Rapid sampling of stochastic displacements in Brownian dynamics simulations with stresslet constraints

Science.gov (United States)

Fiore, Andrew M.; Swan, James W.

2018-01-01

Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material are a significant computational challenge. Here, we present a new method for Brownian dynamics simulations of suspended colloidal scale particles such as colloids, polymers, surfactants, and proteins subject to a particular and important class of hydrodynamic constraints. The total computational cost of the algorithm is practically linear with the number of particles modeled and can be further optimized when the characteristic mass fractal dimension of the suspended particles is known. Specifically, we consider the so-called "stresslet" constraint for which suspended particles resist local deformation. This acts to produce a symmetric force dipole in the fluid and imparts rigidity to the particles. The presented method is an extension of the recently reported positively split formulation for Ewald summation of the Rotne-Prager-Yamakawa mobility tensor to higher order terms in the hydrodynamic scattering series accounting for force dipoles [A. M. Fiore et al., J. Chem. Phys. 146(12), 124116 (2017)]. The hydrodynamic mobility tensor, which is proportional to the covariance of particle Brownian displacements, is constructed as an Ewald sum in a novel way which guarantees that the real-space and wave-space contributions to the sum are independently symmetric and positive-definite for all possible particle configurations. This property of the Ewald sum is leveraged to rapidly sample the Brownian displacements from a superposition of statistically independent processes with the wave-space and real-space contributions as respective covariances. The cost of computing the Brownian displacements in this way is comparable to the cost of computing the deterministic displacements. The addition of a stresslet constraint to the over-damped particle

First passage Brownian functional properties of snowmelt dynamics

Science.gov (United States)

Dubey, Ashutosh; Bandyopadhyay, Malay

2018-04-01

In this paper, we model snow-melt dynamics in terms of a Brownian motion (BM) with purely time dependent drift and difusion and examine its first passage properties by suggesting and examining several Brownian functionals which characterize the lifetime and reactivity of such stochastic processes. We introduce several probability distribution functions (PDFs) associated with such time dependent BMs. For instance, for a BM with initial starting point x0, we derive analytical expressions for : (i) the PDF P(tf|x0) of the first passage time tf which specify the lifetime of such stochastic process, (ii) the PDF P(A|x0) of the area A till the first passage time and it provides us numerous valuable information about the total fresh water availability during melting, (iii) the PDF P(M) associated with the maximum size M of the BM process before the first passage time, and (iv) the joint PDF P(M; tm) of the maximum size M and its occurrence time tm before the first passage time. These P(M) and P(M; tm) are useful in determining the time of maximum fresh water availability and in calculating the total maximum amount of available fresh water. These PDFs are examined for the power law time dependent drift and diffusion which matches quite well with the available data of snowmelt dynamics.

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

International Nuclear Information System (INIS)

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

2011-01-01

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

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.

Molecular dynamics test of the Brownian description of Na+ motion in water

International Nuclear Information System (INIS)

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

1985-01-01

The autocorrelation function of the velocity of an infinitely dilute Na + ion in aqueous solution, and the autocorrelation function of the force exerted on a stationary Na + under the same conditions are evaluated by molecular dynamics calculations. The results are used to test the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dynamics in solution. The self-diffusion coefficient of the Na + ion predicted by Brownian motion theory is (0.65 +- 0.1) x 10 -5 cm 2 /s. This value is about 60% greater than the one obtained for the proper dynamics of the finite mass ion, (0.4 +- 0.1) x 10 -5 cm 2 /s. The numerically correct velocity autocorrelation function is nonexponential, and the autocorrelation of the force on the stationary ion does not decay faster than the ion velocity autocorrelation function. Motivated by previous hydrodynamic modeling of friction kernels, we examine the approximation in which the memory function for the velocity autocorrelation function is identified with the autocorrelation function of the force on the stationary ion. The overall agreement between this approximation for the velocity autocorrelation function and the numerically correct answer is quite good

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.

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.

Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics

NARCIS (Netherlands)

Bailey, A.G.; Lowe, C.P.; Pagonabarraga, I.; Cosentino Lagomarsino, M.

2009-01-01

Microscopic semiflexible filaments suspended in a viscous fluid are widely encountered in biophysical problems. The classic example is the flagella used by microorganisms to generate propulsion. Simulating the dynamics of these filaments numerically is complicated because of the coupling between the

Brownian motion under dynamic disorder: effects of memory on the decay of the non-Gaussianity parameter

Science.gov (United States)

Tyagi, Neha; Cherayil, Binny J.

