meng-Bo

2009-01-01

Dynamics in two-dimensional vortex systems with random pinning centres is investigated using molecular dy-namical simulations. The driving force and temperature dependences of vortex velocity are investigated. Below the critical depinning force Fc, a creep motion of vortex is found at low temperature. At forces slightly above Fc, a part of vortices flow in winding channels at zero temperature. In the vortex channel flow region, we ob-serve the abnormal behaviour of vortex dynamics: the velocity is roughly independent of temperature or even decreases with temperature at low temperatures. A phase diagram that describes different dynamics of vortices is presented.

13. Fast simulation of Brownian dynamics in a crowded environment

CERN Document Server

Smith, Stephen

2016-01-01

Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large spee...

14. Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics

CERN Document Server

Franz, Benjamin; Chapman, S Jonathan; Erban, Radek

2012-01-01

Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface which partitions the domain and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that to accurately compute variances using the PBD simulation requires the overlap region. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.

15. Bias driven coherent carrier dynamics in a two-dimensional aperiodic potential

NARCIS (Netherlands)

de Moura, F. A. B. F.; Viana, L. P.; Lyra, M. L.; Malyshev, Victor; Dominguez-Adame, F.

2008-01-01

We study the dynamics of an electron wave-packet in a two-dimensional square lattice with an aperiodic site potential in the presence of an external uniform electric field. The aperiodicity is described by epsilon(m) = V cos(pi alpha m(x)(nu x)) cos(pi alpha m(y)(nu y)) at lattice sites (m(x),m(y)),

16. The dynamic stiffness matrix of two-dimensional elements: application to Kirchhoff's plate continuous elements

Science.gov (United States)

Casimir, J. B.; Kevorkian, S.; Vinh, T.

2005-10-01

This paper describes a procedure for building the dynamic stiffness matrix of two-dimensional elements with free edge boundary conditions. The dynamic stiffness matrix is the basis of the continuous element method. Then, the formulation is used to build a Kirchhoff rectangular plate element. Gorman's method of boundary condition decomposition and Levy's series are used to obtain the strong solution of the elementary problem. A symbolic computation software partially performs the construction of the dynamic stiffness matrix from this solution. The performances of the element are evaluated from comparisons with harmonic responses of plates obtained by the finite element method.

17. Dynamic effect of overhangs and islands at the depinning transition in two-dimensional magnets.

Science.gov (United States)

Zhou, N J; Zheng, B

2010-09-01

With the Monte Carlo methods, we systematically investigate the short-time dynamics of domain-wall motion in the two-dimensional random-field Ising model with a driving field (DRFIM). We accurately determine the depinning transition field and critical exponents. Through two different definitions of the domain interface, we examine the dynamics of overhangs and islands. At the depinning transition, the dynamic effect of overhangs and islands reaches maximum. We argue that this should be an important mechanism leading the DRFIM model to a different universality class from the Edwards-Wilkinson equation with quenched disorder.

18. Numerical Investigation of Dynamic Effects on Unsteady Flow Measurements Using a Two-Dimensional Probe

Institute of Scientific and Technical Information of China (English)

2000-01-01

The dynamic effects in measurements of unsteady flow when using a probe with quasi-steady calibration curves has been investigated in this paper by numerical simulation of the compressible flow around a fixed two-dimensional 3-hole probe. The unsteady velocity and pressure distributions, as well as the hole-pressures, are calculated for high frequency flow variations. The measurement errors caused by the dynamic effects indicate that considerable measurement errors may occur for high frequency flow fluctuation, e.g., 2000Hz, especially, when the flow around the probe head approaches separation. This work shows how numerical simulation can be used to investigate and correct for the dynamic effects.

19. Hamiltonian dynamics of the two-dimensional lattice {phi}{sup 4} model

Energy Technology Data Exchange (ETDEWEB)

Caiani, Lando [Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), Trieste (Italy); Casetti, Lapo [Istituto Nazionale di Fisica della Materia (INFM), Unita di Ricerca del Politecnico di Torino, Dipartimento di Fisica, Politecnico di Torino, Turin (Italy); Pettini, Marco [Osservatorio Astrofisico di Arcetri, Florence (Italy)

1998-04-17

The Hamiltonian dynamics of the classical {phi}{sup 4} model on a two-dimensional square lattice is investigated by means of numerical simulations. The macroscopic observables are computed as time averages. The results clearly reveal the presence of the continuous phase transition at a finite energy density and are consistent both qualitatively and quantitatively with the predictions of equilibrium statistical mechanics. The Hamiltonian microscopic dynamics also exhibits critical slowing down close to the transition. Moreover, the relationship between chaos and the phase transition is considered, and interpreted in the light of a geometrization of dynamics. (author)

20. Dynamic patterns in a two-dimensional neural field with refractoriness.

Science.gov (United States)

Qi, Yang; Gong, Pulin

2015-08-01

The formation of dynamic patterns such as localized propagating waves is a fascinating self-organizing phenomenon that happens in a wide range of spatially extended systems including neural systems, in which they might play important functional roles. Here we derive a type of two-dimensional neural-field model with refractoriness to study the formation mechanism of localized waves. After comparing this model with existing neural-field models, we show that it is able to generate a variety of localized patterns, including stationary bumps, localized waves rotating along a circular path, and localized waves with longer-range propagation. We construct explicit bump solutions for the two-dimensional neural field and conduct a linear stability analysis on how a stationary bump transitions to a propagating wave under different spatial eigenmode perturbations. The neural-field model is then partially solved in a comoving frame to obtain localized wave solutions, whose spatial profiles are in good agreement with those obtained from simulations. We demonstrate that when there are multiple such propagating waves, they exhibit rich propagation dynamics, including propagation along periodically oscillating and irregular trajectories; these propagation dynamics are quantitatively characterized. In addition, we show that these waves can have repulsive or merging collisions, depending on their collision angles and the refractoriness parameter. Due to its analytical tractability, the two-dimensional neural-field model provides a modeling framework for studying localized propagating waves and their interactions.

1. Brownian dynamics without Green's functions

Energy Technology Data Exchange (ETDEWEB)

Delong, Steven; Donev, Aleksandar, E-mail: donev@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Usabiaga, Florencio Balboa; Delgado-Buscalioni, Rafael [Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Univeridad Autónoma de Madrid, Madrid 28049 (Spain); Griffith, Boyce E. [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, New York 10016 (United States)

2014-04-07

We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finite-volume Stokes solver to generate the action of the response functions “on the fly.” Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically correlated Brownian motion, can be generated by solving the steady Stokes equations numerically only once per time step. This is accomplished by including a stochastic contribution to the stress tensor in the fluid equations consistent with fluctuating hydrodynamics. We develop novel temporal integrators that account for the multiplicative nature of the noise in the equations of Brownian dynamics and the strong dependence of the mobility on the configuration for confined systems. Notably, we propose a random finite difference approach to approximating the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. Through comparisons with analytical and existing computational results, we numerically demonstrate the ability of the FIB method to accurately capture both the static (equilibrium) and dynamic properties of interacting particles in flow.

2. Brownian dynamics of confined rigid bodies

Energy Technology Data Exchange (ETDEWEB)

Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar, E-mail: donev@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States)

2015-10-14

We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the other based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.

3. Dynamics of two-dimensional complex plasmas in a magnetic field

CERN Document Server

Ott, T; Bonitz, M

2013-01-01

We consider a two-dimensional complex plasma layer containing charged dust particles in a perpendicular magnetic field. Computer simulations of both one-component and binary systems are used to explore the equilibrium particle dynamics in the fluid state. The mobility is found to scale with the inverse of the magnetic field strength (Bohm diffusion) for strong fields. For bidisperse mixtures, the magnetic field dependence of the long-time mobility depends on the particle species providing an external control of their mobility ratio. For large magnetic fields, even a two-dimensional model porous matrix can be realized composed by the almost immobilized high-charge particles which act as obstacles for the mobile low-charge particles.

4. Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics

KAUST Repository

Franz, Benjamin

2013-06-19

Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.

5. Signatures of chaos and non-integrability in two-dimensional gravity with dynamical boundary

Directory of Open Access Journals (Sweden)

Fitkevich Maxim

2016-01-01

Full Text Available We propose a model of two-dimensional dilaton gravity with a boundary. In the bulk our model coincides with the classically integrable CGHS model; the dynamical boundary cuts of the CGHS strong-coupling region. As a result, classical dynamics in our model reminds that in the spherically-symmetric gravity: wave packets of matter fields either reflect from the boundary or form black holes. We find large integrable sector of multisoliton solutions in this model. At the same time, we argue that the model is globally non-integrable because solutions at the verge of black hole formation display chaotic properties.

6. Slow dynamics in a quasi-two-dimensional binary complex plasma

CERN Document Server

Du, Cheng-Ran; Thomas, Hubertus M; Morfill, Gregor E; Ivlev, Alexei V

2016-01-01

Slow dynamics in an amorphous quasi-two-dimensional complex plasma, comprised of microparticles of two different sizes, was studied experimentally. The motion of individual particles was observed using video microscopy, and the self part of the intermediate scattering function as well as the mean-squared particle displacement was calculated. The long-time structural relaxation reveals the characteristic behavior near the glass transition. Our results suggest that binary complex plasmas can be an excellent model system to study slow dynamics in classical supercooled fluids.

7. Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Science.gov (United States)

Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng

2006-12-28

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

8. Dynamics of kinks in one- and two-dimensional hyperbolic models with quasidiscrete nonlinearities.

Science.gov (United States)

Rotstein, H G; Mitkov, I; Zhabotinsky, A M; Epstein, I R

2001-06-01

We study the evolution of fronts in the Klein-Gordon equation when the nonlinear term is inhomogeneous. Extending previous works on homogeneous nonlinear terms, we describe the derivation of an equation governing the front motion, which is strongly nonlinear, and, for the two-dimensional case, generalizes the damped Born-Infeld equation. We study the motion of one- and two-dimensional fronts finding a much richer dynamics than in the homogeneous system case, leading, in most cases, to the stabilization of one phase inside the other. For a one-dimensional front, the function describing the inhomogeneity of the nonlinear term acts as a "potential function" for the motion of the front, i.e., a front initially placed between two of its local maxima asymptotically approaches the intervening minimum. Two-dimensional fronts, with radial symmetry and without dissipation can either shrink to a point in finite time, grow unboundedly, or their radius can oscillate, depending on the initial conditions. When dissipation effects are present, the oscillations either decay spirally or not depending on the value of the damping dissipation parameter. For fronts with a more general shape, we present numerical simulations showing the same behavior.

9. Elucidation of population and coherence dynamics using cross-peaks in two-dimensional electronic spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Cheng, Y.-C.; Engel, Gregory S. [Department of Chemistry and QB3 Institute, University of California, Berkeley (United States) and Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Fleming, Graham R. [Department of Chemistry and QB3 Institute, University of California, Berkeley (United States) and Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)], E-mail: GRFleming@lbl.gov

2007-11-15

In this work, we perform a theoretical study on the dynamics and two-dimensional electronic spectroscopy of a model trimer system and compare the results to experimental data on the Fenna-Matthews-Olson protein. We combine a time-nonlocal quantum master equation formalism and the recently developed method for the efficient calculation of third-order photon echo polarization [M.F. Gelin, D. Egorova, W.J. Domcke, J. Chem. Phys. 123 (2005) 164112] to simulate the 2D electronic spectra of the model system, and compare the time-evolution of the amplitude of cross-peaks to the coherent relaxation dynamics of the system following the excitation by a laser pulse. We show that beats of the upper diagonal peaks in the absolute value 2D spectra provide a direct probe for the coherence dynamics in the system, and the time-evolution of the amplitude of the lower diagonal cross-peaks in the real value 2D spectra can be used to reveal the population transfer among exciton states. Our results verify the intuitive description provided by response functions and demonstrate that the full coherent dynamics in a multichromophoric system can be elucidated using two-dimensional electronic spectroscopy.

10. Stochastic Vortex Dynamics in Two-Dimensional Easy Plane Ferromagnets: Multiplicative Versus Additive Noise

Energy Technology Data Exchange (ETDEWEB)

Kamppeter, T.; Mertens, F.G.; Moro, E.; Sanchez, A.; Bishop, A.R.

1998-09-01

We study how thermal fluctuations affect the dynamics of vortices in the two-dimensional anisotropic Heisenberg model depending on their additive or multiplicative character. Using a collective coordinate theory, we analytically show that multiplicative noise, arising from fluctuations in the local field term of the Landau-Lifshitz equations, and Langevin-like additive noise have the same effect on vortex dynamics (within a very plausible assumption consistent with the collective coordinate approach). This is a highly non-trivial result as multiplicative and additive noises usually modify the dynamics in very different ways. We also carry out numerical simulations of both versions of the model finding that they indeed give rise to very similar vortex dynamics.

11. Nonequilibrium critical dynamics of the two-dimensional Ising model quenched from a correlated initial state.

Science.gov (United States)

Környei, László; Pleimling, Michel; Iglói, Ferenc

2008-01-01

The universality class, even the order of the transition, of the two-dimensional Ising model depends on the range and the symmetry of the interactions (Onsager model, Baxter-Wu model, Turban model, etc.), but the critical temperature is generally the same due to self-duality. Here we consider a sudden change in the form of the interaction and study the nonequilibrium critical dynamical properties of the nearest-neighbor model. The relaxation of the magnetization and the decay of the autocorrelation function are found to display a power law behavior with characteristic exponents that depend on the universality class of the initial state.

12. Dynamics in discrete two-dimensional nonlinear Schrödinger equations in the presence of point defects

DEFF Research Database (Denmark)

Christiansen, Peter Leth; Gaididei, Yuri Borisovich; Rasmussen, Kim

1996-01-01

The dynamics of two-dimensional discrete structures is studied in the framework of the generalized two-dimensional discrete nonlinear Schrodinger equation. The nonlinear coupling in the form of the Ablowitz-Ladik nonlinearity and point impurities is taken into account. The stability properties...

13. Dynamics and Structure of Disordered Peptides from Two-Dimensional Infrared Spectroscopy

Science.gov (United States)

Reppert, Mike; Lessing, Joshua; Peng, Chunte; Jones, Kevin; Baiz, Carlos; Tokmakoff, Andrei

2012-02-01

Two-dimensional infrared (IR) spectroscopy is a powerful tool for investigating the ultra-fast dynamics and association of complex biological macromolecules such as proteins and DNA. In addition to the improved spectral discrimination afforded by a two-dimensional spectrum, the ultra-fast time-resolution inherent to the technique provides unique insight (unobtainable by standard linear IR measurements) into the time-scales of macromolecular conformational fluctuations, particularly for intrinsically disordered systems. Here we discuss the use of accurate line shape modeling of peptide amide I vibrations as an advanced method for extracting structural and dynamic information from experimental spectra. The mixed quantum-classical model makes use of standard MD trajectories and a parametrized site energy and coupling map as inputs for excitonic calculations of the delocalized amide I vibrations. We present examples of the application of this method to extract site-specific structural information (such as hydrogen bond number and turn conformation) as well as insight into conformation dynamics and time-scales from experimental data for disordered peptides.

14. Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

CERN Document Server

Butkus, Vytautas; Augulis, Ramūnas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Zigmantas, Donatas; Valkunas, Leonas; Abramavicius, Darius

2015-01-01

The energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on the femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of ${\\rm Q}_{y}$ transitions of chlorophylls $a$ and $c$. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) $a$ and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the ${\\rm Q}_{y}$ transition of Chl $c$ revealed previously not identified mutually non-interacting chlorophyll $c$ states participating in femtosecond or picosecond energy transfer to the Chl $a$ molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the v...

15. Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study.

Science.gov (United States)

Butkus, Vytautas; Gelzinis, Andrius; Augulis, Ramūnas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Zigmantas, Donatas; Valkunas, Leonas; Abramavicius, Darius

2015-06-07

Energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Qy transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Qy transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.

16. Structures and Dynamics of a Two-Dimensional Confined Dusty Plasma System

Institute of Scientific and Technical Information of China (English)

HUANG Feng; LIU Yan-Hong; WANG Long

2005-01-01

The influence of the confining potential strength and temperature on the structures and dynamics of a two-dimensional (2D) dusty plasma system is investigated through molecular dynamic (MD) simulation. The circular symmetric confining potential leads to the nonuniform packing of particles, that is, an inner core with a hexagon lattice surrounded by a few outer circular shells. Under the appropriate confining potential and temperature, the particle trajectories on middle shells form a series of concentric and nested hexagons due to tangential movements of particles.Mean square displacement, self-diffusion constant, pair correlation function, and the nearest bond are used to characterize the structural and dynamical properties of the system. With the increase of the confining potential, the radial and tangential movements of particles have different behaviors. With the increase of temperature, the radial and tangential motions strengthen, particle trajectories gradually become disordered, and the system gradually changes from a crystal or liquid state to a gas state.

17. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

KAUST Repository

Lipková, Jana

2011-01-01

A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.

18. Glassy dynamics of Brownian particles with velocity-dependent friction

Science.gov (United States)

Yazdi, Anoosheh; Sperl, Matthias

2016-09-01

We consider a two-dimensional model system of Brownian particles in which slow particles are accelerated while fast particles are damped. The motion of the individual particles is described by a Langevin equation with Rayleigh-Helmholtz velocity-dependent friction. In the case of noninteracting particles, the time evolution equations lead to a non-Gaussian velocity distribution. The velocity-dependent friction allows negative values of the friction or energy intakes by slow particles, which we consider active motion, and also causes breaking of the fluctuation dissipation relation. Defining the effective temperature proportional to the second moment of velocity, it is shown that for a constant effective temperature the higher the noise strength, the lower the number of active particles in the system. Using the Mori-Zwanzig formalism and the mode-coupling approximation, the equations of motion for the density autocorrelation function are derived. The equations are solved using the equilibrium structure factors. The integration-through-transients approach is used to derive a relation between the structure factor in the stationary state considering the interacting forces, and the conventional equilibrium static structure factor.

19. Switching dynamics of a two-dimensional nonlinear couplers in a photopolymer – A variational approach

T Uthayakumar; K Porsezian

2010-11-01

We study the optical switching of the two-dimensional nonlinear coupler in a doped photopolymer. The coupled nonlinear Schrödinger equations (CNLSEs) describing our coupler system are analysed using Lagrangian variational method. From the Lagrangian, a set of coupled ordinary differential equations (ODEs) describing the system dynamics is obtained. This set of ODE’s is further reduced to single coupled equation and an analytical solution is obtained using the cnoidal functions and the system dynamics is studied. The key factor for switching mechanism of our coupler system is the metal-induced surface plasmon resonance (SPR). This SPR-induced local nonlinear effects results in self-focussing of the optical beam through the launched core. A description of a particle in a well is also made to study the photon switching through the coupler system.

20. Molecular shear heating and vortex dynamics in thermostatted two-dimensional Yukawa liquids

CERN Document Server

Gupta, Akanksha; Joy, Ashwin

2016-01-01

It is well known that two-dimensional macroscale shear flows are susceptible to instabilities leading to macroscale vortical structures. The linear and nonlinear fate of such a macroscale flow in a strongly coupled medium is a fundamental problem. A popular example of a strongly coupled medium is a dusty plasma, often modelled as a Yukawa liquid. Recently, laboratory experiments and MD studies of shear flows in strongly coupled Yukawa liquids, indicated occurrence of strong molecular shear heating, which is found to reduce the coupling strength exponentially leading to destruction of macroscale vorticity. To understand the vortex dynamics of strongly coupled molecular fluids undergoing macroscale shear flows and molecular shear heating, MD simulation has been performed, which allows the macroscopic vortex dynamics to evolve while at the same time, "removes" the microscopically generated heat without using the velocity degrees of freedom. We demonstrate that by using a configurational thermostat in a novel way...

1. CO2 selective dynamic two-dimensional Zn(II) coordination polymer.

Science.gov (United States)

Hwang, In Hong; Bae, Jeong Mi; Hwang, Yong-Kyung; Kim, Ha-Yeong; Kim, Cheal; Huh, Seong; Kim, Sung-Jin; Kim, Youngmee

2013-11-28

A CO2 selective dynamic two-dimensional (2D) MOF system, [Zn(glu)(μ-bpe)]·2H2O (·2H2O) (glu = glutarate, bpe = 1,2-bis(4-pyridyl)ethylene), is prepared. Based on variable temperature PXRD patterns, I·2H2O exhibits a structural transformation of the framework upon desolvation. Various gas sorption analyses at low temperatures reveal that solvent-free I selectively adsorbs CO2 over N2, H2, and CH4. Stepped CO2 isotherms for solvent-free I with a large hysteresis between adsorption and desorption branches at 196 K indicate that I is a dynamic framework. Moreover, I·2H2O shows efficient heterogeneous catalytic reactivity for transesterification of various esters. The catalyst can be recycled multiple times without losing its original activity.

2. Piezoelectricity in two-dimensional materials: Comparative study between lattice dynamics and ab initio calculations

Science.gov (United States)

Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.

2017-03-01

The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.

3. Response Functions for the Two-Dimensional Ultracold Fermi Gas: Dynamical BCS Theory and Beyond

Science.gov (United States)

Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

2017-08-01

Response functions are central objects in physics. They provide crucial information about the behavior of physical systems, and they can be directly compared with scattering experiments involving particles such as neutrons or photons. Calculations of such functions starting from the many-body Hamiltonian of a physical system are challenging and extremely valuable. In this paper, we focus on the two-dimensional (2D) ultracold Fermi atomic gas which has been realized experimentally. We present an application of the dynamical BCS theory to obtain response functions for different regimes of interaction strengths in the 2D gas with zero-range attractive interaction. We also discuss auxiliary-field quantum Monte Carlo (AFQMC) methods for the calculation of imaginary time correlations in these dilute Fermi gas systems. Illustrative results are given and comparisons are made between AFQMC and dynamical BCS theory results to assess the accuracy of the latter.

4. Dynamical Mechanism of Two-Dimensional Plasmon Launching by Swift Electrons

CERN Document Server

Lin, Xiao; Gao, Fei; Kaminer, Ido; Yang, Zhaoju; Gao, Zhen; Buljan, Hrvoje; Joannopoulos, John D; Soljačić, Marin; Chen, Hongsheng; Zhang, Baile

2015-01-01

Launching of surface plasmons by swift electrons has long been utilized to investigate plasmonic properties of ultrathin, or two-dimensional (2D), electron systems, including graphene plasmons recently. However, spatio-temporal dynamics of this process has never been clearly revealed. This is because the impact of an electron will generate not only plasmons, but also photons, demanding both space and time. Here we address this issue within the framework of classical electromagnetics by showing the dynamical process of 2D plasmon launching by swift electrons on graphene. The launching of 2D plasmons on graphene is not immediate, but is delayed after a hydrodynamic splashing-like process, which occurs during the formation time of transition radiation caused by the electron's impact. This newly revealed process also implies that all previous estimates on the yields of graphene plasmons in electron-energy-loss-spectroscopy have been overestimated.

5. CYCLIC HARDENING BEHAVIOR OF POLYCRYSTALS WITH PENETRABLE GRAIN BOUNDARIES: TWO-DIMENSIONAL DISCRETE DISLOCATION DYNAMICS SIMULATION

Institute of Scientific and Technical Information of China (English)

Chuantao Hou; Zhenhuan Li; Minsheng Huang; Chaojun Ouyang

2009-01-01

A two-dimensional discrete dislocation dynamics (DDD) technology by Giessen and Needleman (1995), which has been extended by integrating a dislocation-grain boundary interaction model, is used to computationally analyze the micro-cyclic plastic response of polycrystals containing micron-sized grains, with special attentions to significant influence of dislocationpenetrable grain boundaries (GBs) on the micro-plastic cyclic responses of polycrystals and underlying dislocation mechanism. Toward this end, a typical polycrystalline rectangular specimen under simple tension-compression loading is considered. Results show that, with the increase of cycle accumulative strain, continual dislocation accumulation and enhanced dislocation-dislocation interactions induce the cyclic hardening behavior; however, when a dynamic balance among dislocation nucleation, penetration through GB and dislocation annihilation is approximately established, cyclic stress gradually tends to saturate. In addition, other factors, including the grain size, cyclic strain amplitude and its history, also have considerable influences on the cyclic hardening and saturation.

6. Identification of the dynamics of a two-dimensional grid structure using least square lattice filters

Science.gov (United States)

Montgomery, R. C.; Sundararajan, N.

1984-01-01

The basic theory of least square lattice filters and their use in identification of structural dynamics systems is summarized. Thereafter, this theory is applied to a two-dimensional grid structure made of overlapping bars. Previously, this theory has been applied to an integral beam. System identification results are presented for both simulated and experimental tests and they are compared with those predicted using finite element modelling. The lattice filtering approach works well for simulated data based on finite element modelling. However, considerable discrepancy exists between estimates obtained from experimental data and the finite element analysis. It is believed that this discrepancy is the result of inadequacies in the finite element modelling to represent the damped motion of the laboratory apparatus.

7. Coarse-grained single-particle dynamics in two-dimensional solids and liquids.

Science.gov (United States)

Silbermann, Jörg R; Schoen, Martin; Klapp, Sabine H L

2008-07-01

We consider the dynamics of a single tagged particle in a two-dimensional system governed by Lennard-Jones interactions. Previous work based on the Mori-Zwanzig projection operator formalism has shown that the single-particles dynamics can be described via a generalized Langevin equation (GLE) which is exact within the harmonic approximation, that is, for a low-temperature solid [J. M. Deutch and R. Silbey, Phys. Rev. A 3, 2049 (1971)]. In the present work we explore to what an extent the GLE reproduces the effective dynamics under thermodynamic conditions where the harmonic approximation is no longer justified. To this end we compute characteristic time autocorrelation functions for the tagged particle in molecular dynamics simulations of the full system and compare these functions with those obtained from solving the GLE. At low temperatures we find excellent agreement between both data sets. Deviations emerge at higher temperatures which are, however, surprisingly small even in the high-temperature liquid phase.

8. Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

Energy Technology Data Exchange (ETDEWEB)

Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Augulis, Ramūnas [Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Gall, Andrew; Robert, Bruno [Institut de Biologie et Technologies de Saclay, Bât 532, Commissariat à l’Energie Atomique Saclay, 91191 Gif sur Yvette (France); Büchel, Claudia [Institut für Molekulare Biowissenschaften, Universität Frankfurt, Max-von-Laue-Straße 9, Frankfurt (Germany); Zigmantas, Donatas [Department of Chemical Physics, Lund University, P.O. Box 124, 22100 Lund (Sweden); Abramavicius, Darius, E-mail: darius.abramavicius@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania)

2015-06-07

Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{sub y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.

9. Design considerations for pulsed-flow comprehensive two-dimensional GC: dynamic flow model approach.

Science.gov (United States)

2010-04-01

A dynamic flow model, which maps carrier gas pressures and carrier gas flow rates through the first dimension separation column, the modulator sample loop, and the second dimension separation column(s) in a pulsed-flow modulation comprehensive two-dimensional gas chromatography (PFM-GCxGC) system is described. The dynamic flow model assists design of a PFM-GCxGC modulator and leads to rapid determination of pneumatic conditions, timing parameters, and the dimensions of the separation columns and connecting tubing used to construct the PFM-GCxGC system. Three significant innovations are introduced in this manuscript, which were all uncovered by using the dynamic flow model. A symmetric flow path modulator improves baseline stability, appropriate selection of the flow restrictors in the first dimension column assembly provides a generally more stable and robust system, and these restrictors increase the modulation period flexibility of the PFM-GCxGC system. The flexibility of a PFM-GCxGC system resulting from these innovations is illustrated using the same modulation interface to analyze Special Antarctic Blend (SAB) diesel using 3 s and 9 s modulation periods.

10. Emergent topology and dynamical quantum phase transitions in two-dimensional closed quantum systems

Science.gov (United States)

Bhattacharya, Utso; Dutta, Amit

2017-07-01

Dynamical quantum phase transitions (DQPTs) manifested in the nonanalyticities in the temporal evolution of a closed quantum system generated by the time-independent final Hamiltonian, following a quench (or ramping) of a parameter of the Hamiltonian, is an emerging frontier of nonequilibrium quantum dynamics. We, here, introduce the notion of a dynamical topological order parameter (DTOP) that characterizes these DQPTs occurring in quenched (or ramped) two-dimensional closed quantum systems; this is quite a nontrivial generalization of the notion of DTOP introduced in Budich and Heyl [Phys. Rev. B 93, 085416 (2016), 10.1103/PhysRevB.93.085416] for one-dimensional situations. This DTOP is obtained from the "gauge-invariant" Pancharatnam phase extracted from the Loschmidt overlap, i.e., the modulus of the overlap between the initially prepared state and its time-evolved counterpart reached following a temporal evolution generated by the time-independent final Hamiltonian. This generic proposal is illustrated considering DQPTs occurring in the subsequent temporal evolution following a sudden quench of the staggered mass of the topological Haldane model on a hexagonal lattice where it stays fixed to zero or unity and makes a discontinuous jump between these two values at critical times at which DQPTs occur. What is remarkable is that while the topology of the equilibrium model is characterized by the Chern number, the emergent topology associated with the DQPTs is characterized by a generalized winding number.

11. Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy

Science.gov (United States)

De Marco, Luigi; Fournier, Joseph A.; Thämer, Martin; Carpenter, William; Tokmakoff, Andrei

2016-09-01

Water's extended hydrogen-bond network results in rich and complex dynamics on the sub-picosecond time scale. In this paper, we present a comprehensive analysis of the two-dimensional infrared (2D IR) spectrum of O-H stretching vibrations in liquid H2O and their interactions with bending and intermolecular vibrations. By exploring the dependence of the spectrum on waiting time, temperature, and laser polarization, we refine our molecular picture of water's complex ultrafast dynamics. The spectral evolution following excitation of the O-H stretching resonance reveals vibrational dynamics on the 50-300 fs time scale that are dominated by intermolecular delocalization. These O-H stretch excitons are a result of the anharmonicity of the nuclear potential energy surface that arises from the hydrogen-bonding interaction. The extent of O-H stretching excitons is characterized through 2D depolarization measurements that show spectrally dependent delocalization in agreement with theoretical predictions. Furthermore, we show that these dynamics are insensitive to temperature, indicating that the exciton dynamics alone set the important time scales in the system. Finally, we study the evolution of the O-H stretching mode, which shows highly non-adiabatic dynamics suggestive of vibrational conical intersections. We argue that the so-called heating, commonly observed within ˜1 ps in nonlinear IR spectroscopy of water, is a nonequilibrium state better described by a kinetic temperature rather than a Boltzmann distribution. Our conclusions imply that the collective nature of water vibrations should be considered in describing aqueous solvation.

12. Coupling effect of Brownian motion and laminar shear flow on colloid coagulation: a Brownian dynamics simulation study

Institute of Scientific and Technical Information of China (English)

Xu Sheng-Hua; Sun Zhi-Wei; Li Xu; Jin Tong Wang

2012-01-01

Simultaneous orthokinetic and perikinetic coagulations(SOPCs)are studied for small and large Peclet numbers(Pe)using Brownian dynamics simulation.The results demonstrate that the contributions of the Brownian motion and the shear flow to the overall coagulation rate are basically not additive.At the early stages of coagulation with small Peclet numbers,the ratio of overall coagulation rate to the rate of pure perikinetic coagulation is proportional to Pe1/2,while with high Peclet numbers,the ratio of overall coagulation rate to the rate of pure orthokinetic coagulation is proportional to pe-1/2.Moreover,our results show that the aggregation rate generally changes with time for the SOPC,which is different from that for pure preikinetic and pure orthokinetic coagulations.By comparing the SOPC with pure preikinetic and pure orthokinetic coagulations,we show that the redistribution of particles due to Brownian motion can play a very important role in the SOPC.In addition,the effects of redistribution in the directions perpendicular and parallel to the shear flow direction are different.This perspective explains the behavior of coagulation due to the joint effects of the Brownian motion(perikinetic)and the fluid motion(orthokinetic).

13. Momentum conserving Brownian dynamics propagator for complex soft matter fluids

Energy Technology Data Exchange (ETDEWEB)

Padding, J. T. [Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven (Netherlands); Briels, W. J. [Computational Biophysics, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

2014-12-28

We present a Galilean invariant, momentum conserving first order Brownian dynamics scheme for coarse-grained simulations of highly frictional soft matter systems. Friction forces are taken to be with respect to moving background material. The motion of the background material is described by locally averaged velocities in the neighborhood of the dissolved coarse coordinates. The velocity variables are updated by a momentum conserving scheme. The properties of the stochastic updates are derived through the Chapman-Kolmogorov and Fokker-Planck equations for the evolution of the probability distribution of coarse-grained position and velocity variables, by requiring the equilibrium distribution to be a stationary solution. We test our new scheme on concentrated star polymer solutions and find that the transverse current and velocity time auto-correlation functions behave as expected from hydrodynamics. In particular, the velocity auto-correlation functions display a long time tail in complete agreement with hydrodynamics.

14. Diffusion in crowded biological environments: applications of Brownian dynamics

Directory of Open Access Journals (Sweden)

Długosz Maciej

2011-03-01

Full Text Available Abstract Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.

15. Momentum conserving Brownian dynamics propagator for complex soft matter fluids.

Science.gov (United States)

Padding, J T; Briels, W J

2014-12-28

We present a Galilean invariant, momentum conserving first order Brownian dynamics scheme for coarse-grained simulations of highly frictional soft matter systems. Friction forces are taken to be with respect to moving background material. The motion of the background material is described by locally averaged velocities in the neighborhood of the dissolved coarse coordinates. The velocity variables are updated by a momentum conserving scheme. The properties of the stochastic updates are derived through the Chapman-Kolmogorov and Fokker-Planck equations for the evolution of the probability distribution of coarse-grained position and velocity variables, by requiring the equilibrium distribution to be a stationary solution. We test our new scheme on concentrated star polymer solutions and find that the transverse current and velocity time auto-correlation functions behave as expected from hydrodynamics. In particular, the velocity auto-correlation functions display a long time tail in complete agreement with hydrodynamics.

16. On the two-dimensional dynamical Ising model in the phase coexistence region

Science.gov (United States)

Martinelli, F.

1994-09-01

We consider a Glauber dynamics reversible with respect to the two-dimensional Ising model in a finite square of side L, in the absence of an external field and at large inverse temperature β. We first consider the gap in the spectrum of the generator of the dynamics in two different cases: with plus and open boundary conditions. We prove that, when the symmetry under global spin flip is broken by the boundary conditions, the gap is much larger than the case in which the symmetry is present. For this latter we compute exactly the asymptotics of -(1/β L) log(gap) as L→∞ and show that it coincides with the surface tension along one of the coordinate axes. As a consequence we are able to study quite precisely the large deviations in time of the magnetization and to obtain an upper bound on the spin-spin time correlation in the infinite-volume plus phase. Our results establish a connection between the dynamical large deviations and those of the equilibrium Gibbs measure studied by Shlosman in the framework of the rigorous description of the Wulff shape for the Ising model. Finally we show that, in the case of open boundary conditions, it is possible to rescale the time with L in such a way that, as L→∞, the finite-dimensional distributions of the time-rescaled magnetization converge to those of a symmetric continuous-time Markov chain on the two-state space {- m *(β), m *(β)}, m *(β) being the spontaneous magnetization. Our methods rely upon a novel combination of techniques for bounding from below the gap of symmetric Markov chains on complicated graphs, developed by Jerrum and Sinclair in their Markov chain approach to hard computational problems, and the idea of introducing "block Glauber dynamics" instead of the standard single-site dynamics, in order to put in evidence more effectively the effect of the boundary conditions in the approach to equilibrium.

17. Nonequilibrium critical dynamics of the two-dimensional Ashkin-Teller model at the Baxter line

Science.gov (United States)

Fernandes, H. A.; da Silva, R.; Caparica, A. A.; de Felício, J. R. Drugowich

2017-04-01

We investigate the short-time universal behavior of the two-dimensional Ashkin-Teller model at the Baxter line by performing time-dependent Monte Carlo simulations. First, as preparatory results, we obtain the critical parameters by searching the optimal power-law decay of the magnetization. Thus, the dynamic critical exponents θm and θp, related to the magnetic and electric order parameters, as well as the persistence exponent θg, are estimated using heat-bath Monte Carlo simulations. In addition, we estimate the dynamic exponent z and the static critical exponents β and ν for both order parameters. We propose a refined method to estimate the static exponents that considers two different averages: one that combines an internal average using several seeds with another, which is taken over temporal variations in the power laws. Moreover, we also performed the bootstrapping method for a complementary analysis. Our results show that the ratio β /ν exhibits universal behavior along the critical line corroborating the conjecture for both magnetization and polarization.

18. Superfluidity and relaxation dynamics of a laser-stirred two-dimensional Bose gas

Science.gov (United States)

Singh, Vijay Pal; Weitenberg, Christof; Dalibard, Jean; Mathey, Ludwig

2017-04-01

We investigate the superfluid behavior of a two-dimensional (2D) Bose gas of 87Rb atoms using classical field dynamics. In the experiment by R. Desbuquois et al. [Nat. Phys. 8, 645 (2012), 10.1038/nphys2378], a 2D quasicondensate in a trap is stirred with a blue-detuned laser beam along a circular path around the trap center. Here, we study this experiment from a theoretical perspective. The heating induced by stirring increases rapidly above a velocity vc, which we define as the critical velocity. We identify the superfluid, the crossover, and the thermal regime by a finite, a sharply decreasing, and a vanishing critical velocity, respectively. We demonstrate that the onset of heating occurs due to the creation of vortex-antivortex pairs. A direct comparison of our numerical results to the experimental ones shows a good agreement, if a systematic shift of the critical phase-space density is included. We relate this shift to the absence of thermal equilibrium between the condensate and the thermal wings, which were used in the experiment to extract the temperature. We expand on this observation by studying the full relaxation dynamics between the condensate and the thermal cloud.

19. Spin dynamics and magnetic correlation length in two-dimensional quantum heisenberg antiferromagnets

Science.gov (United States)

Carretta; Ciabattoni; Cuccoli; Mognaschi; Rigamonti; Tognetti; Verrucchi

2000-01-10

The correlated spin dynamics and temperature dependence of the correlation length xi(T) in two-dimensional quantum (S = 1/2) Heisenberg antiferromagnets (2DQHAF) on a square lattice are discussed in light of experimental results of proton spin lattice relaxation in copper formiate tetradeuterate. In this compound the exchange constant is much smaller than the one in recently studied 2DQHAF, such as La2CuO4 and Sr2CuO2Cl2. Thus the spin dynamics can be probed in detail over a wider temperature range. The NMR relaxation rates turn out to be in excellent agreement with a theoretical mode-coupling calculation. The deduced temperature behavior of xi(T) is in agreement with high-temperature expansions, quantum Monte Carlo simulations, and the pure quantum self-consistent harmonic approximation. Contrary to the predictions of the theories based on the nonlinear sigma model, no evidence of crossover between different quantum regimes is observed.

20. Two-dimensional NMR investigations of the dynamic conformations of phospholipids and liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Hong, Mei [Univ. of California, Berkeley, CA (United States). Applied Science and Technology

1996-05-01

Two-dimensional 13C, 1H, and 31P nuclear magnetic resonance (NMR) techniques are developed and used to study molecular structure and dynamics in liquid-crystalline systems, primarily phospholipids and nematic liquid crystals. NMR spectroscopy characterizes molecular conformation in terms of orientations and distances of molecular segments. In anisotropically mobile systems, this is achieved by measuring motionally-averaged nuclear dipolar couplings and chemical shift anisotropies. The short-range couplings yield useful bond order parameters, while the long-range interactions constrain the overall conformation. In this work, techniques for probing proton dipolar local fields are further developed to obtain highlyresolved dipolar couplings between protons and rare spins. By exploiting variable-angle sample spinning techniques, orientation-sensitive NMR spectra are resolved according to sitespecific isotropic chemical shifts. Moreover, the signs and magnitudes of various short-range dipolar couplings are obtained. They are used in novel theoretical analyses that provide information about segmental orientations and their distributions. Such information is obtained in a model-independent fashion or with physically reasonable assumptions. The structural investigation of phospholipids is focused on the dynam

1. Nonequilibrium critical dynamics of two dimensional interacting monomer-dimer model: non-Ising criticality

Science.gov (United States)

Nam, Keekwon; Kim, Bongsoo; Jong Lee, Sung

2014-08-01

We investigate the nonequilibrium relaxation dynamics of an interacting monomer-dimer model with nearest neighbor repulsion on a square lattice, which possesses two symmetric absorbing states. The model is known to exhibit two nearby continuous transitions: the Z2 symmetry-breaking order-disorder transition and the absorbing transition with directed percolation criticality. We performed a more detailed analysis of our extensive simulations on bigger lattice systems which reaffirms that the symmetry-breaking transition exhibits a non-Ising critical behavior with β ≃ 0.149(2) and η ≃ 0.30(1) that are distinct from those values of a pure two dimensional Ising model. Finite size scaling of dimer density near the symmetry breaking transition gives logarithmic scaling (α = 0.0) which is consistent with the hyperscaling relation but the corresponding exponent of νB ≃ 1.37(2) exhibits a conspicuous deviation from the pure Ising value of 1. The value of dynamic critical exponent z, however, is found to be close to that of the kinetic Ising model as 1/z ≃ 0.466(5) from the relaxation of staggered magnetization (and also similar but slightly smaller values from coarsening).

2. Reverse of mixing process with a two-dimensional electro-fluid-dynamic device.

Science.gov (United States)

Liu, Chang; Luo, Yong; Maxwell, E Jane; Fang, Ning; Chen, David D Y

2010-03-15

Mixing of two solutions into one is a spontaneous process with a net increase in entropy. However, the reverse of the mixing process is usually not possible unless certain conditions are met. A continuous solution stream containing a mixture of two compounds can be separated into two channels, each containing a pure compound, thus reversing the mixing process using a two-dimensional microfluidic electro-fluid-dynamic (EFD) device. When the electric field is strategically applied in the interconnecting channels of an EFD device, the pressure required to direct an analyte into a certain channel can be calculated by using the solutions of electric field and fluid dynamics in the mass balance equation. If the pressure and electric potential at various inlets and outlets satisfy these predetermined conditions, the reverse of a mixing process is observed. Conventional microfluidic devices have been used to introduce samples from interconnecting channels or efficiently mix different solutions into a single channel. The EFD devices expand the spatial separation of analytes from one dimension to two using both the differential migration behavior of analytes and the velocity field distribution in different channel geometries. The devices designed according to these basic physicochemical principles can be used for complete processing of minute samples and to obtain pure chemical species from complex mixtures.

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

Energy Technology Data Exchange (ETDEWEB)

Méndez-Bermúdez, J.A. [Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apartado Postal J-48, Puebla 72570 (Mexico); Oliveira, Juliano A. de [UNESP – Univ. Estadual Paulista, Câmpus de São João da Boa Vista, Av. Professora Isette Corrêa Fontão, 505, Jardim Santa Rita das Areias, 13876-750 São João da Boa Vista, SP (Brazil); Leonel, Edson D. [Departamento de Física, UNESP – Univ. Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP (Brazil); Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste (Italy)

2016-05-20

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

4. A two-dimensional global simulation study of inductive-dynamic magnetosphere-ionosphere coupling

Science.gov (United States)

Tu, Jiannan; Song, Paul

2016-12-01

We present the numerical methods and results of a global two-dimensional multifluid-collisional-Hall magnetohydrodynamic (MHD) simulation model of the ionosphere-thermosphere system, an extension of our one-dimensional three-fluid MHD model. The model solves, self-consistently, Maxwell's equations, continuity, momentum, and energy equations for multiple ion and neutral species incorporating photochemistry, collisions among the electron, ion and neutral species, and various heating sources in the energy equations. The inductive-dynamic approach (solving self-consistently Faraday's law and retaining inertia terms in the plasma momentum equations) used in the model retains all possible MHD waves, thus providing faithful physical explanation (not merely description) of the magnetosphere-ionosphere/thermosphere (M-IT) coupling. In the present study, we simulate the dawn-dusk cross-polar cap dynamic responses of the ionosphere to imposed magnetospheric convection. It is shown that the convection velocity at the top boundary launches velocity, magnetic, and electric perturbations propagating with the Alfvén speed toward the bottom of the ionosphere. Within the system, the waves experience reflection, penetration, and rereflection because of the inhomogeneity of the plasma conditions. The reflection of the Alfvén waves may cause overshoot (stronger than the imposed magnetospheric convection) of the plasma velocity in some regions. The simulation demonstrates dynamic propagation of the field-aligned currents and ionospheric electric field carried by the Alfvén waves, as well as formation of closure horizontal currents (Pedersen currents in the E region), indicating that in the dynamic stage the M-I coupling is via the Alfvén waves instead of field-aligned currents or electric field mapping as described in convectional M-I coupling models.

5. Two-dimensional fully dynamic SEM simulations of the 2011 Tohoku earthquake cycle

Science.gov (United States)

Shimizu, H.; Hirahara, K.

2014-12-01

Earthquake cycle simulations have been performed to successfully reproduce the historical earthquake occurrences. Most of them are quasi-dynamic, where inertial effects are approximated using the radiation damping proposed by Rice [1993]. Lapusta et al. [2000, 2009] developed a methodology capable of the detailed description of seismic and aseismic slip and gradual process of earthquake nucleation in the entire earthquake cycle. Their fully dynamic simulations have produced earthquake cycles considerably different from quasi-dynamic ones. Those simulations have, however, never been performed for interplate earthquakes at subduction zones. Many studies showed that on dipping faults such as interplate earthquakes at subduction zones, normal stress is changed during faulting due to the interaction with Earth's free surface. This change in normal stress not only affects the earthquake rupture process, but also causes the residual stress variation that might affect the long-term histories of earthquake cycle. Accounting for such effects, we perform two-dimensional simulations of the 2011 Tohoku earthquake cycle. Our model is in-plane and a laboratory derived rate and state friction acts on a dipping fault embedded on an elastic half-space that reaches the free surface. We extended the spectral element method (SEM) code [Ampuero, 2002] to incorporate a conforming mesh of triangles and quadrangles introduced in Komatitsch et al. [2001], which enables us to analyze the complex geometry with ease. The problem is solved by the methodology almost the same as Kaneko et al. [2011], which is the combined scheme switching in turn a fully dynamic SEM and a quasi-static SEM. The difference is the dip-slip thrust fault in our study in contrast to the vertical strike slip fault. With this method, we can analyze how the dynamic rupture with surface breakout interacting with the free surface affects the long-term earthquake cycle. We discuss the fully dynamic earthquake cycle results

6. Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals.

Science.gov (United States)

Suzuki, Yuta; Cardone, Giovanni; Restrepo, David; Zavattieri, Pablo D; Baker, Timothy S; Tezcan, F Akif

2016-05-19

Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge and an active area of development. More challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamic behaviour in porous three-dimensional (3D) crystalline solids has been exploited for stimuli-responsive functions and adaptive behaviour. As in such 3D materials, integrating flexibility and adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns using a readily accessible design strategy. Three single- or double-point mutants of the C4-symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single-disulfide, double-disulfide and metal-coordination) into crystalline 2D arrays. Owing to the flexibility of the single-disulfide interactions, the lattices of one of the variants ((C98)RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. (C98)RhuA lattices display a Poisson's ratio of -1-the lowest thermodynamically possible value for an isotropic material-making them auxetic.