2018-03-01

The increasingly widespread occurrence in complex fluids of particle motion that is both Brownian and non-Gaussian has recently been found to be successfully modeled by a process (frequently referred to as ‘diffusing diffusivity’) in which the white noise that governs Brownian diffusion is itself stochastically modulated by either Ornstein–Uhlenbeck dynamics or by two-state noise. But the model has so far not been able to account for an aspect of non-Gaussian Brownian motion that is also commonly observed: a non-monotonic decay of the parameter that quantifies the extent of deviation from Gaussian behavior. In this paper, we show that the inclusion of memory effects in the model—via a generalized Langevin equation—can rationalise this phenomenon.

Equivalence of Brownian dynamics and dynamic Monte Carlo simulations in multicomponent colloidal suspensions.

Science.gov (United States)

Cuetos, Alejandro; Patti, Alessandro

2015-08-01

We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.

Collective dynamics of populations of weakly correlated filaments of incoherent white light

International Nuclear Information System (INIS)

Guo, Jinxin; Sheridan, John T; Saravanamuttu, Kalaichelvi

2013-01-01

We examined the dynamics of two populations of self-trapped filaments of spatially and temporally incoherent white light. The populations consisted of (i) independent filaments generated through self-trapping of incandescent speckles, and (ii) co-dependent filaments created through modulation instability of a broad incandescent beam. Both filament populations were positionally stable in conditions where individual pairs of self-trapped beams interact strongly. Both also acquired significantly broad intensity distributions, which were independent of their parent optical fields; a small but persistent number of high-intensity filaments was identified in both cases. These studies provide accessible routes to weakly correlated ensembles, insight into their collective behaviour such as self-stabilization and self-selected intensity distributions, and reveal intriguing similarities between the dynamics of two populations of different origins. (paper)

Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles

Science.gov (United States)

Donev, Aleksandar; Sprinkle, Brennan; Balboa, Florencio; Patankar, Neelesh

2017-11-01

We introduce new numerical methods for simulating the dynamics of passive and active Brownian colloidal suspensions of particles of arbitrary shape sedimented near a bottom wall. The methods also apply for periodic (bulk) suspensions. Our methods scale linearly in the number of particles, and enable previously unprecedented simulations of tens to hundreds of thousands of particles. We demonstrate the accuracy and efficiency of our methods on a suspension of boomerang-shaped colloids. We also model recent experiments on active dynamics of uniform suspensions of spherical microrollers. This work was supported in part by the National Science Foundation under award DMS-1418706, and by the U.S. Department of Energy under award DE-SC0008271.

Structure and dynamics of nonaqueous electrolyte solutions by small angle neutron scattering, brownian dynamics and primitive model theories

International Nuclear Information System (INIS)

Kunz, W.; Turq, P.

1990-01-01

The study of electrolyte solutions by small angle neutron scattering (static) of quasi-elastic neutron scattering (dynamics) gives new perspectives to the primitive model of electrolytes, for both static and dynamic properties of those systems. Whereas all properties can be interpreted by brownian dynamics, integral equations cannot be used at the present time to get transport coefficients in all cases. As regards the choice of the potentials at the McMillan Mayer level, specific Gurney terms for solvation are not needed for tetraalkylammonium salts. (orig.)

Mapping migratory flyways in Asia using dynamic Brownian bridge movement models.

Science.gov (United States)

Palm, Eric C; Newman, Scott H; Prosser, Diann J; Xiao, Xiangming; Ze, Luo; Batbayar, Nyambayar; Balachandran, Sivananinthaperumal; Takekawa, John Y