7. Two-dimensional FSI simulation of closing dynamics of a tilting disc mechanical heart valve.

Science.gov (United States)

Govindarajan, V; Udaykumar, H S; Herbertson, L H; Deutsch, S; Manning, K B; Chandran, K B

2010-03-01

The fluid dynamics during valve closure resulting in high shear flows and large residence times of particles has been implicated in platelet activation and thrombus formation in mechanical heart valves. Our previous studies with bi-leaflet valves have shown that large shear stresses induced in the gap between the leaflet edge and the valve housing results in relatively high platelet activation levels whereas flow between the leaflets results in shed vortices not conducive to platelet damage. In this study we compare the result of closing dynamics of a tilting disc valve with that of a bi-leaflet valve. The two-dimensional fluid-structure interaction analysis of a tilting disc valve closure mechanics is performed with a fixed grid Cartesian mesh flow solver with local mesh refinement, and a Lagrangian particle dynamic analysis for computation of potential for platelet activation. Throughout the simulation the flow remains in the laminar regime and the flow through the gap width is marked by the development of a shear layer which separates from the leaflet downstream of the valve. Zones of re-circulation are observed in the gap between the leaflet edge and the valve housing on the major orifice region of the tilting disc valve and are seen to be migrating towards the minor orifice region. Jet flow is observed at the minor orifice region and a vortex is formed which sheds in the direction of fluid motion as observed in experiments using PIV measurements. The activation parameter computed for the tilting disc valve, at the time of closure was found to be 2.7 times greater than that of the bi-leaflet mechanical valve and was found to be in the vicinity of the minor orifice region mainly due to the migration of vortical structures from the major to the minor orifice region during the leaflet rebound of the closing phase.

8. Quenched dynamics of two-dimensional solitons and vortices in the Gross-Pitaevskii equation

CERN Document Server

Chen, Qian-Yong; Malomed, Boris A

2012-01-01

We consider a two-dimensional (2D) counterpart of the experiment that led to the creation of quasi-1D bright solitons in Bose-Einstein condensates (BECs) [Nature 417, 150--153 (2002)]. We start by identifying the ground state of the 2D Gross-Pitaevskii equation for repulsive interactions, with a harmonic-oscillator (HO) trap, and with or without an optical lattice (OL). Subsequently, we switch the sign of the interaction to induce interatomic attraction and monitor the ensuing dynamics. Regions of the stable self-trapping and catastrophic collapse of 2D fundamental solitons are identified in the parameter plane of the OL strength and BEC norm. The increase of the OL strength expands the persistence domain for the solitons to larger norms. For single-charged solitary vortices, in addition to the survival and collapse regimes, an intermediate one is identified, where the vortex resists the collapse but loses its structure, transforming into a fundamental soliton. The same setting may also be implemented in the ...

9. Dynamical transition in a jammed state of a quasi-two-dimensional foam

Science.gov (United States)

Kurita, Rei; Furuta, Yujiro; Yanagisawa, Naoya; Oikawa, Noriko

2017-06-01

The states of foam are empirically classified into dry foam and wet foam by the volume fraction of the liquid. Recently, a transition between the dry foam state and the wet foam state has been found by characterizing the bubble shapes [Furuta et al., Sci. Rep. 6, 37506 (2016), 10.1038/srep37506]. In the literature, it is indirectly ascertained that the transition from the dry to the wet form is related to the onset of the rearrangement of the bubbles, namely, the liquid fraction at which the bubbles become able to move to replace their positions. The bubble shape is a static property, and the rearrangement of the bubbles is a dynamic property. Thus, we investigate the relation between the bubble shape transition and the rearrangement event occurring in a collapsing process of the bubbles in a quasi-two-dimensional foam system. The current setup brings a good advantage to observe the above transitions, since the liquid fraction of the foam continuously changes in the system. It is revealed that the rearrangement of the bubbles takes place at the dry-wet transition point where the characteristics of the bubble shape change.

10. Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments.

Science.gov (United States)

Chelli, Riccardo; Volkov, Victor V; Righini, Roberto

2008-07-15

We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.

11. Ground-state and dynamical properties of two-dimensional dipolar Fermi liquids

Science.gov (United States)

Abedinpour, Saeed H.; Asgari, Reza; Tanatar, B.; Polini, Marco

2014-01-01

We study the ground-state properties of a two-dimensional spin-polarized fluid of dipolar fermions within the Euler-Lagrange Fermi-hypernetted-chain approximation. Our method is based on the solution of a scattering Schrödinger equation for the "pair amplitude" g(r), where g(r) is the pair distribution function. A key ingredient in our theory is the effective pair potential, which includes a bosonic term from Jastrow-Feenberg correlations and a fermionic contribution from kinetic energy and exchange, which is tailored to reproduce the Hartree-Fock limit at weak coupling. Very good agreement with recent results based on quantum Monte Carlo simulations is achieved over a wide range of coupling constants up to the liquid-to-crystal quantum phase transition. Using the fluctuation-dissipation theorem and a static approximation for the effective inter-particle interactions, we calculate the dynamical density-density response function, and furthermore demonstrate that an undamped zero-sound mode exists for any value of the interaction strength, down to infinitesimally weak couplings.

12. A two-dimensional protein map of Pleurotus ostreatus microsomes-proteome dynamics.

Science.gov (United States)

Petráčková, Denisa; Halada, Petr; Bezoušková, Silvia; Křesinová, Zdena; Svobodová, Kateřina

2016-01-01

Recent studies documented that several processes in filamentous fungi are connected with microsomal enzyme activities. In this work, microsomal subproteomes of Pleurotus ostreatus were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis. To assess proteome dynamics, microsomal proteins were isolated from fungal cultures after 7 and 12 days of cultivation. Additionally, 10 mg/L of 17α-ethinylestradiol (EE2) was treated with the cultures during 2 days. Despite the EE2 degradation by the fungus reached 97 and 76.3 % in 7- and 12-day-old cultures, respectively, only a minor effect on the composition of microsomal proteins was observed. The changes in protein maps related to ageing prevailed over those induced by EE2. Epoxide hydrolase, known to metabolize EE2, was detected in 12-day-old cultures only which suggests differences in EE2 degradation pathways utilized by fungal cultures of different age. The majority (32 %) of identified microsomal proteins were parts of mitochondrial energy metabolism.

13. PRONTO 2D: A two-dimensional transient solid dynamics program

Energy Technology Data Exchange (ETDEWEB)

Taylor, L.M.; Flanagan, D.P.

1987-03-01

PRONTO 2D is a two-dimensional transient solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Four node uniform strain quadrilateral elements are used in the finite element formulation. A number of new numerical algorithms which have been developed for the code are described in this report. An adaptive time step control algorithm is described which greatly improves stability as well as performance in plasticity problems. A robust hourglass control scheme which eliminates hourglass distortions without disturbing the finite element solution is included. All constitutive models in PRONTO are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. An accurate incremental algorithm was developed to determine this rotation and is described in detail. A robust contact algorithm was developed which allows for the impact and interaction of deforming contact surfaces of quite general geometry. A number of numerical examples are presented to demonstrate the utility of these algorithms. 41 refs., 51 figs., 5 tabs.

14. Detection of topological states in two-dimensional Dirac systems by the dynamic spin susceptibility

Science.gov (United States)

Nakamura, Masaaki; Tokuno, Akiyuki

2016-08-01

We discuss dynamic spin susceptibility (DSS) in two-dimensional (2D) Dirac electrons with spin-orbit interactions to characterize topological insulators. The imaginary part of the DSS appears as an absorption rate in response to a transverse ac magnetic field, just as in an electron spin resonance experiment for localized spin systems. We found that when the system is in a static magnetic field, the topological state can be identified by an anomalous resonant peak of the imaginary part of the DSS as a function of the frequency of the transverse magnetic field ω . In the absence of a static magnetic field, the imaginary part of the DSS becomes a continuous function of ω with a threshold frequency ωc. In this case, the topological and the trivial phases can also be distinguished by the values of ωc and by the line shapes. Thus the DSS is an experimentally observable physical quantity to characterize a topological insulator directly from bulk properties, without observing a topological transition.

15. Infiltration effects on a two-dimensional molecular dynamics model of landslides

CERN Document Server

Martelloni, Gianluca

2012-01-01

In this paper we propose a two-dimensional (2D) computational model, based on a molecular dynamics (MD) approach, for deep landslides triggered by rainfall. Our model is based on interacting particles or grains and describes the behavior of a fictitious granular material along a slope consisting of a vertical section, i.e. with a wide thickness. The triggering of the landslide is caused by the passing of two conditions: a threshold speed and a condition on the static friction of the particles, the latter based on the Mohr-Coulomb failure criterion (Coulomb 1776; Mohr 1914). The inter-particle interactions are through a potential that, in the absence of suitable experimental data and due to the arbitrariness of the grain dimension is modeled by means of a potential similar to the Lennard-Jones one (Lennard-Jones 1924), i.e., with an attractive and a repulsive part. For the updating of the particle positions we use a MD method which results to be very suitable to simulate this type of systems (Herrmann and Ludi...

16. From Brownian Dynamics to Markov Chain: An Ion Channel Example

KAUST Repository

Chen, Wan

2014-02-27

A discrete rate theory for multi-ion channels is presented, in which the continuous dynamics of ion diffusion is reduced to transitions between Markovian discrete states. In an open channel, the ion permeation process involves three types of events: an ion entering the channel, an ion escaping from the channel, or an ion hopping between different energy minima in the channel. The continuous dynamics leads to a hierarchy of Fokker-Planck equations, indexed by channel occupancy. From these the mean escape times and splitting probabilities (denoting from which side an ion has escaped) can be calculated. By equating these with the corresponding expressions from the Markov model, one can determine the Markovian transition rates. The theory is illustrated with a two-ion one-well channel. The stationary probability of states is compared with that from both Brownian dynamics simulation and the hierarchical Fokker-Planck equations. The conductivity of the channel is also studied, and the optimal geometry maximizing ion flux is computed. © 2014 Society for Industrial and Applied Mathematics.

17. From Brownian Dynamics to Markov Chain: an Ion Channel Example

CERN Document Server

Chen, Wan; Chapman, S Jonathan

2012-01-01

A discrete rate theory for general multi-ion channels is presented, in which the continuous dynamics of ion diffusion is reduced to transitions between Markovian discrete states. In an open channel, the ion permeation process involves three types of events: an ion entering the channel, an ion escaping from the channel, or an ion hopping between different energy minima in the channel. The continuous dynamics leads to a hierarchy of Fokker-Planck equations, indexed by channel occupancy. From these the mean escape times and splitting probabilities (denoting from which side an ion has escaped) can be calculated. By equating these with the corresponding expressions from the Markov model the Markovian transition rates can be determined. The theory is illustrated with a two-ion one-well channel. The stationary probability of states is compared with that from both Brownian dynamics simulation and the hierarchical Fokker-Planck equations. The conductivity of the channel is also studied, and the optimal geometry maximi...

18. Numerical Modeling of Two-Dimensional Temperature Dynamics Across Ice-Wedge Polygons

Science.gov (United States)

Garayshin, Viacheslav V.

The ice wedges on the North Slope of Alaska have been forming for many millennia, when the ground cracked and the cracks were filled with snowmelt water. The infiltrated water then became frozen and turned into ice. When the annual and summer air temperatures become higher, the depth of the active layer increases. A deeper seasonal thawing may cause melting of ice wedges from their tops. Consequently, the ground starts to settle and a trough begins to form above the ice wedge. The forming trough creates a local temperature anomaly in the surrounding ground, and the permafrost located immediately under the trough starts degrading further. Once the trough is formed, the winter snow cover becomes deeper at the trough area further degrading the permafrost. In this thesis we present a computational approach to study the seasonal temperature dynamics of the ground surrounding an ice wedge and ground subsidence associated with ice wedge degradation. A thermo-mechanical model of the ice wedge based on principles of macroscopic thermodynamics and continuum mechanics was developed and will be presented. The model includes heat conduction and quasi-static mechanical equilibrium equations, a visco-elastic rheology for ground deformation, and an empirical formula which relates unfrozen water content to temperature. The complete system is reduced to a computationally convenient set of coupled equations for temperature, ground displacement and ground porosity in a two-dimensional domain. A finite element method and an implicit scheme in time were utilized to construct a non-linear system of equations, which was solved iteratively. The model employs temperature and moisture content data collected from a field experiment at the Next-Generation Ecosystem Experiments (NGEE) sites in Barrow, Alaska. The model describes seasonal dynamics of temperature and the long-term ground motion near the ice wedges and helps to explain destabilization of the ice wedges north of Alaska's Brooks

19. Exact field-driven interface dynamics in the two-dimensional stochastic Ising model with helicoidal boundary conditions

OpenAIRE

de Mendonça, J. Ricardo G.

2012-01-01

We investigate the interface dynamics of the two-dimensional stochastic Ising model in an external field under helicoidal boundary conditions. At sufficiently low temperatures and fields, the dynamics of the interface is described by an exactly solvable high-spin asymmetric quantum Hamiltonian that is the infinitesimal generator of the zero range process. Generally, the critical dynamics of the interface fluctuations is in the Kardar-Parisi-Zhang universality class of critical behavior. We re...

20. Comparison of lattice-Boltzmann and brownian-dynamics simulations of polymer migration in confined flows.

Science.gov (United States)

Kekre, Rahul; Butler, Jason E; Ladd, Anthony J C

2010-07-01

This paper compares results from lattice-Boltzmann and brownian-dynamics simulations of polymer migration in confined flows bounded by planar walls. We have considered both a uniform shear rate and a constant pressure gradient. Lattice-Boltzmann simulations of the center-of-mass distribution agree quantitatively with brownian-dynamics results, contradicting previously published results. The mean end-to-end distance of the extended polymer is more sensitive to grid resolution Δx and time-step Δt. Nevertheless, for sufficiently small Δx and Δt, convergent results for the polymer stretch are obtained which agree with brownian dynamics within statistical uncertainties. The brownian-dynamics simulations incorporate a mobility matrix for a confined polymer that is both symmetric and positive definite for all physically accessible configurations.

1. Vertical dynamics of a horizontally oscillating active object in a two-dimensional granular medium

Science.gov (United States)

Huang, Ling; Ran, Xianwen; Blumenfeld, Raphael

2016-12-01

We use a discrete-element method simulation and analytical considerations to study the dynamics of a self-energized object, modeled as a disk, oscillating horizontally within a two-dimensional bed of denser and smaller particles. We find that, for given material parameters, the immersed object (IO) may rise, sink, or not change depth, depending on the oscillation amplitude and frequency, as well as on the initial depth. With time, the IO settles at a specific depth that depends on the oscillation parameters. We construct a phase diagram of this behavior in the oscillation frequency and velocity amplitude variable space. We explain the observed rich behavior by two competing effects: climbing on particles, which fill voids opening under the disk, and sinking due to bed fluidization. We present a cavity model that allows us to derive analytically general results, which agree very well with the observations and explain quantitatively the phase diagram. Our specific analytical results are the following. (i) Derivation of a critical frequency, fc, above which the IO cannot float up against gravity. We show that this frequency depends only on the gravitational acceleration and the IO size. (ii) Derivation of a minimal amplitude, Amin, below which the IO cannot rise even if the frequency is below fc. We show that this amplitude also depends only on the gravitational acceleration and the IO size. (iii) Derivation of a critical value, gc, of the IO's acceleration amplitude, below which the IO cannot sink. We show that the value of gc depends on the characteristics of both the IO and the granular bed, as well as on the initial IO's depth.

2. Pattern transition, microstructure, and dynamics in a two-dimensional vibrofluidized granular bed

Science.gov (United States)

Ansari, Istafaul H.; Alam, Meheboob

2016-05-01

Experiments are conducted in a two-dimensional monolayer vibrofluidized bed of glass beads, with a goal to understand the transition scenario and the underlying microstructure and dynamics in different patterned states. At small shaking accelerations (Γ =A ω2/g convection" to "1-roll convection" and finally to a gas-like state. For a given length of the container, the coarsening of multiple convection rolls leading to the genesis of a "single-roll" structure (dubbed the multiroll transition) and its subsequent transition to a granular gas are two findings of this work. We show that the critical shaking intensity (ΓBBLS) for the BB→LS transition has a power-law dependence on the particle loading (F =h0/d , where h0 is the number of particle layers at rest and d is the particle diameter) and the shaking amplitude (A /d ). The characteristics of BB and LS states are studied by calculating (i) the coarse-grained density and temperature profiles and (ii) the pair correlation function. It is shown that while the contact network of particles in the BB state represents a hexagonal-packed structure, the contact network within the "floating cluster" of the LS resembles a liquid-like state. An unsteadiness of the Leidenfrost state has been uncovered wherein the interface (between the floating cluster and the dilute collisional layer underneath) and the top of the bed are found to oscillate sinusoidally, with the oscillation frequency closely matching the frequency of external shaking. Therefore, the granular Leidenfrost state is a period-1 wave as is the case for the BB state.

3. Filamentous Biopolymers on Surfaces: Atomic Force Microscopy Images Compared with Brownian Dynamics Simulation of Filament Deposition

Science.gov (United States)

Mücke, Norbert; Klenin, Konstantin; Kirmse, Robert; Bussiek, Malte; Herrmann, Harald; Hafner, Mathias; Langowski, Jörg

2009-01-01

Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarly on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a ‘trapping’ mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these ‘ideal’ adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica (‘ideal’ trapping) and on glass (‘ideal’ equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions. PMID:19888472

4. Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition.

Directory of Open Access Journals (Sweden)

Norbert Mücke

Full Text Available Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarily on the interaction strength between the filament and the support: i For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a 'trapping' mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these 'ideal' adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica ('ideal' trapping and on glass ('ideal' equilibrated with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions.

5. Local approximation for contour dynamics in effectively two-dimensional ideal electron-magnetohydrodynamic flows

DEFF Research Database (Denmark)

Ruban, V.P.; Senchenko, Sergey

2004-01-01

The evolution of piecewise constant distributions of a conserved quantity related to the frozen-in canonical vorticity in effectively two-dimensional incompressible ideal EMHD flows is analytically investigated by the Hamiltonian method. The study includes the case of axisymmetric flows with zero...

6. Proton dynamics of two-dimensional oxalate-bridged coordination polymers.

Science.gov (United States)

2014-08-28

7. Two-dimensional vertical moisture-pressure dynamics above groundwater waves: Sand flume experiments and modelling

Science.gov (United States)

Shoushtari, Seyed Mohammad Hossein Jazayeri; Cartwright, Nick; Perrochet, Pierre; Nielsen, Peter

2017-01-01

This paper presents a new laboratory dataset on the moisture-pressure relationship above a dispersive groundwater wave in a two-dimensional vertical unconfined sand flume aquifer driven by simple harmonic forcing. A total of five experiments were conducted in which all experimental parameters were kept constant except for the oscillation period, which ranged from 268 s to 2449 s between tests. Moisture content and suction head sensor pairings were co-located at two locations in the unsaturated zone both approximately 0.2 m above the mean watertable elevation and respectively 0.3 m and 0.75 m from the driving head boundary. For all oscillation periods except for the shortest (T = 268s), the formation of a hysteretic moisture-pressure scanning loop was observed. Consistent with the decay of the saturated zone groundwater wave, the size of the observed moisture-pressure scanning loops decayed with increasing distance landward and the decay rate is larger for the shorter oscillation periods. At the shortest period (T = 268s), the observed moisture-pressure relationship was observed to be non-hysteretic but with a capillary capacity that differs from that of the static equilibrium wetting and drying curves. This finding is consistent with observations from existing one-dimensional vertical sand column experiments. The relative damping of the moisture content with distance landward is higher than that for the suction head consistent with the fact that transmission of pressure through a porous medium occurs more readily than mass transfer. This is further supported by the fact that observed phase lags for the unsaturated zone variables (i.e. suction head and moisture content) relative to the driving head are greater than the saturated zone variables (i.e. piezometric head). Harmonic analysis of the data reveals no observable generation of higher harmonics in either moisture or pressure despite the strongly non-linear relationship between the two. In addition, a phase lag

8. An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles

Energy Technology Data Exchange (ETDEWEB)

Ilie, Ioana M.; Briels, Wim J. [Computational Biophysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Otter, Wouter K. den, E-mail: w.k.denotter@utwente.nl [Computational Biophysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

2015-03-21

Brownian Dynamics is the designated technique to simulate the collective dynamics of colloidal particles suspended in a solution, e.g., the self-assembly of patchy particles. Simulating the rotational dynamics of anisotropic particles by a first-order Langevin equation, however, gives rise to a number of complications, ranging from singularities when using a set of three rotational coordinates to subtle metric and drift corrections. Here, we derive and numerically validate a quaternion-based Rotational Brownian Dynamics algorithm that handles these complications in a simple and elegant way. The extension to hydrodynamic interactions is also discussed.

9. Dynamics of two-dimensional vortex system in a strong square pinning array at the second matching field

Energy Technology Data Exchange (ETDEWEB)

Ren, Qing-Bao [Department of Physics, Lishui University, Lishui 323000 (China); Luo, Meng-Bo, E-mail: Luomengbo@zju.edu.cn [Department of Physics, Zhejiang University, Hangzhou 310027 (China)

2013-10-30

We study the dynamics of a two-dimensional vortex system in a strong square pinning array at the second matching field. Two kinds of depinning behaviors, a continuous depinning transition at weak pinning and a discontinuous one at strong pinning, are found. We show that the two different kinds of vortex depinning transitions can be identified in transport as a function of the pinning strength and temperature. Moreover, interstitial vortex state can be probed from the transport properties of vortices.

10. Two-dimensional dynamics of a free molecular chain with a secondary structure

DEFF Research Database (Denmark)

Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

1996-01-01

A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...... of an anharmonic chain in order to include transverse degrees of freedom of the chain molecules. Both the structures are provided by the first- and second-neighbor intermolecular bonds, respectively, resulting in a regular zig-zag (''20 helix'') chain on a plane. The set of two coupled nonlinear field equations...

11. On two-dimensional large-scale primitive equations in oceanic dynamics(Ⅰ)

Institute of Scientific and Technical Information of China (English)

HUANG Dai-wen; GUO Bo-ling

2007-01-01

The initial boundary value problem for the two-dimensional primitive equations of large scale oceanic motion in geophysics is considered.It is assumed that the depth of the ocean is a positive constant.Firstly,if the initial data are square integrable,then by Fadeo-Galerkin method,the existence of the global weak solutions for the problem is obtained.Secondly, if the initial data and their vertical derivatives axe all square integrable,then by Faedo-Galerkin method and anisotropic inequalities,the existerce and uniqueness of the giobal weakly strong solution for the above initial boundary problem axe obtained.

12. On two-dimensional large-scale primitive equations in oceanic dynamics(Ⅱ)

Institute of Scientific and Technical Information of China (English)

HUANG Dai-wen; GUO Bo-ling

2007-01-01

The initial boundary value problem for the two-dimensional primitive equations of largescale oceanic motion in geophysics is considered sequetially.Here the depth of the ocean is positive but not always a constant.By Faedo-Galerkin method and anisotropic inequalities,the existence and uniqueness of the global weakly strong solution and global strong solution for the problem are obtained.Moreover,by studying the asymptotic behavior of solutions for the above problem,the energy is exponential decay with time is proved.

13. Nonlinear low-frequency electrostatic wave dynamics in a two-dimensional quantum plasma

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Samiran, E-mail: sran_g@yahoo.com [Department of Applied Mathematics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata-700 009 (India); Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064 (India)

2016-08-15

The problem of two-dimensional arbitrary amplitude low-frequency electrostatic oscillation in a quasi-neutral quantum plasma is solved exactly by elementary means. In such quantum plasmas we have treated electrons quantum mechanically and ions classically. The exact analytical solution of the nonlinear system exhibits the formation of dark and black solitons. Numerical simulation also predicts the possible periodic solution of the nonlinear system. Nonlinear analysis reveals that the system does have a bifurcation at a critical Mach number that depends on the angle of propagation of the wave. The small-amplitude limit leads to the formation of weakly nonlinear Kadomstev–Petviashvili solitons.

14. Dynamic Effective Medium Theory for Two-Dimensional Non-Magnetic Metamaterial Lattices using Multipole Expansion

CERN Document Server

Chremmos, Ioannis; Giamalaki, Melpomeni; Yannopapas, Vassilios; Paspalakis, Emmanuel

2014-01-01

We present a formulation for deriving effective medium properties of infinitely periodic two-dimensional metamaterial lattice structures beyond the static and quasi-static limits. We utilize the multipole expansions, where the polarization currents associated with the supported Bloch modes are expressed via the electric dipole, magnetic dipole, and electric quadrupole moments per unit length. We then propose a method to calculate the Bloch modes based on the lattice geometry and individual unit element structure. The results revert to well-known formulas in the quasistatic limit and are useful for the homogenization of nanorod-type metamaterials which are frequently used in optical applications.

15. Jamming transition of a two-dimensional traffic dynamics with consideration of optimal current difference

Energy Technology Data Exchange (ETDEWEB)

Gupta, Arvind Kumar, E-mail: akgupta@iitrpr.ac.in; Redhu, Poonam

2013-11-01

A modified two-dimensional lattice hydrodynamic traffic flow model is proposed by incorporating the optimal current difference effect of leading vehicles. Phase transitions and critical phenomenon are investigated near the critical point both analytically and numerically. Based on the configuration of vehicles, it is shown that two distinct jamming transitions occur: conventional jamming transition to the kink jam and jamming transition to the chaotic jam. It is shown that consideration of optimal current difference effect stabilizes the traffic flow and suppresses the traffic jam efficiently for all possible configurations of vehicles on a square lattice.

16. Dynamic Critical Behavior of Multi-Grid Monte Carlo for Two-Dimensional Nonlinear $\\sigma$-Models

OpenAIRE

Mana, Gustavo; Mendes, Tereza; Pelissetto, Andrea; Sokal, Alan D.

1995-01-01

We introduce a new and very convenient approach to multi-grid Monte Carlo (MGMC) algorithms for general nonlinear $\\sigma$-models: it is based on embedding an $XY$ model into the given $\\sigma$-model, and then updating the induced $XY$ model using a standard $XY$-model MGMC code. We study the dynamic critical behavior of this algorithm for the two-dimensional $O(N)$ $\\sigma$-models with $N = 3,4,8$ and for the $SU(3)$ principal chiral model. We find that the dynamic critical exponent $z$ vari...

17. Molecular dynamics test of the Brownian description of Na(+) motion in water

Science.gov (United States)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.

1985-01-01

The present paper provides the results of molecular dynamics calculations on a Na(+) ion in aqueous solution. Attention is given to the sodium-oxygen and sodium-hydrogen radial distribution functions, the velocity autocorrelation function for the Na(+) ion, the autocorrelation function of the force on the stationary ion, and the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dyanmics in solution. It is pointed out that the presented calculations provide accurate data for testing theories of ion dynamics in solution. The conducted tests show that it is feasible to calculate Brownian friction constants for ions in aqueous solutions. It is found that for Na(+) under the considered conditions the Brownian mobility is in error by only 60 percent.

18. Molecular dynamics test of the Brownian description of Na(+) motion in water

Science.gov (United States)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.

1985-01-01

The present paper provides the results of molecular dynamics calculations on a Na(+) ion in aqueous solution. Attention is given to the sodium-oxygen and sodium-hydrogen radial distribution functions, the velocity autocorrelation function for the Na(+) ion, the autocorrelation function of the force on the stationary ion, and the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dyanmics in solution. It is pointed out that the presented calculations provide accurate data for testing theories of ion dynamics in solution. The conducted tests show that it is feasible to calculate Brownian friction constants for ions in aqueous solutions. It is found that for Na(+) under the considered conditions the Brownian mobility is in error by only 60 percent.

19. Evolution of desertification in a two-dimensional energy balance model coupled with thermodynamics and dynamics

Institute of Scientific and Technical Information of China (English)

2010-01-01

The relationship between desert evolution and change in albedo has been investigated quasi-analytically using a zonal mean two-dimensional energy balance model which considers the radiation transmission process due to thermodynamics and bound- ary layer movement caused by kinetics. A climate state including temperature, zonal wind, meridional wind and vertical wind can be simulated according to the current zonal distribution of albedo. Given desert distribution, characterized by the value and distribution of albedo, the response of climate on albedo has been studied to analyze the evolution of desert climate. One significant result is that the simple model can reproduce mean meridional circulation. Another result indicates that climate corresponds to two equilibria. This happens when the junction temperature between vegetation and desert is higher than a certain critical value. As for the first equilibrium, the desert belt is predicted to move southward in the northern hemisphere with the increasing values of albedo, which corresponds to the current trend of climate change. For the second equilibrium, vegetation will expand northward with increasing values of albedo, which would indicate a narrowing of the desert belt. In order to determine if the two equilibria exist, new physical models are needed.

20. Bubble dynamics in a two-dimensional gas-solid fluidized bed

Institute of Scientific and Technical Information of China (English)

2007-01-01

Related referential studies on gas-solid two-phase flows were briefly reviewed. Bubble ascending in a two-dimensional (2D) gas-solid fluidized bed was studied both experimentally and numerically. A modified continuum model expressed in the conservation form was used in numerical simulation. Solid-phase pressure was modeled via local sound speed; gas-phase turbulence was described by the K-ε two-equation model. The modified implicit multiphase formulation (IMF) scheme was used to solve the model equations in 2D Cartesian/cylindrical coordinates. The bubble ascending velocity and particle motion in the 2D fluidized bed were measured using the photochromic dye activation (PDA) technique, which was based on UV light activation of particles impregnated with the dye. Effects of bed height and superficial gas velocity on bubble formation and ascent were investigated numerically. The numerically obtained bubble ascending velocities were compared with experimental measurements. Gas bubble in jetting gas-solids fluidized bed was also simulated numerically.

1. Two-Dimensional Riemann Solver for Euler Equations of Gas Dynamics

Science.gov (United States)

Brio, M.; Zakharian, A. R.; Webb, G. M.

2001-02-01

We construct a Riemann solver based on two-dimensional linear wave contributions to the numerical flux that generalizes the one-dimensional method due to Roe (1981, J. Comput. Phys.43, 157). The solver is based on a multistate Riemann problem and is suitable for arbitrary triangular grids or any other finite volume tessellations of the plane. We present numerical examples illustrating the performance of the method using both first- and second-order-accurate numerical solutions. The numerical flux contributions are due to one-dimensional waves and multidimensional waves originating from the corners of the computational cell. Under appropriate CFL restrictions, the contributions of one-dimensional waves dominate the flux, which explains good performance of dimensionally split solvers in practice. The multidimensional flux corrections increase the accuracy and stability, allowing a larger time step. The improvements are more pronounced on a coarse mesh and for large CFL numbers. For the second-order method, the improvements can be comparable to the improvements resulting from a less diffusive limiter.

2. Fluid dynamics of two-dimensional pollination in Ruppia (widgeon grass)

Science.gov (United States)

Musunuri, Naga; Bunker, Daniel; Pell, Susan; Fischer, Ian; Singh, Pushpendra

2015-11-01

The aim of this work is to understand the physics underlying the mechanisms of two-dimensional aquatic pollen dispersal, known as hydrophily, that have evolved in several genera of aquatic plants, including Halodule, Halophila, Lepilaena, and Ruppia. We selected Ruppia, which grows in the wetlands of the New Jersey/New York metropolitan area, for this study. We observed two mechanisms by which the pollen released from male inflorescences of Ruppia maritime is adsorbed on a water surface: 1) inflorescences rise above the water surface and after they mature their pollen mass falls onto the surface as clumps and disperses as it comes in contact with the surface; 2) inflorescences remain below the surface and produce air bubbles which carry pollen mass to the surface where it disperses. In both cases dispersed pollen masses combined with others to form pollen rafts. The formation of porous pollen rafts increases the probability of pollination since the attractive capillary force on a pollen raft towards a stigma is much larger than on a single pollen grain. The work was supported by National Science Foundation.

3. Finite size scaling study of dynamical phase transitions in two dimensional models: ferromagnet, symmetric and non symmetric spin glasses

Energy Technology Data Exchange (ETDEWEB)

Neumann, A.U.; Derrida, B.

1988-10-01

We study the time evolution of two configurations submitted to the same thermal noise for several two dimensional models (Ising ferromagnet, symmetric spin glass, non symmetric spin glass). For all these models, we find a non zero critical temperature above which the two configurations always meet. Using finite size scaling ideas, we determine for these three models this dynamical phase transition and some of the critical exponents. For the ferromagnet, the transition T/sub c/ approx. = 2.25 coincides with the Curie temperature whereas for the two spin glass models +- J distribution of bonds) we obtain T/sub c/ approx. = 1.5-1.7.

4. On the Dynamics of Two-Dimensional Capillary-Gravity Solitary Waves with a Linear Shear Current

Directory of Open Access Journals (Sweden)

Dali Guo

2014-01-01

Full Text Available The numerical study of the dynamics of two-dimensional capillary-gravity solitary waves on a linear shear current is presented in this paper. The numerical method is based on the time-dependent conformal mapping. The stability of different kinds of solitary waves is considered. Both depression wave and large amplitude elevation wave are found to be stable, while small amplitude elevation wave is unstable to the small perturbation, and it finally evolves to be a depression wave with tails, which is similar to the irrotational capillary-gravity waves.

5. Dynamic Proportional Reinsurance and Approximations for Ruin Probabilities in the Two-Dimensional Compound Poisson Risk Model

Directory of Open Access Journals (Sweden)

Yan Li

2012-01-01

Full Text Available We consider the dynamic proportional reinsurance in a two-dimensional compound Poisson risk model. The optimization in the sense of minimizing the ruin probability which is defined by the sum of subportfolio is being ruined. Via the Hamilton-Jacobi-Bellman approach we find a candidate for the optimal value function and prove the verification theorem. In addition, we obtain the Lundberg bounds and the Cramér-Lundberg approximation for the ruin probability and show that as the capital tends to infinity, the optimal strategies converge to the asymptotically optimal constant strategies. The asymptotic value can be found by maximizing the adjustment coefficient.

6. Two-dimensional optical correlation spectroscopy applied to liquid/glass dynamics

NARCIS (Netherlands)

Lazonder, Kees; Pshenichnikov, Maxim S.; Wiersma, Douwe A.

2006-01-01

Correlation spectroscopy was used to study the effects of temperature and phase changes on liquid and glass solvent dynamics. This method yielded both intuitive clues and a quantitative measure of the dynamics of the system. © 2006 Optical Society of America.

7. A two-dimensional model of the pressing section of a paper machine including dynamic capillary effects

KAUST Repository

Iliev, Oleg P.

2013-05-15

Paper production is a problem with significant importance for society; it is also a challenging topic for scientific investigation. This study is concerned with the simulation of the pressing section of a paper machine. A two-dimensional model is developed to account for the water flow within the pressing zone. A Richards-type equation is used to describe the flow in the unsaturated zone. The dynamic capillary pressure-saturation relation is adopted for the paper production process. The mathematical model accounts for the coexistence of saturated and unsaturated zones in a multilayer computational domain. The discretization is performed by the MPFA-O method. Numerical experiments are carried out for parameters that are typical of the production process. The static and dynamic capillary pressure-saturation relations are tested to evaluate the influence of the dynamic capillary effect. © 2013 Springer Science+Business Media Dordrecht.

8. Water dynamics in small reverse micelles in two solvents: Two-dimensional infrared vibrational echoes with two-dimensional background subtraction

Science.gov (United States)

Fenn, Emily E.; Wong, Daryl B.; Fayer, M. D.

2011-02-01

Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w0 = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w0 = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w0, but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl4 system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.

9. Molecular dynamics computations of two dimensional supersonic rarefied gas flow past blunt bodies

Science.gov (United States)

Greber, Isaac; Wachman, Harold Y.; Woo, Myeung-Jouh

1991-01-01

This paper presents results of molecular dynamics computations of supersonic flow past a circular cylinder and past a flat plate perpendicular to a supersonic stream. The results are for Mach numbers of approximately 5 and 10, for several Knudsen numbers and several ratios of surface to free stream temperatures. A special feature of the computations is the use of relatively small numbers of particles in the molecular dynamics simulation, and an examination of the adequacy of using small numbers of particles to obtain physically useful results.

10. Experimental Evidence of Dynamical Scaling in a Two-Dimensional Fractal Growth

Science.gov (United States)

Miyashita, Satoru; Saito, Yukio; Uwaha, Makio

1997-04-01

A dynamical scaling law of fractal aggregation is testedusing electrochemical deposition without an external electric field.Silver metal leaves grow on the edge of a Cu plate placed in a thin cell containing an AgNO3-water solution due to the difference in ionization tendency between Ag and Cu. We find that the tip height h(t) satisfies the dynamical scaling relationh(t)= c-1/(d-D_f) \\tilde{g}(tc2/(d-D_f)) with respect to the solute concentration cin the space dimension d=2 with the fractal dimension Df=1.71 of the diffusion-limited aggregation.

11. Molecular dynamics computations of two dimensional supersonic rarefied gas flow past blunt bodies

Science.gov (United States)

Greber, Isaac; Wachman, Harold Y.; Woo, Myeung-Jouh

1991-01-01

This paper presents results of molecular dynamics computations of supersonic flow past a circular cylinder and past a flat plate perpendicular to a supersonic stream. The results are for Mach numbers of approximately 5 and 10, for several Knudsen numbers and several ratios of surface to free stream temperatures. A special feature of the computations is the use of relatively small numbers of particles in the molecular dynamics simulation, and an examination of the adequacy of using small numbers of particles to obtain physically useful results.

12. Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

CERN Document Server

Vijaykumar, Adithya; Wolde, Pieter Rein ten; Bolhuis, Peter G

2016-01-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.

13. Light detection and ranging measurements of wake dynamics. Part II: two-dimensional scanning

DEFF Research Database (Denmark)

Trujillo, Juan-José; Bingöl, Ferhat; Larsen, Gunner Chr.;

2011-01-01

A nacelle-mounted lidar system pointing downstream has been used to measure wind turbine wake dynamics. The new measurement and data analysis techniques allow estimation of quasi-instantaneous wind fields in planes perpendicular to the rotor axis. A newly developed wake tracking procedure delivers...

14. Two-dimensional optical correlation spectroscopy applied to liquid/glass dynamics

NARCIS (Netherlands)

Lazonder, Kees; Pshenichnikov, Maxim S.; Wiersma, Douwe A.; Corkum, Paul; Jonas, David M.; Miller, R.J. Dwayne.; Weiner, Andrew M.

2007-01-01

Correlation spectroscopy was used to study the effects of temperature and phase changes on liquid and glass solvent dynamics. By assessing the eccentricity of the elliptic shape of a 2D optical correlation spectrum the value of the underlying frequency-frequency correlation function can be retrieved

15. Identification of the dynamics of a two-dimensional grid structure using least square lattice filters. [for large space structures

Science.gov (United States)

Montgomery, R. C.; Sundararajan, N.

1984-01-01

It is doubtful whether the dynamics of large space structures (LSS) can be predicted well enough for control system design applications. Hence, dynamic modeling from on-orbit measurements followed by a modification of the control system is of interest, taking into account the utilization of adaptive control concepts. The present paper is concerned with the model determination phase of the adaptive control problem. Using spectral decoupling to determine mode shapes, mode frequency and damping data can be obtained with the aid of an equation error parameter identification method. This method employs a second-order auto-regressive moving average (ARMA) model to represent the natural mode amplitudes. The discussed procedure involves an extension of the application of the least square lattice filter in system identification to a nonintegral, two-dimensional grid structure made of overlapping bars.

16. A Two-Dimensional CA Traffic Model with Dynamic Route Choices Between Residence and Workplace

CERN Document Server

Fang, Jun; Chen, Xi-Qun; Qin, Zheng

2015-01-01

The Biham, Middleton and Levine (BML) model is extended to describe dynamic route choices between the residence and workplace in cities. The traffic dynamic in the city with a single workplace is studied from the velocity diagram, arrival time probability distribution, destination arrival rate and convergence time. The city with double workplaces is also investigated to compared with a single workplace within the framework of four modes of urban growth. The transitional region is found in the velocity diagrams where the system undergoes a continuous transition from a moving phase to a completely jamming phase. We perform a finite-size scaling analysis of the critical density from a statistical point of view and the order parameter of this jamming transition is estimated. It is also found that statistical properties of urban traffic are greatly influenced by the urban area, workplace area and urban layout.

17. A two-dimensional model for the dynamics of granular avalanches

OpenAIRE

2005-01-01

Zoning of avalanche risk areas is one important task of land-use planning in alpine areas. The lack of records, due to the low frequency of these events, makes it dicult to implement a statistical analysis. Simulations made with physical and mathematical models can improve the knowledge of the dynamics of these events. In this thesis three didifferent mathematical and numerical models, based on the rheological theory of Savage and Hutter for granular flows, are introduced. A one dimensi...

18. A two-dimensional global simulation study of inductive-dynamic magnetosphere-ionosphere/thermosphere coupling

Science.gov (United States)

Tu, J.; Song, P.

2016-12-01

We have developed a new numerical simulation model of the ionosphere/thermosphere by using an inductive-dynamic approach (including self-consistent solutions of Faraday's law and retaining inertia terms in ion momentum equations), that is, based on magnetic field B and plasma velocity v (B, v paradigm), which is distinctive from the conventional modeling based on electric field E and current j. The model solves self-consistently time-dependent continuity, momentum, and energy equations for multiple species of ions and neutrals including photochemistry, and Maxwell's equations. The governing equations solved in the model are a set of multifluid-collisional-Hall MHD equations which are one of unique features of our ionosphere/thermosphere model. With such an inductive-dynamic approach, not only sound wave mode but also all possible MHD wave modes are retained in the solutions of the governing equations so that the dynamic coupling between the magnetosphere and ionosphere and among different regions of the ionosphere can be self-consistently investigated. In the present study, we demonstrate dynamic propagation of field-aligned currents and ionospheric electric field carried by Alfven waves, as well as formation of closure horizontal currents (Pedersen currents in the E-region), indicating that the M-I coupling is via the Alfven waves instead of the field-aligned currents or electric field mapping. The simulation results also show that the Poynting flux and strongest energy dissipation in the ionosphere/thermosphere is in the regions of the largest ion velocities and not necessarily in the auroral oval where the field-aligned currents reside. The frictional heating increases plasma temperature and thus drives ion upflows. The frictional heating also increase neutral temperature and produces neutral upflows but in a much longer time scale. Furthermore, the coupling of high-to-low latitude ionosphere is investigated in terms of propagation of fast MHD waves.

19. Resonantly excited exciton dynamics in two-dimensional MoSe2 monolayers

Science.gov (United States)

Scarpelli, L.; Masia, F.; Alexeev, E. M.; Withers, F.; Tartakovskii, A. I.; Novoselov, K. S.; Langbein, W.

2017-07-01

We report on the exciton and trion density dynamics in a single layer of MoSe2, resonantly excited and probed using three-pulse four-wave mixing (FWM), at temperatures from 300 K to 77 K. A multiexponential third-order response function for amplitude and phase of the heterodyne-detected FWM signal including four decay processes is used to model the data. We provide a consistent interpretation within the intrinsic band structure, not requiring the inclusion of extrinsic effects. We find an exciton radiative lifetime in the subpicosecond range consistent to what has been recently reported by Jakubczyk et al. [Nano Lett. 16, 5333 (2016), 10.1021/acs.nanolett.6b01060]. After the dominating radiative decay, the remaining exciton density, which has been scattered from the initially excited direct spin-allowed radiative state into dark states of different nature by exciton-phonon scattering or disorder scattering, shows a slower dynamics, covering 10-ps to 10-ns time scales. This includes direct spin-allowed transitions with larger in-plane momentum, as well as indirect and spin-forbidden exciton states. We find that exciton-exciton annihilation is not relevant in the observed dynamics, in variance from previous finding under nonresonant excitation. The trion density at 77 K reveals a decay of the order of 1 ps, similar to what is observed for the exciton. After few tens of picoseconds, the trion dynamics resembles the one of the exciton, indicating that trion ionization occurs on this time scale.

20. Approximation of the Long-term Dynamics of the Dynamical System Generated by the Two-dimensional Thermohydraulics Equations

CERN Document Server

Tone, Florentina

2011-01-01

Pursuing our work in [18], [17], [20], [5], we consider in this article the two-dimensional thermohydraulics equations. We discretize these equations in time using the implicit Euler scheme and we prove that the global attractors generated by the numerical scheme converge to the global attractor of the continuous system as the time-step approaches zero.

1. Unstable shear flows in two dimensional strongly correlated liquids - a hydrodynamic and molecular dynamics study

Science.gov (United States)

Gupta, Akanksha; Ganesh, Rajaraman; Joy, Ashwin

2016-11-01

In Navier-Stokes fluids, shear flows are known to become unstable leading to instability and eventually to turbulence. A class of flow namely, Kolmogorov Flows (K-Flows) exhibit such transition at low Reynolds number. Using fluid and molecular dynamics, we address the physics of transition from laminar to turbulent regime in strongly correlated-liquids such as in multi-species plasmas and also in naturally occurring plasmas with K-Flows as initial condition. A 2D phenomenological generalized hydrodynamic model is invoked wherein the effect of strong correlations is incorporated via a viscoelastic memory. To study the stability of K-Flows or in general any shear flow, a generalized eigenvalue solver has been developed along with a spectral solver for the full nonlinear set of fluid equations. A study of the linear and nonlinear features of K-Flow in incompressible and compressible limit exhibits cyclicity and nonlinear pattern formation in vorticity. A first principles based molecular dynamics simulation of particles interacting via Yukawa potential is performed with features such as configurational and kinetic thermostats for K-Flows. This work reveals several interesting similarities and differences between hydrodynamics and molecular dynamics studies.

2. Short-time dynamics of monomers and dimers in quasi-two-dimensional colloidal mixtures

Science.gov (United States)

Sarmiento-Gómez, Erick; Villanueva-Valencia, José Ramón; Herrera-Velarde, Salvador; Ruiz-Santoyo, José Arturo; Santana-Solano, Jesús; Arauz-Lara, José Luis; Castañeda-Priego, Ramón

2016-07-01

We report on the short-time dynamics in colloidal mixtures made up of monomers and dimers highly confined between two glass plates. At low concentrations, the experimental measurements of colloidal motion agree well with the solution of the Navier-Stokes equation at low Reynolds numbers; the latter takes into account the increase in the drag force on a colloidal particle due to wall-particle hydrodynamic forces. More importantly, we find that the ratio of the short-time diffusion coefficient of the monomer and that of the center of mass of the dimmer is almost independent of both the dimer molar fraction, xd, and the total packing fraction, ϕ , up to ϕ ≈0.5 . At higher concentrations, this ratio displays a small but systematic increase. A similar physical scenario is observed for the ratio between the parallel and the perpendicular components of the short-time diffusion coefficients of the dimer. This dynamical behavior is corroborated by means of molecular dynamics computer simulations that include explicitly the particle-particle hydrodynamic forces induced by the solvent. Our results suggest that the effects of colloid-colloid hydrodynamic interactions on the short-time diffusion coefficients are almost identical and factorable in both species.

3. Dynamics of particle sedimentation in viscoelastic fluids: A numerical study on particle chain in two-dimensional narrow channel

CERN Document Server

Pan, Tsorng-Whay

2016-01-01

In this article we present a numerical method for simulating the sedimentation of circular particles in two-dimensional channel filled with a viscoelastic fluid of FENE-CR type, which is generalized from a domain/distributed Lagrange multiplier method with a factorization approach for Oldroyd-B fluids developed in [J. Non-Newtonian Fluid Mech. 156 (2009) 95]. Numerical results suggest that the polymer extension limit L for the FENE-CR fluid has no effect on the final formation of vertical chain for the cases of two disks and three disks in two-dimensional narrow channel, at least for the values of L considered in this article; but the intermediate dynamics of particle interaction before having a vertical chain can be different for the smaller values of L when increasing the relaxation time. For the cases of six particles sedimenting in FENE-CR type viscoelastic fluid, the formation of chain of 4 to 6 disks does depend on the polymer extension limit L. For the smaller values of L, FENE-CR type viscoelastic flu...

4. Two-dimensional surrogate contact modeling for computationally efficient dynamic simulation of total knee replacements.

Science.gov (United States)

Lin, Yi-Chung; Haftka, Raphael T; Queipo, Nestor V; Fregly, Benjamin J

2009-04-01

Computational speed is a major limiting factor for performing design sensitivity and optimization studies of total knee replacements. Much of this limitation arises from extensive geometry calculations required by contact analyses. This study presents a novel surrogate contact modeling approach to address this limitation. The approach involves fitting contact forces from a computationally expensive contact model (e.g., a finite element model) as a function of the relative pose between the contacting bodies. Because contact forces are much more sensitive to displacements in some directions than others, standard surrogate sampling and modeling techniques do not work well, necessitating the development of special techniques for contact problems. We present a computational evaluation and practical application of the approach using dynamic wear simulation of a total knee replacement constrained to planar motion in a Stanmore machine. The sample points needed for surrogate model fitting were generated by an elastic foundation (EF) contact model. For the computational evaluation, we performed nine different dynamic wear simulations with both the surrogate contact model and the EF contact model. In all cases, the surrogate contact model accurately reproduced the contact force, motion, and wear volume results from the EF model, with computation time being reduced from 13 min to 13 s. For the practical application, we performed a series of Monte Carlo analyses to determine the sensitivity of predicted wear volume to Stanmore machine setup issues. Wear volume was highly sensitive to small variations in motion and load inputs, especially femoral flexion angle, but not to small variations in component placements. Computational speed was reduced from an estimated 230 h to 4 h per analysis. Surrogate contact modeling can significantly improve the computational speed of dynamic contact and wear simulations of total knee replacements and is appropriate for use in design sensitivity

5. Exciton dynamics and non-linearities in two-dimensional hybrid organic perovskites

Science.gov (United States)

Abdel-Baki, K.; Boitier, F.; Diab, H.; Lanty, G.; Jemli, K.; Lédée, F.; Garrot, D.; Deleporte, E.; Lauret, J. S.

2016-02-01

Due to their high potentiality for photovoltaic applications or coherent light sources, a renewed interest in hybrid organic perovskites has emerged for few years. When they are arranged in two dimensions, these materials can be considered as hybrid quantum wells. One consequence of the unique structure of 2D hybrid organic perovskites is a huge exciton binding energy that can be tailored through chemical engineering. We present experimental investigations of the exciton non-linearities by means of femtosecond pump-probe spectroscopy. The exciton dynamics is fitted with a bi-exponential decay with a free exciton life-time of ˜100 ps. Moreover, an ultrafast intraband relaxation (energy.

6. Dynamics of two-dimensional vortex pairs in a spatially varying potential

Science.gov (United States)

Lee, H. H.; Gunn, J. M. F.

1992-10-01

We consider the dynamics of vortices in a superfluid 4He film flowing over a substrate at zero temperature. The vortex trajectories are assumed to be governed by the Magnus-force equation with the effect of the substrate incorporated via the gradient of a potential. We use an equivalent Hamiltonian formulation to show that two vortices in a slowly varying potential can exhibit stochastic behavior. In this regard, there are differences between the cases of two vortices of the same sign and those of the opposite sign, the latter becoming stochastic more readily.

7. An accurate predictor-corrector HOC solver for the two dimensional Riemann problem of gas dynamics

Science.gov (United States)

Gogoi, Bidyut B.

2016-10-01

The work in the present manuscript is concerned with the simulation of twodimensional (2D) Riemann problem of gas dynamics. We extend our recently developed higher order compact (HOC) method from one-dimensional (1D) to 2D solver and simulate the problem on a square geometry with different initial conditions. The method is fourth order accurate in space and second order accurate in time. We then compare our results with the available benchmark results. The comparison shows an excellent agreement of our results with the existing ones in the literature. Being a finite difference solver, it is quite straight-forward and simple.

8. Self-organized Vortex State in Two-dimensional $Dictyostelium$ Dynamics

CERN Document Server

Rappel, W J; Sarkisian, A; Levine, H; Loomis, W F; Rappel, Wouter-Jan; Nicol, Alastair; Sarkissian, Armand; Levine, Herbert; Loomis, William F.

1999-01-01

We present results of experiments on the dynamics of {\\it Dictyostelium discoideum} in a novel set-up which constraints cell motion to a plane. After aggregation, the amoebae collect into round ''pancake" structures in which the cells rotate around the center of the pancake. This vortex state persists for many hours and we have explicitly verified that the motion is not due to rotating waves of cAMP. To provide an alternative mechanism for the self-organization of the {\\it Dictyostelium} cells, we have developed a new model of the dynamics of self-propelled deformable objects. In this model, we show that cohesive energy between the cells, together with a coupling between the self-generated propulsive force and the cell's configuration produces a self-organized vortex state. The angular velocity profiles of the experiment and of the model are qualitatively similar. The mechanism for self-organization reported here can possibly explain similar vortex states in other biological systems.

9. Dynamics of a two-dimensional system of rational difference equations of Leslie--Gower type

Directory of Open Access Journals (Sweden)

Kulenović MRS

2011-01-01

Full Text Available Abstract We investigate global dynamics of the following systems of difference equations x n + 1 = α 1 + β 1 x n A 1 + y n y n + 1 = γ 2 y n A 2 + B 2 x n + y n , n = 0 , 1 , 2 , … where the parameters α 1, β 1, A 1, γ 2, A 2, B 2 are positive numbers, and the initial conditions x 0 and y 0 are arbitrary nonnegative numbers. We show that this system has rich dynamics which depends on the region of parametric space. We show that the basins of attractions of different locally asymptotically stable equilibrium points or non-hyperbolic equilibrium points are separated by the global stable manifolds of either saddle points or non-hyperbolic equilibrium points. We give examples of a globally attractive non-hyperbolic equilibrium point and a semi-stable non-hyperbolic equilibrium point. We also give an example of two local attractors with precisely determined basins of attraction. Finally, in some regions of parameters, we give an explicit formula for the global stable manifold. Mathematics Subject Classification (2000 Primary: 39A10, 39A11 Secondary: 37E99, 37D10

10. Two-dimensional nonlinear dynamics of bidirectional beam-plasma instability

Science.gov (United States)

Pavan, J.; Ziebell, L. F.; Gaelzer, R.; Yoon, P. H.

2009-01-01

Solar wind electrons near 1 AU feature wide-ranging asymmetries in the superthermal tail distribution. Gaelzer et al. (2008) recently demonstrated that a wide variety of asymmetric distributions results if one considers a pair of counterstreaming electron beams interacting with the core solar wind electrons. However, the nonlinear dynamics was investigated under the simplifying assumption of one dimensionality. In the present paper, this problem is revisited by extending the analysis to two dimensions. The classic bump-on-tail instability involves a single electron beam interacting with the background population. The bidirectional or counterstreaming beams excite Langmuir turbulence initially propagating in opposite directions. It is found that the nonlinear mode coupling leads to the redistribution of wave moments along concentric arcs in wave number space, somewhat similar to the earlier findings by Ziebell et al. (2008) in the case of one beam-plasma instability. However, the present result also shows distinctive features. The similarities and differences in the nonlinear wave dynamics are discussed. It is also found that the initial bidirectional beams undergo plateau formation and broadening in perpendicular velocity space. However, the anisotropy persists in the nonlinear stage, implying that an additional pitch angle scattering by transverse electromagnetic fluctuations is necessary in order to bring the system to a truly isotropic state.

11. Vortex formation and dynamics in two-dimensional driven-dissipative condensates

Science.gov (United States)

Hebenstreit, F.

2016-12-01

We investigate the real-time evolution of lattice bosons in two spatial dimensions whose dynamics is governed by a Markovian quantum master equation. We employ the Wigner-Weyl phase space quantization and derive the functional integral for open quantum many-body systems that determines the time evolution of the Wigner function. Using the truncated Wigner approximation, in which quantum fluctuations are only taken into account in the initial state whereas the dynamics is governed by classical evolution equations, we study the buildup of long-range correlations due to the action of non-Hermitean quantum jump operators that constitute a mechanism for dissipative cooling. Starting from an initially disordered state corresponding to a vortex condensate, the dissipative process results in the annihilation of vortex-antivortex pairs and the establishment of quasi-long-range order at late times. We observe that a finite vortex density survives the cooling process, which disagrees with the analytically constructed vortex-free Bose-Einstein condensate at asymptotic times. This indicates that quantum fluctuations beyond the truncated Wigner approximation need to be included to fully capture the physics of dissipative Bose-Einstein condensation.

12. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

CERN Document Server

2015-01-01

Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

13. Two dimensional dynamic analysis of sandwich plates with gradient foam cores

Energy Technology Data Exchange (ETDEWEB)

Mu, Lin; Xiao, Deng Bao; Zhao, Guiping [State Key Laboratory for Mechanical structure Strength and Vibration, School of AerospaceXi' an Jiaotong University, Xi' an (China); Cho, Chong Du [Dept. of Mechanical Engineering, Inha University, Inchon (Korea, Republic of)

2016-09-15

Present investigation is concerned about dynamic response of composite sandwich plates with the functionally gradient foam cores under time-dependent impulse. The analysis is based on a model of the gradient sandwich plate, in which the face sheets and the core adopt the Kirchhoff theory and a [2, 1]-order theory, respectively. The material properties of the gradient foam core vary continuously along the thickness direction. The gradient plate model is validated with the finite element code ABAQUS®. And the results show that the proposed model can predict well the free vibration of composite sandwich plates with gradient foam cores. The influences of gradient foam cores on the natural frequency, deflection and energy absorbing of the sandwich plates are also investigated.

14. An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

Science.gov (United States)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

15. Short-time critical dynamics of damage spreading in the two-dimensional Ising model

Science.gov (United States)

Rubio Puzzo, M. Leticia; Albano, Ezequiel V.

2010-05-01

The short-time critical dynamics of propagation of damage in the Ising ferromagnet in two dimensions is studied by means of Monte Carlo simulations. Starting with equilibrium configurations at T=∞ and magnetization M=0 , an initial damage is created by flipping a small amount of spins in one of the two replicas studied. In this way, the initial damage is proportional to the initial magnetization M0 in one of the configurations upon quenching the system at TC , the Onsager critical temperature of the ferromagnetic-paramagnetic transition. It is found that, at short times, the damage increases with an exponent θD=1.915(3) , which is much larger than the exponent θ=0.197 characteristic of the initial increase of the magnetization M(t) . Also, an epidemic study was performed. It is found that the average distance from the origin of the epidemic (⟨R2(t)⟩) grows with an exponent z∗≈η≈1.9 , which is the same, within error bars, as the exponent θD . However, the survival probability of the epidemics reaches a plateau so that δ=0 . On the other hand, by quenching the system to lower temperatures one observes the critical spreading of the damage at TD≃0.51TC , where all the measured observables exhibit power laws with exponents θD=1.026(3) , δ=0.133(1) , and z∗=1.74(3) .

16. Bubble statistics and coarsening dynamics for quasi-two-dimensional foams with increasing liquid content.

Science.gov (United States)

Roth, A E; Jones, C D; Durian, D J

2013-04-01

We report on the statistics of bubble size, topology, and shape and on their role in the coarsening dynamics for foams consisting of bubbles compressed between two parallel plates. The design of the sample cell permits control of the liquid content, through a constant pressure condition set by the height of the foam above a liquid reservoir. We find that in the scaling regime, all bubble distributions are independent not only of time, but also of liquid content. For coarsening, the average rate decreases with liquid content due to the blocking of gas diffusion by Plateau borders inflated with liquid; we achieve a factor of 4 reduction from the dry limit. By observing the growth rate of individual bubbles, we find that von Neumann's law becomes progressively violated with increasing wetness and decreasing bubble size. We successfully model this behavior by explicitly incorporating the border-blocking effect into the von Neumann argument. Two dimensionless bubble shape parameters naturally arise, one of which is primarily responsible for the violation of von Neumann's law for foams that are not perfectly dry.

17. Parallel implementation of geometrical shock dynamics for two dimensional converging shock waves

Science.gov (United States)

Qiu, Shi; Liu, Kuang; Eliasson, Veronica

2016-10-01

Geometrical shock dynamics (GSD) theory is an appealing method to predict the shock motion in the sense that it is more computationally efficient than solving the traditional Euler equations, especially for converging shock waves. However, to solve and optimize large scale configurations, the main bottleneck is the computational cost. Among the existing numerical GSD schemes, there is only one that has been implemented on parallel computers, with the purpose to analyze detonation waves. To extend the computational advantage of the GSD theory to more general applications such as converging shock waves, a numerical implementation using a spatial decomposition method has been coupled with a front tracking approach on parallel computers. In addition, an efficient tridiagonal system solver for massively parallel computers has been applied to resolve the most expensive function in this implementation, resulting in an efficiency of 0.93 while using 32 HPCC cores. Moreover, symmetric boundary conditions have been developed to further reduce the computational cost, achieving a speedup of 19.26 for a 12-sided polygonal converging shock.

18. Periodic dislocation dynamics in two-dimensional concentrated emulsion flowing in a tapered microchannel

Science.gov (United States)

Gai, Ya; Leong, Chia Min; Cai, Wei; Tang, Sindy K. Y.

2016-11-01

Here we report a surprising order in concentrated emulsion when flowing as a monolayer in a tapered microfluidic channel. The flow of droplets in micro-channels can be non-trivial, and may lead to unexpected phenomena such as long-period oscillations and chaos. Previously, there have been studies on concentrated emulsions in straight channels and channels with bends. The dynamics of how drops flow and rearrange in a tapered geometry has not yet been characterized. At sufficiently slow flow rates, the drops arrange into a hexagonal lattice. At a given x-position, the time-averaged droplet velocities are uniform. The instantaneous drop velocities, however, reveal a different, wave-like pattern. Within the rearrangement zone where the number of rows of drops decreases from N to N-1, there is always a drop moved faster than the others. Close examination reveals the anomalous velocity profile arises from a series of dislocations that are both spatial and temporal periodic. To our knowledge, such reproducible dislocation motion has not been reported before. Our results are useful in novel flow control and mixing strategies in droplet microfluidics as well as modeling crystal plasticity in low-dimensional nanomaterials.

19. Exciton dynamics and non-linearities in two-dimensional hybrid organic perovskites

Energy Technology Data Exchange (ETDEWEB)

Abdel-Baki, K.; Boitier, F.; Diab, H.; Lanty, G.; Jemli, K.; Lédée, F.; Deleporte, E.; Lauret, J. S., E-mail: jean-sebastien.lauret@lac.u-psud.fr [Laboratoire Aimé Cotton, CNRS, Univ. Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay Cedex (France); Garrot, D. [GEMAC, CNRS, UVSQ, Université Paris-Saclay, 45 avenue des États Unis 78035 Versailles Cedex (France)

2016-02-14

Due to their high potentiality for photovoltaic applications or coherent light sources, a renewed interest in hybrid organic perovskites has emerged for few years. When they are arranged in two dimensions, these materials can be considered as hybrid quantum wells. One consequence of the unique structure of 2D hybrid organic perovskites is a huge exciton binding energy that can be tailored through chemical engineering. We present experimental investigations of the exciton non-linearities by means of femtosecond pump-probe spectroscopy. The exciton dynamics is fitted with a bi-exponential decay with a free exciton life-time of ∼100 ps. Moreover, an ultrafast intraband relaxation (<150 fs) is also reported. Finally, the transient modification of the excitonic line is analyzed through the moment analysis and described in terms of reduction of the oscillator strength and linewidth broadening. We show that excitonic non-linearities in 2D hybrid organic perovskites share some behaviours of inorganic semiconductors despite their high exciton binding energy.

20. Two-dimensional intraventricular flow pattern visualization using the image-based computational fluid dynamics.

Science.gov (United States)

Doost, Siamak N; Zhong, Liang; Su, Boyang; Morsi, Yosry S

2016-10-31

The image-based computational fluid dynamics (IB-CFD) technique, as the combination of medical images and the CFD method, is utilized in this research to analyze the left ventricle (LV) hemodynamics. The research primarily aims to propose a semi-automated technique utilizing some freely available and commercial software packages in order to simulate the LV hemodynamics using the IB-CFD technique. In this research, moreover, two different physiological time-resolved 2D models of a patient-specific LV with two different types of aortic and mitral valves, including the orifice-type valves and integrated with rigid leaflets, are adopted to visualize the process of developing intraventricular vortex formation and propagation. The blood flow pattern over the whole cardiac cycle of two models is also compared to investigate the effect of utilizing different valve types in the process of the intraventricular vortex formation. Numerical findings indicate that the model with integrated valves can predict more complex intraventricular flow that can match better the physiological flow pattern in comparison to the orifice-type model.

1. Two-dimensional simulation and modeling for dynamic sheath expansion during plasma immersion ion implantation

Energy Technology Data Exchange (ETDEWEB)

Qin, S.; Zhou, Y.; Chan, C. [Northeastern Univ., Boston, MA (United States)

1996-12-31

Plasma immersion ion implantation (PIII) has been utilized as a low cost, low energy doping method for large area targets with applications to semiconductor manufacturing. They include doping, shallow junction formation, hydrogenation for poly-Si thin film transistors, and SIMOX (Separated by IMplant of OXygen) structure formation. The characteristics of the dynamic sheath expansion during PIII process is very important for the optimum PIII configuration design and process control in order to obtain more accurate doping results such as the implant dose and impurity profile. For example, the sheath thickness is critical to chamber design and monoenergetic ion implant for a more accurate control of as-implanted impurity profile of shallow junction and SIMOX structures. A PDP2 simulation code has been used to simulate PIII process which will aid in understanding the physics of PIII processes and obtain the optimum process parameters. This model was verified by comparing with the PDP2 computer simulations and the experimental results of the PIII doping processes.

2. Molecular-scale dynamics of light-induced spin cross-over in a two-dimensional layer

Science.gov (United States)

Bairagi, Kaushik; Iasco, Olga; Bellec, Amandine; Kartsev, Alexey; Li, Dongzhe; Lagoute, Jérôme; Chacon, Cyril; Girard, Yann; Rousset, Sylvie; Miserque, Frédéric; Dappe, Yannick J; Smogunov, Alexander; Barreteau, Cyrille; Boillot, Marie-Laure; Mallah, Talal; Repain, Vincent

2016-01-01

Spin cross-over molecules show the unique ability to switch between two spin states when submitted to external stimuli such as temperature, light or voltage. If controlled at the molecular scale, such switches would be of great interest for the development of genuine molecular devices in spintronics, sensing and for nanomechanics. Unfortunately, up to now, little is known on the behaviour of spin cross-over molecules organized in two dimensions and their ability to show cooperative transformation. Here we demonstrate that a combination of scanning tunnelling microscopy measurements and ab initio calculations allows discriminating unambiguously between both states by local vibrational spectroscopy. We also show that a single layer of spin cross-over molecules in contact with a metallic surface displays light-induced collective processes between two ordered mixed spin-state phases with two distinct timescale dynamics. These results open a way to molecular scale control of two-dimensional spin cross-over layers. PMID:27425776

3. Dynamics of laser-imploded core plasmas observed by ultrafast two-dimensional x-ray imaging with animation display

Energy Technology Data Exchange (ETDEWEB)

Heya, Manabu; Shiraga, Hiroyuki; Shimada, Kyoko; Miyanaga, Noriaki; Takabe, Hideaki; Yamanaka, Tatsuhiko; Mima, Kunioki [Osaka Univ., Inst. of Laser Engineering, Suita, Osaka (Japan)

1999-05-01

In order to observe time-resolved, two-dimensional (2D) spatial distribution of x rays emitted from core plasmas at the final stage of the implosion, we have developed a multi-imaging x-ray streak camera (MIXS) and a multi-channel MIXS (McMIXS) methods as new ultrafast 2D x-ray imaging techniques. The observed time-resolved 2D x-ray and electron-temperature images of core plasmas, which are sequentially changing with time, have been displayed by using an animation method. Temporal evolutions of nonuniform structures, including shape, size, and movement of core plasmas can be observed instinctively with the animated display. The ultrafast 2D x-ray imaging with the animation display is a new powerful tool for understanding the dynamics of laser-imploded core plasmas. (author)

4. Study on two-dimensional equilibrium structure of magnetized complex plasmas based on a Langevin dynamics simulation

Science.gov (United States)

Kong, Wei; Yang, Fang; Liu, Songfen; Shi, Feng

2016-10-01

A Langevin dynamics simulation method is used to study the two-dimensional (2D) equilibrium structure of complex plasmas while considering an external magnetic field. The traditional Yukawa potential and a modified Yukawa potential according to Shukla et al. [Phys. Lett. A 291, 413 (2001); Shukla and Mendonca, Phys. Scr. T113 82 (2004)] and Salimullah et al. [Phys. Plasmas 10, 3047 (2003)] respectively, are employed to account for the interaction of the charged dust particles. It is found that the collisions between neutral gas and charged dust particles have minor effects on the 2D equilibrium structure of the system. Based on the modified Yukawa potential, studies on the 2D equilibrium structure show that the traditional Yukawa potential is still suitable for describing the magnetized complex plasmas, even if the shielding distance of charged dust particles is affected by the strong external magnetic field.

5. Synthesis of a Two-Dimensional Covalent Organic Monolayer through Dynamic Imine Chemistry at the Air/Water Interface.

Science.gov (United States)

Dai, Wenyang; Shao, Feng; Szczerbiński, Jacek; McCaffrey, Ryan; Zenobi, Renato; Jin, Yinghua; Schlüter, A Dieter; Zhang, Wei

2016-01-01

A two-dimensional covalent organic monolayer was synthesized from simple aromatic triamine and dialdehyde building blocks by dynamic imine chemistry at the air/water interface (Langmuir-Blodgett method). The obtained monolayer was characterized by optical microscopy, scanning electron microscopy, and atomic force microscopy, which unambiguously confirmed the formation of a large (millimeter range), unimolecularly thin aromatic polyimine sheet. The imine-linked chemical structure of the obtained monolayer was characterized by tip-enhanced Raman spectroscopy, and the peak assignment was supported by spectra simulated by density functional theory. Given the modular nature and broad substrate scope of imine formation, the work reported herein opens up many new possibilities for the synthesis of customizable 2D polymers and systematic studies of their structure-property relationships.

6. Signatures of correlated excitonic dynamics in two-dimensional spectroscopy of the Fenna-Matthew-Olson photosynthetic complex

Energy Technology Data Exchange (ETDEWEB)

Caram, Justin R.; Lewis, Nicholas H. C.; Fidler, Andrew F.; Engel, Gregory S. [Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States)

2012-03-14

Long-lived excitonic coherence in photosynthetic proteins has become an exciting area of research because it may provide design principles for enhancing the efficiency of energy transfer in a broad range of materials. In this publication, we provide new evidence that long-lived excitonic coherence in the Fenna-Mathew-Olson pigment-protein (FMO) complex is consistent with the assumption of cross correlation in the site basis, indicating that each site shares bath fluctuations. We analyze the structure and character of the beating crosspeak between the two lowest energy excitons in two-dimensional (2D) electronic spectra of the FMO Complex. To isolate this dynamic signature, we use the two-dimensional linear prediction Z-transform as a platform for filtering coherent beating signatures within 2D spectra. By separating signals into components in frequency and decay rate representations, we are able to improve resolution and isolate specific coherences. This strategy permits analysis of the shape, position, character, and phase of these features. Simulations of the crosspeak between excitons 1 and 2 in FMO under different regimes of cross correlation verify that statistically independent site fluctuations do not account for the elongation and persistence of the dynamic crosspeak. To reproduce the experimental results, we invoke near complete correlation in the fluctuations experienced by the sites associated with excitons 1 and 2. This model contradicts ab initio quantum mechanic/molecular mechanics simulations that observe no correlation between the energies of individual sites. This contradiction suggests that a new physical model for long-lived coherence may be necessary. The data presented here details experimental results that must be reproduced for a physical model of quantum coherence in photosynthetic energy transfer.

7. A Brownian Dynamics Approach to ESR Line Shape Calculations

Science.gov (United States)

Wright, Matthew P.

The work presented in this thesis uses a Monte Carlo technique to simulate spectra for 14N spin-labels and 15N spin labels. The algorithm presented here also has the capability to produce simulated spectra for any admixture of 14N and 15N. The algorithm makes use of iterative loops' to model Brownian rotational diffusion and for the repeated evaluation of the spectral correlation function (relaxation function). The method described in this work starts with a derivation of an angular dependent "Spin Hamiltonian" that when diagonalized yields orientation dependent eigenvalues. The resulting eigenvalue equations are later used to calculate the energy trajectories of a nitroxide spin-label undergoing rotational diffusion. The energy trajectories are then used to evaluate the relaxation function. The absorption spectrum is obtained by applying a Fourier transform to the relaxation function. However, the application of the Fourier transform to the relaxation function produces "leakage" effects that manifest as spurious peaks in the first derivative spectrum. To counter "leakage" effects a data windowing function was applied to the relaxation function prior to the Fourier transform. In order to test the accuracy of this algorithm, simulated spectra for 14N, and 15N spin labels diffusing in a glycerol-water mixture as well as a 14N-15N admixture diffusing in the same solvent were produced and compared to experimental spectra. An attempt to quantify the level of agreement was made by calculating the mean square residual of the simulated and experimental spectra. The main spectral features were reproduced with reasonable fidelity by the simulated spectra.

8. Dynamic cortical activity during the perception of three-dimensional object shape from two-dimensional random-dot motion.

Science.gov (United States)

Iwaki, Sunao; Bonmassar, Giorgio; Belliveau, John W

2013-09-01

Recent neuroimaging studies implicate that both the dorsal and ventral visual pathways, as well as the middle temporal (MT) areas which are critical for the perception of visual motion, are involved in the perception of three-dimensional (3D) structure from two-dimensional (2D) motion (3D-SFM). However, the neural dynamics underlying the reconstruction of a 3D object from 2D optic flow is not known. Here we combined magnetoencephalography (MEG) and functional MRI (fMRI) measurements to investigate the spatiotemporal brain dynamics during 3D-SFM. We manipulated parametrically the coherence of randomly moving groups of dots to create different levels of 3D perception and to study the associated changes in brain activity. At different latencies, the posterior infero-temporal (pIT), the parieto-occipital (PO), and the intraparietal (IP) regions showed increased neural activity during highly coherent motion conditions in which subjects perceived a robust 3D object. Causality analysis between these regions indicated significant causal influence from IP to pIT and from pIT to PO only in conditions where subjects perceived a robust 3D object. Current results suggest that the perception of a 3D object from 2D motion includes integration of global motion and 3D mental image processing, as well as object recognition that are accomplished by interactions between the dorsal and ventral visual pathways.

9. Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

CERN Document Server

Bellesia, Giovanni

2015-01-01

We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

10. Estimating the contribution of Brownian and Néel relaxation in a magnetic fluid through dynamic magnetic susceptibility measurements

Energy Technology Data Exchange (ETDEWEB)

Maldonado-Camargo, L. [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); Torres-Díaz, I. [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States); Chiu-Lam, A. [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); Hernández, M. [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States); Rinaldi, C., E-mail: carlos.rinaldi@bme.ufl.edu [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States)

2016-08-15

We demonstrate how dynamic magnetic susceptibility measurements (DMS) can be used to estimate the relative contributions of Brownian and Néel relaxation to the dynamic magnetic response of a magnetic fluid, a suspension of magnetic nanoparticles. The method applies to suspensions with particles that respond through Brownian or Néel relaxation and for which the characteristic Brownian and Néel relaxation times are widely separated. First, we illustrate this using magnetic fluids consisting of mixtures of particles that relax solely by the Brownian or Néel mechanisms. Then, it is shown how the same approach can be applied to estimate the relative contributions of Brownian and Néel relaxation in a suspension consisting of particles obtained from a single synthesis and whose size distribution straddles the transition from Néel to Brownian relaxation. - Highlights: • Method to estimate the contributions of the relaxation mechanism to the magnetic response. • Method applies to cases where the Brownian and Néel peaks do not overlap. • The method applies for ferrofluids prepared with as–synthesized particles.

11. A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures

Science.gov (United States)

Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.

2014-03-01

Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.

12. Dynamical observations on the crack tip zone and stress corrosion of two-dimensional MoS2

Science.gov (United States)

Ly, Thuc Hue; Zhao, Jiong; Cichocka, Magdalena Ola; Li, Lain-Jong; Lee, Young Hee

2017-01-01

Whether and how fracture mechanics needs to be modified for small length scales and in systems of reduced dimensionality remains an open debate. Here, employing in situ transmission electron microscopy, atomic structures and dislocation dynamics in the crack tip zone of a propagating crack in two-dimensional (2D) monolayer MoS2 membrane are observed, and atom-to-atom displacement mapping is obtained. The electron beam is used to initiate the crack; during in situ observation of crack propagation the electron beam effect is minimized. The observed high-frequency emission of dislocations is beyond previous understanding of the fracture of brittle MoS2. Strain analysis reveals dislocation emission to be closely associated with the crack propagation path in nanoscale. The critical crack tip plastic zone size of nearly perfect 2D MoS2 is between 2 and 5 nm, although it can grow to 10 nm under corrosive conditions such as ultraviolet light exposure, showing enhanced dislocation activity via defect generation.

13. Size-Dependent Biexciton Quantum Yields and Carrier Dynamics of Quasi-Two-Dimensional Core/Shell Nanoplatelets.

Science.gov (United States)

Ma, Xuedan; Diroll, Benjamin T; Cho, Wooje; Fedin, Igor; Schaller, Richard D; Talapin, Dmitri V; Gray, Stephen K; Wiederrecht, Gary P; Gosztola, David J

2017-09-05

Quasi-two-dimensional nanoplatelets (NPLs) possess fundamentally different excitonic properties from zero-dimensional quantum dots. We study lateral size-dependent photon emission statistics and carrier dynamics of individual NPLs using second-order photon correlation (g((2))(τ)) spectroscopy and photoluminescence (PL) intensity-dependent lifetime analysis. Room-temperature radiative lifetimes of NPLs can be derived from maximum PL intensity periods in PL time traces. It first decreases with NPL lateral size and then stays constant, deviating from the electric dipole approximation. Analysis of the PL time traces further reveals that the single exciton quantum yield in NPLs decreases with NPL lateral size and increases with protecting shell thickness, indicating the importance of surface passivation on NPL emission quality. Second-order photon correlation (g((2))(τ)) studies of single NPLs show that the biexciton quantum yield is strongly dependent on the lateral size and single exciton quantum yield of the NPLs. In large NPLs with unity single exciton quantum yield, the corresponding biexciton quantum yield can reach unity. These findings reveal that by careful growth control and core-shell material engineering, NPLs can be of great potential for light amplification and integrated quantum photonic applications.

14. Dynamical observations on the crack tip zone and stress corrosion of two-dimensional MoS2

KAUST Repository

Ly, Thuc Hue

2017-01-18

Whether and how fracture mechanics needs to be modified for small length scales and in systems of reduced dimensionality remains an open debate. Here, employing in situ transmission electron microscopy, atomic structures and dislocation dynamics in the crack tip zone of a propagating crack in two-dimensional (2D) monolayer MoS2 membrane are observed, and atom-to-atom displacement mapping is obtained. The electron beam is used to initiate the crack; during in situ observation of crack propagation the electron beam effect is minimized. The observed high-frequency emission of dislocations is beyond previous understanding of the fracture of brittle MoS2. Strain analysis reveals dislocation emission to be closely associated with the crack propagation path in nanoscale. The critical crack tip plastic zone size of nearly perfect 2D MoS2 is between 2 and 5 nm, although it can grow to 10 nm under corrosive conditions such as ultraviolet light exposure, showing enhanced dislocation activity via defect generation.

15. Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow.

Science.gov (United States)

Yang, Xiao-Dong; Melnik, Roderick V N

2007-04-01

The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity.

16. Noncommutative Brownian motion

CERN Document Server

Santos, Willien O; Souza, Andre M C

2016-01-01

We investigate the Brownian motion of a particle in a two-dimensional noncommutative (NC) space. Using the standard NC algebra embodied by the sympletic Weyl-Moyal formalism we find that noncommutativity induces a non-vanishing correlation between both coordinates at different times. The effect itself stands as a signature of spatial noncommutativity and offers further alternatives to experimentally detect the phenomena.

17. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

Science.gov (United States)

Votapka, Lane W; Amaro, Rommie E

2015-10-01

The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.

18. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

Directory of Open Access Journals (Sweden)

Lane W Votapka

2015-10-01

Full Text Available The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.

19. BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms.

Science.gov (United States)

Solano, Carlos J F; Pothula, Karunakar R; Prajapati, Jigneshkumar D; De Biase, Pablo M; Noskov, Sergei Yu; Kleinekathöfer, Ulrich

2016-05-10

All-atom molecular dynamics simulations have a long history of applications studying ion and substrate permeation across biological and artificial pores. While offering unprecedented insights into the underpinning transport processes, MD simulations are limited in time-scales and ability to simulate physiological membrane potentials or asymmetric salt solutions and require substantial computational power. While several approaches to circumvent all of these limitations were developed, Brownian dynamics simulations remain an attractive option to the field. The main limitation, however, is an apparent lack of protein flexibility important for the accurate description of permeation events. In the present contribution, we report an extension of the Brownian dynamics scheme which includes conformational dynamics. To achieve this goal, the dynamics of amino-acid residues was incorporated into the many-body potential of mean force and into the Langevin equations of motion. The developed software solution, called BROMOCEA, was applied to ion transport through OmpC as a test case. Compared to fully atomistic simulations, the results show a clear improvement in the ratio of permeating anions and cations. The present tests strongly indicate that pore flexibility can enhance permeation properties which will become even more important in future applications to substrate translocation.

20. Conserved linear dynamics of single-molecule Brownian motion

KAUST Repository

Serag, Maged F.

2017-06-06

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

1. The Effect of Buoyancy Force in Computational Fluid Dynamics Simulation of a Two-Dimensional Continuous Ohmic Heating Process

Directory of Open Access Journals (Sweden)

Elzubier A. Salih

2009-01-01

Full Text Available Problem statement: Earlier research on ohmic heating technique focused on viscous food and foods containing solid particles. In this study, use of ohmic heating on sterilization of guava juice is carried out. Computational fluid dynamics was used to model and simulate the system. Investigate the buoyancy effect on the CFD simulation of continuous ohmic heating systems of fluid foods. Approach: A two-dimensional model describing the flow, temperature and electric field distribution of non-Newtonian power law guava juice fluid in a cylindrical continuous ohmic heating cell was developed. The electrical conductivity, thermo physical and rheological properties of the fluid was temperature dependent. Numerical simulation was carried out using FLUENT 6.1 software package. A user defined functions available in FLUENT 6.1 was employed for the electric field equation. The heating cell used consisted of a cylindrical tube of diameter 0.05 m, height 0.50 m and having three collinear electrodes of 0.02 m width separated by a distance of 0.22 m. The sample was subjected to zero voltage at the top and bottom of electrodes while electrical potential of 90 volts (AC 50-60 Hz was set at the middle electrode. The inlet velocity is 0.003 m sec-1 and the temperature is in the range of 30-90°C. Results: Simulation was carried with and without buoyancy driven force effect. The ohmic heating was successfully simulated using CFD and the results showed that the buoyancy had a strong effect in temperature profiles and flow pattern of the collinear electrodes configuration ohmic heating. A more uniform velocity and temperature profiles were obtained with the buoyancy effect included. Conclusion: For accurate results, the inclusion of buoyancy effect into the CFD simulation is important.

2. Two-dimensional electron-electron double resonance and electron spin-echo study of solute dynamics in smectics

Science.gov (United States)

Gorcester, Jeff; Rananavare, Shankar B.; Freed, Jack H.

1989-05-01

Electron spin-echo (ESE) and two-dimensional electron-electron double resonance (2D ELDOR) experiments have been performed as a function of director orientation and temperature in the smectic A phase of the liquid crystal S2 for the spin-probe PD-tempone(2×10-3 M). Over the entire temperature range studied (288-323 K) we observe significant 2D ELDOR cross peaks only for ΔMI =±1 indicative of 14N spin-relaxation and negligible Heisenberg exchange. From the angular dependent 14N spin-relaxation rates we obtain the dipolar spectral densities at the hyperfine (hf) frequency, whereas from a combination of ESE and 2D ELDOR we obtain the dipolar and Zeeman-dipolar spectral densities at zero frequency. The angular dependent spectral densities were successfully decomposed into their basic components in accordance with theory. The angular dependent spectral densities at the hf frequency are not predicted by a model of anisotropic rotational diffusion in a nematic orienting potential, but are consistent with predictions of a model due to Moro and Nordio of solute rototranslational diffusion in a McMillan-type potential. The angular dependence also indicates that order director fluctuations in the smectic phase are suppressed at frequencies on the order of 10 MHz. An additional contribution to solute reorientation due to cooperative hydrocarbon chain fluctuations is suggested to account for the behavior of the observed spectral densities at zero frequency. An evaluation of the relevance of several other dynamical models to this experimental work is also presented.

3. Harmonic functions on Walsh's Brownian motion

OpenAIRE

Jehring, Kristin Elizabeth

2009-01-01

In this dissertation we examine a variation of two- dimensional Brownian motion introduced in 1978 by Walsh. Walsh's Brownian motion can be described as a Brownian motion on the spokes of a (rimless) bicycle wheel. We will construct such a process by randomly assigning an angle to the excursions of a reflecting Brownian motion from 0. With this construction we see that Walsh's Brownian motion in R² behaves like one-dimensional Brownian motion away from the origin, but at the origin behaves di...

4. Polymer deformation in Brownian ratchets: theory and molecular dynamics simulations.

Science.gov (United States)

Kenward, Martin; Slater, Gary W

2008-11-01

We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U0 on the order of several kBT. The application of the ratchet potential also deforms the polymer chains. With increasing U0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=35 (U0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=34 for moderate U0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D3D to that of a pancaked-shaped polymer moving parallel to its minor axis D2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, toff, is defined in terms of the relaxation time of the polymer, tauR. We also derive a modified version of the Bader ratchet model [Bader, Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.

5. Solitary wave solutions of two-dimensional nonlinear Kadomtsev–Petviashvili dynamic equation in dust-acoustic plasmas

2017-09-01

Nonlinear two-dimensional Kadomtsev–Petviashvili (KP) equation governs the behaviour of nonlinear waves in dusty plasmas with variable dust charge and two temperature ions. By using the reductive perturbation method, the two-dimensional dust-acoustic solitary waves (DASWs) in unmagnetized cold plasma consisting of dust fluid, ions and electrons lead to a KP equation. We derived the solitary travelling wave solutions of the twodimensional nonlinear KP equation by implementing sech–tanh, sinh–cosh, extended direct algebraic and fraction direct algebraicmethods. We found the electrostatic field potential and electric field in the form travellingwave solutions for two-dimensional nonlinear KP equation. The solutions for the KP equation obtained by using these methods can be demonstrated precisely and efficiency. As an illustration, we used the readymade package of $\\it{Mathematica}$ program 10.1 to solve the original problem. These solutions are in good agreement with the analytical one.

6. Structure Analysis of Jungle-Gym-Type Gels by Brownian Dynamics Simulation

Science.gov (United States)

Ohta, Noriyoshi; Ono, Kohki; Takasu, Masako; Furukawa, Hidemitsu

2008-02-01

We investigated the structure and the formation process of two kinds of gels by Brownian dynamics simulation. The effect of flexibility of main chain oligomer was studied. From our results, hard gel with rigid main chain forms more homogeneous network structure than soft gel with flexible main chain. In soft gel, many small loops are formed, and clusters tend to shrink. This heterogeneous network structure may be caused by microgels. In the low density case, soft gel shows more heterogeneity than the high density case.

7. Brownian dynamics simulations on CPU and GPU with BD_BOX.

Science.gov (United States)

Długosz, Maciej; Zieliński, Paweł; Trylska, Joanna

2011-09-01

There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU. Copyright © 2011 Wiley Periodicals, Inc.

8. Brownian Dynamics Simulation of Microstructures and Elongational Viscosities of Micellar Surfactant Solution

Institute of Scientific and Technical Information of China (English)

WEI Jin-Jia; KAWAGUCHI Yasuo; YU Bo; LI Feng-Chen

2008-01-01

@@ Brownian dynamics simulation is conducted for a dilute surfactant solution under a steady uniaxial elongational flow.A new inter-cluster potential is used for the interaction among surfactant micelles to determine the micellar network structures in the surfactant solution.The micellar network is successfully simulated.It is formed at low elongation rates and destroyed by high elongation rates.The computed elongational viscosities show elongation-thinning characteristics.The relationship between the elongational viscosities and the microstructure of the surfactant solution is revealed.

9. Dynamic phase transition in the two-dimensional kinetic Ising model in an oscillating field: universality with respect to the stochastic dynamics.

Science.gov (United States)

Buendía, G M; Rikvold, P A

2008-11-01

We study the dynamical response of a two-dimensional Ising model subject to a square-wave oscillating external field. In contrast to earlier studies, the system evolves under a so-called soft Glauber dynamic [Rikvold and Kolesik, J. Phys. A 35, L117 (2002)], for which both nucleation and interface propagation are slower and the interfaces smoother than for the standard Glauber dynamic. We choose the temperature and magnitude of the external field such that the metastable decay of the system following field reversal occurs through nucleation and growth of many droplets of the stable phase, i.e., the multidroplet regime. Using kinetic Monte Carlo simulations, we find that the system undergoes a nonequilibrium phase transition, in which the symmetry-broken dynamic phase corresponds to an asymmetric stationary limit cycle for the time-dependent magnetization. The critical point is located where the half period of the external field is approximately equal to the metastable lifetime of the system. We employ finite-size scaling analysis to investigate the characteristics of this dynamical phase transition. The critical exponents and the fixed-point value of the fourth-order cumulant are found to be consistent with the universality class of the two-dimensional equilibrium Ising model. This universality class has previously been established for the same nonequilibrium model evolving under the standard Glauber dynamic, as well as in a different nonequilibrium model of CO oxidation. The results reported in the present paper support the hypothesis that this far-from-equilibrium phase transition is universal with respect to the choice of the stochastic dynamics.

10. Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

CERN Document Server

Jo, Ju-Yeon; Tanimura, Yoshitaka

2016-01-01

Frequency-domain two-dimensional Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid MD simulation algorithm. We elucidate mechanisms governing the 2D signal pro?les involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal pro?les and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently.

11. Deterministic Brownian motion: The effects of perturbing a dynamical system by a chaotic semi-dynamical system

Energy Technology Data Exchange (ETDEWEB)

Mackey, Michael C. [Departments of Physiology, Physics and Mathematics and Centre for Nonlinear Dynamics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6 (Canada)]. E-mail: mackey@cnd.mcgill.ca; Tyran-Kaminska, Marta [Institute of Mathematics, Silesian University, ul. Bankowa 14, 40-007 Katowice (Poland)]. E-mail: mtyran@us.edu.pl

2006-01-15

Here we review and extend central limit theorems for chaotic deterministic semi-dynamical discrete time systems. We then apply these results to show how Brownian motion-like behavior can be recovered and how an Ornstein-Uhlenbeck process can be constructed within a totally deterministic framework. These results illustrate that under certain circumstances the contamination of experimental data by 'noise' may be alternately interpreted as the signature of an underlying chaotic process.

12. On the large-scale structure and spectral dynamics of two-dimensional turbulence in a periodic channel

NARCIS (Netherlands)

Kramer, W.; Clercx, H.J.H.; van Heijst, G.J.F.

2008-01-01

This paper reports on a numerical study of forced two-dimensional turbulence in a periodic channel with flat no-slip walls. Since corners or curved domain boundaries, which are met in the standard rectangular, square, or circular geometries, are absent in this geometry, the (statistical) analysis of

13. Inertial-range dynamics and scaling laws of two-dimensional magnetohydrodynamic turbulence in the weak-field regime.

Science.gov (United States)

Blackbourn, Luke A K; Tran, Chuong V

2014-08-01

We study inertial-range dynamics and scaling laws in unforced two-dimensional magnetohydrodynamic turbulence in the regime of moderately small and small initial magnetic-to-kinetic-energy ratio r(0), with an emphasis on the latter. The regime of small r(0) corresponds to a relatively weak field and strong magnetic stretching, whereby the turbulence is characterized by an intense conversion of kinetic into magnetic energy (dynamo action in the three-dimensional context). This conversion is an inertial-range phenomenon and, upon becoming quasisaturated, deposits the converted energy within the inertial range rather than transferring it to the small scales. As a result, the magnetic-energy spectrum E(b)(k) in the inertial range can become quite shallow and may not be adequately explained or understood in terms of conventional cascade theories. It is demonstrated by numerical simulations at high Reynolds numbers (and unity magnetic Prandtl number) that the energetics and inertial-range scaling depend strongly on r(0). In particular, for fully developed turbulence with r(0) in the range [1/4,1/4096], E(b)(k) is found to scale as k(α), where α≳-1, including α>0. The extent of such a shallow spectrum is limited, becoming broader as r(0) is decreased. The slope α increases as r(0) is decreased, appearing to tend to +1 in the limit of small r(0). This implies equipartition of magnetic energy among the Fourier modes of the inertial range and the scaling k(-1) of the magnetic potential variance, whose flux is direct rather than inverse. This behavior of the potential resembles that of a passive scalar. However, unlike a passive scalar whose variance dissipation rate slowly vanishes in the diffusionless limit, the dissipation rate of the magnetic potential variance scales linearly with the diffusivity in that limit. Meanwhile, the kinetic-energy spectrum is relatively steep, followed by a much shallower tail due to strong antidynamo excitation. This gives rise to a total

14. Generalized Scaling and the Master Variable for Brownian Magnetic Nanoparticle Dynamics.

Directory of Open Access Journals (Sweden)

Daniel B Reeves

Full Text Available Understanding the dynamics of magnetic particles can help to advance several biomedical nanotechnologies. Previously, scaling relationships have been used in magnetic spectroscopy of nanoparticle Brownian motion (MSB to measure biologically relevant properties (e.g., temperature, viscosity, bound state surrounding nanoparticles in vivo. Those scaling relationships can be generalized with the introduction of a master variable found from non-dimensionalizing the dynamical Langevin equation. The variable encapsulates the dynamical variables of the surroundings and additionally includes the particles' size distribution and moment and the applied field's amplitude and frequency. From an applied perspective, the master variable allows tuning to an optimal MSB biosensing sensitivity range by manipulating both frequency and field amplitude. Calculation of magnetization harmonics in an oscillating applied field is also possible with an approximate closed-form solution in terms of the master variable and a single free parameter.

15. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling.

Science.gov (United States)

Metzger, Vincent T; Eun, Changsun; Kekenes-Huskey, Peter M; Huber, Gary; McCammon, J Andrew

2014-11-18

We perform Brownian dynamics simulations and Smoluchowski continuum modeling of the bifunctional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (P. falciparum DHFR-TS) with the objective of understanding the electrostatic channeling of dihydrofolate generated at the TS active site to the DHFR active site. The results of Brownian dynamics simulations and Smoluchowski continuum modeling suggest that compared to Leishmania major DHFR-TS, P. falciparum DHFR-TS has a lower but significant electrostatic-mediated channeling efficiency (?15-25%) at physiological pH (7.0) and ionic strength (150 mM). We also find that removing the electric charges from key basic residues located between the DHFR and TS active sites significantly reduces the channeling efficiency of P. falciparum DHFR-TS. Although several protozoan DHFR-TS enzymes are known to have similar tertiary and quaternary structure, subtle differences in structure, active-site geometry, and charge distribution appear to influence both electrostatic-mediated and proximity-based substrate channeling.

16. Studies of spin relaxation and molecular dynamics in liquid crystals by two-dimensional Fourier transform electron spin resonance. II. Perdeuterated-tempone in butoxy benzylidene octylaniline and dynamic cage effects

Science.gov (United States)

Sastry, V. S. S.; Polimeno, Antonino; Crepeau, Richard H.; Freed, Jack H.

1996-10-01

Two-dimensional Fourier transform (2D-FT)-electron spin resonance (ESR) studies on the small globular spin probe perdeuterated tempone (PDT) in the liquid crystal solvent 4O,8 (butoxy benzylidene octylaniline) are reported. These experiments, over the temperature range of 95 °C to 24 °C, cover the isotropic (I), nematic (N), smectic A (SA), smectic B (SB), and crystal (C) phases. The 2D-ELDOR (two-dimensional electron-electron double resonance) spectra confirm the anomalously rapid reorientation of PDT, especially in the lower temperature phases. The model of a slowly relaxing local structure (SRLS) leads to generally very good non-linear least squares (NLLS) global fits to the sets of 2D-ELDOR spectra obtained at each temperature. These fits are significantly better than those achieved by the standard model of Brownian reorientation in a macroscopic orienting potential. The SRLS model is able to account for anomalies first observed in an earlier 2D-ELDOR study on PDT in a different liquid crystal in its smectic phases. Although it is instructional to extract the various spectral densities from the COSY (correlation spectroscopy) and 2D-ELDOR spectra, the use of NLLS global fitting to a full set of 2D-ELDOR spectra is shown to be more reliable and convenient for obtaining optimum model parameters, especially in view of possible (incipient) slow motional effects from the SRLS or dynamic cage. The cage potential is found to remain fairly constant at about kBT over the various phases (with only a small drop in the SB phase), but its asymmetry increases with decreasing temperature T. This value is significantly larger than the weak macroscopic orienting potential which increases from 0.1 to 0.3kBT with decreasing T. The cage relaxation rate, given by Rc is about 3×107 s-1 in the I phase, but increases to about 108 s-1 in the SA, SB, and C phases. The rotational diffusion tensor for PDT shows only a small T-independent asymmetry, and its mean rotational diffusion

17. Coexistence of chaotic and non-chaotic states in the two-dimensional Gauss-Navier-Stokes dynamics

Science.gov (United States)

Giberti, C.; Rondoni, L.; Vernia, C.

2004-01-01

Recently, Gallavotti proposed an Equivalence Conjecture in hydrodynamics, which states that forced-damped fluids can be equally well represented by means of the Navier-Stokes equations (NS) and by means of time reversible modifications of NS called Gauss-Navier-Stokes equations (GNS). This Equivalence Conjecture received numerical support in several recent papers concerning two-dimensional fluid mechanics. The corresponding results rely on the fact that the NS and GNS systems only have one attracting set. Performing similar two-dimensional simulations, we find that there are conditions to be met by the GNS system for this to be the case. In particular, increasing the Reynolds number, while keeping fixed the number of Fourier modes, leads to the coexistence of different attractors. This makes difficult a test of the Equivalence Conjecture, but constitutes a spurious effect due to the insufficient spectral resolution. With sufficiently fine spectral resolution, the steady states are unique and the Equivalence Conjecture can be conveniently established.

18. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

Science.gov (United States)

Kuznetsov, Igor R; Evans, Evan A

2013-04-01

We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

19. A Study of Electron and Phonon Dynamics by Broadband Two-Dimensional THz Time-Domain Spectroscopy

Science.gov (United States)

Fu, Zhengping

Terahertz (THz) wave interacts with semiconductors in many ways, such as resonant excitation of lattice vibration, intraband transition and polaron formation. Different from the optical waves, THz wave has lower photon energy (1 THz = 4.14 meV) and is suitable for studying dynamics of low-energy excitations. Recently the studies of the interaction of THz wave and semiconductors have been extending from the linear regime to the nonlinear regime, owing to the advance of the high-intensity THz generation and detection methods. Two-dimensional (2D) spectroscopy, as a useful tool to unravel the nonlinearity of materials, has been well developed in nuclear magnetic resonance and infrared region. However, the counterpart in THz region has not been well developed and was only demonstrated at frequency around 20 THz due to the lack of intense broadband THz sources. Using laser-induced plasma as the THz source, we developed collinear broadband 2D THz time-domain spectroscopy covering from 0.5 THz to 20 THz. Broadband intense THz pulses emitted from laser-induced plasma provide access to a variety of nonlinear properties of materials. Ultrafast optical and THz pulses make it possible to resolve the transient change of the material properties with temporal resolution of tens of femtoseconds. This thesis focuses on the linear and nonlinear interaction of the THz wave with semiconductors. Since a great many physical processes, including vibrational motion of lattice and plasma oscillation, has resonant frequency in the THz range, rich physics can be studies in our experiment. The thesis starts from the linear interaction of the THz wave with semiconductors. In the narrow band gap semiconductor InSb, the plasma absorption edge, Restrahlen band and dispersion of polaritons are observed. The nonlinear response of InSb in high THz field is verified in the frequency-resolved THz Z-scan experiment. The third harmonic generations due to the anharmonicity of plasma oscillation and the

20. Effective diffusion of confined active Brownian swimmers

Science.gov (United States)

Sandoval, Mario; Dagdug, Leonardo

2014-11-01

We find theoretically the effect of confinement and thermal fluctuations, on the diffusivity of a spherical active swimmer moving inside a two-dimensional narrow cavity of general shape. The explicit formulas for the effective diffusion coefficient of a swimmer moving inside two particular cavities are presented. We also compare our analytical results with Brownian Dynamics simulations and we obtain excellent agreement. L.D. thanks Consejo Nacional de Ciencia y Tecnologia (CONACyT) Mexico, for partial support by Grant No. 176452. M. S. thanks CONACyT and Programa de Mejoramiento de Profesorado (PROMEP) for partially funding this work under Grant No. 103.5/13/6732.

1. The van Hove distribution function for brownian hard spheres: dynamical test particle theory and computer simulations for bulk dynamics.

Science.gov (United States)

Hopkins, Paul; Fortini, Andrea; Archer, Andrew J; Schmidt, Matthias

2010-12-14

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.

2. Brownian dynamics simulation of the effect of histone modification on nucleosome structure

Science.gov (United States)

Li, Wei; Dou, Shuo-Xing; Xie, Ping; Wang, Peng-Ye

2007-05-01

Using Brownian dynamics we simulate the effect of histone modification, such as phosphorylation, acetylation, and methylation, on nucleosome structure by varying the interaction force between DNA and the histone octamer. The simulation shows that the structural stability of nucleosome is very sensitive to the interaction force, and the DNA unwrapping from the modified histone octamer usually occurs turn by turn. Furthermore, the effects of temperature and DNA break as well as the competition between modified and normal histone octamers are investigated, with the simulation results being in agreement with the experimental observation that phosphorylated nucleosomes near DNA breaks are more easily depleted. Though the simulation study may only give a coarse grained view of the DNA unwrapping process for the modified histone octamer, it may provide insight into the mechanism of DNA repair.

3. Full evaporation dynamic headspace in combination with selectable one-dimensional/two-dimensional gas chromatography-mass spectrometry for the determination of suspected fragrance allergens in cosmetic products.

Science.gov (United States)

Devos, Christophe; Ochiai, Nobuo; Sasamoto, Kikuo; Sandra, Pat; David, Frank

2012-09-14

Suspected fragrance allergens were determined in cosmetic products using a combination of full evaporation-dynamic headspace (FEDHS) with selectable one-dimensional/two-dimensional GC-MS. The full evaporation dynamic headspace approach allows the non-discriminating extraction and injection of both apolar and polar fragrance compounds, without contamination of the analytical system by high molecular weight non-volatile matrix compounds. The method can be applied to all classes of cosmetic samples, including water containing matrices such as shower gels or body creams. In combination with selectable (1)D/(2)D GC-MS, consisting of a dedicated heart-cutting GC-MS configuration using capillary flow technology (CFT) and low thermal mass GC (LTM-GC), a highly flexible and easy-to-use analytical solution is offered. Depending on the complexity of the perfume fraction, analyses can be performed in one-dimensional GC-MS mode or in heart-cutting two-dimensional GC-MS mode, without the need of hardware reconfiguration. The two-dimensional mode with independent temperature control of the first and second dimension column is especially useful to confirm the presence of detected allergen compounds when mass spectral deconvolution is not possible.

4. Two-dimensional fluorescence-detected coherent spectroscopy with absolute phasing by confocal imaging of a dynamic grating and 27-step phase-cycling

Energy Technology Data Exchange (ETDEWEB)

De, Arijit K., E-mail: akde@lbl.gov; Fleming, Graham R., E-mail: grfleming@lbl.gov [Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94702 (United States); Department of Chemistry, University of California at Berkeley, Berkeley, California 94702 (United States); Monahan, Daniele; Dawlaty, Jahan M. [Department of Chemistry, University of California at Berkeley, Berkeley, California 94702 (United States)

2014-05-21

We present a novel experimental scheme for two-dimensional fluorescence-detected coherent spectroscopy (2D-FDCS) using a non-collinear beam geometry with the aid of “confocal imaging” of dynamic (population) grating and 27-step phase-cycling to extract the signal. This arrangement obviates the need for distinct experimental designs for previously developed transmission detected non-collinear two-dimensional coherent spectroscopy (2D-CS) and collinear 2D-FDCS. We also describe a novel method for absolute phasing of the 2D spectrum. We apply this method to record 2D spectra of a fluorescent dye in solution at room temperature and observe “spectral diffusion.”.

5. Dynamical scaling, domain-growth kinetics, and domain-wall shapes of quenched two-dimensional anisotropic XY models

DEFF Research Database (Denmark)

Mouritsen, Ole G.; Praestgaard, Eigil

1988-01-01

temperature, the domain-growth kinetics is found to be independent of the value of this parameter over several decades of its range. This suggests that a universal principle is operative. The domain-wall shape is analyzed and shown to be well represented by a hyperbolic tangent function. The growth process......The domain-growth kinetics in two different anisotropic two-dimensional XY-spin models is studied by computer simulation. The models have uniaxial and cubic anisotropy which leads to ground-state orderings which are twofold and fourfold degenerate, respectively. The models are quenched from...... infinite to zero temperature as well as to nonzero temperatures below the ordering transition. The continuous nature of the spin variables causes the domain walls to be ‘‘soft’’ and characterized by a finite thickness. The steady-state thickness of the walls can be varied by a model parameter, P. At zero...

6. Accurate method for the Brownian dynamics simulation of spherical particles with hard-body interactions

Science.gov (United States)

Barenbrug, Theo M. A. O. M.; Peters, E. A. J. F. (Frank); Schieber, Jay D.

2002-11-01

In Brownian Dynamics simulations, the diffusive motion of the particles is simulated by adding random displacements, proportional to the square root of the chosen time step. When computing average quantities, these Brownian contributions usually average out, and the overall simulation error becomes proportional to the time step. A special situation arises if the particles undergo hard-body interactions that instantaneously change their properties, as in absorption or association processes, chemical reactions, etc. The common "naı̈ve simulation method" accounts for these interactions by checking for hard-body overlaps after every time step. Due to the simplification of the diffusive motion, a substantial part of the actual hard-body interactions is not detected by this method, resulting in an overall simulation error proportional to the square root of the time step. In this paper we take the hard-body interactions during the time step interval into account, using the relative positions of the particles at the beginning and at the end of the time step, as provided by the naı̈ve method, and the analytical solution for the diffusion of a point particle around an absorbing sphere. Öttinger used a similar approach for the one-dimensional case [Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996), p. 270]. We applied the "corrected simulation method" to the case of a simple, second-order chemical reaction. The results agree with recent theoretical predictions [K. Hyojoon and Joe S. Kook, Phys. Rev. E 61, 3426 (2000)]. The obtained simulation error is proportional to the time step, instead of its square root. The new method needs substantially less simulation time to obtain the same accuracy. Finally, we briefly discuss a straightforward way to extend the method for simulations of systems with additional (deterministic) forces.

7. Hadamard States and Two-dimensional Gravity

CERN Document Server

Salehi, H

2001-01-01

We have used a two-dimensional analog of the Hadamard state-condition to study the local constraints on the two-point function of a linear quantum field conformally coupled to a two-dimensional gravitational background. We develop a dynamical model in which the determination of the state of the quantum field is essentially related to the determination of a conformal frame. A particular conformal frame is then introduced in which a two-dimensional gravitational equation is established.

8. Dynamics of a multimode system coupled to multiple heat baths probed by two-dimensional infrared spectroscopy.

Science.gov (United States)

Ishizaki, Akihito; Tanimura, Yoshitaka

2007-09-27

Reduced equation of motion for a multimode system coupled to multiple heat baths is constructed by extending the quantum Fokker-Planck equation with low-temperature correction terms (J. Phys. Soc. Jpn. 2005, 74, 3131). Unlike such common approaches used to describe intramolecular multimode vibration as a Bloch-Redfield theory and a stochastic theory, the present formalism is defined by the molecular coordinates. To explore the correlation among different modes through baths, we consider two cases of system-bath couplings. One is a correlated case in which two modes are coupled to a single bath, and the other is an uncorrelated case in which each mode is coupled to a different bath. We further classify the correlated case into two cases, the plus- and minus-correlated cases, according to distinct correlation manners. For these, one-dimensional and two-dimensional infrared (2D-IR) spectra are calculated numerically by solving the equation of motion. It is demonstrated that 2D-IR spectroscopy has the ability to analyze the correlation of fluctuation-dissipation processes among different modes.

9. Classical Solution of a Two-Dimensional Dynamics System for Pure Forest%一个二维纯林发展系统的古典解

Institute of Scientific and Technical Information of China (English)

徐龙封; 吴慧

2011-01-01

The research of two-dimensional forest dynamics system model is still open. First, for the peculiarity of two-dimensional forest dynamics systems with initial state depending only on total quantity of forest, and boundary condition depending only on initial state again, boundary of system not satisfying one of 3 kinds common conditions, by introducing a class of special family curves in presence region of " stand age-diameter", the problem of boundary conditions is avoided. Secondly, using the technique of selecting measure dimension of lumber diameter properly, a well-posed two-dimensional forest dynamics system model is propounded. At last, colligating the technique of pulling characteristic curve, a prior estimate, structuring integral equation of initial state, iteration, the existence and uniqueness of the global classical solution are proved for this system.%二维森林发展系统模型的研究还未见到任何结果.针对这类系统初始状态依赖于林木总量,而边界状态又依赖于初始状态,系统的边界不满足通常的三类条件之一的特点,采用在“树龄-直径”存在区域内引进一类特殊的曲线族,避开了提边界条件问题.再利用适当地选择林木直径尺度量纲的技巧,提出了一个适定的二维纯林发展系统模型,最后综合拉特征线、先验估计、构造初始状态积分方程、迭代等技巧证明了这个系统整体古典解的存在唯一性.

10. Studies of spin relaxation and molecular dynamics in liquid crystals by two-dimensional Fourier transform electron spin resonance. I. Cholestane in butoxy benzylidene-octylaniline and dynamic cage effects

Science.gov (United States)

Sastry, V. S. S.; Polimeno, Antonino; Crepeau, Richard H.; Freed, Jack H.

1996-10-01

Two-dimensional Fourier transform (2D-FT) electron spin resonance (ESR) studies on the rigid rodlike cholestane (CSL) spin-label in the liquid crystal solvent 4O,8 (butoxy benzylidene octylaniline) are reported. These experiments were performed over a wide temperature range: 96 °C to 25 °C covering the isotropic (I), nematic (N), smectic A (SA), smectic B (SB), and crystal (C) phases. It is shown that 2D-FT-ESR, especially in the form of 2D-ELDOR (two-dimensional electron-electron double resonance) provides greatly enhanced sensitivity to rotational dynamics than previous cw-ESR studies on this and related systems. This sensitivity is enhanced by obtaining a series of 2D-ELDOR spectra as a function of mixing time, Tm, yielding essentially a three-dimensional experiment. Advantage is taken of this sensitivity to study the applicability of the model of a slowly relaxing local structure (SRLS). In this model, a dynamic cage of solvent molecules, which relaxes on a slower time scale than the CSL solute, provides a local orienting potential in addition to that of the macroscopic aligning potential in the liquid crystalline phase. The theory of Polimeno and Freed for SRLS in the ESR slow motional regime is extended by utilizing the theory of Lee et al. to include 2D-FT-ESR experiments, and it serves as the basis for the analysis of the 2D-ELDOR experiments. It is shown that the SRLS model leads to significantly improved non-linear least squares fits to experiment over those obtained with the standard model of Brownian reorientation in a macroscopic aligning potential. This is most evident for the SA phase, and the use of the SRLS model also removes the necessity of fitting with the unreasonably large CSL rotational asymmetries in the smectic phases that are required in both the cw-ESR and 2D-ELDOR fits with the standard model. The cage potential is found to vary from about kBT in the isotropic phase to greater than 2kBT in the N and SA phases, with an abrupt drop to

11. Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry.

Science.gov (United States)

Hua, Xin; Marshall, Matthew J; Xiong, Yijia; Ma, Xiang; Zhou, Yufan; Tucker, Abigail E; Zhu, Zihua; Liu, Songqin; Yu, Xiao-Ying

2015-05-01

A vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface), was employed for in situ chemical imaging of live biofilms using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Depth profiling by sputtering materials in sequential layers resulted in live biofilm spatial chemical mapping. Two-dimensional (2D) images were reconstructed to report the first three-dimensional images of hydrated biofilm elucidating spatial and chemical heterogeneity. 2D image principal component analysis was conducted among biofilms at different locations in the microchannel. Our approach directly visualized spatial and chemical heterogeneity within the living biofilm by dynamic liquid ToF-SIMS.

12. Dynamic Critical Exponents of Three-Dimensional Ising Models and Two-Dimensional Three-States Potts Models

Science.gov (United States)

2008-01-01

Values of dynamic critical exponents are numerically estimated for various models with the nonequilibrium relaxation method to test the dynamic universality hypothesis. The dynamics used here are single-spin update with Metropolis-type transition probabities. The estimated values of nonequilibrium relaxation exponent of magnetization λm (=β/zν) of Ising models on bcc and fcc lattices are estimated to be 0.251(3) and 0.252(3), respectively, which are consistent with the value of the model on simple-cubic lattice, 0.250(2). The dynamic critical exponents of three-states Potts models on square, honeycomb and triangular lattices are also estimated to be 2.193(5), 2.198(4), and 2.199(3), respectively. They are consistent within the error bars. It is also confirmed that Ising models with regularly modulated coupling constants on square lattice have the same dynamic critical exponents with the uniformly ferromagnetic Ising model.

13. Simulation for Sludge Flocculation I: Brownian Dynamic Simulation for Perikinetic Flocculation of Charged Particle

Directory of Open Access Journals (Sweden)

Linshuang Liu

2012-01-01

Full Text Available To investigate sludge drying process, a numerical simulation based on Brownian dynamic for the floc with uncharged and charged particles was conducted. The Langevin equation is used as dynamical equation for tracking each particle in a floc. An initial condition and periodic boundary condition which well conformed to reality is used for calculating the floc growth process. Each cell consists of 1000 primary particles with diameter 0.1 ∼ 4 μm. Floc growth is related to the thermal force and the electrostatic force. The electrostatic force on a particle in the simulation cell is considered as the sum of electrostatic forces from other particles in the original cell and its replicate cells. It is assumed that flocs are charged with precharged primary particles in dispersion system by ionization. By the analysis of the simulation figures, on one hand, the effects of initial particle size and sludge density on floc smashing time, floc radius of gyration, and fractal dimension were discussed. On the other hand, the effects of ionization on floc smashing time and floc structure were presented. This study has important practical value in the high-turbidity water treatment, especially for sludge drying.

14. COMPUTER SIMULATION OF LOCAL MOBILITY IN DENDRIMERS WITH ASYMMETRIC BRANCHING BY BROWNIAN DYNAMICS METHOD

Directory of Open Access Journals (Sweden)

O. V. Shavykin

2016-09-01

Full Text Available The Brownian dynamics method has been used to study the effect of the branching asymmetry on the local orientational mobility of segments and bonds in dendrimers in good solvent. “Coarse-grained” models of flexible dendrimers with different branching symmetry but with the same average segment length were considered. The frequency dependences of the rate of the spin-lattice relaxation nuclear magnetic resonance (NMR [1/T1H(H] for segments or bonds located at different distances from terminal monomers were calculated. After the exclusion of the contribution of the overall dendrimer rotation the position of the maxima of the frequency dependences [1/T1H(ωH] for different segments with the same length doesn’t depend on their location inside a dendrimer both for phantom models and for models with excluded volume interactions. This effect doesn’t depend also on the branching symmetry, but the position of the maximum [1/T1H(ωH] is determined by the segment length. For bonds inside segments the positions of the maximum [1/T1H(ωH] coincide for all models considered. Therefore, the obtained earlier conclusion about the weak influence of the excluded volume interactions on the local dynamics in the flexible symmetric dendrimers can be generalized for dendrimers with an asymmetric branching.

15. Self-assembly of actin monomers into long filaments: Brownian Dynamics simulations

DEFF Research Database (Denmark)

Shillcock, Julian C.

2009-01-01

/detachment events. When a single filament is allowed to grow in a bath of constant concentration of free ADP-actin monomers, its growth rate increases linearly with the free monomer concentration in quantitative agreement with in vitro experiments. Theresults also show that the waiting time is governed by exponential......Brownian dynamics simulations are used to study the dynamical process of self-assembly of actin monomers into long filaments containing up to 1000 actin protomers. In order to overcome the large separation of time scales between the diffusive motion of the freemonomers and the relatively slow...... states corresponding to a bound adenosine triphosphate (ATP), adenosine diphosphate with inorganic phosphate (ADP/P), and ADP molecule. The simplest situation that has been studied experimentally is provided by the polymerization of ADP-actin, for which all protomers are identical. This case is used...

16. Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

Science.gov (United States)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

17. A Brownian dynamics study on ferrofluid colloidal dispersions using an iterative constraint method to satisfy Maxwell's equations

Science.gov (United States)

Dubina, Sean Hyun; Wedgewood, Lewis Edward

2016-07-01

Ferrofluids are often favored for their ability to be remotely positioned via external magnetic fields. The behavior of particles in ferromagnetic clusters under uniformly applied magnetic fields has been computationally simulated using the Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. However, few methods have been established that effectively handle the basic principles of magnetic materials, namely, Maxwell's equations. An iterative constraint method was developed to satisfy Maxwell's equations when a uniform magnetic field is imposed on ferrofluids in a heterogeneous Brownian dynamics simulation that examines the impact of ferromagnetic clusters in a mesoscale particle collection. This was accomplished by allowing a particulate system in a simple shear flow to advance by a time step under a uniformly applied magnetic field, then adjusting the ferroparticles via an iterative constraint method applied over sub-volume length scales until Maxwell's equations were satisfied. The resultant ferrofluid model with constraints demonstrates that the magnetoviscosity contribution is not as substantial when compared to homogeneous simulations that assume the material's magnetism is a direct response to the external magnetic field. This was detected across varying intensities of particle-particle interaction, Brownian motion, and shear flow. Ferroparticle aggregation was still extensively present but less so than typically observed.

18. A Brownian dynamics study on ferrofluid colloidal dispersions using an iterative constraint method to satisfy Maxwell’s equations

Energy Technology Data Exchange (ETDEWEB)

Dubina, Sean Hyun, E-mail: sdubin2@uic.edu; Wedgewood, Lewis Edward, E-mail: wedge@uic.edu [Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St. (MC 110), Chicago, Illinois 60607-4408 (United States)

2016-07-15

Ferrofluids are often favored for their ability to be remotely positioned via external magnetic fields. The behavior of particles in ferromagnetic clusters under uniformly applied magnetic fields has been computationally simulated using the Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. However, few methods have been established that effectively handle the basic principles of magnetic materials, namely, Maxwell’s equations. An iterative constraint method was developed to satisfy Maxwell’s equations when a uniform magnetic field is imposed on ferrofluids in a heterogeneous Brownian dynamics simulation that examines the impact of ferromagnetic clusters in a mesoscale particle collection. This was accomplished by allowing a particulate system in a simple shear flow to advance by a time step under a uniformly applied magnetic field, then adjusting the ferroparticles via an iterative constraint method applied over sub-volume length scales until Maxwell’s equations were satisfied. The resultant ferrofluid model with constraints demonstrates that the magnetoviscosity contribution is not as substantial when compared to homogeneous simulations that assume the material’s magnetism is a direct response to the external magnetic field. This was detected across varying intensities of particle-particle interaction, Brownian motion, and shear flow. Ferroparticle aggregation was still extensively present but less so than typically observed.

19. Brownian dynamics simulation of peeling a strongly-adsorbed polymer molecule from a frictionless substrate.

Science.gov (United States)

Iliafar, Sara; Vezenov, Dmitri; Jagota, Anand

2013-02-01

We used brownian dynamics to study the peeling of a polymer molecule, represented by a freely jointed chain, from a frictionless surface in an implicit solvent with parameters representative of single-stranded DNA adsorbed on graphite. For slow peeling rates, simulations match the predictions of an equilibrium statistical thermodynamic model. We show that deviations from equilibrium peeling forces are dominated by a combination of Stokes (viscous) drag forces acting on the desorbed section of the chain and a finite rate of hopping over a desorption barrier. Characteristic velocities separating equilibrium and nonequilibrium regimes are many orders of magnitude higher than values accessible in force spectroscopy experiments. Finite probe stiffness resulted in disappearance of force spikes due to desorption of individual links predicted by the statistical thermodynamic model under displacement control. Probe fluctuations also masked sharp transitions in peeling force between blocks of distinct sequences, indicating limitation in the ability of single-molecule force spectroscopy to distinguish small differences in homologous molecular structures.

20. Conductance properties of the inwardly rectifying channel, Kir3.2: molecular and Brownian dynamics study.

Science.gov (United States)

Hilder, Tamsyn A; Chung, Shin-Ho

2013-02-01

Using the recently unveiled crystal structure, and molecular and Brownian dynamics simulations, we elucidate several conductance properties of the inwardly rectifying potassium channel, Kir3.2, which is implicated in cardiac and neurological disorders. We show that the pore is closed by a hydrophobic gating mechanism similar to that observed in Kv1.2. Once open, potassium ions move into, but not out of, the cell. The asymmetrical current-voltage relationship arises from the lack of negatively charged residues at the narrow intracellular mouth of the channel. When four phenylalanine residues guarding the intracellular gate are mutated to glutamate residues, the channel no longer shows inward rectification. Inward rectification is restored in the mutant Kir3.2 when it becomes blocked by intracellular Mg(2+). Tertiapin, a polypeptide toxin isolated from the honey bee, is known to block several subtypes of the inwardly rectifying channels with differing affinities. We identify critical residues in the toxin and Kir3.2 for the formation of the stable complex. A lysine residue of tertiapin protrudes into the selectivity filter of Kir3.2, while two other basic residues of the toxin form hydrogen bonds with acidic residues located just outside the channel entrance. The depth of the potential of mean force encountered by tertiapin is -16.1kT, thus indicating that the channel will be half-blocked by 0.4μM of the toxin.

1. Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study

Science.gov (United States)

Haliloglu, Turkan; Bahar, Ivet; Erman, Burak

1996-08-01

The behavior of a single polyethylene chain grafted to an impenetrable surface, under shear flow, is investigated using Brownian dynamics simulations. Both short-range conformational energies and excluded volume effects are included in the model. Simulations are performed in good and poor solvent conditions in order to explore the effect of solvent quality. The shear flow is represented by the superposition of a force profile increasing linearly with the distance from the surface. Distribution of rotational angles, chain dimensions, components of the radius of gyration, segment density distribution, average layer thickness, and average orientation of bond vectors with respect to flow direction are determined and compared with other studies. Above a certain value of the shear rate, a significant increase in chain dimensions is observed for both good and poor solvents, the transition from coiled to stretched state being sharper in poor solvent. In good solvent, chain dimensions along the two perpendicular directions to the flow direction diminish with increasing shear rate. On the other hand, in poor solvent, there is an overall expansion in chain dimensions in all directions at low shear rates, which is subsequently followed by the orientation and alignment of the chain along the direction of flow. The experimentally observed increase in chain dimensions normal to the flow field at low shear rates is evidenced for the first time by simulations.

2. Average hydrodynamic correction for the Brownian dynamics calculation of flocculation rates in concentrated dispersions

Science.gov (United States)

Urbina-Villalba, German; García-Sucre, Máximo; Toro-Mendoza, Jhoan

2003-12-01

In order to account for the hydrodynamic interaction (HI) between suspended particles in an average way, Honig et al. [J. Colloid Interface Sci. 36, 97 (1971)] and more recently Heyes [Mol. Phys. 87, 287 (1996)] proposed different analytical forms for the diffusion constant. While the formalism of Honig et al. strictly applies to a binary collision, the one from Heyes accounts for the dependence of the diffusion constant on the local concentration of particles. However, the analytical expression of the latter approach is more complex and depends on the particular characteristics of each system. Here we report a combined methodology, which incorporates the formula of Honig et al. at very short distances and a simple local volume-fraction correction at longer separations. As will be shown, the flocculation behavior calculated from Brownian dynamics simulations employing the present technique, is found to be similar to that of Batchelor’s tensor [J. Fluid. Mech. 74, 1 (1976); 119, 379 (1982)]. However, it corrects the anomalous coalescence found in concentrated systems as a result of the overestimation of many-body HI.

3. Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study

Science.gov (United States)

Mielke, Steven P.; Fink, William H.; Krishnan, V. V.; Grønbech-Jensen, Niels; Benham, Craig J.

2004-10-01

The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume. The chain, linear when relaxed, is looped to form two open but topologically constrained subdomains. This permits the dynamic introduction of torsional stress via a centrally applied torque. We simulate by Brownian dynamics the 100 μs response of a 477-base pair B-DNA template to the localized torque generated by the prokaryotic transcription ensemble. Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe. The magnitude of writhe surpasses that of twist before also leveling off when the structure reaches mechanical equilibrium with the torsional load. Superhelicity is simultaneously right handed in one subdomain and left handed in the other, as predicted by the "transcription-induced twin-supercoiled-domain" model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987)]. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA.

4. Low-energy dynamics of the two-dimensional S=1/2 Heisenberg antiferromagnet on percolating clusters.

Science.gov (United States)

Wang, Ling; Sandvik, Anders W

2006-09-15

We investigate the quantum dynamics of site diluted S=1/2 Heisenberg antiferromagnetic clusters at the 2D percolation threshold. We use Lanczos diagonalization to calculate the lowest excitation gap Delta and, to reach larger sizes, use quantum Monte Carlo simulations to study an upper bound for Delta obtained from sum rules involving the staggered structure factor and susceptibility. Scaling the gap distribution with the cluster length L, Delta approximately L(-), we obtain a dynamic exponent z approximately 2D(f), where D(f)=91/48 is the fractal dimensionality of the percolating cluster. This is in contrast with previous expectations of z=D(f). We argue that the low-energy excitations are due to weakly coupled effective moments formed due to local imbalance in sublattice occupation.

5. Effects of electric field on structures and dynamics in a two-dimensional dust dipole particle system

Science.gov (United States)

Hou, X. N.; Liu, Y. H.; Huang, F.; Jiang, S. Z.; Chen, Z. Y.; Zhang, R. Y.

2016-09-01

Effects of radial electric field on the structures and dynamics of dust dipoles are studied by molecular dynamics simulations. The dipoles' configuration and mean distance to the system center are used to illustrate the structures of the whole system. It is shown that the dipole particles can arrange themselves into ring-like structures in the absence of external electric field, which can gradually transform to vortex, and then to radial arrangement with the increase of the strength of electric field. The trajectories, mean square displacement, and the mean speed in radial and tangential directions of dipoles are investigated to depict the effects of the radial electric filed on the collective motion of dust dipolar particles, which are closely associated with the growth of dust particle, especially for the formation of rod-like and some other complex fractal dust particles.

6. Size-Dependent Transition to High-Dimensional Chaotic Dynamics in a Two-Dimensional Excitable Medium

CERN Document Server

Strain, M C; Strain, Matthew C.; Greenside, Henry S.

1997-01-01

The spatiotemporal dynamics of an excitable medium with multiple spiral defects is shown to vary smoothly with system size from short-lived transients for small systems to extensive chaos for large systems. A comparison of the Lyapunov dimension density with the average spiral defect density suggests an average dimension per spiral defect varying between three and seven. We discuss some implications of these results for experimental studies of ventricular fibrillation.

7. Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase.

Science.gov (United States)

Ono, Junichi; Takada, Shoji; Saito, Shinji

2015-06-07

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

8. Two-dimensional calculus

CERN Document Server

Osserman, Robert

2011-01-01

The basic component of several-variable calculus, two-dimensional calculus is vital to mastery of the broader field. This extensive treatment of the subject offers the advantage of a thorough integration of linear algebra and materials, which aids readers in the development of geometric intuition. An introductory chapter presents background information on vectors in the plane, plane curves, and functions of two variables. Subsequent chapters address differentiation, transformations, and integration. Each chapter concludes with problem sets, and answers to selected exercises appear at the end o

9. Two dimensional vernier

Science.gov (United States)

Juday, Richard D. (Inventor)

1992-01-01

A two-dimensional vernier scale is disclosed utilizing a cartesian grid on one plate member with a polar grid on an overlying transparent plate member. The polar grid has multiple concentric circles at a fractional spacing of the spacing of the cartesian grid lines. By locating the center of the polar grid on a location on the cartesian grid, interpolation can be made of both the X and Y fractional relationship to the cartesian grid by noting which circles coincide with a cartesian grid line for the X and Y direction.

10. Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a Light Harvesting 2 complex.

Science.gov (United States)

van der Vegte, C P; Prajapati, J D; Kleinekathöfer, U; Knoester, J; Jansen, T L C

2015-01-29

The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient manner. A general description of the chromophores and the interaction with their local environment is crucial to understand this highly efficient energy transport. Here we include this interaction in an atomistic way using mixed quantum-classical (molecular dynamics) simulations of spectra. In particular, we present the first atomistic simulation of nonlinear optical spectra for LH2 and use it to study the energy transport within the complex. We show that the frequency distributions of the pigments strongly depend on their positions with respect to the protein scaffold and dynamics of their local environment. Furthermore, we show that although the pigments are closely packed the transition frequencies of neighboring pigments are essentially uncorrelated. We present the simulated linear absorption spectra for the LH2 complex and provide a detailed explanation of the states responsible for the observed two-band structure. Finally, we discuss the energy transfer within the complex by analyzing population transfer calculations and 2D spectra for different waiting times. We conclude that the energy transfer from the B800 ring to the B850 ring is mediated by intermediate states that are delocalized over both rings, allowing for a stepwise downhill energy transport.

11. Virial theorem and dynamical evolution of self-gravitating Brownian particles in an unbounded domain. II. Inertial models.

Science.gov (United States)

Chavanis, Pierre-Henri; Sire, Clément

2006-06-01

We propose a general kinetic and hydrodynamic description of self-gravitating Brownian particles in d dimensions. We go beyond the usual approximations by considering inertial effects and finite-N effects while previous works use a mean-field approximation valid in a proper thermodynamic limit (N --> +infinity) and consider an overdamped regime (xi --> +infinity). We recover known models in some particular cases of our general description. We derive the expression of the virial theorem for self-gravitating Brownian particles and study the linear dynamical stability of isolated clusters of particles and uniform systems by using techniques introduced in astrophysics. We investigate the influence of the equation of state, of the dimension of space, and of the friction coefficient on the dynamical stability of the system. We obtain the exact expression of the critical temperature Tc for a multicomponents self-gravitating Brownian gas in d = 2. We also consider the limit of weak frictions, xi --> 0, and derive the orbit-averaged Kramers equation.

12. Brownian Dynamics of a Suspension of Particles with Constrained Voronoi Cell Volumes

KAUST Repository

Singh, John P.

2015-06-23

© 2015 American Chemical Society. Solvent-free polymer-grafted nanoparticle fluids consist of inorganic core particles fluidized by polymers tethered to their surfaces. The attachment of the suspending fluid to the particle surface creates a strong penalty for local variations in the fluid volume surrounding the particles. As a model of such a suspension we perform Brownian dynamics of an equilibrium system consisting of hard spheres which experience a many-particle potential proportional to the variance of the Voronoi volumes surrounding each particle (E = α(Vi-V0)2). The coefficient of proportionality α can be varied such that pure hard sphere dynamics is recovered as α → 0, while an incompressible array of hairy particles is obtained as α →. As α is increased the distribution of Voronoi volumes becomes narrower, the mean coordination number of the particle increases and the variance in the number of nearest neighbors decreases. The nearest neighbor peaks in the pair distribution function are suppressed and shifted to larger radial separations as the constraint acts to maintain relatively uniform interstitial regions. The structure factor of the model suspension satisfies S(k=0) → 0 as α → in accordance with expectation for a single component (particle plus tethered fluid) incompressible system. The tracer diffusivity of the particles is reduced by the volume constraint and goes to zero at φ 0.52, indicating an earlier glass transition than has been observed in hard sphere suspensions. The total pressure of the suspension grows in proportion to (αkBT)1/2 as the strength of the volume-constraint potential grows. This stress arises primarily from the interparticle potential forces, while the hard-sphere collisional contribution to the stress is suppressed by the volume constraint.

13. Oscillatory shear response of dilute ferrofluids: predictions from rotational Brownian dynamics simulations and ferrohydrodynamics modeling.

Science.gov (United States)

Soto-Aquino, D; Rosso, D; Rinaldi, C

2011-11-01

Ferrofluids are colloidal suspensions of magnetic nanoparticles that exhibit normal liquid behavior in the absence of magnetic fields but respond to imposed magnetic fields by changing their viscosity without loss of fluidity. The response of ferrofluids to constant shear and magnetic fields has received a lot of attention, but the response of ferrofluids to oscillatory shear remains largely unexplored. In the present work we used rotational Brownian dynamics to study the dynamic properties of ferrofluids with thermally blocked nanoparticles under oscillatory shear and constant magnetic fields. Comparisons between simulations and modeling using the ferrohydrodynamics equations were also made. Simulation results show that, for small rotational Péclet number, the in-phase and out-of-phase components of the complex viscosity depend on the magnitude of the magnetic field and frequency of the shear, following a Maxwell-like model with field-dependent viscosity and characteristic time equal to the field-dependent transverse magnetic relaxation time of the nanoparticles. Comparison between simulations and the numerical solution of the ferrohydrodynamic equations shows that the oscillatory rotational magnetoviscosity for an oscillating shear field obtained using the kinetic magnetization relaxation equation quantitatively agrees with simulations for a wide range of Péclet number and Langevin parameter but has quantitative deviations from the simulations at high values of the Langevin parameter. These predictions indicate an apparent elastic character to the rheology of these suspensions, even though we are considering the infinitely dilute limit in which there are negligible particle-particle interactions and, as such, chains do not form. Additionally, an asymptotic analytical solution of the ferrohydrodynamics equations, valid for Pe<2, was used to demonstrate that the Cox-Merz rule applies for dilute ferrofluids under conditions of small shear rates. At higher shear

14. Brownian Dynamics of a Suspension of Particles with Constrained Voronoi Cell Volumes.

Science.gov (United States)

Singh, John P; Walsh, Stuart D C; Koch, Donald L

2015-06-23

Solvent-free polymer-grafted nanoparticle fluids consist of inorganic core particles fluidized by polymers tethered to their surfaces. The attachment of the suspending fluid to the particle surface creates a strong penalty for local variations in the fluid volume surrounding the particles. As a model of such a suspension we perform Brownian dynamics of an equilibrium system consisting of hard spheres which experience a many-particle potential proportional to the variance of the Voronoi volumes surrounding each particle (E = α(Vi-V0)(2)). The coefficient of proportionality α can be varied such that pure hard sphere dynamics is recovered as α → 0, while an incompressible array of hairy particles is obtained as α → ∞. As α is increased the distribution of Voronoi volumes becomes narrower, the mean coordination number of the particle increases and the variance in the number of nearest neighbors decreases. The nearest neighbor peaks in the pair distribution function are suppressed and shifted to larger radial separations as the constraint acts to maintain relatively uniform interstitial regions. The structure factor of the model suspension satisfies S(k=0) → 0 as α → ∞ in accordance with expectation for a single component (particle plus tethered fluid) incompressible system. The tracer diffusivity of the particles is reduced by the volume constraint and goes to zero at ϕ ∼ 0.52, indicating an earlier glass transition than has been observed in hard sphere suspensions. The total pressure of the suspension grows in proportion to (αkBT)(1/2) as the strength of the volume-constraint potential grows. This stress arises primarily from the interparticle potential forces, while the hard-sphere collisional contribution to the stress is suppressed by the volume constraint.

15. Testing a one-dimensional prescription of dynamical shear mixing with a two-dimensional hydrodynamic simulation

Science.gov (United States)

Edelmann, P. V. F.; Röpke, F. K.; Hirschi, R.; Georgy, C.; Jones, S.

2017-07-01

Context. The treatment of mixing processes is still one of the major uncertainties in 1D stellar evolution models. This is mostly due to the need to parametrize and approximate aspects of hydrodynamics in hydrostatic codes. In particular, the effect of hydrodynamic instabilities in rotating stars, for example, dynamical shear instability, evades consistent description. Aims: We intend to study the accuracy of the diffusion approximation to dynamical shear in hydrostatic stellar evolution models by comparing 1D models to a first-principle hydrodynamics simulation starting from the same initial conditions. Methods: We chose an initial model calculated with the stellar evolution code GENEC that is just at the onset of a dynamical shear instability but does not show any other instabilities (e.g., convection). This was mapped to the hydrodynamics code SLH to perform a 2D simulation in the equatorial plane. We compare the resulting profiles in the two codes and compute an effective diffusion coefficient for the hydro simulation. Results: Shear instabilities develop in the 2D simulation in the regions predicted by linear theory to become unstable in the 1D stellar evolution model. Angular velocity and chemical composition is redistributed in the unstable region, thereby creating new unstable regions. After a period of time, the system settles in a symmetric, steady state, which is Richardson stable everywhere in the 2D simulation, whereas the instability remains for longer in the 1D model due to the limitations of the current implementation in the 1D code. A spatially resolved diffusion coefficient is extracted by comparing the initial and final profiles of mean atomic mass. Conclusions: The presented simulation gives a first insight on hydrodynamics of shear instabilities in a real stellar environment and even allows us to directly extract an effective diffusion coefficient. We see evidence for a critical Richardson number of 0.25 as regions above this threshold remain

16. Equation of state calculations for two-dimensional dust coulomb crystal at near zero temperature by molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Djouder, M., E-mail: djouder-madjid@ummto.dz; Kermoun, F.; Mitiche, M. D.; Lamrous, O. [Laboratoire de Physique et Chimie Quantique, Université Mouloud Mammeri Tizi-Ouzou, BP 17 RP, 15000 Tizi-Ouzou (Algeria)

2016-01-15

Dust particles observed in universe as well as in laboratory and technological plasma devices are still under investigation. At low temperature, these particles are strongly negatively charged and are able to form a 2D or 3D coulomb crystal. In this work, our aim was to check the ideal gas law validity for a 2D single-layer dust crystal recently reported in the literature. For this purpose, we have simulated, using the molecular dynamics method, its thermodynamic properties for different values of dust particles number and confinement parameters. The obtained results have allowed us to invalidate the ideal gas behaviour and to propose an effective equation of state which assumes a near zero dust temperature. Furthermore, the value of the calculated sound velocity was found to be in a good agreement with experimental data published elsewhere.

17. Spatiotemporal periodicity of dislocation dynamics in a two-dimensional microfluidic crystal flowing in a tapered channel

Science.gov (United States)

Gai, Ya; Leong, Chia Min; Cai, Wei; Tang, Sindy K. Y.

2016-10-01

When a many-body system is driven away from equilibrium, order can spontaneously emerge in places where disorder might be expected. Here we report an unexpected order in the flow of a concentrated emulsion in a tapered microfluidic channel. The velocity profiles of individual drops in the emulsion show periodic patterns in both space and time. Such periodic patterns appear surprising from both a fluid and a solid mechanics point of view. In particular, when the emulsion is considered as a soft crystal under extrusion, a disordered scenario might be expected based on the stochastic nature of dislocation dynamics in microscopic crystals. However, an orchestrated sequence of dislocation nucleation and migration is observed to give rise to a highly ordered deformation mode. This discovery suggests that nanocrystals can be made to deform more controllably than previously thought. It can also lead to novel flow control and mixing strategies in droplet microfluidics.

18. Random walk approach to spin dynamics in a two-dimensional electron gas with spin-orbit coupling

Energy Technology Data Exchange (ETDEWEB)

Yang, Luyi; Orenstein, J.; Lee, Dung-Hai

2010-09-27

We introduce and solve a semiclassical random walk (RW) model that describes the dynamics of spin polarization waves in zinc-blende semiconductor quantum wells. We derive the dispersion relations for these waves, including the Rashba, linear and cubic Dresselhaus spin-orbit interactions, as well as the effects of an electric field applied parallel to the spin polarization wave vector. In agreement with calculations based on quantum kinetic theory [P. Kleinert and V. V. Bryksin, Phys. Rev. B 76, 205326 (2007)], the RW approach predicts that spin waves acquire a phase velocity in the presence of the field that crosses zero at a nonzero wave vector, q{sub 0}. In addition, we show that the spin-wave decay rate is independent of field at q{sub 0} but increases as (q-q{sub 0}){sup 2} for q {ne} q{sub 0}. These predictions can be tested experimentally by suitable transient spin grating experiments.