2015-01-01

Identifying movement routes and stopover sites is necessary for developing effective management and conservation strategies for migratory animals. In the case of migratory birds, a collection of migration routes, known as a flyway, is often hundreds to thousands of kilometers long and can extend across political boundaries. Flyways encompass the entire geographic range between the breeding and non-breeding areas of a population, species, or a group of species, and they provide spatial frameworks for management and conservation across international borders. Existing flyway maps are largely qualitative accounts based on band returns and survey data rather than observed movement routes. In this study, we use satellite and GPS telemetry data and dynamic Brownian bridge movement models to build upon existing maps and describe waterfowl space use probabilistically in the Central Asian and East Asian-Australasian Flyways. Our approach provided new information on migratory routes that was not easily attainable with existing methods to describe flyways. Utilization distributions from dynamic Brownian bridge movement models identified key staging and stopover sites, migration corridors and general flyway outlines in the Central Asian and East Asian-Australasian Flyways. A map of space use from ruddy shelducks depicted two separate movement corridors within the Central Asian Flyway, likely representing two distinct populations that show relatively strong connectivity between breeding and wintering areas. Bar-headed geese marked at seven locations in the Central Asian Flyway showed heaviest use at several stopover sites in the same general region of high-elevation lakes along the eastern Qinghai-Tibetan Plateau. Our analysis of data from multiple Anatidae species marked at sites throughout Asia highlighted major movement corridors across species and confirmed that the Central Asian and East Asian-Australasian Flyways were spatially distinct. The dynamic Brownian bridge

Dynamic properties of polydisperse colloidal particles in the presence of thermal gradient studied by a modified Brownian dynamic model

Science.gov (United States)

Song, Dongxing; Jin, Hui; Jing, Dengwei; Wang, Xin

2018-03-01

Aggregation and migration of colloidal particles under the thermal gradient widely exists in nature and many industrial processes. In this study, dynamic properties of polydisperse colloidal particles in the presence of thermal gradient were studied by a modified Brownian dynamic model. Other than the traditional forces on colloidal particles, including Brownian force, hydrodynamic force, and electrostatic force from other particles, the electrostatic force from the asymmetric ionic diffusion layer under a thermal gradient has been considered and introduced into the Brownian dynamic model. The aggregation ratio of particles (R A), the balance time (t B) indicating the time threshold when {{R}A} becomes constant, the porosity ({{P}BA} ), fractal dimension (D f) and distributions of concentration (DISC) and aggregation (DISA) for the aggregated particles were discussed based on this model. The aggregated structures formed by polydisperse particles are less dense and the particles therein are loosely bonded. Also it showed a quite large compressibility as the increases of concentration and interparticle potential can significantly increase the fractal dimension. The thermal gradient can induce two competitive factors leading to a two-stage migration of particles. When t{{t}B} , the thermophoresis becomes dominant thus the migrations of particles are against the thermal gradient. The effect of thermophoresis on the aggregate structures was found to be similar to the effect of increasing particle concentration. This study demonstrates how the thermal gradient affects the aggregation of monodisperse and polydisperse particles and can be a guide for the biomimetics and precise control of colloid system under the thermal gradient. Moreover, our model can be easily extended to other more complex colloidal systems considering shear, temperature fluctuation, surfactant, etc.

The self-assembly, elasticity, and dynamics of cardiac thin filaments.

Science.gov (United States)

Tassieri, M; Evans, R M L; Barbu-Tudoran, L; Trinick, J; Waigh, T A

2008-03-15

Solutions of intact cardiac thin filaments were examined with transmission electron microscopy, dynamic light scattering (DLS), and particle-tracking microrheology. The filaments self-assembled in solution with a bell-shaped distribution of contour lengths that contained a population of filaments of much greater length than the in vivo sarcomere size ( approximately 1 mum) due to a one-dimensional annealing process. Dynamic semiflexible modes were found in DLS measurements at fast timescales (12.5 ns-0.0001 s). The bending modulus of the fibers is found to be in the range 4.5-16 x 10(-27) Jm and is weakly dependent on calcium concentration (with Ca2+ > or = without Ca2+). Good quantitative agreement was found for the values of the fiber diameter calculated from transmission electron microscopy and from the initial decay of DLS correlation functions: 9.9 nm and 9.7 nm with and without Ca2+, respectively. In contrast, at slower timescales and high polymer concentrations, microrheology indicates that the cardiac filaments act as short rods in solution according to the predictions of the Doi-Edwards chopsticks model (viscosity, eta approximately c(3), where c is the polymer concentration). This differs from the semiflexible behavior of long synthetic actin filaments at comparable polymer concentrations and timescales (elastic shear modulus, G' approximately c(1.4), tightly entangled) and is due to the relative ratio of the contour lengths ( approximately 30). The scaling dependence of the elastic shear modulus on the frequency (omega) for cardiac thin filaments is G' approximately omega(3/4 +/- 0.03), which is thought to arise from flexural modes of the filaments.