19. Spin dynamics in high-mobility two-dimensional electron systems embedded in GaAs/AlGaAs quantum wells

Energy Technology Data Exchange (ETDEWEB)

Griesbeck, Michael

2012-11-22

Since many years there has been great effort to explore the spin dynamics in low-dimensional electron systems embedded in GaAs/AlGaAs based heterostructures for the purpose of quantum computation and spintronics applications. Advances in technology allow for the design of high quality and well-defined two-dimensional electron systems (2DES), which are perfectly suited for the study of the underlying physics that govern the dynamics of the electron spin system. In this work, spin dynamics in high-mobility 2DES is studied by means of the all-optical time-resolved Kerr/Faraday rotation technique. In (001)-grown 2DES, a strong in-plane spin dephasing anisotropy is studied, resulting from the interference of comparable Rashba and Dresselhaus contributions to the spin-orbit field (SOF). The dependence of this anisotropy on parameters like the confinement length of the 2DES, the sample temperature, as well as the electron density is demonstrated. Furthermore, coherent spin dynamics of an ensemble of ballistically moving electrons is studied without and within an applied weak magnetic field perpendicular to the sample plane, which forces the electrons to move on cyclotron orbits. Finally, strongly anisotropic spin dynamics is investigated in symmetric (110)-grown 2DES, using the resonant spin amplification method. Here, extremely long out-of-plane spin dephasing times can be achieved, in consequence of the special symmetry of the Dresselhaus SOF.

20. Wavelength selection based on two-dimensional correlation spectroscopy: application to noninvasive hemoglobin measurement by dynamic spectrum

Science.gov (United States)

Zhang, Shengzhao; Zhang, Linna; Li, Zhe; Li, Gang; Lin, Ling

2016-10-01

Dynamic spectrum (DS) method is one of the noninvasive approaches to measure the concentration of components in human blood based on the application of photoplethysmogram (PPG). One of the targets of the DS method is to predict the hemoglobin concentration in human blood noninvasively. In previous works, the usually used wavelength in the spectrum is 600-1100 nm which is regarded as the analysis "window" in human tissues. Optimum wavelengths for measurements of hemoglobin concentration have not been investigated yet. In order to improve the precision and reliability of hemoglobin measurements, a method for wavelength selection based on two-dimension (2D) correlation spectroscopy has been studied in this paper. By analyzing the 2D correlation spectroscopy which is generated by the DS data from subject with different blood hemoglobin concentrations, the wavelength bands which are sensible to hemoglobin concentrations in DS can be found. We developed calibration models between the DS data and hemoglobin concentration based on data from 57 subjects. The correlation coefficient is 0.68 in the test set of the model using the whole wavelength band (600-1100nm), while in the test set of the model using the selected wavelength band (850- 950nm) the correlation coefficient is 0.87. Results show the feasibility of wavelength selection utilizing 2Dcorrelation spectroscopy.

1. Two-dimensional electron gas in the regime of strong light-matter coupling: Dynamical conductivity and all-optical measurements of Rashba and Dresselhaus coupling

Science.gov (United States)

Yudin, Dmitry; Shelykh, Ivan A.

2016-10-01

A nonperturbative interaction of an electronic system with a laser field can substantially modify its physical properties. In particular, in two-dimensional (2D) materials with a lack of inversion symmetry, the achievement of a regime of strong light-matter coupling allows direct optical tuning of the strength of the Rashba spin-orbit interaction (SOI). Capitalizing on these results, we build a theory of the dynamical conductivity of a 2D electron gas with both Rashba and Dresselhaus SOIs coupled to an off-resonant high-frequency electromagnetic wave. We argue that strong light-matter coupling modifies qualitatively the dispersion of the electrons and can be used as a powerful tool to probe and manipulate the coupling strengths and adjust the frequency range where optical conductivity is essentially nonzero.

2. Towards a microchannel-based X-ray detector with two-dimensional spatial and time resolution and high dynamic range.

Science.gov (United States)

Adams, Bernhard W; Mane, Anil U; Elam, Jeffrey W; Obaid, Razib; Wetstein, Matthew; Chollet, Matthieu

2015-09-01

X-ray detectors that combine two-dimensional spatial resolution with a high time resolution are needed in numerous applications of synchrotron radiation. Most detectors with this combination of capabilities are based on semiconductor technology and are therefore limited in size. Furthermore, the time resolution is often realised through rapid time-gating of the acquisition, followed by a slower readout. Here, a detector technology is realised based on relatively inexpensive microchannel plates that uses GHz waveform sampling for a millimeter-scale spatial resolution and better than 100 ps time resolution. The technology is capable of continuous streaming of time- and location-tagged events at rates greater than 10(7) events per cm(2). Time-gating can be used for improved dynamic range.

3. Towards a microchannel-based X-ray detector with two-dimensional spatial and time resolution and high dynamic range

Energy Technology Data Exchange (ETDEWEB)

Adams, Bernhard W.; Mane, Anil; Elam, Jeffrey; Obaid, Razib; Wetstein, Matthew J.

2015-09-01

X-ray detectors that combine two-dimensional spatial resolution with a high time resolution are needed in numerous applications of synchrotron radiation. Most detectors with this combination of capabilities are based on semiconductor technology and are therefore limited in size. Furthermore, the time resolution is often realised through rapid time-gating of the acquisition, followed by a slower readout. Here, a detector technology is realised based on relatively inexpensive microchannel plates that uses GHz waveform sampling for a millimeter-scale spatial resolution and better than 100 ps time resolution. The technology is capable of continuous streaming of time- and location-tagged events at rates greater than 10(7) events per cm(2). Time-gating can be used for improved dynamic range.

4. Brownian dynamics simulations of polyelectrolyte adsorption in shear flow with hydrodynamic interaction.

Science.gov (United States)

Hoda, Nazish; Kumar, Satish

2007-12-21

The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N(1/3)Wi(2/3) at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N(-1/2)kappa(-3)(l(B)|sigmaq|)(3/2), where kappa is the inverse screening length, l(B) is the Bjerrum length, sigma is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.

5. The special theory of Brownian relativity: equivalence principle for dynamic and static random paths and uncertainty relation for diffusion.

Science.gov (United States)

Mezzasalma, Stefano A

2007-03-15

The theoretical basis of a recent theory of Brownian relativity for polymer solutions is deepened and reexamined. After the problem of relative diffusion in polymer solutions is addressed, its two postulates are formulated in all generality. The former builds a statistical equivalence between (uncorrelated) timelike and shapelike reference frames, that is, among dynamical trajectories of liquid molecules and static configurations of polymer chains. The latter defines the "diffusive horizon" as the invariant quantity to work with in the special version of the theory. Particularly, the concept of universality in polymer physics corresponds in Brownian relativity to that of covariance in the Einstein formulation. Here, a "universal" law consists of a privileged observation, performed from the laboratory rest frame and agreeing with any diffusive reference system. From the joint lack of covariance and simultaneity implied by the Brownian Lorentz-Poincaré transforms, a relative uncertainty arises, in a certain analogy with quantum mechanics. It is driven by the difference between local diffusion coefficients in the liquid solution. The same transformation class can be used to infer Fick's second law of diffusion, playing here the role of a gauge invariance preserving covariance of the spacetime increments. An overall, noteworthy conclusion emerging from this view concerns the statistics of (i) static macromolecular configurations and (ii) the motion of liquid molecules, which would be much more related than expected.

6. Brownian agents and active particles collective dynamics in the natural and social sciences

CERN Document Server

Schweitzer, Frank

2007-01-01

""This book lays out a vision for a coherent framework for understanding complex systems"" (from the foreword by J. Doyne Farmer). By developing the genuine idea of Brownian agents, the author combines concepts from informatics, such as multiagent systems, with approaches of statistical many-particle physics. This way, an efficient method for computer simulations of complex systems is developed which is also accessible to analytical investigations and quantitative predictions. The book demonstrates that Brownian agent models can be successfully applied in many different contexts, ranging from

7. Two-dimensional optical spectroscopy

CERN Document Server

Cho, Minhaeng

2009-01-01

Discusses the principles and applications of two-dimensional vibrational and optical spectroscopy techniques. This book provides an account of basic theory required for an understanding of two-dimensional vibrational and electronic spectroscopy.

8. Large scale spatio-temporal behaviour in surface growth. Scaling and dynamics of slow height variations in generalized two-dimensional Kuramoto-Sivashinsky equations

Science.gov (United States)

Juknevičius, Vaidas; Ruseckas, Julius; Armaitis, Jogundas

2017-09-01

This paper presents new findings concerning the dynamics of the slow height variations in surfaces produced by the two-dimensional isotropic Kuramoto-Sivashinsky equation with an additional nonlinear term. In addition to the disordered cellular patterns of specific size evident at small scales, slow height variations of scale-free character become increasingly evident when the system size is increased. This paper focuses on the parameter range in which the kinetic roughening with eventual saturation in surface roughness and coarseness is obtained, and the statistical and dynamical properties of surfaces in the long-time stationary regime are investigated. The resulting long-range scaling properties of the saturated surface roughness consistent with the power-law shape of the surface spectrum at small wave numbers are obtained in a wider parameter range than previously reported. The temporal properties of these long-range height variations are investigated by analysing the time series of surface roughness fluctuations. The resulting power-spectral densities can be expressed as a generalized Lorentzian whose cut-off frequency varies with system size. The dependence of this lower cut-off frequency on the smallest wave number connects spatial and temporal properties and gives new insight into the surface evolution on large scales.

9. Dynamics and microinstabilities at perpendicular collisionless shock: A comparison of large-scale two-dimensional full particle simulations with different ion to electron mass ratio

CERN Document Server

Umeda, Takayuki; Matsukiyo, Shuichi; Yamazaki, Ryo

2014-01-01

Large-scale two-dimensional (2D) full particle-in-cell simulations are carried out for studying the relationship between the dynamics of a perpendicular shock and microinstabilities generated at the shock foot. The structure and dynamics of collisionless shocks are generally determined by Alfven Mach number and plasma beta, while microinstabilities at the shock foot are controlled by the ratio of the upstream bulk velocity to the electron thermal velocity and the ratio of the plasma-to-cyclotron frequency. With a fixed Alfven Mach number and plasma beta, the ratio of the upstream bulk velocity to the electron thermal velocity is given as a function of the ion-to-electron mass ratio. The present 2D full PIC simulations with a relatively low Alfven Mach number (M_A ~ 6) show that the modified two-stream instability is dominant with higher ion-to-electron mass ratios. It is also confirmed that waves propagating downstream are more enhanced at the shock foot near the shock ramp as the mass ratio becomes higher. T...

10. Optical probing of spin dynamics of two-dimensional and bulk electrons in a GaAs/AlGaAs heterojunction system

Energy Technology Data Exchange (ETDEWEB)

Rizo, P J; Pugzlys, A; Slachter, A; Denega, S Z; Van Loosdrecht, P H M; Van der Wal, C H [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, NL-9747AG Groningen (Netherlands); Reuter, D; Wieck, A D, E-mail: c.h.van.der.wal@rug.n [Angewandte Festkoerperphysik, Ruhr-Universitaet Bochum, D-44780 Bochum (Germany)

2010-11-15

The electron spin dynamics in a GaAs/AlGaAs heterojunction system containing a high-mobility two-dimensional electron gas (2DEG) have been studied in this paper by using pump-probe time-resolved Kerr rotation experiments. Owing to the complex layer structure of this material, the transient Kerr response contains information about electron spins in the 2DEG, an epilayer and the substrate. We analyzed the physics that underlies this Kerr response, and established the conditions under which it is possible to unravel the signatures of the various photo-induced spin populations. This was used to explore how the electron spin dynamics of the various populations depend on the temperature, magnetic field and pump-photon density. The results show that the D'Yakonov-Perel' mechanism for spin dephasing (by spin-orbit fields) plays a prominent role in both the 2DEG and bulk populations over a wide range of temperatures and magnetic fields. Our results are of importance for future studies on the 2DEG in this type of heterojunction system, which offers interesting possibilities for spin manipulation and control of spin relaxation via tunable spin-orbit effects.

11. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies

Science.gov (United States)

Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

2016-09-01

Dynamics of the hydration structure around small vibrational probes have been extensively studied over the past few decades. However, we need to gain insight into how vibrational dynamics is affected by the molecular nature of the probe molecules in water. In this study, 2-nitro-5-thiocyanate benzoic acid (NTBA), which has an SCN group attached to an aromatic ring, and thiocyanate ion (SCN-) were used to investigate the vibrational dynamics of two vibrational probes, including vibrational frequency fluctuations and rotational relaxation. By performing two-dimensional infrared spectroscopic measurements, the vibrational frequency fluctuations of the SCN anti-stretching modes of these solutes were compared. The frequency-frequency time correlation function (FFTCF) of these solutes can be modeled by a delta function plus an exponential function and a constant. The FFTCF of NTBA was characterized by a time constant of 1.1 ps, which is similar to that of SCN-. Moreover, no component was longer than this constant. Consequently, the loss of the correlation in frequency fluctuations of the SCN anti-stretching mode of NTBA may be controlled by a mechanism similar to that of the ionic probe, which involves the hydrogen bonding dynamics of water. Polarization-controlled IR pump-probe measurements were performed for these vibrational probes in water to study the vibrational energy relaxation (VER) and reorientational relaxation processes. The VER rate of NTBA is much smaller than that of SCN-, which indicates that the intramolecular relaxation process is significant for VER of NTBA. Based on the rotational relaxation time of NTBA being shorter than that of SCN-, the internal rotational motion of the SCN group around the Cphenyl-S bond axis, where Cphenyl denotes a carbon atom of the aromatic ring to which the SCN group is attached, may play an important role in the anisotropic decay of NTBA in H2O.

12. Dynamics of ions in the selectivity filter of the KcsA channel: Towards a coupled Brownian particle description

CERN Document Server

Cosseddu, Salvatore M; Allen, Michael P; Rodger, P M; Luchinsky, Dmitry G; McClintock, Peter V E

2013-01-01

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion's dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.

13. Blood rheology using a Brownian dynamics simulation of bead spring ring with a constant area

Science.gov (United States)

Lopez, Rogelio

Coronary artery disease is epidemic in the western world. Occlusive vascular disease, when considered in terms of total incidence rather than separated to organ involvement, is the leading human's health hazard. A better understanding of occlusive vascular disease is so important that does not need to be justified. Blood theological properties are important factors in the occurrence and onset development of these diseases and may help in a rational approach to predictive and anticipatory therapies. Blood is a suspension of red blood cells (RBC) and therefore has a complex flow behavior. This research presents a Brownian dynamics (BD) model that captures the complex rheological behavior of blood; a three-bead-spring ring with a holonomic constant area constraint is being used to model the RBC in a dilute Newtonian solvent. The BD model has been used in simulations of RBCs to generate the RBC configuration. The stress tensor or momentum flux tensor is obtained as an ensemble average over molecular configurations by Giesekus expression of the stress calculator. This stress calculator makes it possible to obtain the RBC rheological properties of the model blood suspension under different flow conditions: homogeneous simple shear flow, elongational flow, inception of a steady shear flow, stress relaxation after cessation of steady shear flow and flow within narrow vessels by considering the blood microstructure scale process. The model's main results obtained for the specified flows are as follows: (a) Simulations in steady shear flow in an unbounded space the dilute blood suspension model expresses both shear thinning behavior for the viscosity and first normal stress coefficient. (b) In steady elongational flow, the elongational viscosity of the dilute blood suspension increases when the elongational rate increases. (c) Stress growth upon inception of steady shear flow; increasing shear rates does the shear stress approach its steady state monotonically. (d) Stress

14. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA

Science.gov (United States)

Mielke, Steven P.; Grønbech-Jensen, Niels; Krishnan, V. V.; Fink, William H.; Benham, Craig J.

2005-09-01

The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.

15. Brownian Ratchets in Biophysics: from Diffusing Phospholipids to Polymerizing Actin Filaments

Science.gov (United States)

van Oudenaarden, Alexander

2000-03-01

In the 'Feynman Lectures on Physics' Feynman introduces a mechanical ratchet and pawl subjected to thermal fluctuations to demonstrate the impossibility to violate the second law of thermodynamics. Since this introduction the Brownian ratchet has evolved from Gedanken experiments to real experiments in the interdisciplinary sciences such as biophysics and biochemistry. In this symposium I will present two experiments in which the concept Brownian ratchet is of key importance. The first experiment addresses a so-called geometrical Brownian ratchet [1]. This ratchet consists of a two-dimensional microfabricated periodic array of asymmetric diffusion barriers. As an experimental realization of a two-dimensional fluid of Brownian particles, a bilayer of phospholipid molecules is used. I will demonstrate that the geometrical Brownian ratchet can be used as a molecular sieve to separate mixtures of membrane molecules without the need to extract them from the membrane. In the second experiment I explore the spontaneous symmetry breaking of polymerizing actin networks [2]. Small submicron size beads coated uniformly with a protein that catalyzes actin polymerization, are initially surrounded by a symmetrical cloud of actin filaments. This symmetry can be broken spontaneously after which the beads undergo directional motion with constant velocity. I will present a simple stochastic theory, in which each filament is modeled as an elastic Brownian ratchet that qualitatively reproduces the experimental results. The presence of the bead couples the dynamics of different filaments which results in a complex collective system of interacting Brownian ratchets that exhibits an emergent symmetry breaking behavior. [1] A. van Oudenaarden and S. G. Boxer, Science 285, 1046 (1999). [2] A. van Oudenaarden and J. A. Theriot, Nature Cell Biology 1, 493 (1999).

16. Carrier dynamics of optical emission from two-dimensional electron gas in undoped AlGaN/GaN single heterojunctions

Energy Technology Data Exchange (ETDEWEB)

Kwack, H.S.; Cho, Y.H. [Department of Physics and Institute for Basic Science Research, Chungbuk National University, Cheongju 361-763 (Korea); Kim, G.H. [School of Information and Communication Engineering, Sungkyunkwan University, Suwon 440-746 (Korea); Park, M.R.; Youn, D.H.; Bae, S.B.; Lee, K.S. [Basic Research Laboratory, Electronics and Telecommunications Research Institute, Daejeon 305-350 (Korea); Lee, J.H.; Lee, J.H. [Department of Electric and Electronic Engineering, Kyungpook National University, Taegu 702-701 (Korea)

2006-06-15

The structural and optical properties of undoped AlGaN/GaN single heterojunctions (HJs) were studied by means of high-resolution x-ray diffraction, photoluminescence (PL), cathodoluminescence (CL), and time-resolved PL spectroscopy. An additional two-dimensional electron gas (2DEG)-related PL and CL emission appeared at about 40 meV below the GaN band-edge emission energy and persisted up to about 100 K, while this peak disappeared when the top AlGaN layer was removed by reactive ion etching. Depth-resolved CL spectra reveal the presence of a 2DEG at the heterointerface. The additional PL and CL emission below the GaN band-edge emission is attributed to the recombination between photogenerated holes and electrons confined at 2DEG states in the triangular-shaped interface potential. For the 2DEG emission, we observed an about 50-ps delayed rise time than the GaN and AlGaN emissions by using time-resolved PL, indicating effective carrier transfer from the GaN flatband and AlGaN regions to the heterointerface. From the results, we explained the optical properties and carrier recombination dynamics of 2DEG, GaN, and AlGaN emissions in undoped AlGaN/GaN single HJs. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

17. Carrier dynamics of optical emission from two-dimensional electron gas in undoped AlGaN/GaN single heterojunctions

Science.gov (United States)

Kwack, H. S.; Cho, Y. H.; Kim, G. H.; Park, M. R.; Youn, D. H.; Bae, S. B.; Lee, K.-S.; Lee, J. H.; Lee, J. H.

2006-06-01

The strucutral and optical properties of undoped AlGaN/GaN single heterojunctions (HJs) were studied by means of high-resolution x-ray diffraction, photoluminescence (PL), cathodoluminescence (CL), and time-resolved PL spectroscopy. An additional two-dimensional electron gas (2DEG)-related PL and CL emission appeared at about 40 meV below the GaN band-edge emission energy and persisted up to about 100 K, while this peak disappeared when the top AlGaN layer was removed by reactive ion etching. Depth-resolved CL spectra reveal the presence of a 2DEG at the heterointerface. The additional PL and CL emission below the GaN band-edge emission is attributed to the recombination between photogenerated holes and electrons confined at 2DEG states in the triangular-shaped interface potential. For the 2DEG emission, we observed an about 50-ps delayed rise time than the GaN and AlGaN emissions by using time-resolved PL, indicating effective carrier transfer from the GaN flatband and AlGaN regions to the heterointerface. From the results, we explained the optical properties and carrier recombination dynamics of 2DEG, GaN, and AlGaN emissions in undoped AlGaN/GaN single HJs.

18. Control of dynamical self-assembly of strongly Brownian nanoparticles through convective forces induced by ultrafast laser

Science.gov (United States)

Ilday, Serim; Akguc, Gursoy B.; Tokel, Onur; Makey, Ghaith; Yavuz, Ozgun; Yavuz, Koray; Pavlov, Ihor; Ilday, F. Omer; Gulseren, Oguz

We report a new dynamical self-assembly mechanism, where judicious use of convective and strong Brownian forces enables effective patterning of colloidal nanoparticles that are almost two orders of magnitude smaller than the laser beam. Optical trapping or tweezing effects are not involved, but the laser is used to create steep thermal gradients through multi-photon absorption, and thereby guide the colloids through convective forces. Convective forces can be thought as a positive feedback mechanism that helps to form and reinforce pattern, while Brownian motion act as a competing negative feedback mechanism to limit the growth of the pattern, as well as to increase the possibilities of bifurcation into different patterns, analogous to the competition observed in reaction-diffusion systems. By steering stochastic processes through these forces, we are able to gain control over the emergent pattern such as to form-deform-reform of a pattern, to change its shape and transport it spatially within seconds. This enables us to dynamically initiate and control large patterns comprised of hundreds of colloids. Further, by not relying on any specific chemical, optical or magnetic interaction, this new method is, in principle, completely independent of the material type being assembled.

19. Virial theorem and dynamical evolution of self-gravitating Brownian particles in an unbounded domain. I. Overdamped models.

Science.gov (United States)

Chavanis, Pierre-Henri; Sire, Clément

2006-06-01

We derive the virial theorem appropriate to the generalized Smoluchowski-Poisson (GSP) system describing self-gravitating Brownian particles in an overdamped limit. We extend previous works by considering the case of an unbounded domain and an arbitrary equation of state. We use the virial theorem to study the diffusion (evaporation) of an isothermal Brownian gas above the critical temperature Tc in dimension d = 2 and show how the effective diffusion coefficient and the Einstein relation are modified by self-gravity. We also study the collapse at T = Tc and show that the central density increases logarithmically with time instead of exponentially in a bounded domain. Finally, for d > 2, we show that the evaporation of the system is essentially a pure diffusion slightly slowed down by self-gravity. We also study the linear dynamical stability of stationary solutions of the GSP system representing isolated clusters of particles and investigate the influence of the equation of state and of the dimension of space on the dynamical stability of the system.

20. Normal versus anomalous self-diffusion in two-dimensional fluids: memory function approach and generalized asymptotic Einstein relation.

Science.gov (United States)

Shin, Hyun Kyung; Choi, Bongsik; Talkner, Peter; Lee, Eok Kyun

2014-12-07

Based on the generalized Langevin equation for the momentum of a Brownian particle a generalized asymptotic Einstein relation is derived. It agrees with the well-known Einstein relation in the case of normal diffusion but continues to hold for sub- and super-diffusive spreading of the Brownian particle's mean square displacement. The generalized asymptotic Einstein relation is used to analyze data obtained from molecular dynamics simulations of a two-dimensional soft disk fluid. We mainly concentrated on medium densities for which we found super-diffusive behavior of a tagged fluid particle. At higher densities a range of normal diffusion can be identified. The motion presumably changes to sub-diffusion for even higher densities.

1. Brownian earthworm

CERN Document Server

Burdzy, Krzysztof; Pal, Soumik

2010-01-01

We prove that the distance between two reflected Brownian motions outside a sphere in a 3-dimensional flat torus does not converge to 0, a.s., if the radius of the sphere is sufficiently small, relative to the size of the torus.

2. Mathematical modelling and computational study of two-dimensional and three-dimensional dynamics of receptor-ligand interactions in signalling response mechanisms.

Science.gov (United States)

García-Peñarrubia, Pilar; Gálvez, Juan J; Gálvez, Jesús

2014-09-01

Cell signalling processes involve receptor trafficking through highly connected networks of interacting components. The binding of surface receptors to their specific ligands is a key factor for the control and triggering of signalling pathways. But the binding process still presents many enigmas and, by analogy with surface catalytic reactions, two different mechanisms can be conceived: the first mechanism is related to the Eley-Rideal (ER) mechanism, i.e. the bulk-dissolved ligand interacts directly by pure three-dimensional (3D) diffusion with the specific surface receptor; the second mechanism is similar to the Langmuir-Hinshelwood (LH) process, i.e. 3D diffusion of the ligand to the cell surface followed by reversible ligand adsorption and subsequent two-dimensional (2D) surface diffusion to the receptor. A situation where both mechanisms simultaneously contribute to the signalling process could also occur. The aim of this paper is to perform a computational study of the behavior of the signalling response when these different mechanisms for ligand-receptor interactions are integrated into a model for signal transduction and ligand transport. To this end, partial differential equations have been used to develop spatio-temporal models that show trafficking dynamics of ligands, cell surface components, and intracellular signalling molecules through the different domains of the system. The mathematical modeling developed for these mechanisms has been applied to the study of two situations frequently found in cell systems: (a) dependence of the signal response on cell density; and (b) enhancement of the signalling response in a synaptic environment.

3. Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

Science.gov (United States)

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.

4. Brownian Emitters

Science.gov (United States)

Tsekov, Roumen

2016-06-01

A Brownian harmonic oscillator, which dissipates energy either by friction or via emission of electromagnetic radiation, is considered. This Brownian emitter is driven by the surrounding thermo-quantum fluctuations, which are theoretically described by the fluctuation-dissipation theorem. It is shown how the Abraham-Lorentz force leads to dependence of the half-width on the peak frequency of the oscillator amplitude spectral density. It is found that for the case of a charged particle moving in vacuum at zero temperature, its root-mean-square velocity fluctuation is a universal constant, equal to roughly 1/18 of the speed of light. The relevant Fokker-Planck and Smoluchowski equations are also derived.

5. Kinetics of Hexagonal Cylinders to Face-centered Cubic Spheres Transition of Triblock Copolymer in Selective Solvent: Brownian Dynamics Simulation

CERN Document Server

Li, Minghai; Bansil, Rama

2010-01-01

The kinetics of the transformation from the hexagonal packed cylinder (HEX) phase to the face-centered-cubic (FCC) phase was simulated using Brownian Dynamics for an ABA triblock copolymer in a selective solvent for the A block. The kinetics was obtained by instantaneously changing either the temperature of the system or the well-depth of the Lennard-Jones potential. Detailed analysis showed that the transformation occurred via a rippling mechanism. The simulation results indicated that the order-order transformation (OOT) was a nucleation and growth process when the temperature of the system instantly jumped from 0.8 to 0.5. The time evolution of the structure factor obtained by Fourier Transformation showed that the peak intensities of the HEX and FCC phases could be fit well by an Avrami equation.

6. Two-Dimensional Self-Propelled Fish Motion in Medium:An Integrated Method for Deforming Body Dynamics and Unsteady Fluid Dynamics

Institute of Scientific and Technical Information of China (English)

YANG Yan; Wu Guan-Hao; YU Yong-Liang; TONG Bing-Gang

2008-01-01

We present(1)the dynamical equations of deforming body and(2)an integrated method for deforming body dynamics and unsteady fluid dynamics,to investigate a modelled freely serf-propelled fish.The theoretical model and practical method is applicable for studies on the general mechanics of animal locomotion such as flying in air and swimming in water,particularly of free self-propulsion.The present results behave more credibly than the previous numerical studies and are close to the experimental results,and the aligned vortices pattern is discovered in cruising swimming.

7. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

Science.gov (United States)

Roberts, Christopher C; Chang, Chia-En A

2016-08-25

We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

8. GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA

CERN Document Server

Spiechowicz, J; Machura, L

2014-01-01

This work presents an updated and extended guide on methods of a proper acceleration of the Monte Carlo integration of stochastic differential equations with the commonly available NVIDIA Graphics Processing Units using the CUDA programming environment. We outline the general aspects of the scientific computing on graphics cards and demonstrate them with two models of a well known phenomenon of the noise induced transport of Brownian motors in periodic structures. As a source of fluctuations in the considered systems we selected the three most commonly occurring noises: the Gaussian white noise, the white Poissonian noise and the dichotomous process also known as a random telegraph signal. The detailed discussion on various aspects of the applied numerical schemes is also presented. The measured speedup can be of the astonishing order of 2000 when compared to a typical CPU. This number significantly expands the range of problems solvable by use of stochastic simulations, allowing even an interactive research ...

9. GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA

Science.gov (United States)

Spiechowicz, J.; Kostur, M.; Machura, L.

2015-06-01

This work presents an updated and extended guide on methods of a proper acceleration of the Monte Carlo integration of stochastic differential equations with the commonly available NVIDIA Graphics Processing Units using the CUDA programming environment. We outline the general aspects of the scientific computing on graphics cards and demonstrate them with two models of a well known phenomenon of the noise induced transport of Brownian motors in periodic structures. As a source of fluctuations in the considered systems we selected the three most commonly occurring noises: the Gaussian white noise, the white Poissonian noise and the dichotomous process also known as a random telegraph signal. The detailed discussion on various aspects of the applied numerical schemes is also presented. The measured speedup can be of the astonishing order of about 3000 when compared to a typical CPU. This number significantly expands the range of problems solvable by use of stochastic simulations, allowing even an interactive research in some cases.

10. Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

Energy Technology Data Exchange (ETDEWEB)

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

11. Dynamic effects on the transition between two-dimensional regular and Mach reflection of shock waves in an ideal, steady supersonic free stream

CSIR Research Space (South Africa)

Naidoo, K

2011-06-01

Full Text Available et al. (1999) investigated the effect of continuous rapid wedge rotation on the point of transition with Euler CFD on moving meshes. In contrast to the work by Markelov et al. (1999), Khotyanovsky et al. (1999) considered larger move- ments... between the three-dimensional Euler CFD predictions of Ivanov et al. (2001) and their measurements from experiments with the finite aspect ratio wedge. This agreement established confidence in their two-dimensional Mach stem predictions with Euler CFD...

12. Shape-induced chiral ordering in two-dimensional packing of snowmanlike dimeric particles.

Science.gov (United States)

Han, Youngkyu; Lee, Juncheol; Choi, Siyoung Q; Choi, Myung Chul; Kim, Mahn Won

2013-10-01

Understanding the distinctive phase behaviors in random packing due to particle shapes is an important issue in condensed matter physics. In this paper, we investigate the random packing structure of two-dimensional (2D) snowmen via wax-snowman packing experiments and Brownian dynamics simulations. Both experiments and simulations reveal that neighboring snowmen have a strong short-range orientational correlation and consequently locally form particular conformations. A chiral conformation is dominant for high area fractions near the jamming condition (φ>0.8), and the proportion of the chiral conformation increases with γ. We also found that the attractive interaction does not have a significant impact on the results. The geometry of chirally ordered snowmen causes a mismatch with 2D crystalline symmetries and thus inhibits the development of long-range spatial order, despite the strong orientational correlation between neighbors.

13. Confined Brownian ratchets.

Science.gov (United States)

Malgaretti, Paolo; Pagonabarraga, Ignacio; Rubi, J Miguel

2013-05-21

We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases of a flashing ratchet, a two-state model, and a ratchet under the influence of a temperature gradient are analyzed in detail. We show the emergence of a strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may take place in situations where none of those mechanisms leads to rectification when acting individually. The combined rectification mechanisms may lead to bidirectional transport and to new routes to segregation phenomena. Confined Brownian ratchets could be used to control transport in mesostructures and to engineer new and more efficient devices for transport at the nanoscale.

14. Tunable spin wave dynamics in two-dimensional Ni{sub 80}Fe{sub 20} nanodot lattices by varying dot shape

Energy Technology Data Exchange (ETDEWEB)

Mahato, Bipul Kumar; Rana, Bivas; Kumar, Dheeraj; Barman, Saswati; Barman, Anjan, E-mail: abarman@bose.res.in [Thematic Unit of Excellence on Nanodevice Technology, Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098 (India); Sugimoto, Satoshi [Institute for Solid State Physics, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Otani, YoshiChika [Institute for Solid State Physics, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); CEMS-RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2014-07-07

We demonstrate tunable spin wave spectrum in two-dimensional Ni{sub 80}Fe{sub 20} nanodot lattices by varying dot shape. A single collective mode in elliptical dot lattices transforms into three distinct modes for the half-elliptical, rectangular, and diamond dot lattices, albeit with different peak frequencies and intensities. A drastic change is observed for the triangular dots, where eight modes covering a broad band are observed. Using micromagnetic simulations, we characterized the modes as different localized, extended, and quantized modes, whose frequencies and spatial profiles are determined by a combination of internal field profiles within the nanodots and the stray magnetic field within the lattice.

15. Brownian vortexes

Science.gov (United States)

Sun, Bo; Lin, Jiayi; Darby, Ellis; Grosberg, Alexander Y.; Grier, David G.

2009-07-01

Mechanical equilibrium at zero temperature does not necessarily imply thermodynamic equilibrium at finite temperature for a particle confined by a static but nonconservative force field. Instead, the diffusing particle can enter into a steady state characterized by toroidal circulation in the probability flux, which we call a Brownian vortex. The circulatory bias in the particle’s thermally driven trajectory is not simply a deterministic response to the solenoidal component of the force but rather reflects interplay between advection and diffusion in which thermal fluctuations extract work from the nonconservative force field. As an example of this previously unrecognized class of stochastic heat engines, we consider a colloidal sphere diffusing in a conventional optical tweezer. We demonstrate both theoretically and experimentally that nonconservative optical forces bias the particle’s fluctuations into toroidal vortexes whose circulation can reverse direction with temperature or laser power.

16. Two-dimensional liquid chromatography

DEFF Research Database (Denmark)

Græsbøll, Rune

of this thesis is on online comprehensive two-dimensional liquid chromatography (online LC×LC) with reverse phase in both dimensions (online RP×RP). Since online RP×RP has not been attempted before within this research group, a significant part of this thesis consists of knowledge and experience gained...

17. Development of a two-dimensional zonally averaged statistical-dynamical model. III - The parameterization of the eddy fluxes of heat and moisture

Science.gov (United States)

Stone, Peter H.; Yao, Mao-Sung

1990-01-01

A number of perpetual January simulations are carried out with a two-dimensional zonally averaged model employing various parameterizations of the eddy fluxes of heat (potential temperature) and moisture. The parameterizations are evaluated by comparing these results with the eddy fluxes calculated in a parallel simulation using a three-dimensional general circulation model with zonally symmetric forcing. The three-dimensional model's performance in turn is evaluated by comparing its results using realistic (nonsymmetric) boundary conditions with observations. Branscome's parameterization of the meridional eddy flux of heat and Leovy's parameterization of the meridional eddy flux of moisture simulate the seasonal and latitudinal variations of these fluxes reasonably well, while somewhat underestimating their magnitudes. New parameterizations of the vertical eddy fluxes are developed that take into account the enhancement of the eddy mixing slope in a growing baroclinic wave due to condensation, and also the effect of eddy fluctuations in relative humidity. The new parameterizations, when tested in the two-dimensional model, simulate the seasonal, latitudinal, and vertical variations of the vertical eddy fluxes quite well, when compared with the three-dimensional model, and only underestimate the magnitude of the fluxes by 10 to 20 percent.

18. Two dimensional unstable scar statistics.

Energy Technology Data Exchange (ETDEWEB)

Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; Lee, Kelvin S. H. (ITT Industries/AES Los Angeles, CA)

2006-12-01

This report examines the localization of time harmonic high frequency modal fields in two dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This paper examines the enhancements for these unstable orbits when the opposing mirrors are both convex and concave. In the latter case the construction includes the treatment of interior foci.

19. Two-Dimensional Vernier Scale

Science.gov (United States)

Juday, Richard D.

1992-01-01

Modified vernier scale gives accurate two-dimensional coordinates from maps, drawings, or cathode-ray-tube displays. Movable circular overlay rests on fixed rectangular-grid overlay. Pitch of circles nine-tenths that of grid and, for greatest accuracy, radii of circles large compared with pitch of grid. Scale enables user to interpolate between finest divisions of regularly spaced rule simply by observing which mark on auxiliary vernier rule aligns with mark on primary rule.

20. Two-dimensional confocal laser scanning microscopy image correlation for nanoparticle flow velocimetry

Science.gov (United States)

Jun, Brian; Giarra, Matthew; Golz, Brian; Main, Russell; Vlachos, Pavlos

2016-11-01

We present a methodology to mitigate the major sources of error associated with two-dimensional confocal laser scanning microscopy (CLSM) images of nanoparticles flowing through a microfluidic channel. The correlation-based velocity measurements from CLSM images are subject to random error due to the Brownian motion of nanometer-sized tracer particles, and a bias error due to the formation of images by raster scanning. Here, we develop a novel ensemble phase correlation with dynamic optimal filter that maximizes the correlation strength, which diminishes the random error. In addition, we introduce an analytical model of CLSM measurement bias error correction due to two-dimensional image scanning of tracer particles. We tested our technique using both synthetic and experimental images of nanoparticles flowing through a microfluidic channel. We observed that our technique reduced the error by up to a factor of ten compared to ensemble standard cross correlation (SCC) for the images tested in the present work. Subsequently, we will assess our framework further, by interrogating nanoscale flow in the cell culture environment (transport within the lacunar-canalicular system) to demonstrate our ability to accurately resolve flow measurements in a biological system.

1. In- and out-of-plane dynamic flexural behaviors of two-dimensional ensembles of vertically aligned single-walled carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Kiani, Keivan, E-mail: k_kiani@kntu.ac.ir

2014-09-15

Useful nonlocal discrete and continuous models are developed to explain free vibration of two-dimensional (2D) ensembles of single-walled carbon nanotubes (SWCNTs) in bending. For this purpose, the models are constructed based on the nonlocal Rayleigh, Timoshenko, and higher-order beam theories. In contrast to an individual SWCNT exhibits identical bending behavior in different directions, for 2D ensemble networks of SWCNTs, it is shown that such a fact is completely dissimilar. Such an important issue leads to the definition of in-plane and out-of-plane flexural behaviors for such nanostructures. Subsequently, their corresponding fundamental frequencies are evaluated based on the proposed nonlocal models. The capabilities of the proposed nonlocal continuous models in predicting flexural frequencies of SWCNTs' ensembles with different numbers of SWCNTs as well as various levels of slenderness ratios are then explained. Such investigations confirm the high efficiency of the proposed continuous models. This matter would be of great importance in vibration analysis of highly populated ensembles of SWCNTs in which the discrete models may suffer from the size of the governing equations. The roles of the number of SWCNTs, slenderness ratio, intertube distance, small-scale parameter, and radius of the SWCNT on both in-plane and out-of-plane fundamental frequencies are addressed.

2. A time-domain numerical modeling of two-dimensional wave propagation in porous media with frequency-dependent dynamic permeability.

Science.gov (United States)

Blanc, Emilie; Chiavassa, Guillaume; Lombard, Bruno

2013-12-01

An explicit finite-difference scheme is presented for solving the two-dimensional Biot equations of poroelasticity across the full range of frequencies. The key difficulty is to discretize the Johnson-Koplik-Dashen (JKD) model which describes the viscous dissipations in the pores. Indeed, the time-domain version of Biot-JKD model involves order 1/2 fractional derivatives which amount to a time convolution product. To avoid storing the past values of the solution, a diffusive representation of fractional derivatives is used: The convolution kernel is replaced by a finite number of memory variables that satisfy local-in-time ordinary differential equations. The coefficients of the diffusive representation follow from an optimization procedure of the dispersion relation. Then, various methods of scientific computing are applied: The propagative part of the equations is discretized using a fourth-order finite-difference scheme, whereas the diffusive part is solved exactly. An immersed interface method is implemented to discretize the geometry on a Cartesian grid, and also to discretize the jump conditions at interfaces. Numerical experiments are proposed in various realistic configurations.

3. Ultrafast optical dynamics of HITCI in ethylene glycol. A non-Markovian Brownian oscillator description

NARCIS (Netherlands)

de Boeij, Wim P; Pshenichnikov, Maxim S.; Duppen, Koos; Wiersma, Douwe A.

1994-01-01

Femtosecond photon echo, chirped four-wave mixing and pump-probe experiments are reported, using a 13 fs cavity-dumped Ti: sapphire laser for excitation. It is shown that the optical dynamics of HITCI in ethylene glycol occurs on distinctly different time scales. The ultrafast solvent response is

4. Decoherence in a Landau Quantized Two Dimensional Electron Gas

Directory of Open Access Journals (Sweden)

McGill Stephen A.

2013-03-01

Full Text Available We have studied the dynamics of a high mobility two-dimensional electron gas as a function of temperature. The presence of satellite reflections in the sample and magnet can be modeled in the time-domain.

5. Two-dimensional liquid chromatography

DEFF Research Database (Denmark)

Græsbøll, Rune

Two-dimensional liquid chromatography has received increasing interest due to the rise in demand for analysis of complex chemical mixtures. Separation of complex mixtures is hard to achieve as a simple consequence of the sheer number of analytes, as these samples might contain hundreds or even...... dimensions. As a consequence of the conclusions made within this thesis, the research group has, for the time being, decided against further development of online LC×LC systems, since it was not deemed ideal for the intended application, the analysis of the polar fraction of oil. Trap-and...

6. Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS

CERN Document Server

Brackley, C A; Marenduzzo, D

2014-01-01

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

7. Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

Science.gov (United States)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

2016-11-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume. This work is funded by NSF under Grant DMS-1222550.

8. Development of a Two-Dimensional Zonally Averaged Statistical-Dynamical Model. Part III: The Parameterization of the Eddy Fluxes of Heat and Moisture.

Science.gov (United States)

Stone, Peter H.; Yao, Mao-Sung

1990-07-01

A number of perpetual January simulations are carried out with a two-dimensional (2-D) zonally averaged model employing various parameterizations of the eddy fluxes of heat (potential temperature) and moisture. The parameterizations are evaluated by comparing these results with the eddy fluxes calculated in a parallel simulation using a three-dimensional (3-D) general circulation model with zonally symmetric forcing. The 3-D model's performance in turn is evaluated by comparing its results using realistic (nonsymmetric) boundary conditions with observations.Branscome's parameterization of the meridional eddy flux of heat and Leovy's parameterization of the meridional eddy flux of moisture simulate the seasonal and latitudinal variations of these fluxes reasonably well, while somewhat underestimating their magnitudes. In particular, Branscome's parameterization underestimates the vertically integrated flux of heat by about 30%, mainly because it misses out the secondary peak in this flux near the tropopause; and Leovy's parameterization of the meridional eddy flux of moisture underestimates the magnitude of this flux by about 20%. The analogous parameterizations of the vertical eddy fluxes of heat and moisture are found to perform much more poorly, i.e., they give fluxes only one quarter to one half as strong as those calculated in the 3-D model. New parameterizations of the vertical eddy fluxes are developed that take into account the enhancement of the eddy mixing slope in a growing baroclinic wave due to condensation, and also the effect of eddy fluctuations in relative humidity. The new parameterizations, when tested in the 2-D model, simulate the seasonal, latitudinal, and vertical variations of the vertical eddy fluxes quite well, when compared with the 3-D model, and only underestimate the magnitude of the fluxes by 10% to 20%.

9. Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains

Science.gov (United States)

2017-02-01

The computational efficiency of Brownian dynamics (BD) simulation of the constrained model of a polymeric chain (bead-rod) with n beads and in the presence of hydrodynamic interaction (HI) is reduced to the order of n2 via an efficient algorithm which utilizes the conjugate-gradient (CG) method within a Picard iteration scheme. Moreover, the utility of the Barnes and Hut (BH) multipole method in BD simulation of polymeric solutions in the presence of HI, with regard to computational cost, scaling, and accuracy, is discussed. Overall, it is determined that this approach leads to a scaling of O (n1.2) . Furthermore, a stress algorithm is developed which accurately captures the transient stress growth in the startup of flow for the bead-rod model with HI and excluded volume (EV) interaction. Rheological properties of the chains up to n =350 in the presence of EV and HI are computed via the former algorithm. The result depicts qualitative differences in shear thinning behavior of the polymeric solutions in the intermediate values of the Weissenburg number (10

10. Two-dimensional capillary origami

Energy Technology Data Exchange (ETDEWEB)

Brubaker, N.D., E-mail: nbrubaker@math.arizona.edu; Lega, J., E-mail: lega@math.arizona.edu

2016-01-08

We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid. - Highlights: • Full solution set of the two-dimensional capillary origami problem. • Fluid does not necessarily wet the entire plate. • Global energy approach provides exact differential equations satisfied by minimizers. • Bifurcation diagrams highlight three different regimes. • Conditions for spontaneous encapsulation are identified.

11. Brownian Motion and General Relativity

CERN Document Server

O'Hara, Paul

2013-01-01

We construct a model of Brownian Motion on a pseudo-Riemannian manifold associated with general relativity. There are two aspects of the problem: The first is to define a sequence of stopping times associated with the Brownian "kicks" or impulses. The second is to define the dynamics of the particle along geodesics in between the Brownian kicks. When these two aspects are taken together, we can associate various distributions with the motion. We will find that the statistics of space-time events will obey a temperature dependent four dimensional Gaussian distribution defined over the quaternions which locally can be identified with Minkowski space. Analogously, the statistics of the 4-velocities will obey a kind of Maxwell-Juttner distribution. In contrast to previous work, our processes are characterized by two independent proper time variables defined with respect to the laboratory frame: a discrete one corresponding to the stopping times when the impulses take place and a continuous one corresponding to th...

12. 反场构形的二维磁流体力学描述%Two-dimensional magneto-hydro dynamic description of field reversed configuration

Institute of Scientific and Technical Information of China (English)

李璐璐; 张华; 杨显俊

2014-01-01

磁化靶聚变技术作为实现纯聚变的一种途径,不需要惯性约束聚变的高初始密度(约1026 cm-3),也不需要磁约束聚变的长约束时间(秒量级),可能是一种实现纯聚变更低廉更有效的途径。开发了一个二维磁流体力学模拟程序MPF-2D,用于描述反场构形的形成过程。采用该程序对美国洛斯阿拉莫斯国家实验室在反场构形形成装置上形成反场构形的实验进行了二维模拟和分析,理论值与实验值符合得较好；同时也对中国工程物理研究院流体物理研究所设计的“荧光-1”实验装置上形成的反场构形进行了模拟与评估,结果表明该装置上的反场构形基本达到设计指标。%Magnetized target fusion (MTF) is an alternative approach to fusion, of which the plasma lifetime and density are those between inertial confinement fusion and magnetic confinement fusion. Field-reversed configuration (FRC) is a candidate target plasma of MTF. In this paper, a two-dimensional magneto-hydrodynamic code MPF-2D is developed, and it is used to simulate the formation process of FRC on experimental devices FRX series at Los Alamos National Laboratory. In addition, design parameters of FRC on“Yingguang-1”device are also evaluated, which will be constructed in 2015 at the Institute of Fluid Physics, China Academy of Engineering Physics.

13. Two-dimensional quantum repeaters

Science.gov (United States)

Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.