Active Polymers — Emergent Conformational and Dynamical Properties: A Brief Review

Science.gov (United States)

Winkler, Roland G.; Elgeti, Jens; Gompper, Gerhard

2017-10-01

Active matter exhibits a wealth of emerging nonequilibrium behaviours. A paradigmatic example is the interior of cells, where active components, such as the cytoskeleton, are responsible for its structural organization and the dynamics of the various components. Of particular interest are the properties of polymers and filaments. The intimate coupling of thermal and active noise, hydrodynamic interactions, and polymer conformations implies the emergence of novel structural and dynamical features. In this article, we review recent theoretical and simulation developments and results for the structural and dynamical properties of polymers exposed to activity. Two- and three-dimensional filaments are considered propelled by different mechanisms such as active Brownian particles or hydrodynamically-coupled force dipoles.

Ergodicity breaking and ageing of underdamped Brownian dynamics with quenched disorder

Science.gov (United States)

Guo, Wei; Li, Yong; Song, Wen-Hua; Du, Lu-Chun

2018-03-01

The dynamics of an underdamped Brownian particle moving in one-dimensional quenched disorder under the action of an external force is investigated. Within the tailored parameter regime, the transiently anomalous diffusion and ergodicity breaking, spanning several orders of magnitude in time, have been obtained. The ageing nature of the system weakens as the dissipation of the system increases for other given parameters. Its origin is ascribed to the highly local heterogeneity of the disorder. Two kinds of approximations (in the stationary state), respectively, for large bias and large damping are derived. These results may be helpful in further understanding the nontrivial response of nonlinear dynamics, and also have potential applications to experiments and activities of biological processes.

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.

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

International Nuclear Information System (INIS)

Dubina, Sean Hyun; Wedgewood, Lewis Edward

2016-01-01

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.

Microscopic derivation of open quantum Brownian motion: a particular example

International Nuclear Information System (INIS)

Sinayskiy, Ilya; Petruccione, Francesco

2015-01-01

The microscopic derivation of a new type of Brownian motion, namely open quantum Brownian motion (OQBM) is presented. The quantum master equation for OQBM is derived for a weakly driven system interacting with a decoherent environment. Examples of the dynamics for initial Gaussian and non-Gaussian distributions are presented. Both examples demonstrate convergence of the OQBM dynamics to Gaussian distributions. (topical article)

Stochastic Severing of Actin Filaments by Actin Depolymerizing Factor/Cofilin Controls the Emergence of a Steady Dynamical Regime

Science.gov (United States)

Roland, Jeremy; Berro, Julien; Michelot, Alphée; Blanchoin, Laurent; Martiel, Jean-Louis

2008-01-01

Actin dynamics (i.e., polymerization/depolymerization) powers a large number of cellular processes. However, a great deal remains to be learned to explain the rapid actin filament turnover observed in vivo. Here, we developed a minimal kinetic model that describes key details of actin filament dynamics in the presence of actin depolymerizing factor (ADF)/cofilin. We limited the molecular mechanism to 1), the spontaneous growth of filaments by polymerization of actin monomers, 2), the ageing of actin subunits in filaments, 3), the cooperative binding of ADF/cofilin to actin filament subunits, and 4), filament severing by ADF/cofilin. First, from numerical simulations and mathematical analysis, we found that the average filament length, 〈L〉, is controlled by the concentration of actin monomers (power law: 5/6) and ADF/cofilin (power law: −2/3). We also showed that the average subunit residence time inside the filament, 〈T〉, depends on the actin monomer (power law: −1/6) and ADF/cofilin (power law: −2/3) concentrations. In addition, filament length fluctuations are ∼20% of the average filament length. Moreover, ADF/cofilin fragmentation while modulating filament length keeps filaments in a high molar ratio of ATP- or ADP-Pi versus ADP-bound subunits. This latter property has a protective effect against a too high severing activity of ADF/cofilin. We propose that the activity of ADF/cofilin in vivo is under the control of an affinity gradient that builds up dynamically along growing actin filaments. Our analysis shows that ADF/cofilin regulation maintains actin filaments in a highly dynamical state compatible with the cytoskeleton dynamics observed in vivo. PMID:18065447

Force-velocity measurements of a few growing actin filaments.