2016-11-01

The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

14. Two-dimensional capillary origami

Science.gov (United States)

Brubaker, N. D.; Lega, J.

2016-01-01

We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid.

15. Two-dimensional cubic convolution.

Science.gov (United States)

Reichenbach, Stephen E; Geng, Frank

2003-01-01

The paper develops two-dimensional (2D), nonseparable, piecewise cubic convolution (PCC) for image interpolation. Traditionally, PCC has been implemented based on a one-dimensional (1D) derivation with a separable generalization to two dimensions. However, typical scenes and imaging systems are not separable, so the traditional approach is suboptimal. We develop a closed-form derivation for a two-parameter, 2D PCC kernel with support [-2,2] x [-2,2] that is constrained for continuity, smoothness, symmetry, and flat-field response. Our analyses, using several image models, including Markov random fields, demonstrate that the 2D PCC yields small improvements in interpolation fidelity over the traditional, separable approach. The constraints on the derivation can be relaxed to provide greater flexibility and performance.

16. Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar.

Science.gov (United States)

Spaar, Alexander; Helms, Volkhard

2005-07-01

Over the past years Brownian dynamics (BD) simulations have been proven to be a suitable tool for the analysis of protein-protein association. The computed rates and relative trends for protein mutants and different ionic strength are generally in good agreement with experimental results, e.g. see ref 1. By design, BD simulations correspond to an intensive sampling over energetically favorable states, rather than to a systematic sampling over all possible states which is feasible only at rather low resolution. On the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional encounter, we report here the computation of the 6-dimensional free energy landscape for the encounter process of two proteins by a novel, careful analysis of the trajectories from BD simulations. The aim of these studies was the clarification of the encounter state. Along the trajectories, the individual positions and orientations of one protein (relative to the other) are recorded and stored in so-called occupancy maps. Since the number of simulated trajectories is sufficiently high, these occupancy maps can be interpreted as a probability distribution which allows the calculation of the entropy landscape by the use of a locally defined entropy function. Additionally, the configuration dependent electrostatic and desolvation energies are recorded in separate maps. The free energy landscape of protein-protein encounter is finally obtained by summing the energy and entropy contributions. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape, a minimum shows up suggesting this to be used as the definition of the encounter state. This minimum describes a state of reduced diffusion velocity where the electrostatic attraction is compensated by the repulsion due to the unfavorable desolvation of the charged residues and the entropy loss due to the increasing restriction of the

17. Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Hua, Xin; Marshall, Matthew J.; Xiong, Yijia; Ma, Xiang; Zhou, Yufan; Tucker, Abigail E.; Zhu, Zihua; Liu, Songqin; Yu, Xiao-Ying

2015-05-01

A vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface) was employed for in situ chemical imaging of live biofilms using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Depth profiling by sputtering materials in sequential layers resulted in live biofilm spatial chemical mapping. 2D images were reconstructed to report the first 3D images of hydrated biofilm elucidating spatial and chemical heterogeneity. 2D image principal component analysis (PCA) was conducted among biofilms at different locations in the microchannel. Our approach directly visualized spatial and chemical heterogeneity within the living biofilm by dynamic liquid ToF-SIMS.

18. Classifying Two-dimensional Hyporeductive Triple Algebras

CERN Document Server

Issa, A Nourou

2010-01-01

Two-dimensional real hyporeductive triple algebras (h.t.a.) are investigated. A classification of such algebras is presented. As a consequence, a classification of two-dimensional real Lie triple algebras (i.e. generalized Lie triple systems) and two-dimensional real Bol algebras is given.

19. Dynamics of two disks settling in a two-dimensional narrow channel: From periodic motion to vertical chain in Oldroyd-B fluid

CERN Document Server

Pan, Tsorng-Whay

2016-01-01

In this article we present a numerical study of the dynamics of two disks settling in a narrow vertical channel filled with Oldroyd-B fluid. Two kinds of particle dynamics are obtained: (i) periodic interaction between two disks and (ii) the chain formation of two disks. For the periodic interaction of two disks, two different motions are obtained: (a) two disks stay far apart and interact periodically and (b) two disks interact closely and then far apart in a periodic way, like the drafting, kissing and tumbling of two disks sedimenting in Newtonian fluid, due to the lack of strong enough elastic force. For the formation of two disk chain occurred at higher values of the elasticity number, it is either a tilted chain or a vertical chain. The tilted chain can be obtained for either that the elasticity number is less than the critical value for having the vertical chain or that the Mach number is greater than the critical value for a long body to fall broadside-on. Hence the values of the elasticity number and...

20. First-Principle Molecular Dynamics Study of Selected Schiff and Mannich Bases:  Application of Two-Dimensional Potential of Mean Force to Systems with Strong Intramolecular Hydrogen Bonds.

Science.gov (United States)

Jezierska, Aneta; Panek, Jarosław J

2008-03-01

Car-Parrinello Molecular Dynamics simulations were performed for selected anharmonic systems, i.e., Schiff and Mannich base-type compounds, to investigate the vibrational properties associated with O-H stretching. All calculations were performed in the gas phase to compare them with available experimental data. First the vibrational properties of the two compounds were analyzed on the basis of well-established approaches:  Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. Then path integral molecular dynamics simulations were performed to demonstrate the influence of quantum effects on the proton's position in the hydrogen bridge. In addition, quantum effects were incorporated a posteriori into calculations of O-H stretching envelopes for the Schiff and Mannich bases. Proton potential snapshots were extracted from the ab initio molecular dynamics trajectory. Vibrational Schrödinger equations (one- and two-dimensional) were solved numerically for the snapshots, and the O-H stretching envelopes were calculated as a superposition of the 0→1 transitions. Subsequently, one- and two-dimensional potentials of mean force (1D and 2D pmf) were calculated for the proton stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The results show that the applied methodologies are in good agreement with experimental infrared spectra. Additionally, it is demonstrated that the 2D pmf method could be applied in systems with strong anharmonicity to describe the properties of the O-H stretching mode more accurately. Future applications of the 2D pmf technique include, in principle, large biomolecular systems treated within the QM/MM framework.

1. Reduction of Z classification of a two-dimensional weak topological insulator: Real-space dynamical mean-field theory study

Science.gov (United States)

Yoshida, Tsuneya; Kawakami, Norio

2017-01-01

One of the remarkable interaction effects on topological insulators is the reduction of topological classification in free-fermion systems. We address this issue in a bilayer honeycomb lattice model by taking into account temperature effects on the reduction. Our analysis, based on the real-space dynamical mean-field theory, elucidates the following results. (i) Even when the reduction occurs, the winding number defined by the Green's function can take a nontrivial value at zero temperature. (ii) The winding number taking the nontrivial value becomes consistent with the absence of gapless edge modes due to Mott behaviors emerging only at the edges. (iii) Temperature effects can restore the gapless edge modes, provided that the energy scale of interactions is smaller than the bulk gap. In addition, we observe the topological edge Mott behavior only in some finite-temperature region.

2. Two-dimensional function photonic crystals

CERN Document Server

Wu, Xiang-Yao; Liu, Xiao-Jing; Liang, Yu

2016-01-01

In this paper, we have firstly proposed two-dimensional function photonic crystals, which the dielectric constants of medium columns are the functions of space coordinates $\\vec{r}$, it is different from the two-dimensional conventional photonic crystals constituting by the medium columns of dielectric constants are constants. We find the band gaps of two-dimensional function photonic crystals are different from the two-dimensional conventional photonic crystals, and when the functions form of dielectric constants are different, the band gaps structure should be changed, which can be designed into the appropriate band gaps structures by the two-dimensional function photonic crystals.

3. Blending Brownian motion and heat equation

CERN Document Server

Cristiani, Emiliano

2015-01-01

In this short communication we present an original way to couple the Brownian motion and the heat equation. More in general, we suggest a way for coupling the Langevin equation for a particle, which describes a single realization of its trajectory, with the associated Fokker-Planck equation, which instead describes the evolution of the particle's probability density function. Numerical results show that it is indeed possible to obtain a regularized Brownian motion and a Brownianized heat equation still preserving the global statistical properties of the solutions. The results also suggest that the more macroscale leads the dynamics the more one can reduce the microscopic degrees of freedom.

4. Effects of Obstacles on the Dynamics of Kinesins, Including Velocity and Run Length, Predicted by a Model of Two Dimensional Motion.

Directory of Open Access Journals (Sweden)

Woochul Nam

Full Text Available Kinesins are molecular motors which walk along microtubules by moving their heads to different binding sites. The motion of kinesin is realized by a conformational change in the structure of the kinesin molecule and by a diffusion of one of its two heads. In this study, a novel model is developed to account for the 2D diffusion of kinesin heads to several neighboring binding sites (near the surface of microtubules. To determine the direction of the next step of a kinesin molecule, this model considers the extension in the neck linkers of kinesin and the dynamic behavior of the coiled-coil structure of the kinesin neck. Also, the mechanical interference between kinesins and obstacles anchored on the microtubules is characterized. The model predicts that both the kinesin velocity and run length (i.e., the walking distance before detaching from the microtubule are reduced by static obstacles. The run length is decreased more significantly by static obstacles than the velocity. Moreover, our model is able to predict the motion of kinesin when other (several motors also move along the same microtubule. Furthermore, it suggests that the effect of mechanical interaction/interference between motors is much weaker than the effect of static obstacles. Our newly developed model can be used to address unanswered questions regarding degraded transport caused by the presence of excessive tau proteins on microtubules.

5. A particle-in-mesh method for Brownian Dynamics simulation of many-particle systems with hydrodynamics interactions in a confined geometry

Science.gov (United States)

Zhao, Xujun; Hernandez-Ortiz, Juan; Karpeyev, Dmitry; de Pablo, Juan; Smith, Barry

In this work, we present an efficient parallel particle-in-mesh method for Brownian Dynamics simulations of many-particle systems confined in micro- and nano-fluidic devices. A general geometry Ewald-like method (GGEM) combined with finite element method is used to account for the hydrodynamic interaction. A fast parallel Krylov-type iterative solver with hybrid preconditioning techniques is developed for solving the large sparse systems of equations arising from finite element discretization of the Stokes equations. In addition, the current computer code is developed based on PETSc, a scalable library of numerical algorithms developed at Argonne, SLEPc - Scalable Library for Eigenvalue Problem Computations, and libMesh, a finite element library for numerical solution of PDEs built on top of PETSc, which allows for direct simulation of large scale systems with arbitrary confined geometries. This scheme is applied to Brownian dynamics simulations of flowing confined polymer solutions and colloidal dispersions in micro-fluid channels. The effects of hydrodynamics interactions and geometric confinement on the migration phenomena are illustrated.

6. Spatiotemporal dissipative solitons in two-dimensional photonic lattices.

Science.gov (United States)

Mihalache, Dumitru; Mazilu, Dumitru; Lederer, Falk; Kivshar, Yuri S

2008-11-01

We analyze spatiotemporal dissipative solitons in two-dimensional photonic lattices in the presence of gain and loss. In the framework of the continuous-discrete cubic-quintic Ginzburg-Landau model, we demonstrate the existence of novel classes of two-dimensional spatiotemporal dissipative lattice solitons, which also include surface solitons located in the corners or at the edges of the truncated two-dimensional photonic lattice. We find the domains of existence and stability of such spatiotemporal dissipative solitons in the relevant parameter space, for both on-site and intersite lattice solitons. We show that the on-site solitons are stable in the whole domain of their existence, whereas most of the intersite solitons are unstable. We describe the scenarios of the instability-induced dynamics of dissipative solitons in two-dimensional lattices.

7. Two-dimensional optical thermal ratchets based on Fibonacci spirals.

Science.gov (United States)

Xiao, Ke; Roichman, Yael; Grier, David G

2011-07-01

An ensemble of symmetric potential energy wells arranged at the vertices of a Fibonacci spiral can serve as the basis for an irreducibly two-dimensional thermal ratchet. Periodic rotation of the potential energy landscape through a three-step cycle drives trapped Brownian particles along spiral trajectories through the pattern. Which spiral is selected depends on the angular displacement at each step, with transitions between selected spirals arising at rational proportions of the golden angle. Fibonacci spiral ratchets therefore display an exceptionally rich range of transport properties, including inhomogeneous states in which different parts of the pattern induce motion in different directions. Both the radial and angular components of these trajectories can undergo flux reversal as a function of the scale of the pattern or the rate of rotation.

8. Optimal excitation of two dimensional Holmboe instabilities

CERN Document Server

Constantinou, Navid C

2010-01-01

Highly stratified shear layers are rendered unstable even at high stratifications by Holmboe instabilities when the density stratification is concentrated in a small region of the shear layer. These instabilities may cause mixing in highly stratified environments. However these instabilities occur in tongues for a limited range of parameters. We perform Generalized Stability analysis of the two dimensional perturbation dynamics of an inviscid Boussinesq stratified shear layer and show that Holmboe instabilities at high Richardson numbers can be excited by their adjoints at amplitudes that are orders of magnitude larger than by introducing initially the unstable mode itself. We also determine the optimal growth that obtains for parameters for which there is no instability. We find that there is potential for large transient growth regardless of whether the background flow is exponentially stable or not and that the characteristic structure of the Holmboe instability asymptotically emerges for parameter values ...

9. Janus Spectra in Two-Dimensional Flows

Science.gov (United States)

Liu, Chien-Chia; Cerbus, Rory T.; Chakraborty, Pinaki

2016-09-01

In large-scale atmospheric flows, soap-film flows, and other two-dimensional flows, the exponent of the turbulent energy spectra, α , may theoretically take either of two distinct values, 3 or 5 /3 , but measurements downstream of obstacles have invariably revealed α =3 . Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which α transitions from 3 to 5 /3 for the streamwise fluctuations but remains equal to 3 for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows.

10. Two-dimensional fourier transform spectrometer

Energy Technology Data Exchange (ETDEWEB)

DeFlores, Lauren; Tokmakoff, Andrei

2016-10-25

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

11. Two-dimensional fourier transform spectrometer

Science.gov (United States)

DeFlores, Lauren; Tokmakoff, Andrei

2013-09-03

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

12. 经会阴二维超声动态观察和评估未育女性盆底%Dynamic observation and evaluation on pelvic floor in nulliparous women with trans-perineum two-dimensional ultrasound

Institute of Scientific and Technical Information of China (English)

邵春娟; 应涛; 朱兆领; 胡兵

2011-01-01

目的 应用经会阴二维超声动态观察并评估未育女性盆底器官的形态、位置及运动,探索一种可有效观察盆底器官的影像学方法.方法 对50例未育女性行经会阴二维超声检查,分别在静息期、缩肛期和张力期动态观察盆底器官的形态、位置及运动,并获取位置的测量参数.结果 经会阴二维超声可清晰显示未育女性盆底器官的形态和位置.盆底器官静息期位于参照线头侧,缩肛期向头腹侧移动,张力期向足背侧移动,但始终位于参照线头侧;盆底器官有一定的向正常方向的移动度.结论 经会阴二维超声能清晰地显示女性盆底器官的形态、位置及运动,是一种有效的影像学方法.%Objective To dynamically observe and evaluate the shape , position and movement of pelvic floor organs in　 nulliparous women with trans-perineum two-dimensional ultrasound, and to seek for effective imaging method for pelvic　 floor. Methods Trans-perineal two-dimensional ultrasound was performed on 50 nulliparous women to observe the shape , position and movement of pelvic floor organs during quiet period , anus-contracting period and tension period . Linear parameters of location were measured . Results The shape and position of pelvic floor organs of nulliparous women were clearly　 displayed . Pelvic floor organs located at the head side of the reference line in quiet period , but moved to the cephalic and　 ventral direction during anus-contracting period while to the caudal and dorsal direction during tension period . Pelvic floor　 organs could move appropriately towards the right direction . Conclusion The trans-perineum two-dimensional ultrasound　 can clearly display and estimate the shape , location and movement of nulliparous women's pelvic floor organs . It is an effective imaging pattern to observe pelvic floor .

13. Nonlinear excitations in two-dimensional molecular structures with impurities

DEFF Research Database (Denmark)

Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

1995-01-01

We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp......We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

14. Equivalency of two-dimensional algebras

Energy Technology Data Exchange (ETDEWEB)

Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S. [Universidade Federal da Bahia (UFBA), BA (Brazil). Inst. de Fisica

2011-07-01

Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

15. Ratcheted electrophoresis of Brownian particles

Science.gov (United States)

Kowalik, Mikołaj; Bishop, Kyle J. M.

2016-05-01

The realization of nanoscale machines requires efficient methods by which to rectify unbiased perturbations to perform useful functions in the presence of significant thermal noise. The performance of such Brownian motors often depends sensitively on their operating conditions—in particular, on the relative rates of diffusive and deterministic motions. In this letter, we present a type of Brownian motor that uses contact charge electrophoresis of a colloidal particle within a ratcheted channel to achieve directed transport or perform useful work against an applied load. We analyze the stochastic dynamics of this model ratchet to show that it functions under any operating condition—even in the limit of strong thermal noise and in contrast to existing ratchets. The theoretical results presented here suggest that ratcheted electrophoresis could provide a basis for electrochemically powered, nanoscale machines capable of transport and actuation of nanoscale components.

16. Radiation Reaction on Brownian Motions

CERN Document Server

Seto, Keita

2016-01-01

Tracking the real trajectory of a quantum particle is one of the interpretation problem and it is expressed by the Brownian (stochastic) motion suggested by E. Nelson. Especially the dynamics of a radiating electron, namely, radiation reaction which requires us to track its trajectory becomes important in the high-intensity physics by PW-class lasers at present. It has been normally treated by the Furry picture in non-linear QED, but it is difficult to draw the real trajectory of a quantum particle. For the improvement of this, I propose the representation of a stochastic particle interacting with fields and show the way to describe radiation reaction on its Brownian motion.

17. Strongly interacting two-dimensional Dirac fermions

NARCIS (Netherlands)

Lim, L.K.; Lazarides, A.; Hemmerich, Andreas; de Morais Smith, C.

2009-01-01

We show how strongly interacting two-dimensional Dirac fermions can be realized with ultracold atoms in a two-dimensional optical square lattice with an experimentally realistic, inherent gauge field, which breaks time reversal and inversion symmetries. We find remarkable phenomena in a temperature

18. Topology optimization of two-dimensional waveguides

DEFF Research Database (Denmark)

Jensen, Jakob Søndergaard; Sigmund, Ole

2003-01-01

In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss.......In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss....

19. Structural analysis of a dipole system in two-dimensional channels.

Science.gov (United States)

Haghgooie, Ramin; Doyle, Patrick S

2004-12-01

A system of magnetic dipoles in two-dimensional (2D) channels was studied using Brownian dynamics simulations. The dipoles interact with a purely repulsive r(-3) potential and are confined by two hard walls in one of the dimensions. Solid crystals were annealed in the 2D channels and the structural properties of the crystals were investigated. The long-ranged nature of the purely repulsive dipoles combined with the presence of hard walls led to structural deviations from the unbounded (infinite) 2D dipolar crystal. The structures in the channels were characterized by a high density of particles along the walls. The particles along the wall became increasingly localized as the channel width was increased. The spacing of the walls was important in determining the properties of the structures formed in the channel. Small changes in the width of the channel induced significant structural changes in the crystal. These structural changes were manifested in the density profiles, defect concentrations, and local bond-orientation order of the system. Oscillations in the structural properties were observed as the channel width was increased, indicating the existence of magic-number channel widths for this system. As the channel width was increased the properties of the confined system approached those of the unbounded system surprisingly slowly.

20. Spin-orbit torques in two-dimensional Rashba ferromagnets

NARCIS (Netherlands)

Qaiumzadeh, A.; Duine, R. A.|info:eu-repo/dai/nl/304830127; Titov, M.

2015-01-01

Magnetization dynamics in single-domain ferromagnets can be triggered by a charge current if the spin-orbit coupling is sufficiently strong. We apply functional Keldysh theory to investigate spin-orbit torques in metallic two-dimensional Rashba ferromagnets in the presence of spin-dependent

1. Easy interpretation of optical two-dimensional correlation spectra

NARCIS (Netherlands)

Lazonder, K.; Pshenichnikov, M.S.; Wiersma, D.A.

2006-01-01

We demonstrate that the value of the underlying frequency-frequency correlation function can be retrieved from a two-dimensional optical correlation spectrum through a simple relationship. The proposed method yields both intuitive clues and a quantitative measure of the dynamics of the system. The t

2. Two-dimensional lattice Boltzmann model for magnetohydrodynamics.

Science.gov (United States)

Schaffenberger, Werner; Hanslmeier, Arnold

2002-10-01

We present a lattice Boltzmann model for the simulation of two-dimensional magnetohydro dynamic (MHD) flows. The model is an extension of a hydrodynamic lattice Boltzman model with 9 velocities on a square lattice resulting in a model with 17 velocities. Earlier lattice Boltzmann models for two-dimensional MHD used a bidirectional streaming rule. However, the use of such a bidirectional streaming rule is not necessary. In our model, the standard streaming rule is used, allowing smaller viscosities. To control the viscosity and the resistivity independently, a matrix collision operator is used. The model is then applied to the Hartmann flow, giving reasonable results.

3. Characterization of sulfur compounds in whisky by full evaporation dynamic headspace and selectable one-dimensional/two-dimensional retention time locked gas chromatography-mass spectrometry with simultaneous element-specific detection.

Science.gov (United States)

Ochiai, Nobuo; Sasamoto, Kikuo; MacNamara, Kevin

2012-12-28

A method is described for characterization of sulfur compounds in unaged and aged whisky. The method is based on full evaporation dynamic headspace (FEDHS) of 100 μL of whisky samples followed by selectable one-dimensional ((1)D) or two-dimensional ((2)D) retention-time-locked (RTL) gas chromatography (GC)-mass spectrometry (MS) with simultaneous element-specific detection using a sulfur chemiluminescence detector (SCD) and a nitrogen chemiluminescence detector (NCD). Sequential heart-cuts of the 16 sulfur fractions were used to identify each individual sulfur compound in the unaged whisky. Twenty sulfur compounds were positively identified by a MS library search, linear retention indices (LRI), and formula identification using MS calibration software. Additionally eight formulas were also identified for unknown sulfur compounds. Simultaneous heart-cuts of the 16 sulfur fractions were used to produce the (2)D RTL GC-SCD chromatograms for principal component analysis. PCA of the (2)D RTL GC-SCD data clearly demonstrated the difference between unaged and aged whisky, as well as two different whisky samples. Fourteen sulfur compounds could be characterized as key sulfur compounds responsible for the changes in the aging step and/or the difference between two kinds of whisky samples. The determined values of the key sulfur compounds were in the range of 0.3-210 ng mL(-1) (RSD: 0.37-12%, n=3).

4. Janus spectra in two-dimensional flows

CERN Document Server

Liu, Chien-Chia; Chakraborty, Pinaki

2016-01-01

In theory, large-scale atmospheric flows, soap-film flows and other two-dimensional flows may host two distinct types of turbulent energy spectra---in one, $\\alpha$, the spectral exponent of velocity fluctuations, equals $3$ and the fluctuations are dissipated at the small scales, and in the other, $\\alpha=5/3$ and the fluctuations are dissipated at the large scales---but measurements downstream of obstacles have invariably revealed $\\alpha = 3$. Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which $\\alpha$ has transitioned from $3$ to $5/3$ for the streamwise fluctuations but remains equal to $3$ for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows...

5. Comment on 'Finding viscosity of liquids from Brownian motion at students' laboratory' and 'Brownian motion using video capture'

Energy Technology Data Exchange (ETDEWEB)

Greczylo, Tomasz; Debowska, Ewa [Institute of Experimental Physics, Wroclaw University, pl. Maxa Borna 9, 50-204 Wroclaw (Poland)

2007-09-15

The authors make comments and remarks on the papers by Salmon et al (2002 Eur. J. Phys. 23 249-53) and their own (2005 Eur. J. Phys. 26 827-33) concerning Brownian motion in two-dimensional space. New, corrected results of calculations and measurements for students' experiments on finding the viscosity of liquids from Brownian motion are presented. (letters and comments)

6. Chiral brownian heat pump.

Science.gov (United States)

van den Broek, M; Van den Broeck, C

2008-04-04

We present the exact analysis of a chiral Brownian motor and heat pump. Optimization of the construction predicts, for a nanoscale device, frequencies of the order of kHz and cooling rates of the order of femtojoule per second.

7. Chiral Brownian heat pump

OpenAIRE

Van Den Broek, Martijn; Van Den Broeck, Christian

2007-01-01

We present the exact analysis of a chiral Brownian motor and heat pump. Optimization of the construction predicts, for a nanoscale device, frequencies of the order of kHz and cooling rates of the order of femtojoule per second.

8. Active Brownian rods

Science.gov (United States)

Peruani, Fernando

2016-11-01

Bacteria, chemically-driven rods, and motility assays are examples of active (i.e. self-propelled) Brownian rods (ABR). The physics of ABR, despite their ubiquity in experimental systems, remains still poorly understood. Here, we review the large-scale properties of collections of ABR moving in a dissipative medium. We address the problem by presenting three different models, of decreasing complexity, which we refer to as model I, II, and III, respectively. Comparing model I, II, and III, we disentangle the role of activity and interactions. In particular, we learn that in two dimensions by ignoring steric or volume exclusion effects, large-scale nematic order seems to be possible, while steric interactions prevent the formation of orientational order at large scales. The macroscopic behavior of ABR results from the interplay between active stresses and local alignment. ABR exhibit, depending on where we locate ourselves in parameter space, a zoology of macroscopic patterns that ranges from polar and nematic bands to dynamic aggregates.

9. Two Dimensional Plasmonic Cavities on Moire Surfaces

Science.gov (United States)

Balci, Sinan; Kocabas, Askin; Karabiyik, Mustafa; Kocabas, Coskun; Aydinli, Atilla

2010-03-01

We investigate surface plasmon polariton (SPP) cavitiy modes on two dimensional Moire surfaces in the visible spectrum. Two dimensional hexagonal Moire surface can be recorded on a photoresist layer using Interference lithography (IL). Two sequential exposures at slightly different angles in IL generate one dimensional Moire surfaces. Further sequential exposure for the same sample at slightly different angles after turning the sample 60 degrees around its own axis generates two dimensional hexagonal Moire cavity. Spectroscopic reflection measurements have shown plasmonic band gaps and cavity states at all the azimuthal angles (omnidirectional cavity and band gap formation) investigated. The plasmonic band gap edge and the cavity states energies show six fold symmetry on the two dimensional Moire surface as measured in reflection measurements.

10. Two-dimensional function photonic crystals

Science.gov (United States)

Liu, Xiao-Jing; Liang, Yu; Ma, Ji; Zhang, Si-Qi; Li, Hong; Wu, Xiang-Yao; Wu, Yi-Heng

2017-01-01

In this paper, we have studied two-dimensional function photonic crystals, in which the dielectric constants of medium columns are the functions of space coordinates , that can become true easily by electro-optical effect and optical kerr effect. We calculated the band gap structures of TE and TM waves, and found the TE (TM) wave band gaps of function photonic crystals are wider (narrower) than the conventional photonic crystals. For the two-dimensional function photonic crystals, when the dielectric constant functions change, the band gaps numbers, width and position should be changed, and the band gap structures of two-dimensional function photonic crystals can be adjusted flexibly, the needed band gap structures can be designed by the two-dimensional function photonic crystals, and it can be of help to design optical devices.

11. Two-Dimensional Planetary Surface Lander

Science.gov (United States)

Hemmati, H.; Sengupta, A.; Castillo, J.; McElrath, T.; Roberts, T.; Willis, P.

2014-06-01

A systems engineering study was conducted to leverage a new two-dimensional (2D) lander concept with a low per unit cost to enable scientific study at multiple locations with a single entry system as the delivery vehicle.

12. Interpolation by two-dimensional cubic convolution

Science.gov (United States)

Shi, Jiazheng; Reichenbach, Stephen E.

2003-08-01

This paper presents results of image interpolation with an improved method for two-dimensional cubic convolution. Convolution with a piecewise cubic is one of the most popular methods for image reconstruction, but the traditional approach uses a separable two-dimensional convolution kernel that is based on a one-dimensional derivation. The traditional, separable method is sub-optimal for the usual case of non-separable images. The improved method in this paper implements the most general non-separable, two-dimensional, piecewise-cubic interpolator with constraints for symmetry, continuity, and smoothness. The improved method of two-dimensional cubic convolution has three parameters that can be tuned to yield maximal fidelity for specific scene ensembles characterized by autocorrelation or power-spectrum. This paper illustrates examples for several scene models (a circular disk of parametric size, a square pulse with parametric rotation, and a Markov random field with parametric spatial detail) and actual images -- presenting the optimal parameters and the resulting fidelity for each model. In these examples, improved two-dimensional cubic convolution is superior to several other popular small-kernel interpolation methods.

13. Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces.

Science.gov (United States)

d'Auvergne, Edward J; Gooley, Paul R

2008-02-01

The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, however, the long chain of dependencies required for its calculation complicates the model-free chi-squared space. Convolutions are induced by the Lorentzian form of the spectral density functions, the linear recombinations of certain spectral density values to obtain the relaxation rates, the calculation of the NOE using the ratio of two of these rates, and finally the quadratic form of the chi-squared equation itself. Two major topological features of the model-free space complicate optimisation. The first is a long, shallow valley which commences at infinite correlation times and gradually approaches the minimum. The most severe convolution occurs for motions on two timescales in which the minimum is often located at the end of a long, deep, curved tunnel or multidimensional valley through the space. A large number of optimisation algorithms will be investigated and their performance compared to determine which techniques are suitable for use in model-free analysis. Local optimisation algorithms will be shown to be sufficient for minimisation not only within the model-free space but also for the minimisation of the Brownian rotational diffusion tensor. In addition the performance of the programs Modelfree and Dasha are investigated. A number of model-free optimisation failures were identified: the inability to slide along the limits, the singular matrix failure of the Levenberg-Marquardt minimisation algorithm, the low precision of both programs, and a bug in Modelfree. Significantly, the singular matrix failure of the Levenberg-Marquardt algorithm occurs when internal correlation times are undefined and is greatly amplified in model-free analysis by

14. TWO-DIMENSIONAL TOPOLOGY OF COSMOLOGICAL REIONIZATION

Energy Technology Data Exchange (ETDEWEB)

Wang, Yougang; Xu, Yidong; Chen, Xuelei [Key Laboratory of Computational Astrophysics, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100012 China (China); Park, Changbom [School of Physics, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of); Kim, Juhan, E-mail: wangyg@bao.ac.cn, E-mail: cbp@kias.re.kr [Center for Advanced Computation, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of)

2015-11-20

We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two-dimensional genus curve for the early, middle, and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometre Array.

15. Two dimensional topology of cosmological reionization

CERN Document Server

Wang, Yougang; Xu, Yidong; Chen, Xuelei; Kim, Juhan

2015-01-01

We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two dimensional genus curve for the early, middle and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometer Array.

16. Two-dimensional x-ray diffraction

CERN Document Server

He, Bob B

2009-01-01

Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

17. Matching Two-dimensional Gel Electrophoresis' Spots

DEFF Research Database (Denmark)

Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza

2012-01-01

This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar......This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches...

18. Mobility anisotropy of two-dimensional semiconductors

Science.gov (United States)

Lang, Haifeng; Zhang, Shuqing; Liu, Zhirong

2016-12-01

The carrier mobility of anisotropic two-dimensional semiconductors under longitudinal acoustic phonon scattering was theoretically studied using deformation potential theory. Based on the Boltzmann equation with the relaxation time approximation, an analytic formula of intrinsic anisotropic mobility was derived, showing that the influence of effective mass on mobility anisotropy is larger than those of deformation potential constant or elastic modulus. Parameters were collected for various anisotropic two-dimensional materials (black phosphorus, Hittorf's phosphorus, BC2N , MXene, TiS3, and GeCH3) to calculate their mobility anisotropy. It was revealed that the anisotropic ratio is overestimated by the previously described method.

19. Towards two-dimensional search engines

OpenAIRE

Ermann, Leonardo; Chepelianskii, Alexei D.; Shepelyansky, Dima L.

2011-01-01

We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way the ranking of nodes becomes two-dimensional that paves the way for development of two-dimensional search engines of new type. Statistical properties of inf...

20. Brownian particles in supramolecular polymer solutions

NARCIS (Netherlands)

Gucht, van der J.; Besseling, N.A.M.; Knoben, W.; Bouteiller, L.; Cohen Stuart, M.A.

2003-01-01

The Brownian motion of colloidal particles embedded in solutions of hydrogen-bonded supramolecular polymers has been studied using dynamic light scattering. At short times, the motion of the probe particles is diffusive with a diffusion coefficient equal to that in pure solvent. At intermediate time

1. Brownian particles in supramolecular polymer solutions

NARCIS (Netherlands)

Gucht, van der J.; Besseling, N.A.M.; Knoben, W.; Bouteiller, L.; Cohen Stuart, M.A.

2003-01-01

The Brownian motion of colloidal particles embedded in solutions of hydrogen-bonded supramolecular polymers has been studied using dynamic light scattering. At short times, the motion of the probe particles is diffusive with a diffusion coefficient equal to that in pure solvent. At intermediate time

2. On Dirichlet eigenvectors for neutral two-dimensional Markov chains

CERN Document Server

Champagnat, Nicolas; Miclo, Laurent

2012-01-01

We consider a general class of discrete, two-dimensional Markov chains modeling the dynamics of a population with two types, without mutation or immigration, and neutral in the sense that type has no influence on each individual's birth or death parameters. We prove that all the eigenvectors of the corresponding transition matrix or infinitesimal generator \\Pi\\ can be expressed as the product of "universal" polynomials of two variables, depending on each type's size but not on the specific transitions of the dynamics, and functions depending only on the total population size. These eigenvectors appear to be Dirichlet eigenvectors for \\Pi\\ on the complement of triangular subdomains, and as a consequence the corresponding eigenvalues are ordered in a specific way. As an application, we study the quasistationary behavior of finite, nearly neutral, two-dimensional Markov chains, absorbed in the sense that 0 is an absorbing state for each component of the process.

3. Penalising Brownian paths

CERN Document Server

Roynette, Bernard

2009-01-01

Penalising a process is to modify its distribution with a limiting procedure, thus defining a new process whose properties differ somewhat from those of the original one. We are presenting a number of examples of such penalisations in the Brownian and Bessel processes framework. The Martingale theory plays a crucial role. A general principle for penalisation emerges from these examples. In particular, it is shown in the Brownian framework that a positive sigma-finite measure takes a large class of penalisations into account.

4. Minor magnetization loops in two-dimensional dipolar Ising model

Energy Technology Data Exchange (ETDEWEB)

Sarjala, M. [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland); Seppaelae, E.T., E-mail: eira.seppala@nokia.co [Nokia Research Center, Itaemerenkatu 11-13, FI-00180 Helsinki (Finland); Alava, M.J., E-mail: mikko.alava@tkk.f [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland)

2011-05-15

The two-dimensional dipolar Ising model is investigated for the relaxation and dynamics of minor magnetization loops. Monte Carlo simulations show that in a stripe phase an exponential decrease can be found for the magnetization maxima of the loops, M{approx}exp(-{alpha}N{sub l}) where N{sub l} is the number of loops. We discuss the limits of this behavior and its relation to the equilibrium phase diagram of the model.

5. SU(1,2) invariance in two-dimensional oscillator

CERN Document Server

Krivonos, Sergey

2016-01-01

Performing the Hamiltonian analysis we explicitly established the canonical equivalence of the deformed oscillator, constructed in arXiv:1607.03756[hep-th], with the ordinary one. As an immediate consequence, we proved that the SU(1,2) symmetry is the dynamical symmetry of the ordinary two-dimensional oscillator. The characteristic feature of this SU(1,2) symmetry is a non-polynomial structure of its generators written it terms of the oscillator variables.

6. Multiple Potts Models Coupled to Two-Dimensional Quantum Gravity

CERN Document Server

Baillie, C F

1992-01-01

We perform Monte Carlo simulations using the Wolff cluster algorithm of {\\it multiple} $q=2,3,4$ state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the $c>1$ region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for $c>1$. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for $c>1$.

7. Multiple Potts models coupled to two-dimensional quantum gravity

Science.gov (United States)

Baillie, C. F.; Johnston, D. A.

1992-07-01

We perform Monte Carlo simulations using the Wolff cluster algorithm of multiple q=2, 3, 4 state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the c>1 region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for c>1. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for c>1.

8. Velocity Statistics in the Two-Dimensional Granular Turbulence

OpenAIRE

Isobe, Masaharu

2003-01-01

We studied the macroscopic statistical properties on the freely evolving quasi-elastic hard disk (granular) system by performing a large-scale (up to a few million particles) event-driven molecular dynamics systematically and found that remarkably analogous to an enstrophy cascade process in the decaying two-dimensional fluid turbulence. There are four typical stages in the freely evolving inelastic hard disk system, which are homogeneous, shearing (vortex), clustering and final state. In the...

9. Statistical study of approximations to two dimensional inviscid turbulence

Energy Technology Data Exchange (ETDEWEB)

Glaz, H.M.

1977-09-01

A numerical technique is developed for studying the ergodic and mixing hypotheses for the dynamical systems arising from the truncated Fourier transformed two-dimensional inviscid Navier-Stokes equations. This method has the advantage of exactly conserving energy and entropy (i.e., total vorticity) in the inviscid case except for numerical error in solving the ordinary differential equations. The development of the mathematical model as an approximation to a real physical (turbulent) flow and the numerical results obtained are discussed.

10. Nonequilibrium Brownian dynamics analysis of negative viscosity induced in a magnetic fluid subjected to both ac magnetic and shear flow fields.

Science.gov (United States)

Morimoto, Hisao; Maekawa, Toru; Matsumoto, Yoichiro

2002-06-01

We study the rheological and magnetic characteristics of a magnetic fluid. The system, which we investigate, is as follows. Ferromagnetic particles are dispersed in a solvent, which is subjected to both ac magnetic and shear flow fields. The translational and rotational motions of particles are calculated by the Brownian dynamics method based on Langevin equations and the rheological and magnetic characteristics of the magnetic fluid system are estimated. First, we investigate the rheological and magnetic characteristics of the system in a dc magnetic field and then we analyze the effect of an ac magnetic field on those characteristics. We find that the negative viscosity effect is induced at a certain frequency range of the ac magnetic field. We also find that there are two main mechanisms responsible for the occurrence of negative viscosity. (1) Resonance between the rotational motions of the dipoles of particles and the fluctuation of ac magnetic fields occurs when applied magnetic fields are weak compared to the shear rate, in which case particles can still rotate in magnetic fields. Beyond this resonance frequency, negative viscosity appears. (2) The magnetic dipole moments of particles are forced to stay in the direction of the magnetic field when strong magnetic fields are applied in relatively low shear flow fields. However, negative viscosity occurs when the frequency of external magnetic fields exceeds a critical value, in which case the dipoles rotate continuously in a shear flow without stopping. In both cases, the mean angular velocity of the particles becomes higher than that of the solvent.

11. Piezoelectricity in Two-Dimensional Materials

KAUST Repository

Wu, Tao

2015-02-25

Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards embedding low-dimensional materials into future disruptive technologies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

12. Kronecker Product of Two-dimensional Arrays

Institute of Scientific and Technical Information of China (English)

Lei Hu

2006-01-01

Kronecker sequences constructed from short sequences are good sequences for spread spectrum communication systems. In this paper we study a similar problem for two-dimensional arrays, and we determine the linear complexity of the Kronecker product of two arrays. Our result shows that similar good property on linear complexity holds for Kronecker product of arrays.

13. Two-Dimensional Toda-Heisenberg Lattice

Directory of Open Access Journals (Sweden)

2013-06-01

Full Text Available We consider a nonlinear model that is a combination of the anisotropic two-dimensional classical Heisenberg and Toda-like lattices. In the framework of the Hirota direct approach, we present the field equations of this model as a bilinear system, which is closely related to the Ablowitz-Ladik hierarchy, and derive its N-soliton solutions.

14. A novel two dimensional particle velocity sensor

NARCIS (Netherlands)

Pjetri, Olti; Wiegerink, Remco J.; Lammerink, Theo S.; Krijnen, Gijs J.

2013-01-01

In this paper we present a two wire, two-dimensional particle velocity sensor. The miniature sensor of size 1.0x2.5x0.525 mm, consisting of only two crossed wires, shows excellent directional sensitivity in both directions, thus requiring no directivity calibration, and is relatively easy to fabrica

15. Two-dimensional microstrip detector for neutrons

Energy Technology Data Exchange (ETDEWEB)

Oed, A. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

1997-04-01

Because of their robust design, gas microstrip detectors, which were developed at ILL, can be assembled relatively quickly, provided the prefabricated components are available. At the beginning of 1996, orders were received for the construction of three two-dimensional neutron detectors. These detectors have been completed. The detectors are outlined below. (author). 2 refs.

16. Two-dimensional magma-repository interactions

NARCIS (Netherlands)

Bokhove, O.

2001-01-01

Two-dimensional simulations of magma-repository interactions reveal that the three phases --a shock tube, shock reflection and amplification, and shock attenuation and decay phase-- in a one-dimensional flow tube model have a precursor. This newly identified phase `zero'' consists of the impact of

17. Two-dimensional subwavelength plasmonic lattice solitons

CERN Document Server

Ye, F; Hu, B; Panoiu, N C

2010-01-01

We present a theoretical study of plasmonic lattice solitons (PLSs) formed in two-dimensional (2D) arrays of metallic nanowires embedded into a nonlinear medium with Kerr nonlinearity. We analyze two classes of 2D PLSs families, namely, fundamental and vortical PLSs in both focusing and defocusing media. Their existence, stability, and subwavelength spatial confinement are studied in detai

18. A two-dimensional Dirac fermion microscope

DEFF Research Database (Denmark)

Bøggild, Peter; Caridad, Jose; Stampfer, Christoph

2017-01-01

in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2...

19. Langevin model for a Brownian system with directed motion

Science.gov (United States)

Ambía, Francisco; Híjar, Humberto

2016-08-01

We propose a model for an active Brownian system that exhibits one-dimensional directed motion. This system consists of two Brownian spherical particles that interact through an elastic potential and have time-dependent radii. We suggest an algorithm by which the sizes of the particles can be varied, such that the center of mass of the system is able to move at an average constant speed in one direction. The dynamics of the system is studied theoretically using a Langevin model, as well as from Brownian Dynamics simulations.

20. Existence of Random Attractors for a Class of Second-Order Lattice Dynamical Systems with Brownian Motions

Directory of Open Access Journals (Sweden)

Yamin Wang

2014-01-01

Full Text Available This paper is concerned with the random attractors for a class of second-order stochastic lattice dynamical systems. We first prove the uniqueness and existence of the solutions of second-order stochastic lattice dynamical systems in the space F=lλ2×l2. Then, by proving the asymptotic compactness of the random dynamical systems, we establish the existence of the global random attractor. The system under consideration is quite general, and many existing results can be regarded as the special case of our results.

1. Stress Wave Propagation in Two-dimensional Buckyball Lattice

Science.gov (United States)

Xu, Jun; Zheng, Bowen

2016-11-01

Orderly arrayed granular crystals exhibit extraordinary capability to tune stress wave propagation. Granular system of higher dimension renders many more stress wave patterns, showing its great potential for physical and engineering applications. At nanoscale, one-dimensionally arranged buckyball (C60) system has shown the ability to support solitary wave. In this paper, stress wave behaviors of two-dimensional buckyball (C60) lattice are investigated based on square close packing and hexagonal close packing. We show that the square close packed system supports highly directional Nesterenko solitary waves along initially excited chains and hexagonal close packed system tends to distribute the impulse and dissipates impact exponentially. Results of numerical calculations based on a two-dimensional nonlinear spring model are in a good agreement with the results of molecular dynamics simulations. This work enhances the understanding of wave properties and allows manipulations of nanoscale lattice and novel design of shock mitigation and nanoscale energy harvesting devices.

2. Topological defect motifs in two-dimensional Coulomb clusters

CERN Document Server

2012-01-01

The most energetically favourable arrangement of low-density electrons in an infinite two-dimensional plane is the ordered triangular Wigner lattice. However, in most instances of contemporary interest one deals instead with finite clusters of strongly interacting particles localized in potential traps, for example, in complex plasmas. In the current contribution we study distribution of topological defects in two-dimensional Coulomb clusters with parabolic lateral confinement. The minima hopping algorithm based on molecular dynamics is used to efficiently locate the ground- and low-energy metastable states, and their structure is analyzed by means of the Delaunay triangulation. The size, structure and distribution of geometry-induced lattice imperfections strongly depends on the system size and the energetic state. Besides isolated disclinations and dislocations, classification of defect motifs includes defect compounds --- grain boundaries, rosette defects, vacancies and interstitial particles. Proliferatio...

3. Statistical mechanics of two-dimensional and geophysical flows

CERN Document Server

Bouchet, Freddy

2011-01-01

The theoretical study of the self-organization of two-dimensional and geophysical turbulent flows is addressed based on statistical mechanics methods. This review is a self-contained presentation of classical and recent works on this subject; from the statistical mechanics basis of the theory up to applications to Jupiter's troposphere and ocean vortices and jets. Emphasize has been placed on examples with available analytical treatment in order to favor better understanding of the physics and dynamics. The equilibrium microcanonical measure is built from the Liouville theorem. On this theoretical basis, we predict the output of the long time evolution of complex turbulent flows as statistical equilibria. This is applied to make quantitative models of two-dimensional turbulence, the Great Red Spot and other Jovian vortices, ocean jets like the Gulf-Stream, and ocean vortices. We also present recent results for non-equilibrium situations, for the studies of either the relaxation towards equilibrium or non-equi...

4. Two Dimensional Lattice Boltzmann Method for Cavity Flow Simulation

Directory of Open Access Journals (Sweden)

Panjit MUSIK

2004-01-01

Full Text Available This paper presents a simulation of incompressible viscous flow within a two-dimensional square cavity. The objective is to develop a method originated from Lattice Gas (cellular Automata (LGA, which utilises discrete lattice as well as discrete time and can be parallelised easily. Lattice Boltzmann Method (LBM, known as discrete Lattice kinetics which provide an alternative for solving the Navier–Stokes equations and are generally used for fluid simulation, is chosen for the study. A specific two-dimensional nine-velocity square Lattice model (D2Q9 Model is used in the simulation with the velocity at the top of the cavity kept fixed. LBM is an efficient method for reproducing the dynamics of cavity flow and the results which are comparable to those of previous work.

5. Transport behavior of water molecules through two-dimensional nanopores

Energy Technology Data Exchange (ETDEWEB)

Zhu, Chongqin; Li, Hui; Meng, Sheng, E-mail: smeng@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

2014-11-14

Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

6. Transport behavior of water molecules through two-dimensional nanopores

Science.gov (United States)

Zhu, Chongqin; Li, Hui; Meng, Sheng

2014-11-01

Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

7. Thermodynamics of two-dimensional Yukawa systems across coupling regimes

Science.gov (United States)

Kryuchkov, Nikita P.; Khrapak, Sergey A.; Yurchenko, Stanislav O.

2017-04-01

Thermodynamics of two-dimensional Yukawa (screened Coulomb or Debye-Hückel) systems is studied systematically using molecular dynamics (MD) simulations. Simulations cover very broad parameter range spanning from weakly coupled gaseous states to strongly coupled fluid and crystalline states. Important thermodynamic quantities, such as internal energy and pressure, are obtained and accurate physically motivated fits are proposed. This allows us to put forward simple practical expressions to describe thermodynamic properties of two-dimensional Yukawa systems. For crystals, in addition to numerical simulations, the recently developed shortest-graph interpolation method is applied to describe pair correlations and hence thermodynamic properties. It is shown that the finite-temperature effects can be accounted for by using simple correction of peaks in the pair correlation function. The corresponding correction coefficients are evaluated using MD simulation. The relevance of the obtained results in the context of colloidal systems, complex (dusty) plasmas, and ions absorbed to interfaces in electrolytes is pointed out.

8. Two-dimensional localized structures in harmonically forced oscillatory systems

Science.gov (United States)

Ma, Y.-P.; Knobloch, E.

2016-12-01

Two-dimensional spatially localized structures in the complex Ginzburg-Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turing-stable and Turing-unstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defect-mediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully two-dimensional system.

9. Biased Brownian motion in narrow channels with asymmetry and anisotropy

Science.gov (United States)

To, Kiwing; Peng, Zheng

2016-11-01

We study Brownian motion of a single millimeter size bead confined in a quasi-two-dimensional horizontal channel with built-in anisotropy and asymmetry. Channel asymmetry is implemented by ratchet walls while anisotropy is introduced using a channel base that is grooved along the channel axis so that a bead can acquire a horizontal impulse perpendicular to the longitudinal direction when it collides with the base. When energy is injected to the channel by vertical vibration, the combination of asymmetric walls and anisotropic base induces an effective force which drives the bead into biased diffusive motion along the channel axis with diffusivity and drift velocity increase with vibration strength. The magnitude of this driving force, which can be measured in experiments of tilted channel, is found to be consistent to those obtained from dynamic mobility and position probability distribution measurements. These results are explained by a simple collision model that suggests the random kinetic energies transfer between different translational degrees of freedom may be turned into useful work in the presence of asymmetry and anisotropy.

10. Electronics based on two-dimensional materials.

Science.gov (United States)

Fiori, Gianluca; Bonaccorso, Francesco; Iannaccone, Giuseppe; Palacios, Tomás; Neumaier, Daniel; Seabaugh, Alan; Banerjee, Sanjay K; Colombo, Luigi

2014-10-01

The compelling demand for higher performance and lower power consumption in electronic systems is the main driving force of the electronics industry's quest for devices and/or architectures based on new materials. Here, we provide a review of electronic devices based on two-dimensional materials, outlining their potential as a technological option beyond scaled complementary metal-oxide-semiconductor switches. We focus on the performance limits and advantages of these materials and associated technologies, when exploited for both digital and analog applications, focusing on the main figures of merit needed to meet industry requirements. We also discuss the use of two-dimensional materials as an enabling factor for flexible electronics and provide our perspectives on future developments.

11. Two-dimensional ranking of Wikipedia articles

Science.gov (United States)

Zhirov, A. O.; Zhirov, O. V.; Shepelyansky, D. L.

2010-10-01

The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists ab aeterno. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

12. Two-Dimensional NMR Lineshape Analysis

Science.gov (United States)

Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

2016-04-01

NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.

13. Towards two-dimensional search engines

CERN Document Server

Ermann, Leonardo; Shepelyansky, Dima L

2011-01-01

We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way the ranking of nodes becomes two-dimensional that paves the way for development of two-dimensional search engines of new type. Information flow properties on PageRank-CheiRank plane are analyzed for networks of British, French and Italian Universities, Wikipedia, Linux Kernel, gene regulation and other networks. Methods of spam links control are also analyzed.

14. Toward two-dimensional search engines

Science.gov (United States)

Ermann, L.; Chepelianskii, A. D.; Shepelyansky, D. L.

2012-07-01

We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way, the ranking of nodes becomes two dimensional which paves the way for the development of two-dimensional search engines of a new type. Statistical properties of information flow on the PageRank-CheiRank plane are analyzed for networks of British, French and Italian universities, Wikipedia, Linux Kernel, gene regulation and other networks. A special emphasis is done for British universities networks using the large database publicly available in the UK. Methods of spam links control are also analyzed.

15. A two-dimensional Dirac fermion microscope

Science.gov (United States)

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-06-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

16. A two-dimensional Dirac fermion microscope.

Science.gov (United States)

Bøggild, Peter; Caridad, José M; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-06-09

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

17. Two-Dimensional Scheduling: A Review

Directory of Open Access Journals (Sweden)

Zhuolei Xiao

2013-07-01

Full Text Available In this study, we present a literature review, classification schemes and analysis of methodology for scheduling problems on Batch Processing machine (BP with both processing time and job size constraints which is also regarded as Two-Dimensional (TD scheduling. Special attention is given to scheduling problems with non-identical job sizes and processing times, with details of the basic algorithms and other significant results.

18. Two dimensional fermions in four dimensional YM

CERN Document Server

Narayanan, R

2009-01-01

Dirac fermions in the fundamental representation of SU(N) live on a two dimensional torus flatly embedded in $R^4$. They interact with a four dimensional SU(N) Yang Mills vector potential preserving a global chiral symmetry at finite $N$. As the size of the torus in units of $\\frac{1}{\\Lambda_{SU(N)}}$ is varied from small to large, the chiral symmetry gets spontaneously broken in the infinite $N$ limit.

19. Two-dimensional Kagome photonic bandgap waveguide

DEFF Research Database (Denmark)

Nielsen, Jens Bo; Søndergaard, Thomas; Libori, Stig E. Barkou;

2000-01-01

The transverse-magnetic photonic-bandgap-guidance properties are investigated for a planar two-dimensional (2-D) Kagome waveguide configuration using a full-vectorial plane-wave-expansion method. Single-moded well-localized low-index guided modes are found. The localization of the optical modes...... is investigated with respect to the width of the 2-D Kagome waveguide, and the number of modes existing for specific frequencies and waveguide widths is mapped out....

20. String breaking in two-dimensional QCD

CERN Document Server

Hornbostel, K J

1999-01-01

I present results of a numerical calculation of the effects of light quark-antiquark pairs on the linear heavy-quark potential in light-cone quantized two-dimensional QCD. I extract the potential from the Q-Qbar component of the ground-state wavefunction, and observe string breaking at the heavy-light meson pair threshold. I briefly comment on the states responsible for the breaking.

1. Two-dimensional supramolecular electron spin arrays.

Science.gov (United States)

Wäckerlin, Christian; Nowakowski, Jan; Liu, Shi-Xia; Jaggi, Michael; Siewert, Dorota; Girovsky, Jan; Shchyrba, Aneliia; Hählen, Tatjana; Kleibert, Armin; Oppeneer, Peter M; Nolting, Frithjof; Decurtins, Silvio; Jung, Thomas A; Ballav, Nirmalya

2013-05-07

A bottom-up approach is introduced to fabricate two-dimensional self-assembled layers of molecular spin-systems containing Mn and Fe ions arranged in a chessboard lattice. We demonstrate that the Mn and Fe spin states can be reversibly operated by their selective response to coordination/decoordination of volatile ligands like ammonia (NH3). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

2. Two dimensional echocardiographic detection of intraatrial masses.

Science.gov (United States)

DePace, N L; Soulen, R L; Kotler, M N; Mintz, G S

1981-11-01

With two dimensional echocardiography, a left atrial mass was detected in 19 patients. Of these, 10 patients with rheumatic mitral stenosis had a left atrial thrombus. The distinctive two dimensional echocardiographic features of left atrial thrombus included a mass of irregular nonmobile laminated echos within an enlarged atrial cavity, usually with a broad base of attachment to the posterior left atrial wall. Seven patients had a left atrial myxoma. Usually, the myxoma appeared as a mottled ovoid, sharply demarcated mobile mass attached to the interatrial septum. One patient had a right atrial angiosarcoma that appeared as a nonmobile mass extending from the inferior vena caval-right atrial junction into the right atrial cavity. One patient had a left atrial leiomyosarcoma producing a highly mobile mass attached to the lateral wall of the left atrium. M mode echocardiography detected six of the seven myxomas, one thrombus and neither of the other tumors. Thus, two dimensional echocardiography appears to be the technique of choice in the detection, localization and differentiation of intraatrial masses.

3. Intensity Coding in Two-Dimensional Excitable Neural Networks

CERN Document Server

Copelli, Mauro

2016-01-01

In the light of recent experimental findings that gap junctions are essential for low level intensity detection in the sensory periphery, the Greenberg-Hastings cellular automaton is employed to model the response of a two-dimensional sensory network to external stimuli. We show that excitable elements (sensory neurons) that have a small dynamical range are shown to give rise to a collective large dynamical range. Therefore the network transfer (gain) function (which is Hill or Stevens law-like) is an emergent property generated from a pool of small dynamical range cells, providing a basis for a "neural psychophysics". The growth of the dynamical range with the system size is approximately logarithmic, suggesting a functional role for electrical coupling. For a fixed number of neurons, the dynamical range displays a maximum as a function of the refractory period, which suggests experimental tests for the model. A biological application to ephaptic interactions in olfactory nerve fascicles is proposed.

4. Open Quantum System Dynamics from a Measurement Perspective: Applications to Coherent Particle Transport and to Quantum~Brownian Motion

CERN Document Server

Kamleitner, Ingo

2010-01-01

We employ the theoretical framework of positive operator valued measures, to study Markovian open quantum systems. In particular, we discuss how a quantum system influences its environment. Using the theory of indirect measurements, we then draw conclusions about the information we could hypothetically obtain about the system by observing the environment. Although the environment is not actually observed, we can use these results to describe the change of the quantum system due to its interaction with the environment. We apply this technique to two different problems. In the first part, we study the coherently driven dynamics of a particle on a rail of quantum dots. This tunnelling between adjacent quantum dots can be controlled externally. We employ an adiabatic scheme similar to stimulated Raman adiabatic passage, to transfer the particle between different quantum dots. We compare two fundamentally different sources of decoherence. In the second part, we study the dynamics of a free quantum particle, which ...

5. Anomalous Brownian Refrigerator

OpenAIRE

Rana, Shubhashis; Pal, P. S.; Saha, Arnab; Jayannavar, A. M.

2015-01-01

We present a detailed study of a Brownian particle driven by Carnot-type refrigerating protocol operating between two thermal baths. Both the underdamped as well as the overdamped limits are investigated. The particle is in a harmonic potential with time-periodic strength that drives the particle cyclically between the baths. Each cycle consists of two isothermal steps at different temperatures and two adiabatic steps connecting them. Besides working as a stochastic refrigerator, it is shown ...

6. Electromagnetically induced two-dimensional grating assisted by incoherent pump

Energy Technology Data Exchange (ETDEWEB)

Chen, Yu-Yuan; Liu, Zhuan-Zhuan; Wan, Ren-Gang, E-mail: wrg@snnu.edu.cn

2017-04-25

We propose a scheme for realizing electromagnetically induced two-dimensional grating in a double-Λ system driven simultaneously by a coherent field and an incoherent pump field. In such an atomic configuration, the absorption is suppressed owing to the incoherent pumping process and the probe can be even amplified, while the refractivity is mainly attributed to the dynamically induced coherence. With the help of a standing-wave pattern coherent field, we obtain periodically modulated refractive index without or with gain, and therefore phase grating or gain-phase grating which diffracts a probe light into high-order direction efficiently can be formed in the medium via appropriate manipulation of the system parameters. The diffraction efficiency attainable by the present gratings can be controlled by tuning the coherent field intensity or the interaction length. Hence, the two-dimensional grating can be utilized as all-optical splitter or router in optical networking and communication. - Highlights: • Two-dimensional grating is coherently induced in four-level atoms. • Phase and gain-phase gratings are obtained assisted by incoherent pump. • The diffraction power is improved due to the enhanced refraction modulation. • The gratings can be utilized as multi-channel all-optical splitter and router.

7. Two-dimensional capillary electrophoresis using tangentially connected capillaries.

Science.gov (United States)

Sahlin, Eskil

2007-06-22

A novel type of fused silica capillary system is described where channels with circular cross-sections are tangentially in contact with each other and connected through a small opening at the contact area. Since the channels are not crossing each other in the same plane, the capillaries can easily be filled with different solutions, i.e. different solutions will be in contact with each other at the contact point. The system has been used to perform different types of two-dimensional separations and the complete system is fully automated where a high voltage switch is used to control the location of the high voltage in the system. Using two model compounds it is demonstrated that a type of two-dimensional separation can be performed using capillary zone electrophoresis at two different pH values. It is also shown that a compound with acid/base properties can be concentrated using a dynamic pH junction mechanism when transferred from the first separation to the second separation. In addition, the system has been used to perform a comprehensive two-dimensional capillary electrophoresis separation of tryptic digest of bovine serum albumin using capillary zone electrophoresis followed by micellar electrokinetic chromatography.

8. Conductance simulation of the purinergic P2X2, P2X4, and P2X7 ionic channels using a combined Brownian dynamics and molecular dynamics approach.

Science.gov (United States)

Turchenkov, Dmitry A; Bystrov, Vladimir S

2014-08-07

This paper investigates the application of an original combined approach of molecular and Brownian dynamic methods with quantum chemistry calculations for modeling the process of conductance of ion channels using purinergic P2X family receptors P2X2, P2X4, and P2X7 as a case study. A simplified model of the ionic channel in the lipid bilayer has been developed. A high level of conductance (30 pS) of P2X2 ionic channel together with the key role of Asp349 in forming the selectivity filter of P2X2 has been shown by using this approach. Calculated P2X2 permeability to monovalent cations Li(+), Na(+), and K(+) conforms to the free diffusion coefficient of these ions, which shows the low selectivity of P2X2 ionic channel.

9. Brownian Motion, "Diverse and Undulating"

CERN Document Server

Duplantier, Bertrand

2016-01-01

We describe in detail the history of Brownian motion, as well as the contributions of Einstein, Sutherland, Smoluchowski, Bachelier, Perrin and Langevin to its theory. The always topical importance in physics of the theory of Brownian motion is illustrated by recent biophysical experiments, where it serves, for instance, for the measurement of the pulling force on a single DNA molecule. In a second part, we stress the mathematical importance of the theory of Brownian motion, illustrated by two chosen examples. The by-now classic representation of the Newtonian potential by Brownian motion is explained in an elementary way. We conclude with the description of recent progress seen in the geometry of the planar Brownian curve. At its heart lie the concepts of conformal invariance and multifractality, associated with the potential theory of the Brownian curve itself.

10. Open Quantum System Dynamics from a Measurement Perspective: Applications to Coherent Particle Transport and to Quantum~Brownian Motion

Science.gov (United States)

Kamleitner, Ingo

2010-09-01

We employ the theoretical framework of positive operator valued measures, to study Markovian open quantum systems. In particular, we discuss how a quantum system influences its environment. Using the theory of indirect measurements, we then draw conclusions about the information we could hypothetically obtain about the system by observing the environment. Although the environment is not actually observed, we can use these results to describe the change of the quantum system due to its interaction with the environment. We apply this technique to two different problems. In the first part, we study the coherently driven dynamics of a particle on a rail of quantum dots. This tunnelling between adjacent quantum dots can be controlled externally. We employ an adiabatic scheme similar to stimulated Raman adiabatic passage, to transfer the particle between different quantum dots. We compare two fundamentally different sources of decoherence. In the second part, we study the dynamics of a free quantum particle, which experiences random collisions with gas particles. Previous studies on this topic applied scattering theory to momentum eigenstates. We present a supplementary approach, where we develop a rigorous measurement interpretation of the collision process to derive a master equation. Finally, we study the collisional decoherence process in terms of the Wigner function. We restrict ourselves to one spatial dimension. Nevertheless, we find some interesting new insight, including that the previously celebrated quantum contribution to position diffusion is not real, but a consequence of the Markovian approximation. Further, we discover that the leading decoherence process is due to phase averaging, rather than induced by the information transfer between the colliding particles.

11. Weakly disordered two-dimensional Frenkel excitons

Science.gov (United States)

Boukahil, A.; Zettili, Nouredine

2004-03-01

We report the results of studies of the optical properties of weakly disordered two- dimensional Frenkel excitons in the Coherent Potential Approximation (CPA). An approximate complex Green's function for a square lattice with nearest neighbor interactions is used in the self-consistent equation to determine the coherent potential. It is shown that the Density of States is very much affected by the logarithmic singularities in the Green's function. Our CPA results are in excellent agreement with previous investigations by Schreiber and Toyozawa using the Monte Carlo simulation.

12. Two-dimensional photonic crystal surfactant detection.

Science.gov (United States)

Zhang, Jian-Tao; Smith, Natasha; Asher, Sanford A

2012-08-07

We developed a novel two-dimensional (2-D) crystalline colloidal array photonic crystal sensing material for the visual detection of amphiphilic molecules in water. A close-packed polystyrene 2-D array monolayer was embedded in a poly(N-isopropylacrylamide) (PNIPAAm)-based hydrogel film. These 2-D photonic crystals placed on a mirror show intense diffraction that enables them to be used for visual determination of analytes. Binding of surfactant molecules attaches ions to the sensor that swells the PNIPAAm-based hydrogel. The resulting increase in particle spacing red shifts the 2-D diffracted light. Incorporation of more hydrophobic monomers increases the sensitivity to surfactants.

13. Theory of two-dimensional transformations

OpenAIRE

Kanayama, Yutaka J.; Krahn, Gary W.

1998-01-01

The article of record may be found at http://dx.doi.org/10.1109/70.720359 Robotics and Automation, IEEE Transactions on This paper proposes a new "heterogeneous" two-dimensional (2D) transformation group ___ to solve motion analysis/planning problems in robotics. In this theory, we use a 3×1 matrix to represent a transformation as opposed to a 3×3 matrix in the homogeneous formulation. First, this theory is as capable as the homogeneous theory, Because of the minimal size, its implement...

14. Two-dimensional ranking of Wikipedia articles

CERN Document Server

Zhirov, A O; Shepelyansky, D L

2010-01-01

The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists {\\it ab aeterno}. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. We analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

15. Mobility anisotropy of two-dimensional semiconductors

CERN Document Server

Lang, Haifeng; Liu, Zhirong

2016-01-01

The carrier mobility of anisotropic two-dimensional (2D) semiconductors under longitudinal acoustic (LA) phonon scattering was theoretically studied with the deformation potential theory. Based on Boltzmann equation with relaxation time approximation, an analytic formula of intrinsic anisotropic mobility was deduced, which shows that the influence of effective mass to the mobility anisotropy is larger than that of deformation potential constant and elastic modulus. Parameters were collected for various anisotropic 2D materials (black phosphorus, Hittorf's phosphorus, BC$_2$N, MXene, TiS$_3$, GeCH$_3$) to calculate their mobility anisotropy. It was revealed that the anisotropic ratio was overestimated in the past.

16. Sums of two-dimensional spectral triples

DEFF Research Database (Denmark)

Christensen, Erik; Ivan, Cristina

2007-01-01

construct a sum of two dimensional modules which reflects some aspects of the topological dimensions of the compact metric space, but this will only give the metric back approximately. At the end we make an explicit computation of the last module for the unit interval in. The metric is recovered exactly......, the Dixmier trace induces a multiple of the Lebesgue integral but the growth of the number of eigenvalues is different from the one found for the standard differential operator on the unit interval....

17. Binding energy of two-dimensional biexcitons

DEFF Research Database (Denmark)

Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

1996-01-01

Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

18. Two-dimensional conformal field theory and the butterfly effect

CERN Document Server

Roberts, Daniel A

2014-01-01

We study chaotic dynamics in two-dimensional conformal field theory through out-of-time order thermal correlators of the form $\\langle W(t)VW(t)V\\rangle$. We reproduce bulk calculations similar to those of [1], by studying the large $c$ Virasoro identity block. The contribution of this block to the above correlation function begins to decrease exponentially after a delay of $\\sim t_* - \\frac{\\beta}{2\\pi}\\log \\beta^2E_w E_v$, where $t_*$ is the scrambling time $\\frac{\\beta}{2\\pi}\\log c$, and $E_w,E_v$ are the energy scales of the $W,V$ operators.

19. Size-dispersity effects in two-dimensional melting.

Science.gov (United States)

Watanabe, Hiroshi; Yukawa, Satoshi; Ito, Nobuyasu

2005-01-01

In order to investigate the effect of size dispersity on two-dimensional melting transitions, hard-disk systems with equimolar bidispersity are studied by means of particle dynamics simulations. From the nonequilibrium relaxation behaviors of bond-orientational order parameters, we find that (i) there is a critical dispersity at which the melting transition of the hexagonal solid vanishes and (ii) the quadratic structure is metastable in a certain region of the dispersity-density parameter space. These results suggest that the dispersity not only destroys order but produces new structures under certain specific conditions.

20. The XY model coupled to two-dimensional quantum gravity

Science.gov (United States)

Baillie, C. F.; Johnston, D. A.

1992-09-01

We perform Monte Carlo simulations using the Wolff cluster algorithm of the XY model on both fixed and dynamical phi-cubed graphs (i.e. without and with coupling to two-dimensional quantum gravity). We compare the numerical results with the theoretical expectation that the phase transition remains of KT type when the XY model is coupled to gravity. We also examine whether the universality we discovered in our earlier work on various Potts models with the same value of the central charge, c, carries over to the XY model, which has c=1.

1. The XY Model Coupled to Two-Dimensional Quantum Gravity

CERN Document Server

Baillie, C F; 10.1016/0370-2693(92)91037-A

2009-01-01

We perform Monte Carlo simulations using the Wolff cluster algorithm of the XY model on both fixed and dynamical phi-cubed graphs (i.e. without and with coupling to two-dimensional quantum gravity). We compare the numerical results with the theoretical expectation that the phase transition remains of KT type when the XY model is coupled to gravity. We also examine whether the universality we discovered in our earlier work on various Potts models with the same value of the central charge, $c$, carries over to the XY model, which has $c=1$.

2. Smoothed Particle Hydrodynamics Method for Two-dimensional Stefan Problem

CERN Document Server

Tarwidi, Dede

2016-01-01

Smoothed particle hydrodynamics (SPH) is developed for modelling of melting and solidification. Enthalpy method is used to solve heat conduction equations which involved moving interface between phases. At first, we study the melting of floating ice in the water for two-dimensional system. The ice objects are assumed as solid particles floating in fluid particles. The fluid and solid motion are governed by Navier-Stokes equation and basic rigid dynamics equation, respectively. We also propose a strategy to separate solid particles due to melting and solidification. Numerical results are obtained and plotted for several initial conditions.

3. QUANTUM STOCHASTIC PROCESSES: BOSON AND FERMION BROWNIAN MOTION

Directory of Open Access Journals (Sweden)

A.E.Kobryn

2003-01-01

Full Text Available Dynamics of quantum systems which are stochastically perturbed by linear coupling to the reservoir can be studied in terms of quantum stochastic differential equations (for example, quantum stochastic Liouville equation and quantum Langevin equation. In order to work it out one needs to define the quantum Brownian motion. As far as only its boson version has been known until recently, in the present paper we present the definition which makes it possible to consider the fermion Brownian motion as well.

4. Vibrational wave packet induced oscillations in two-dimensional electronic spectra. I. Experiments

CERN Document Server

Nemeth, Alexandra; Mancal, Tomas; Lukes, Vladimir; Hauer, Juergen; Kauffmann, Harald F; Sperling, Jaroslaw

2010-01-01

This is the first in a series of two papers investigating the effect of electron-phonon coupling in two-dimensional Fourier transformed electronic spectroscopy. We present a series of one- and two-dimensional nonlinear spectroscopic techniques for studying a dye molecule in solution. Ultrafast laser pulse excitation of an electronic transition coupled to vibrational modes induces a propagating vibrational wave packet that manifests itself in oscillating signal intensities and line-shapes. For the two-dimensional electronic spectra we can attribute the observed modulations to periodic enhancement and decrement of the relative amplitudes of rephasing and non-rephasing contributions to the total response. Different metrics of the two-dimensional signals are shown to relate to the frequency-frequency correlation function which provides the connection between experimentally accessible observations and the underlying microscopic molecular dynamics. A detailed theory of the time-dependent two-dimensional spectral li...

5. Two-dimensional Insect Flight on an Air-Water Interface is a Chaotic Oscillator

CERN Document Server

Mukundarajan, Haripriya; Prakash, Manu

2014-01-01

Two-dimensional flapping wing insect flight on an air-water interface provides a successful foraging strategy to explore an ecological niche on the surface of a pond. However, the complex interplay of surface tension, aerodynamic forces, biomechanics and neural control that enables two-dimensional flight is unknown. Here we report the discovery of two-dimensional flight in the waterlily beetle Galerucella nymphaeae, which is the fastest reported propulsion mode for an insect on a fluid interface. Using kinematics derived from high-speed videography coupled with analytical models, we demonstrate that two-dimensional flight is a chaotic interfacial oscillator, thus significantly constraining the possible range of flight parameters. Discovery of this complex dynamics in two-dimensional flight on time scales similar to neural responses indicates the challenge of evolving active flight control on a fluid interface.

6. Two-dimensional gauge theoretic supergravities

Science.gov (United States)

Cangemi, D.; Leblanc, M.

1994-05-01

We investigate two-dimensional supergravity theories, which can be built from a topological and gauge invariant action defined on an ordinary surface. One is the N = 1 supersymmetric extension of the Jackiw-Teitelboim model presented by Chamseddine in a superspace formalism. We complement the proof of Montano, Aoaki and Sonnenschein that this extension is topological and gauge invariant, based on the graded de Sitter algebra. Not only do the equations of motion correspond to the supergravity ones and do gauge transformations encompass local supersymmetries, but we also identify the ∫-theory with the superfield formalism action written by Chamseddine. Next, we show that the N = 1 supersymmetric extension of string-inspired two-dimensional dilaton gravity put forward by Park and Strominger cannot be written as a ∫-theory. As an alternative, we propose two topological and gauge theories that are based on a graded extension of the extended Poincaré algebra and satisfy a vanishing-curvature condition. Both models are supersymmetric extensions of the string-inspired dilaton gravity.

7. Two-Dimensional Theory of Scientific Representation

Directory of Open Access Journals (Sweden)

A Yaghmaie

2013-03-01

Full Text Available Scientific representation is an interesting topic for philosophers of science, many of whom have recently explored it from different points of view. There are currently two competing approaches to the issue: cognitive and non-cognitive, and each of them claims its own merits over the other. This article tries to provide a hybrid theory of scientific representation, called Two-Dimensional Theory of Scientific Representation, which has the merits of the two accounts and is free of their shortcomings. To do this, we will argue that although scientific representation needs to use the notion of intentionality, such a notion is defined and realized in a simply structural form contrary to what cognitive approach says about intentionality. After a short introduction, the second part of the paper is devoted to introducing theories of scientific representation briefly. In the third part, the structural accounts of representation will be criticized. The next step is to introduce the two-dimensional theory which involves two key components: fixing and structural fitness. It will be argued that fitness is an objective and non-intentional relation, while fixing is intentional.

8. Two-dimensional shape memory graphene oxide

Science.gov (United States)

Chang, Zhenyue; Deng, Junkai; Chandrakumara, Ganaka G.; Yan, Wenyi; Liu, Jefferson Zhe

2016-06-01

Driven by the increasing demand for micro-/nano-technologies, stimuli-responsive shape memory materials at nanoscale have recently attracted great research interests. However, by reducing the size of conventional shape memory materials down to approximately nanometre range, the shape memory effect diminishes. Here, using density functional theory calculations, we report the discovery of a shape memory effect in a two-dimensional atomically thin graphene oxide crystal with ordered epoxy groups, namely C8O. A maximum recoverable strain of 14.5% is achieved as a result of reversible phase transition between two intrinsically stable phases. Our calculations conclude co-existence of the two stable phases in a coherent crystal lattice, giving rise to the possibility of constructing multiple temporary shapes in a single material, thus, enabling highly desirable programmability. With an atomic thickness, excellent shape memory mechanical properties and electric field stimulus, the discovery of a two-dimensional shape memory graphene oxide opens a path for the development of exceptional micro-/nano-electromechanical devices.

9. Existence and Stability of Two-Dimensional Compact-Like Discrete Breathers in Discrete Two-Dimensional Monatomic Square Lattices

Institute of Scientific and Technical Information of China (English)

XU Quan; TIAN Qiang

2007-01-01

Two-dimensional compact-like discrete breathers in discrete two-dimensional monatomic square lattices are investigated by discussing a generafized discrete two-dimensional monatomic model.It is proven that the twodimensional compact-like discrete breathers exist not only in two-dimensional soft Ф4 potentials but also in hard two-dimensional Ф4 potentials and pure two-dimensional K4 lattices.The measurements of the two-dimensional compact-like discrete breather cores in soft and hard two-dimensional Ф4 potential are determined by coupling parameter K4,while those in pure two-dimensional K4 lattices have no coupling with parameter K4.The stabilities of the two-dimensional compact-like discrete breathers correlate closely to the coupling parameter K4 and the boundary condition of lattices.

10. Simulations of magnetic nanoparticle Brownian motion.

Science.gov (United States)

Reeves, Daniel B; Weaver, John B

2012-12-15

Magnetic nanoparticles are useful in many medical applications because they interact with biology on a cellular level thus allowing microenvironmental investigation. An enhanced understanding of the dynamics of magnetic particles may lead to advances in imaging directly in magnetic particle imaging or through enhanced MRI contrast and is essential for nanoparticle sensing as in magnetic spectroscopy of Brownian motion. Moreover, therapeutic techniques like hyperthermia require information about particle dynamics for effective, safe, and reliable use in the clinic. To that end, we have developed and validated a stochastic dynamical model of rotating Brownian nanoparticles from a Langevin equation approach. With no field, the relaxation time toward equilibrium matches Einstein's model of Brownian motion. In a static field, the equilibrium magnetization agrees with the Langevin function. For high frequency or low amplitude driving fields, behavior characteristic of the linearized Debye approximation is reproduced. In a higher field regime where magnetic saturation occurs, the magnetization and its harmonics compare well with the effective field model. On another level, the model has been benchmarked against experimental results, successfully demonstrating that harmonics of the magnetization carry enough information to infer environmental parameters like viscosity and temperature.

11. Phonon hydrodynamics in two-dimensional materials.

Science.gov (United States)

Cepellotti, Andrea; Fugallo, Giorgia; Paulatto, Lorenzo; Lazzeri, Michele; Mauri, Francesco; Marzari, Nicola

2015-03-06

The conduction of heat in two dimensions displays a wealth of fascinating phenomena of key relevance to the scientific understanding and technological applications of graphene and related materials. Here, we use density-functional perturbation theory and an exact, variational solution of the Boltzmann transport equation to study fully from first-principles phonon transport and heat conductivity in graphene, boron nitride, molybdenum disulphide and the functionalized derivatives graphane and fluorographene. In all these materials, and at variance with typical three-dimensional solids, normal processes keep dominating over Umklapp scattering well-above cryogenic conditions, extending to room temperature and more. As a result, novel regimes emerge, with Poiseuille and Ziman hydrodynamics, hitherto typically confined to ultra-low temperatures, characterizing transport at ordinary conditions. Most remarkably, several of these two-dimensional materials admit wave-like heat diffusion, with second sound present at room temperature and above in graphene, boron nitride and graphane.

12. Two-dimensional position sensitive neutron detector

A M Shaikh; S S Desai; A K Patra

2004-08-01

A two-dimensional position sensitive neutron detector has been developed. The detector is a 3He + Kr filled multiwire proportional counter with charge division position readout and has a sensitive area of 345 mm × 345 mm, pixel size 5 mm × 5 mm, active depth 25 mm and is designed for efficiency of 70% for 4 Å neutrons. The detector is tested with 0.5 bar 3He + 1.5 bar krypton gas mixture in active chamber and 2 bar 4He in compensating chamber. The pulse height spectrum recorded at an anode potential of 2000 V shows energy resolution of ∼ 25% for the 764 keV peak. A spatial resolution of 8 mm × 6 mm is achieved. The detector is suitable for SANS studies in the range of 0.02–0.25 Å-1.

13. Two-dimensional heterostructures for energy storage

Science.gov (United States)

Pomerantseva, Ekaterina; Gogotsi, Yury

2017-07-01

Two-dimensional (2D) materials provide slit-shaped ion diffusion channels that enable fast movement of lithium and other ions. However, electronic conductivity, the number of intercalation sites, and stability during extended cycling are also crucial for building high-performance energy storage devices. While individual 2D materials, such as graphene, show some of the required properties, none of them can offer all properties needed to maximize energy density, power density, and cycle life. Here we argue that stacking different 2D materials into heterostructured architectures opens an opportunity to construct electrodes that would combine the advantages of the individual building blocks while eliminating the associated shortcomings. We discuss characteristics of common 2D materials and provide examples of 2D heterostructured electrodes that showed new phenomena leading to superior electrochemical performance. We also consider electrode fabrication approaches and finally outline future steps to create 2D heterostructured electrodes that could greatly expand current energy storage technologies.

14. Rationally synthesized two-dimensional polymers.

Science.gov (United States)

Colson, John W; Dichtel, William R

2013-06-01

Synthetic polymers exhibit diverse and useful properties and influence most aspects of modern life. Many polymerization methods provide linear or branched macromolecules, frequently with outstanding functional-group tolerance and molecular weight control. In contrast, extending polymerization strategies to two-dimensional periodic structures is in its infancy, and successful examples have emerged only recently through molecular framework, surface science and crystal engineering approaches. In this Review, we describe successful 2D polymerization strategies, as well as seminal research that inspired their development. These methods include the synthesis of 2D covalent organic frameworks as layered crystals and thin films, surface-mediated polymerization of polyfunctional monomers, and solid-state topochemical polymerizations. Early application targets of 2D polymers include gas separation and storage, optoelectronic devices and membranes, each of which might benefit from predictable long-range molecular organization inherent to this macromolecular architecture.

15. Local doping of two-dimensional materials

Science.gov (United States)

Wong, Dillon; Velasco, Jr, Jairo; Ju, Long; Kahn, Salman; Lee, Juwon; Germany, Chad E.; Zettl, Alexander K.; Wang, Feng; Crommie, Michael F.

2016-09-20

This disclosure provides systems, methods, and apparatus related to locally doping two-dimensional (2D) materials. In one aspect, an assembly including a substrate, a first insulator disposed on the substrate, a second insulator disposed on the first insulator, and a 2D material disposed on the second insulator is formed. A first voltage is applied between the 2D material and the substrate. With the first voltage applied between the 2D material and the substrate, a second voltage is applied between the 2D material and a probe positioned proximate the 2D material. The second voltage between the 2D material and the probe is removed. The first voltage between the 2D material and the substrate is removed. A portion of the 2D material proximate the probe when the second voltage was applied has a different electron density compared to a remainder of the 2D material.

16. FACE RECOGNITION USING TWO DIMENSIONAL LAPLACIAN EIGENMAP

Institute of Scientific and Technical Information of China (English)

Chen Jiangfeng; Yuan Baozong; Pei Bingnan

2008-01-01

Recently,some research efforts have shown that face images possibly reside on a nonlinear sub-manifold. Though Laplacianfaces method considered the manifold structures of the face images,it has limits to solve face recognition problem. This paper proposes a new feature extraction method,Two Dimensional Laplacian EigenMap (2DLEM),which especially considers the manifold structures of the face images,and extracts the proper features from face image matrix directly by using a linear transformation. As opposed to Laplacianfaces,2DLEM extracts features directly from 2D images without a vectorization preprocessing. To test 2DLEM and evaluate its performance,a series of ex-periments are performed on the ORL database and the Yale database. Moreover,several experiments are performed to compare the performance of three 2D methods. The experiments show that 2DLEM achieves the best performance.

17. Regime of aggregate structures and magneto-rheological characteristics of a magnetic rod-like particle suspension: Monte Carlo and Brownian dynamics simulations

Science.gov (United States)

2017-09-01

In the present study, we address a suspension composed ferromagnetic rod-like particles to elucidate a regime change in the aggregate structures and the magneto-rheological characteristics. Monte Carlo simulations have been employed for investigating the aggregate structures in thermodynamic equilibrium, and Brownian dynamics simulations for magneto-rheological features in a simple shear flow. The main results obtained here are summarized as follows. For the case of thermodynamic equilibrium, the rod-like particles aggregate to form thick chain-like clusters and the neighboring clusters incline in opposite directions. If the external magnetic field is increased, the thick chain-like clusters in the magnetic field direction grow thicker by adsorbing the neighboring clusters that incline in the opposite direction. Hence, a significant phase change in the particle aggregates is not induced by an increase in the magnetic field strength. For the case of a simple shear flow, even a weak shear flow induces a significant regime change from the thick chain-like clusters of thermodynamic equilibrium into wall-like aggregates composed of short raft-like clusters. A strong external magnetic field drastically changes these aggregates into wall-like aggregates composed of thick chain-like clusters rather than the short raft-like clusters. The internal structure of these aggregates is not strongly influenced by a shear flow, and the formation of the short raft-like clusters is maintained inside the aggregates. The main contribution to the net viscosity is the viscosity component due to magnetic particle-particle interaction forces in relation to the present volumetric fraction. Hence, a larger magnetic interaction strength and also a stronger external magnetic field give rise to a larger magneto-rheological effect. However, the dependence of the viscosity on these factors is governed in a complex manner by whether or not the wall-like aggregates are composed mainly of short raft

18. Approximations of fractional Brownian motion

CERN Document Server

Li, Yuqiang; 10.3150/10-BEJ319

2012-01-01

Approximations of fractional Brownian motion using Poisson processes whose parameter sets have the same dimensions as the approximated processes have been studied in the literature. In this paper, a special approximation to the one-parameter fractional Brownian motion is constructed using a two-parameter Poisson process. The proof involves the tightness and identification of finite-dimensional distributions.

19. Driven Brownian transport through arrays of symmetric obstacles.

Science.gov (United States)

Ghosh, P K; Hänggi, P; Marchesoni, F; Martens, S; Nori, F; Schimansky-Geier, L; Schmid, G

2012-01-01

We numerically investigate the transport of a suspended overdamped Brownian particle which is driven through a two-dimensional rectangular array of circular obstacles with finite radius. Two limiting cases are considered in detail, namely, when the constant drive is parallel to the principal or the diagonal array axes. This corresponds to studying the Brownian transport in periodic channels with reflecting walls of different topologies. The mobility and diffusivity of the transported particles in such channels are determined as functions of the drive and the array geometric parameters. Prominent transport features, like negative differential mobilities, excess diffusion peaks, and unconventional asymptotic behaviors, are explained in terms of two distinct lengths, the size of single obstacles (trapping length), and the lattice constant of the array (local correlation length). Local correlation effects are further analyzed by continuously rotating the drive between the two limiting orientations. © 2012 American Physical Society

20. Rotation of Magnetization Derived from Brownian Relaxation in Magnetic Fluids of Different Viscosity Evaluated by Dynamic Hysteresis Measurements over a Wide Frequency Range.

Science.gov (United States)

Ota, Satoshi; Kitaguchi, Ryoichi; Takeda, Ryoji; Yamada, Tsutomu; Takemura, Yasushi

2016-09-10

The dependence of magnetic relaxation on particle parameters, such as the size and anisotropy, has been conventionally discussed. In addition, the influences of external conditions, such as the intensity and frequency of the applied field, the surrounding viscosity, and the temperature on the magnetic relaxation have been researched. According to one of the basic theories regarding magnetic relaxation, the faster type of relaxation dominates the process. However, in this study, we reveal that Brownian and Néel relaxations coexist and that Brownian relaxation can occur after Néel relaxation despite having a longer relaxation time. To understand the mechanisms of Brownian rotation, alternating current (AC) hysteresis loops were measured in magnetic fluids of different viscosities. These loops conveyed the amplitude and phase delay of the magnetization. In addition, the intrinsic loss power (ILP) was calculated using the area of the AC hysteresis loops. The ILP also showed the magnetization response regarding the magnetic relaxation over a wide frequency range. To develop biomedical applications of magnetic nanoparticles, such as hyperthermia and magnetic particle imaging, it is necessary to understand the mechanisms of magnetic relaxation.

1. Rotation of Magnetization Derived from Brownian Relaxation in Magnetic Fluids of Different Viscosity Evaluated by Dynamic Hysteresis Measurements over a Wide Frequency Range

Directory of Open Access Journals (Sweden)

Satoshi Ota

2016-09-01

Full Text Available The dependence of magnetic relaxation on particle parameters, such as the size and anisotropy, has been conventionally discussed. In addition, the influences of external conditions, such as the intensity and frequency of the applied field, the surrounding viscosity, and the temperature on the magnetic relaxation have been researched. According to one of the basic theories regarding magnetic relaxation, the faster type of relaxation dominates the process. However, in this study, we reveal that Brownian and Néel relaxations coexist and that Brownian relaxation can occur after Néel relaxation despite having a longer relaxation time. To understand the mechanisms of Brownian rotation, alternating current (AC hysteresis loops were measured in magnetic fluids of different viscosities. These loops conveyed the amplitude and phase delay of the magnetization. In addition, the intrinsic loss power (ILP was calculated using the area of the AC hysteresis loops. The ILP also showed the magnetization response regarding the magnetic relaxation over a wide frequency range. To develop biomedical applications of magnetic nanoparticles, such as hyperthermia and magnetic particle imaging, it is necessary to understand the mechanisms of magnetic relaxation.

2. On numerical evaluation of two-dimensional phase integrals

DEFF Research Database (Denmark)

Lessow, H.; Rusch, W.; Schjær-Jacobsen, Hans

1975-01-01

The relative advantages of several common numerical integration algorithms used in computing two-dimensional phase integrals are evaluated.......The relative advantages of several common numerical integration algorithms used in computing two-dimensional phase integrals are evaluated....

3. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

Energy Technology Data Exchange (ETDEWEB)

El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens, E-mail: bredenbeck@biophysik.uni-frankfurt.org, E-mail: bredenbeck@biophysik.uni-frankfurt.de [Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt (Germany)

2015-08-15

A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

4. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

Science.gov (United States)

El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens

2015-08-01

A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

5. Ultrafast laser control of vibrational dynamics for a two-dimensional model of HONO 2 in the ground electronic state: separation of conformers, control of the bond length, selective preparation of the discrete and the continuum states

Science.gov (United States)

Oppel, M.; Paramonov, G. K.

1998-06-01

Selective excitation of the vibrational bound and the continuum states, controlled by subpicosecond infrared (IR) laser pulses, is simulated within the Schrödinger wave function formalism for a two-dimensional model of the HONO 2 molecule in the ground electronic state. State-selective excitation of the OH bond is achieved by single optimal laser pulses, with the probability being 97% for the bound states and more than 91% for the resonances. Stable, long-living continuum states are prepared with more than 96% probability by two optimal laser pulses, with the expectation energy of the molecule being well above the dissociation threshold of the ON single bond, and its life-time being at least 100 ps. The length of the ON single bond can be controlled selectively: stretching and contraction by about 45% of its equilibrium length are demonstrated. Laser separation of spatial conformers of HONO 2 in inhomogeneous conditions occurring on an anisotropic surface or created by a direct current (DC) electric field is analysed. The relative yields of target conformers may be very high, ranging from 10 to 10 8, and the absolute yields of up to 40% and more are calculated.

6. Two-Dimensional Crystallization of the Ca(2+)-ATPase for Electron Crystallography.

Science.gov (United States)

Glaves, John Paul; Primeau, Joseph O; Young, Howard S

2016-01-01

Electron crystallography of two-dimensional crystalline arrays is a powerful alternative for the structure determination of membrane proteins. The advantages offered by this technique include a native membrane environment and the ability to closely correlate function and dynamics with crystalline preparations and structural data. Herein, we provide a detailed protocol for the reconstitution and two-dimensional crystallization of the sarcoplasmic reticulum calcium pump (also known as Ca(2+)-ATPase or SERCA) and its regulatory subunits phospholamban and sarcolipin.

7. Perspective: Two-dimensional resonance Raman spectroscopy

Science.gov (United States)

Molesky, Brian P.; Guo, Zhenkun; Cheshire, Thomas P.; Moran, Andrew M.

2016-11-01

Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in complex systems. The 2DRR method can leverage electronic resonance enhancement to selectively probe chromophores embedded in complex environments (e.g., a cofactor in a protein). In addition, correlations between the two dimensions of the 2DRR spectrum reveal information that is not available in traditional Raman techniques. For example, distributions of reactant and product geometries can be correlated in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this perspective article, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin. We also address key differences between the signal generation mechanisms for 2DRR and off-resonant 2D Raman spectroscopies. Most notably, it has been shown that these two techniques are subject to a tradeoff between sensitivity to anharmonicity and susceptibility to artifacts. Overall, recent experimental developments and applications of the 2DRR method suggest great potential for the future of the technique.

8. Comparative Two-Dimensional Fluorescence Gel Electrophoresis.

Science.gov (United States)

Ackermann, Doreen; König, Simone

2018-01-01

Two-dimensional comparative fluorescence gel electrophoresis (CoFGE) uses an internal standard to increase the reproducibility of coordinate assignment for protein spots visualized on 2D polyacrylamide gels. This is particularly important for samples, which need to be compared without the availability of replicates and thus cannot be studied using differential gel electrophoresis (DIGE). CoFGE corrects for gel-to-gel variability by co-running with the sample proteome a standardized marker grid of 80-100 nodes, which is formed by a set of purified proteins. Differentiation of reference and analyte is possible by the use of two fluorescent dyes. Variations in the y-dimension (molecular weight) are corrected by the marker grid. For the optional control of the x-dimension (pI), azo dyes can be used. Experiments are possible in both vertical and horizontal (h) electrophoresis devices, but hCoFGE is much easier to perform. For data analysis, commercial software capable of warping can be adapted.

9. Two-dimensional hexagonal semiconductors beyond graphene

Science.gov (United States)

Nguyen, Bich Ha; Hieu Nguyen, Van

2016-12-01

The rapid and successful development of the research on graphene and graphene-based nanostructures has been substantially enlarged to include many other two-dimensional hexagonal semiconductors (THS): phosphorene, silicene, germanene, hexagonal boron nitride (h-BN) and transition metal dichalcogenides (TMDCs) such as MoS2, MoSe2, WS2, WSe2 as well as the van der Waals heterostructures of various THSs (including graphene). The present article is a review of recent works on THSs beyond graphene and van der Waals heterostructures composed of different pairs of all THSs. One among the priorities of new THSs compared to graphene is the presence of a non-vanishing energy bandgap which opened up the ability to fabricate a large number of electronic, optoelectronic and photonic devices on the basis of these new materials and their van der Waals heterostructures. Moreover, a significant progress in the research on TMDCs was the discovery of valley degree of freedom. The results of research on valley degree of freedom and the development of a new technology based on valley degree of freedom-valleytronics are also presented. Thus the scientific contents of the basic research and practical applications os THSs are very rich and extremely promising.

10. Two-Dimensional Phononic Crystals: Disorder Matters.

Science.gov (United States)

Wagner, Markus R; Graczykowski, Bartlomiej; Reparaz, Juan Sebastian; El Sachat, Alexandros; Sledzinska, Marianna; Alzina, Francesc; Sotomayor Torres, Clivia M

2016-09-14

The design and fabrication of phononic crystals (PnCs) hold the key to control the propagation of heat and sound at the nanoscale. However, there is a lack of experimental studies addressing the impact of order/disorder on the phononic properties of PnCs. Here, we present a comparative investigation of the influence of disorder on the hypersonic and thermal properties of two-dimensional PnCs. PnCs of ordered and disordered lattices are fabricated of circular holes with equal filling fractions in free-standing Si membranes. Ultrafast pump and probe spectroscopy (asynchronous optical sampling) and Raman thermometry based on a novel two-laser approach are used to study the phononic properties in the gigahertz (GHz) and terahertz (THz) regime, respectively. Finite element method simulations of the phonon dispersion relation and three-dimensional displacement fields furthermore enable the unique identification of the different hypersonic vibrations. The increase of surface roughness and the introduction of short-range disorder are shown to modify the phonon dispersion and phonon coherence in the hypersonic (GHz) range without affecting the room-temperature thermal conductivity. On the basis of these findings, we suggest a criteria for predicting phonon coherence as a function of roughness and disorder.

11. Two-dimensional topological photonic systems

Science.gov (United States)

Sun, Xiao-Chen; He, Cheng; Liu, Xiao-Ping; Lu, Ming-Hui; Zhu, Shi-Ning; Chen, Yan-Feng

2017-09-01

The topological phase of matter, originally proposed and first demonstrated in fermionic electronic systems, has drawn considerable research attention in the past decades due to its robust transport of edge states and its potential with respect to future quantum information, communication, and computation. Recently, searching for such a unique material phase in bosonic systems has become a hot research topic worldwide. So far, many bosonic topological models and methods for realizing them have been discovered in photonic systems, acoustic systems, mechanical systems, etc. These discoveries have certainly yielded vast opportunities in designing material phases and related properties in the topological domain. In this review, we first focus on some of the representative photonic topological models and employ the underlying Dirac model to analyze the edge states and geometric phase. On the basis of these models, three common types of two-dimensional topological photonic systems are discussed: 1) photonic quantum Hall effect with broken time-reversal symmetry; 2) photonic topological insulator and the associated pseudo-time-reversal symmetry-protected mechanism; 3) time/space periodically modulated photonic Floquet topological insulator. Finally, we provide a summary and extension of this emerging field, including a brief introduction to the Weyl point in three-dimensional systems.

12. Radiation effects on two-dimensional materials

Energy Technology Data Exchange (ETDEWEB)

Walker, R.C. II; Robinson, J.A. [Department of Materials Science, Penn State, University Park, PA (United States); Center for Two-Dimensional Layered Materials, Penn State, University Park, PA (United States); Shi, T. [Department of Mechanical and Nuclear Engineering, Penn State, University Park, PA (United States); Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI (United States); Silva, E.C. [GlobalFoundries, Malta, NY (United States); Jovanovic, I. [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI (United States)

2016-12-15

The effects of electromagnetic and particle irradiation on two-dimensional materials (2DMs) are discussed in this review. Radiation creates defects that impact the structure and electronic performance of materials. Determining the impact of these defects is important for developing 2DM-based devices for use in high-radiation environments, such as space or nuclear reactors. As such, most experimental studies have been focused on determining total ionizing dose damage to 2DMs and devices. Total dose experiments using X-rays, gamma rays, electrons, protons, and heavy ions are summarized in this review. We briefly discuss the possibility of investigating single event effects in 2DMs based on initial ion beam irradiation experiments and the development of 2DM-based integrated circuits. Additionally, beneficial uses of irradiation such as ion implantation to dope materials or electron-beam and helium-beam etching to shape materials have begun to be used on 2DMs and are reviewed as well. For non-ionizing radiation, such as low-energy photons, we review the literature on 2DM-based photo-detection from terahertz to UV. The majority of photo-detecting devices operate in the visible and UV range, and for this reason they are the focus of this review. However, we review the progress in developing 2DMs for detecting infrared and terahertz radiation. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

13. Photodetectors based on two dimensional materials

Science.gov (United States)

Zheng, Lou; Zhongzhu, Liang; Guozhen, Shen

2016-09-01

Two-dimensional (2D) materials with unique properties have received a great deal of attention in recent years. This family of materials has rapidly established themselves as intriguing building blocks for versatile nanoelectronic devices that offer promising potential for use in next generation optoelectronics, such as photodetectors. Furthermore, their optoelectronic performance can be adjusted by varying the number of layers. They have demonstrated excellent light absorption, enabling ultrafast and ultrasensitive detection of light in photodetectors, especially in their single-layer structure. Moreover, due to their atomic thickness, outstanding mechanical flexibility, and large breaking strength, these materials have been of great interest for use in flexible devices and strain engineering. Toward that end, several kinds of photodetectors based on 2D materials have been reported. Here, we present a review of the state-of-the-art in photodetectors based on graphene and other 2D materials, such as the graphene, transition metal dichalcogenides, and so on. Project supported by the National Natural Science Foundation of China (Nos. 61377033, 61574132, 61504136) and the State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences.

14. Asymptotics for Two-dimensional Atoms

DEFF Research Database (Denmark)

Nam, Phan Thanh; Portmann, Fabian; Solovej, Jan Philip

2012-01-01

We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E^{\\TF}(\\lambd......We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge$Z>0$and$N$quantum electrons of charge -1 is$E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$when$Z\\to \\infty$and$N/Z\\to \\lambda$, where$E......^{\\TF}(\\lambda)$is given by a Thomas-Fermi type variational problem and$c^{\\rm H}\\approx -2.2339$is an explicit constant. We also show that the radius of a two-dimensional neutral atom is unbounded when$Z\\to \\infty$, which is contrary to the expected behavior of three-dimensional atoms.... 15. Predicting Two-Dimensional Silicon Carbide Monolayers. Science.gov (United States) Shi, Zhiming; Zhang, Zhuhua; Kutana, Alex; Yakobson, Boris I 2015-10-27 Intrinsic semimetallicity of graphene and silicene largely limits their applications in functional devices. Mixing carbon and silicon atoms to form two-dimensional (2D) silicon carbide (SixC1-x) sheets is promising to overcome this issue. Using first-principles calculations combined with the cluster expansion method, we perform a comprehensive study on the thermodynamic stability and electronic properties of 2D SixC1-x monolayers with 0 ≤ x ≤ 1. Upon varying the silicon concentration, the 2D SixC1-x presents two distinct structural phases, a homogeneous phase with well dispersed Si (or C) atoms and an in-plane hybrid phase rich in SiC domains. While the in-plane hybrid structure shows uniform semiconducting properties with widely tunable band gap from 0 to 2.87 eV due to quantum confinement effect imposed by the SiC domains, the homogeneous structures can be semiconducting or remain semimetallic depending on a superlattice vector which dictates whether the sublattice symmetry is topologically broken. Moreover, we reveal a universal rule for describing the electronic properties of the homogeneous SixC1-x structures. These findings suggest that the 2D SixC1-x monolayers may present a new "family" of 2D materials, with a rich variety of properties for applications in electronics and optoelectronics. 16. Two-dimensional nuclear magnetic resonance of quadrupolar systems Energy Technology Data Exchange (ETDEWEB) Wang, Shuanhu 1997-09-17 This dissertation describes two-dimensional nuclear magnetic resonance theory and experiments which have been developed to study quadruples in the solid state. The technique of multiple-quantum magic-angle spinning (MQMAS) is extensively reviewed and expanded upon in this thesis. Specifically, MQMAS is first compared with another technique, dynamic-angle spinning (DAS). The similarity between the two techniques allows us to extend much of the DAS work to the MQMAS case. Application of MQMAS to a series of aluminum containing materials is then presented. The superior resolution enhancement through MQMAS is exploited to detect the five- and six-coordinated aluminum in many aluminosilicate glasses. Combining the MQMAS method with other experiments, such as HETCOR, greatly expands the possibility of the use of MQMAS to study a large range of problems and is demonstrated in Chapter 5. Finally, the technique switching-angle spinning (SAS) is applied to quadrupolar nuclei to fully characterize a quadrupolar spin system in which all of the 8 NMR parameters are accurately determined. This dissertation is meant to demonstrate that with the combination of two-dimensional NMR concepts and new advanced spinning technologies, a series of multiple-dimensional NMR techniques can be designed to allow a detailed study of quadrupolar nuclei in the solid state. 17. Two-Dimensional turbulence in the inverse cascade range CERN Document Server Yakhot, V 1999-01-01 A theory of two-dimensional turbulence in the inverse energy cascade range is presented. Strong time-dependence of the large-scale features of the flow ($\\bar{u^{2}}\\propto t\$) results in decoupling of the large-scale dynamics from statistically steady-state small-scale random processes. This time-dependence is also a reason for the localness of the pressure-gradient terms in the equations governing the small-scale velocity difference PDF's. The derived expressions for the pressure gradient contributions lead to a gaussian statistics of transverse velocity differences. The solution for the PDF of longitudinal velocity differences is based on a smallness of the energy flux in two-dimensional turbulence. The theory makes a few quantitative predictions which can be tested experimentally. One of the most surprising results, derived in this paper, is that the small-scale transverse velocity differences are governed by a linear Langevin-like equation, strirred by a non-local universal gaussian random force. This ex...

18. Two-Dimensional Impact Reconstruction Method for Rail Defect Inspection

Directory of Open Access Journals (Sweden)

Jie Zhao

2014-01-01

Full Text Available The safety of train operating is seriously menaced by the rail defects, so it is of great significance to inspect rail defects dynamically while the train is operating. This paper presents a two-dimensional impact reconstruction method to realize the on-line inspection of rail defects. The proposed method utilizes preprocessing technology to convert time domain vertical vibration signals acquired by wireless sensor network to space signals. The modern time-frequency analysis method is improved to reconstruct the obtained multisensor information. Then, the image fusion processing technology based on spectrum threshold processing and node color labeling is proposed to reduce the noise, and blank the periodic impact signal caused by rail joints and locomotive running gear. This method can convert the aperiodic impact signals caused by rail defects to partial periodic impact signals, and locate the rail defects. An application indicates that the two-dimensional impact reconstruction method could display the impact caused by rail defects obviously, and is an effective on-line rail defects inspection method.

19. Interaction of two-dimensional magnetoexcitons

Science.gov (United States)

Dumanov, E. V.; Podlesny, I. V.; Moskalenko, S. A.; Liberman, M. A.

2017-04-01

We study interaction of the two-dimensional magnetoexcitons with in-plane wave vector k→∥ = 0 , taking into account the influence of the excited Landau levels (ELLs) and of the external electric field perpendicular to the surface of the quantum well and parallel to the external magnetic field. It is shown that the account of the ELLs gives rise to the repulsion between the spinless magnetoexcitons with k→∥ = 0 in the Fock approximation, with the interaction constant g decreasing inverse proportional to the magnetic field strength B (g (0) ∼ 1 / B) . In the presence of the perpendicular electric field the Rashba spin-orbit coupling (RSOC), Zeeman splitting (ZS) and nonparabolicity of the heavy-hole dispersion law affect the Landau quantization of the electrons and holes. They move along the new cyclotron orbits, change their Coulomb interactions and cause the interaction between 2D magnetoexcitons with k→∥ = 0 . The changes of the Coulomb interactions caused by the electrons and by the holes moving with new cyclotron orbits are characterized by some coefficients, which in the absence of the electric field turn to be unity. The differences between these coefficients of the electron-hole pairs forming the magnetoexcitons determine their affinities to the interactions. The interactions between the homogeneous, semihomogeneous and heterogeneous magnetoexcitons forming the symmetric states with the same signs of their affinities are attractive whereas in the case of different sign affinities are repulsive. In the heterogeneous asymmetric states the interactions have opposite signs in comparison with the symmetric states. In all these cases the interaction constant g have the dependence g (0) 1 /√{ B} .

20. Two-dimensional materials and their prospects in transistor electronics.

Science.gov (United States)

Schwierz, F; Pezoldt, J; Granzner, R

2015-05-14

During the past decade, two-dimensional materials have attracted incredible interest from the electronic device community. The first two-dimensional material studied in detail was graphene and, since 2007, it has intensively been explored as a material for electronic devices, in particular, transistors. While graphene transistors are still on the agenda, researchers have extended their work to two-dimensional materials beyond graphene and the number of two-dimensional materials under examination has literally exploded recently. Meanwhile several hundreds of different two-dimensional materials are known, a substantial part of them is considered useful for transistors, and experimental transistors with channels of different two-dimensional materials have been demonstrated. In spite of the rapid progress in the field, the prospects of two-dimensional transistors still remain vague and optimistic opinions face rather reserved assessments. The intention of the present paper is to shed more light on the merits and drawbacks of two-dimensional materials for transistor electronics and to add a few more facets to the ongoing discussion on the prospects of two-dimensional transistors. To this end, we compose a wish list of properties for a good transistor channel material and examine to what extent the two-dimensional materials fulfill the criteria of the list. The state-of-the-art two-dimensional transistors are reviewed and a balanced view of both the pros and cons of these devices is provided.

1. Interacting Brownian Swarms: Some Analytical Results

Directory of Open Access Journals (Sweden)

Guillaume Sartoretti

2016-01-01

Full Text Available We consider the dynamics of swarms of scalar Brownian agents subject to local imitation mechanisms implemented using mutual rank-based interactions. For appropriate values of the underlying control parameters, the swarm propagates tightly and the distances separating successive agents are iid exponential random variables. Implicitly, the implementation of rank-based mutual interactions, requires that agents have infinite interaction ranges. Using the probabilistic size of the swarm’s support, we analytically estimate the critical interaction range below that flocked swarms cannot survive. In the second part of the paper, we consider the interactions between two flocked swarms of Brownian agents with finite interaction ranges. Both swarms travel with different barycentric velocities, and agents from both swarms indifferently interact with each other. For appropriate initial configurations, both swarms eventually collide (i.e., all agents interact. Depending on the values of the control parameters, one of the following patterns emerges after collision: (i Both swarms remain essentially flocked, or (ii the swarms become ultimately quasi-free and recover their nominal barycentric speeds. We derive a set of analytical flocking conditions based on the generalized rank-based Brownian motion. An extensive set of numerical simulations corroborates our analytical findings.

2. Brownian Motion Theory and Experiment

CERN Document Server

Basu, K; Basu, Kasturi; Baishya, Kopinjol

2003-01-01

Brownian motion is the perpetual irregular motion exhibited by small particles immersed in a fluid. Such random motion of the particles is produced by statistical fluctuations in the collisions they suffer with the molecules of the surrounding fluid. Brownian motion of particles in a fluid (like milk particles in water) can be observed under a microscope. Here we describe a simple experimental set-up to observe Brownian motion and a method of determining the diffusion coefficient of the Brownian particles, based on a theory due to Smoluchowski. While looking through the microscope we focus attention on a fixed small volume, and record the number of particles that are trapped in that volume, at regular intervals of time. This gives us a time-series data, which is enough to determine the diffusion coefficient of the particles to a good degree of accuracy.

3. Isotropic model of fractional transport in two-dimensional bounded domains.

Science.gov (United States)

Kullberg, A; del-Castillo-Negrete, D; Morales, G J; Maggs, J E

2013-05-01

A two-dimensional fractional Laplacian operator is derived and used to model nonlocal, nondiffusive transport. This integro-differential operator appears in the long-wavelength, fluid description of quantities undergoing non-Brownian random walks without characteristic length scale. To study bounded domains, a mask function is introduced that modifies the kernel in the fractional Laplacian and removes singularities at the boundary. Green's function solutions to the fractional diffusion equation are presented for the unbounded domain and compared to the one-dimensional Cartesian approximations. A time-implicit numerical integration scheme is presented to study fractional diffusion in a circular disk with azimuthal symmetry. Numerical studies of steady-state reveal temperature profiles in which the heat flux and temperature gradient are in the same direction, i.e., uphill transport. The response to off-axis heating, scaling of confinement time with system size, and propagation of cold pulses are investigated.

4. Nonlinear transport in a two dimensional holographic superconductor

Science.gov (United States)

Zeng, Hua Bi; Tian, Yu; Fan, Zhe Yong; Chen, Chiang-Mei

2016-06-01

The problem of nonlinear transport in a two-dimensional superconductor with an applied oscillating electric field is solved by the holographic method. The complex conductivity can be computed from the dynamics of the current for both the near- and nonequilibrium regimes. The limit of weak electric field corresponds to the near-equilibrium superconducting regime, where the charge response is linear and the conductivity develops a gap determined by the condensate. A larger electric field drives the system into a superconducting nonequilibrium steady state, where the nonlinear conductivity is quadratic with respect to the electric field. Increasing the amplitude of the applied electric field results in a far-from-equilibrium nonsuperconducting steady state with a universal linear conductivity of one. In the lower temperature regime we also find chaotic behavior of the superconducting gap, which results in a nonmonotonic field-dependent nonlinear conductivity.

5. Nonlinear Transport in a Two Dimensional Holographic Superconductor

CERN Document Server

Zeng, Hua Bi; Fan, Zhe Yong; Chen, Chiang-Mei

2016-01-01

The problem of nonlinear transport in a two dimensional superconductor with an applied oscillating electric field is solved by the holographic method. The complex conductivity can be computed from the dynamics of the current for both near- and non-equilibrium regimes. The limit of weak electric field corresponds to the near equilibrium superconducting regime, where the charge response is linear and the conductivity develops a gap determined by the condensate. A larger electric field drives the system into a superconducting non-equilibrium steady state, where the nonlinear conductivity is quadratic with respect to the electric field. Keeping increasing the amplitude of applied electric field results in a far-from-equilibrium non-superconducting steady state with a universal linear conductivity of one. In lower temperature regime we also find chaotic behavior of superconducting gap, which results in a non-monotonic field dependent nonlinear conductivity.

6. Thermal conductivity of disordered two-dimensional binary alloys.

Science.gov (United States)

Zhou, Yang; Guo, Zhi-Xin; Cao, Hai-Yuan; Chen, Shi-You; Xiang, Hong-Jun; Gong, Xin-Gao

2016-10-20

Using non-equilibrium molecular dynamics simulations, we have studied the effect of disorder on the thermal conductivity of two-dimensional (2D) C1-xNx alloys. We find that the thermal conductivity not only depends on the substitution concentration of nitrogen, but also strongly depends on the disorder distribution. A general linear relationship is revealed between the thermal conductivity and the participation ratio of phonons in 2D alloys. Localization mode analysis further indicates that the thermal conductivity variation in the ordered alloys can be attributed to the number of inequivalent atoms. As for the disordered alloys, we find that the thermal conductivity variation can be described by a simple linear formula with the disorder degree and the substitution concentration. The present study suggests some general guidance for phonon manipulation and thermal engineering in low dimensional alloys.

7. Vibrational Properties of a Two-Dimensional Silica Kagome Lattice.

Science.gov (United States)

Björkman, Torbjörn; Skakalova, Viera; Kurasch, Simon; Kaiser, Ute; Meyer, Jannik C; Smet, Jurgen H; Krasheninnikov, Arkady V

2016-12-27

Kagome lattices are structures possessing fascinating magnetic and vibrational properties, but in spite of a large body of theoretical work, experimental realizations and investigations of their dynamics are scarce. Using a combination of Raman spectroscopy and density functional theory calculations, we study the vibrational properties of two-dimensional silica (2D-SiO2), which has a kagome lattice structure. We identify the signatures of crystalline and amorphous 2D-SiO2 structures in Raman spectra and show that, at finite temperatures, the stability of 2D-SiO2 lattice is strongly influenced by phonon-phonon interaction. Our results not only provide insights into the vibrational properties of 2D-SiO2 and kagome lattices in general but also suggest a quick nondestructive method to detect 2D-SiO2.

8. Coherent two-dimensional spectroscopy of a Fano model

CERN Document Server

Poulsen, Felipe; Pullerits, Tõnu; Hansen, Thorsten

2016-01-01

The Fano lineshape arises from the interference of two excitation pathways to reach a continuum. Its generality has resulted in a tremendous success in explaining the lineshapes of many one-dimensional spectroscopies - absorption, emission, scattering, conductance, photofragmentation - applied to very varied systems - atoms, molecules, semiconductors and metals. Unravelling a spectroscopy into a second dimension reveals the relationship between states in addition to decongesting the spectra. Femtosecond-resolved two-dimensional electronic spectroscopy (2DES) is a four-wave mixing technique that measures the time-evolution of the populations, and coherences of excited states. It has been applied extensively to the dynamics of photosynthetic units, and more recently to materials with extended band-structures. In this letter, we solve the full time-dependent third-order response, measured in 2DES, of a Fano model and give the new system parameters that become accessible.

9. Isolated structures in two-dimensional optical superlattice

Science.gov (United States)

Zou, Xin-Hao; Yang, Bao-Guo; Xu, Xia; Tang, Peng-Ju; Zhou, Xiao-Ji

2017-10-01

Overlaying commensurate optical lattices with various configurations called superlattices can lead to exotic lattice topologies and, in turn, a discovery of novel physics. In this study, by overlapping the maxima of lattices, a new isolated structure is created, while the interference of minima can generate various "sublattice" patterns. Three different kinds of primitive lattices are used to demonstrate isolated square, triangular, and hexagonal "sublattice" structures in a two-dimensional optical superlattice, the patterns of which can be manipulated dynamically by tuning the polarization, frequency, and intensity of laser beams. In addition, we propose the method of altering the relative phase to adjust the tunneling amplitudes in "sublattices". Our configurations provide unique opportunities to study particle entanglement in "lattices" formed by intersecting wells and to implement special quantum logic gates in exotic lattice geometries.

10. Surface Ship Shock Modeling and Simulation: Two-Dimensional Analysis

Directory of Open Access Journals (Sweden)

Young S. Shin

1998-01-01

Full Text Available The modeling and simulation of the response of a surface ship system to underwater explosion requires an understanding of many different subject areas. These include the process of underwater explosion events, shock wave propagation, explosion gas bubble behavior and bubble-pulse loading, bulk and local cavitation, free surface effect, fluid-structure interaction, and structural dynamics. This paper investigates the effects of fluid-structure interaction and cavitation on the response of a surface ship using USA-NASTRAN-CFA code. First, the one-dimensional Bleich-Sandler model is used to validate the approach, and second, the underwater shock response of a two-dimensional mid-section model of a surface ship is predicted with a surrounding fluid model using a constitutive equation of a bilinear fluid which does not allow transmission of negative pressures.

11. Transport of Bose-Einstein condensates through two dimensional cavities

Energy Technology Data Exchange (ETDEWEB)

Hartmann, Timo

2015-06-01

The recent experimental advances in manipulating ultra-cold atoms make it feasible to study coherent transport of Bose-Einstein condensates (BEC) through various mesoscopic structures. In this work the quasi-stationary propagation of BEC matter waves through two dimensional cavities is investigated using numerical simulations within the mean-field approach of the Gross-Pitaevskii equation. The focus is on the interplay between interference effects and the interaction term in the non-linear wave equation. One sees that the transport properties show a complicated behaviour with multi-stability, hysteresis and dynamical instabilities for non-vanishing interaction. Furthermore, the prominent weak localization effect, which is a robust interference effect emerging after taking a configuration average, is reduced and partially inverted for non-vanishing interaction.

12. Diffusion in the two-dimensional nonoverlapping Lorentz gas

Science.gov (United States)

James, Corinne P.; Evans, Glenn T.

1987-10-01

The self-diffusion coefficient, velocity autocorrelation function, and distribution of collision times for a two-dimensional nonoverlapping Lorentz gas were calculated using molecular dynamics simulation. The systems studied covered a range of densities, from a packing fraction (πNr2/L2) of 0.01 to 0.8. Self-diffusion coefficients were found to agree to all densities with kinetic theory predictions [A. Weijland and J. M. J. van Leeuwen, Physica 38, 35 (1968)] if the radial distribution function (rdf) was taken into account. The density dependence of the decay of the velocity autocorrelation function was qualitatively different from that predicted by kinetic theory. The distribution of collision times was nearly exponential for all but the highest density studied.

13. Large scale instabilities in two-dimensional magnetohydrodynamics

Science.gov (United States)

Boffetta; Celani; Prandi

2000-04-01

The stability of a sheared magnetic field is analyzed in two-dimensional magnetohydrodynamics with resistive and viscous dissipation. Using a multiple-scale analysis, it is shown that at large enough Reynolds numbers the basic state describing a motionless fluid and a layered magnetic field, becomes unstable with respect to large scale perturbations. The exact expressions for eddy-viscosity and eddy-resistivity are derived in the nearby of the critical point where the instability sets in. In this marginally unstable case the nonlinear phase of perturbation growth obeys to a Cahn-Hilliard-like dynamics characterized by coalescence of magnetic islands leading to a final new equilibrium state. High resolution numerical simulations confirm quantitatively the predictions of multiscale analysis.

14. Velocity statistics in two-dimensional granular turbulence

Science.gov (United States)

Isobe, Masaharu

2003-10-01

We studied the macroscopic statistical properties on the freely evolving quasielastic hard disk (granular) system by performing a large-scale (up to a few million particles) event-driven molecular dynamics systematically and found it to be remarkably analogous to an enstrophy cascade process in the decaying two-dimensional fluid turbulence. There are four typical stages in the freely evolving inelastic hard disk system, which are homogeneous, shearing (vortex), clustering, and final state. In the shearing stage, the self-organized macroscopic coherent vortices become dominant. In the clustering stage, the energy spectra are close to the expectation of Kraichnan-Batchelor theory and the squared two-particle separation strictly obeys Richardson law.

15. The modified cumulant expansion for two-dimensional isotropic turbulence

Science.gov (United States)

Tatsumi, T.; Yanase, S.

1981-09-01

The two-dimensional isotropic turbulence in an incompressible fluid is investigated using the modified zero fourth-order cumulant approximation. The dynamical equation for the energy spectrum obtained under this approximation is solved numerically and the similarity laws governing the solution in the energy-containing and enstrophy-dissipation ranges are derived analytically. At large Reynolds numbers the numerical solutions yield the k to the -3rd power inertial subrange spectrum which was predicted by Kraichnan (1967), Leith (1968) and Batchelor (1969), assuming a finite enstrophy dissipation in the inviscid limit. The energy-containing range is found to satisfy an inviscid similarity while the enstrophy-dissipation range is governed by the quasi-equilibrium similarity with respect to the enstrophy dissipation as proposed by Batchelor (1969). There exists a critical time which separates the initial period and the similarity period in which the enstrophy dissipation vanishes and remains non-zero respectively in the inviscid limit.

16. Current fluctuations in a two dimensional model of heat conduction

Science.gov (United States)

Pérez-Espigares, Carlos; Garrido, Pedro L.; Hurtado, Pablo I.

2011-03-01

In this work we study numerically and analytically current fluctuations in the two-dimensional Kipnis-Marchioro-Presutti (KMP) model of heat conduction. For that purpose, we use a recently introduced algorithm which allows the direct evaluation of large deviations functions. We compare our results with predictions based on the Hydrodynamic Fluctuation Theory (HFT) of Bertini and coworkers, finding very good agreement in a wide interval of current fluctuations. We also verify the existence of a well-defined temperature profile associated to a given current fluctuation which depends exclusively on the magnitude of the current vector, not on its orientation. This confirms the recently introduced Isometric Fluctuation Relation (IFR), which results from the time-reversibility of the dynamics, and includes as a particular instance the Gallavotti-Cohen fluctuation theorem in this context but adds a completely new perspective on the high level of symmetry imposed by timereversibility on the statistics of nonequilibrium fluctuations.

17. Collective Modes in Two Dimensional Binary Yukawa Systems

CERN Document Server

Kalman, Gabor J; Donko, Zoltan; Golden, Kenneth I; Kyrkos, Stamatios

2013-01-01

We analyze via theoretical approaches and molecular dynamics simulations the collective mode structure of strongly coupled two-dimensional binary Yukawa systems, for selected density, mass and charge ratios, both in the liquid and crystalline solid phases. Theoretically, the liquid phase is described through the Quasi-Localized Charge Approximation (QLCA) approach, while in the crystalline phase we study the centered honeycomb and the staggered rectangular crystal structures through the standard harmonic phonon approximation. We identify "longitudinal" and "transverse" acoustic and optic modes and find that the longitudinal acoustic mode evolves from its weakly coupled counterpart in a discontinuous non-perturbative fashion. The low frequency acoustic excitations are governed by the oscillation frequency of the average atom, while the high frequency optic excitation frequencies are related to the Einstein frequencies of the systems.

18. Isolated Structures in Two-Dimensional Optical Superlattice

CERN Document Server

Zou, Xinhao; Xu, Xia; Tang, Pengju; Zhou, Xiaoji

2016-01-01

Overlaying commensurate optical lattices with various configurations called superlattices can lead to exotic lattice topologies and, in turn, a discovery of novel physics. In this study, by overlapping the maxima of lattices, a new isolated structure is created, while the interference of minima can generate various "sublattice" patterns. Three different kinds of primitive lattices are used to demonstrate isolated square, triangular, and hexagonal "sublattice" structures in a two-dimensional optical superlattice, the patterns of which can be manipulated dynamically by tuning the polarization, frequency, and intensity of laser beams. In addition, we propose the method of altering the relative phase to adjust the tunneling amplitudes in "sublattices." Our configurations provide unique opportunities to study particle entanglement in "lattices" formed by intersecting wells and to implement special quantum logic gates in exotic lattice geometries.

19. Archimedes' principle for Brownian liquid

CERN Document Server

Burdzy, Krzysztof; Pal, Soumik

2009-01-01

We consider a family of hard core objects moving as independent Brownian motions confined to a vessel by reflection. These are subject to gravitational forces modeled by drifts. The stationary distribution for the process has many interesting implications, including an illustration of the Archimedes' principle. The analysis rests on constructing reflecting Brownian motion with drift in a general open connected domain and studying its stationary distribution. In dimension two we utilize known results about sphere packing.

20. Archimedes' principle for Brownian liquid

OpenAIRE

Burdzy, Krzysztof; Chen, Zhen-Qing; Pal, Soumik

2009-01-01

We consider a family of hard core objects moving as independent Brownian motions confined to a vessel by reflection. These are subject to gravitational forces modeled by drifts. The stationary distribution for the process has many interesting implications, including an illustration of the Archimedes’ principle. The analysis rests on constructing reflecting Brownian motion with drift in a general open connected domain and studying its stationary distribution. In dimension two we utilize known ...

1. Ultrafast two dimensional infrared chemical exchange spectroscopy

Science.gov (United States)

Fayer, Michael

2011-03-01

The method of ultrafast two dimensional infrared (2D IR) vibrational echo spectroscopy is described. Three ultrashort IR pulses tuned to the frequencies of the vibrational transitions of interest are directed into the sample. The interaction of these pulses with the molecular vibrational oscillators produces a polarization that gives rise to a fourth pulse, the vibrational echo. The vibrational echo pulse is combined with another pulse, the local oscillator, for heterodyne detection of the signal. For fixed time between the second and third pulses, the waiting time, the first pulse is scanned. Two Fourier transforms of the data yield a 2D IR spectrum. The waiting time is increased, and another spectrum is obtained. The change in the 2D IR spectra with increased waiting time provides information on the time evolution of the structure of the molecular system under observation. In a 2D IR chemical exchange experiment, two species A and B, are undergoing chemical exchange. A's are turning into B's, and B's are turning into A's, but the overall concentrations of the species are not changing. The kinetics of the chemical exchange on the ground electronic state under thermal equilibrium conditions can be obtained 2D IR spectroscopy. A vibration that has a different frequency for the two species is monitored. At very short time, there will be two peaks on the diagonal of the 2D IR spectrum, one for A and one for B. As the waiting time is increased, chemical exchange causes off-diagonal peaks to grow in. The time dependence of the growth of these off-diagonal peaks gives the chemical exchange rate. The method is applied to organic solute-solvent complex formation, orientational isomerization about a carbon-carbon single bond, migration of a hydrogen bond from one position on a molecule to another, protein structural substate interconversion, and water hydrogen bond switching between ions and water molecules. This work was supported by the Air Force Office of Scientific

2. Molecular assembly on two-dimensional materials

Science.gov (United States)

Kumar, Avijit; Banerjee, Kaustuv; Liljeroth, Peter

2017-02-01

Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy. The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule–substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging

3. Anomalous Brownian refrigerator

Science.gov (United States)

Rana, Shubhashis; Pal, P. S.; Saha, Arnab; Jayannavar, A. M.

2016-02-01

We present a detailed study of a Brownian particle driven by Carnot-type refrigerating protocol operating between two thermal baths. Both the underdamped as well as the overdamped limits are investigated. The particle is in a harmonic potential with time-periodic strength that drives the system cyclically between the baths. Each cycle consists of two isothermal steps at different temperatures and two adiabatic steps connecting them. Besides working as a stochastic refrigerator, it is shown analytically that in the quasistatic regime the system can also act as stochastic heater, depending on the bath temperatures. Interestingly, in non-quasistatic regime, our system can even work as a stochastic heat engine for certain range of cycle time and bath temperatures. We show that the operation of this engine is not reliable. The fluctuations of stochastic efficiency/coefficient of performance (COP) dominate their mean values. Their distributions show power law tails, however the exponents are not universal. Our study reveals that microscopic machines are not the microscopic equivalent of the macroscopic machines that we come across in our daily life. We find that there is no one to one correspondence between the performance of our system under engine protocol and its reverse.

4. Brownian Carnot engine.

Science.gov (United States)

Martínez, I A; Roldán, É; Dinis, L; Petrov, D; Parrondo, J M R; Rica, R A

2016-01-01

The Carnot cycle imposes a fundamental upper limit to the efficiency of a macroscopic motor operating between two thermal baths1. However, this bound needs to be reinterpreted at microscopic scales, where molecular bio-motors2 and some artificial micro-engines3-5 operate. As described by stochastic thermodynamics6,7, energy transfers in microscopic systems are random and thermal fluctuations induce transient decreases of entropy, allowing for possible violations of the Carnot limit8. Here we report an experimental realization of a Carnot engine with a single optically trapped Brownian particle as the working substance. We present an exhaustive study of the energetics of the engine and analyse the fluctuations of the finite-time efficiency, showing that the Carnot bound can be surpassed for a small number of non-equilibrium cycles. As its macroscopic counterpart, the energetics of our Carnot device exhibits basic properties that one would expect to observe in any microscopic energy transducer operating with baths at different temperatures9-11. Our results characterize the sources of irreversibility in the engine and the statistical properties of the efficiency-an insight that could inspire new strategies in the design of efficient nano-motors.

5. Brownian Carnot engine

Science.gov (United States)

Martínez, I. A.; Roldán, É.; Dinis, L.; Petrov, D.; Parrondo, J. M. R.; Rica, R. A.

2016-01-01

The Carnot cycle imposes a fundamental upper limit to the efficiency of a macroscopic motor operating between two thermal baths. However, this bound needs to be reinterpreted at microscopic scales, where molecular bio-motors and some artificial micro-engines operate. As described by stochastic thermodynamics, energy transfers in microscopic systems are random and thermal fluctuations induce transient decreases of entropy, allowing for possible violations of the Carnot limit. Here we report an experimental realization of a Carnot engine with a single optically trapped Brownian particle as the working substance. We present an exhaustive study of the energetics of the engine and analyse the fluctuations of the finite-time efficiency, showing that the Carnot bound can be surpassed for a small number of non-equilibrium cycles. As its macroscopic counterpart, the energetics of our Carnot device exhibits basic properties that one would expect to observe in any microscopic energy transducer operating with baths at different temperatures. Our results characterize the sources of irreversibility in the engine and the statistical properties of the efficiency--an insight that could inspire new strategies in the design of efficient nano-motors.

6. Brownian versus Newtonian devitrification of hard-sphere glasses

Science.gov (United States)

Montero de Hijes, Pablo; Rosales-Pelaez, Pablo; Valeriani, Chantal; Pusey, Peter N.; Sanz, Eduardo

2017-08-01

In a recent molecular dynamics simulation work it has been shown that glasses composed of hard spheres crystallize via cooperative, stochastic particle displacements called avalanches [E. Sanz et al., Proc. Natl. Acad. Sci. USA 111, 75 (2014), 10.1073/pnas.1308338110]. In this Rapid Communication we investigate if such a devitrification mechanism is also present when the dynamics is Brownian rather than Newtonian. The research is motivated in part by the fact that colloidal suspensions, an experimental realization of hard-sphere systems, undergo Brownian motion. We find that Brownian hard-sphere glasses do crystallize via avalanches with very similar characteristics to those found in the Newtonian case. We briefly discuss the implications of these findings for experiments on colloids.

7. Generalization of Brownian Motion with Autoregressive Increments

CERN Document Server

Fendick, Kerry

2011-01-01

This paper introduces a generalization of Brownian motion with continuous sample paths and stationary, autoregressive increments. This process, which we call a Brownian ray with drift, is characterized by three parameters quantifying distinct effects of drift, volatility, and autoregressiveness. A Brownian ray with drift, conditioned on its state at the beginning of an interval, is another Brownian ray with drift over the interval, and its expected path over the interval is a ray with a slope that depends on the conditioned state. This paper shows how Brownian rays can be applied in finance for the analysis of queues or inventories and the valuation of options. We model a queue's net input process as a superposition of Brownian rays with drift and derive the transient distribution of the queue length conditional on past queue lengths and on past states of the individual Brownian rays comprising the superposition. The transient distributions of Regulated Brownian Motion and of the Regulated Brownian Bridge are...

8. Effect of interfaces on the nearby Brownian motion

CERN Document Server

Huang, Kai

2016-01-01

Near-boundary Brownian motion is a classic hydrodynamic problem of great importance in a variety of fields, from biophysics to micro-/nanofluidics. However, due to challenges in experimental measurements of near-boundary dynamics, the effect of interfaces on Brownian motion has remained elusive. Here, we report a computational study of this effect using microsecond-long large-scale molecular dynamics simulations and our newly developed Green-Kubo relation for friction at the liquid-solid interface. Our computer experiment unambiguously reveals that the t^(-3/2) long-time decay of the velocity autocorrelation function of a Brownian particle in bulk liquid is replaced by a t^(-5/2) decay near a boundary. We discover a general breakdown of traditional no-slip boundary condition at short time scales and we show that this breakdown has a profound impact on the near-boundary Brownian motion. Our results demonstrate the potential of Brownian-particle based micro-/nano-sonar to probe the local wettability of liquid-s...

9. Electrical and optoelectronic properties of two-dimensional materials

Science.gov (United States)

Wang, Qiaoming

Electrical and optoelectronic properties of bulk semiconductor materials have been extensively explored in last century. However, when reduced to one-dimensional and two-dimensional, many semiconductors start to show unique electrical and optoelectronic behaviors. In this dissertation, electrical and optoelectronic properties of one-dimensional (nanowires) and two-dimensional semiconductor materials are investigated by various techniques, including scanning photocurrent microscopy, scanning Kelvin probe microscopy, Raman spectroscopy, photoluminescence, and finite-element simulations. In our work, gate-tunable photocurrent in ZnO nanowires has been observed under optical excitation in the visible regime, which originates from the nanowire/substrate interface states. This gate tunability in the visible regime can be used to enhance the photon absorption efficiency, and suppress the undesirable visible-light photodetection in ZnO-based solar cells. The power conversion efficiency of CuInSe2/CdS core-shell nanowire solar cells has been investigated. The highest power conversion efficiency per unit area/volume is achieved with core diameter of 50 nm and the thinnest shell thickness. The existence of the optimal geometrical parameters is due to a combined effect of optical resonances and carrier transport/dynamics. Significant current crowding in two-dimensional black phosphorus field-effect transistors has been found, which has been significantly underestimated by the commonly used transmission-line model. This current crowding can lead to Joule heating close to the contacts. New van der Waals metal-semiconductor junctions have been mechanically constructed and systematically studied. The photocurrent on junction area has been demonstrated to originate from the photothermal effect rather than the photovoltaic effect. Our findings suggest that a reasonable control of interface/surface state properties can enable new and beneficial functionalities in nanostructures. We

10. The convolution theorem for two-dimensional continuous wavelet transform

Institute of Scientific and Technical Information of China (English)

ZHANG CHI

2013-01-01

In this paper , application of two -dimensional continuous wavelet transform to image processes is studied. We first show that the convolution and correlation of two continuous wavelets satisfy the required admissibility and regularity conditions ,and then we derive the convolution and correlation theorem for two-dimensional continuous wavelet transform. Finally, we present numerical example showing the usefulness of applying the convolution theorem for two -dimensional continuous wavelet transform to perform image restoration in the presence of additive noise.

11. Two-Dimensional Electron-Spin Resonance

Science.gov (United States)

Freed, Jack H.

2000-03-01

The extension of the concepts of 2D-NMR to ESR posed significant technological challenges, especially for liquids. ESR relaxation times are very short, as low as 10-15 ns. for T_2's. Spectral bandwidths are 100-250 MHz for nitroxide spin labels. Adequate coverage is obtained with 3-5 ns. π/2 (9-17 GHz) microwave pulses into a small low Q resonator. Dead-times are currently 25-30 ns. Additional requirements are rapid phase shifting for phase cycling, nsec. data acquisition, and fast repetition rates (10-100 kHz). 2D-ELDOR (electron-electron double resonance), which is a 3-pulse 2D-exchange experiment, takes about 30 minutes with just 0.5 nanomole spin-probe in solution (SNR 200). 2D-ELDOR is very useful in studies of molecular dynamics and local structure in complex fluids. For such media, the slow rotational dynamics requires a theory based upon the stochastic Liouville equation which enables quantitative interpretation of 2D-ELDOR experiments. In studies of spin-probes in a liquid crystal new insights could be obtained on the dynamic structure in different phases. One obtains, in addition to ordering and reorientation rates of the probes, details of the local dynamic cage: its orienting potential and (slow) relaxation rate. 2D-ELDOR overcomes the loss of resolution resulting from microscopically ordered but macroscopically disordered complex fluids. This is illustrated by studies of the dynamic structure of lipid membrane vesicles, and the effects of adding a peptide. The short dead times enable the observation of both the bulk lipids and the more immobilized lipids that coat (or are trapped) by the (aggregates of) peptides. Also, new developments of multi-quantum (2D) FT-ESR from nitroxide spin labels interacting by dipolar interactions show considerable promise in measuring distances of ca. 15-70A in macromolecules.

12. Quantum Darwinism in Quantum Brownian Motion

Science.gov (United States)

Blume-Kohout, Robin; Zurek, Wojciech H.

2008-12-01

Quantum Darwinism—the redundant encoding of information about a decohering system in its environment—was proposed to reconcile the quantum nature of our Universe with apparent classicality. We report the first study of the dynamics of quantum Darwinism in a realistic model of decoherence, quantum Brownian motion. Prepared in a highly squeezed state—a macroscopic superposition—the system leaves records whose redundancy increases rapidly with initial delocalization. Redundancy appears rapidly (on the decoherence time scale) and persists for a long time.

13. On final states of two-dimensional decaying turbulence

Science.gov (United States)

Yin, Z.

2004-12-01

Numerical and analytical studies of final states of two-dimensional (2D) decaying turbulence are carried out. The first part of this work is trying to give a definition for final states of 2D decaying turbulence. The functional relation of ω-ψ, which is frequently adopted as the characterization of those final states, is merely a sufficient but not necessary condition; moreover, it is not proper to use it as the definition. It is found that the method through the value of the effective area S covered by the scatter ω-ψ plot, initially suggested by Read, Rhines, and White ["Geostrophic scatter diagrams and potential vorticity dynamics," J. Atmos. Sci. 43, 3226 (1986)] is more general and suitable for the definition. Based on this concept, a definition is presented, which covers all existing results in late states of decaying 2D flows (including some previous unexplainable weird double-valued ω-ψ scatter plots). The remaining part of the paper is trying to further study 2D decaying turbulence with the assistance of this definition. Some numerical results, leading to "bar" final states and further verifying the predictive ability of statistical mechanics [Yin, Montgomery, and Clercx, "Alternative statistical-mechanical descriptions of decaying two-dimensional turbulence in terms of patches and points," Phys. Fluids 15, 1937 (2003)], are reported. It is realized that some simulations with narrow-band energy spectral initial conditions result in some final states that cannot be very well interpreted by the statistical theory (meanwhile, those final states are still in the scope of the definition).

14. Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase

CERN Document Server

Lu, Jian; Hwang, Harold Y; Ofori-Okai, Benjamin K; Fleischer, Sharly; Nelson, Keith A

2016-01-01

Ultrafast two-dimensional spectroscopy utilizes correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum. Its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. Here we report ultrafast two-dimensional terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by three terahertz field-dipole interactions. The nonlinear time-domain orientation signals are mapped into the frequency domain in two-dimensional rotational spectra which reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.

15. Entropic forces in Brownian motion

CERN Document Server

Roos, Nico

2013-01-01

The interest in the concept of entropic forces has risen considerably since E. Verlinde proposed to interpret the force in Newton s second law and Gravity as entropic forces. Brownian motion, the motion of a small particle (pollen) driven by random impulses from the surrounding molecules, may be the first example of a stochastic process in which such forces are expected to emerge. In this note it is shown that at least two types of entropic motion can be identified in the case of 3D Brownian motion (or random walk). This yields simple derivations of known results of Brownian motion, Hook s law and, applying an external (nonradial) force, Curie s law and the Langevin-Debye equation.

16. The Chandrasekhar's Equation for Two-Dimensional Hypothetical White Dwarfs

CERN Document Server

De, Sanchari

2014-01-01

In this article we have extended the original work of Chandrasekhar on the structure of white dwarfs to the two-dimensional case. Although such two-dimensional stellar objects are hypothetical in nature, we strongly believe that the work presented in this article may be prescribed as Master of Science level class problem for the students in physics.

17. Beginning Introductory Physics with Two-Dimensional Motion

Science.gov (United States)

Huggins, Elisha

2009-01-01

During the session on "Introductory College Physics Textbooks" at the 2007 Summer Meeting of the AAPT, there was a brief discussion about whether introductory physics should begin with one-dimensional motion or two-dimensional motion. Here we present the case that by starting with two-dimensional motion, we are able to introduce a considerable…

18. Spatiotemporal surface solitons in two-dimensional photonic lattices.

Science.gov (United States)

Mihalache, Dumitru; Mazilu, Dumitru; Lederer, Falk; Kivshar, Yuri S

2007-11-01

We analyze spatiotemporal light localization in truncated two-dimensional photonic lattices and demonstrate the existence of two-dimensional surface light bullets localized in the lattice corners or the edges. We study the families of the spatiotemporal surface solitons and their properties such as bistability and compare them with the modes located deep inside the photonic lattice.

19. Explorative data analysis of two-dimensional electrophoresis gels

DEFF Research Database (Denmark)

Schultz, J.; Gottlieb, D.M.; Petersen, Marianne Kjerstine;

2004-01-01

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening...

20. Mechanics of Apparent Horizon in Two Dimensional Dilaton Gravity

CERN Document Server

Cai, Rong-Gen

2016-01-01

In this article, we give a definition of apparent horizon in a two dimensional general dilaton gravity theory. With this definition, we construct the mechanics of the apparent horizon by introducing a quasi-local energy of the theory. Our discussion generalizes the apparent horizons mechanics in general spherically symmetric spactimes in four or higher dimensions to the two dimensional dilaton gravity case.