Directory of Open Access Journals (Sweden)

Coraline Brangbour

2011-04-01

Full Text Available The polymerization of actin in filaments generates forces that play a pivotal role in many cellular processes. We introduce a novel technique to determine the force-velocity relation when a few independent anchored filaments grow between magnetic colloidal particles. When a magnetic field is applied, the colloidal particles assemble into chains under controlled loading or spacing. As the filaments elongate, the beads separate, allowing the force-velocity curve to be precisely measured. In the widely accepted Brownian ratchet model, the transduced force is associated with the slowing down of the on-rate polymerization. Unexpectedly, in our experiments, filaments are shown to grow at the same rate as when they are free in solution. However, as they elongate, filaments are more confined in the interspace between beads. Higher repulsive forces result from this higher confinement, which is associated with a lower entropy. In this mechanism, the production of force is not controlled by the polymerization rate, but is a consequence of the restriction of filaments' orientational fluctuations at their attachment point.

Mathematical modeling of alignment dynamics in active motor-filament systems

Science.gov (United States)

Swaminathan, Sumanth

The formation of the cytoskeleton, via motor-mediated microtubule self-organization, is an important subject of study in the biological sciences as well as in nonequilibrium, soft matter physics. Accurate modeling of the dynamics is a formidable task as it involves intrinsic nonlinearities, structural anisotropies, nonequilibrium processes, and a broad window of time scales, length scales, and densities. In this thesis, we study the ordering dynamics and pattern formations arising from motor-mediated microtubule self-organization in dilute and semi-dilute filament solutions. In the dilute case, we use a probabilistic model in which microtubules interact through motor induced, inelastic binary collisions. This model shows that initially disordered filament solutions exhibit an ordering transition resulting in the emergence of well aligned rod bundles. We study the existence and dynamic interaction of microtubule bundles analytically and numerically. Our results show a long term attraction and coalescing of bundles indicating a clear coarsening in the system; microtubule bundles concentrate into fewer orientations on a slow logarithmic time scale. In the semi-dilute case, multiple motors can bind a filament to several others and, for a critical motor density, induce a transition to an ordered state with a nonzero mean orientation. We develop a spatially homogeneous, mean-field theory that explicitly accounts for motor forcing and thermal fluctuations which enter into the model as multiplicative and additive noises respectively. Our model further incorporates a force-dependent detachment rate of motors, which in turn affects the mean and the fluctuations of the net force acting on a filament. We demonstrate that the transition to the oriented state changes from second order to first order when the force-dependent detachment becomes important. In our final analysis, we add complex spatial inhomogeneities to our mean field theory. The revised model consists of a system

Generalized Langevin Theory Of The Brownian Motion And The Dynamics Of Polymers In Solution

International Nuclear Information System (INIS)

Tothova, J.; Lisy, V.

2015-01-01

The review deals with a generalization of the Rouse and Zimm bead-spring models of the dynamics of flexible polymers in dilute solutions. As distinct from these popular theories, the memory in the polymer motion is taken into account. The memory naturally arises as a consequence of the fluid and bead inertia within the linearized Navier-Stokes hydrodynamics. We begin with a generalization of the classical theory of the Brownian motion, which forms the basis of any theory of the polymer dynamics. The random force driving the Brownian particles is not the white one as in the Langevin theory, but “colored”, i.e., statistically correlated in time, and the friction force on the particles depends on the history of their motion. An efficient method of solving the resulting generalized Langevin equations is presented and applied to the solution of the equations of motion of polymer beads. The memory effects lead to several peculiarities in the time correlation functions used to describe the dynamics of polymer chains. So, the mean square displacement of the polymer coils contains algebraic long-time tails and at short times it is ballistic. It is shown how these features reveal in the experimentally observable quantities, such as the dynamic structure factors of the scattering or the viscosity of polymer solutions. A phenomenological theory is also presented that describes the dependence of these quantities on the polymer concentration in solution. (author)

Efficient Brownian Dynamics of rigid colloids in linear flow fields based on the grand mobility matrix

Science.gov (United States)

Palanisamy, Duraivelan; den Otter, Wouter K.

2018-05-01

We present an efficient general method to simulate in the Stokesian limit the coupled translational and rotational dynamics of arbitrarily shaped colloids subject to external potential forces and torques, linear flow fields, and Brownian motion. The colloid's surface is represented by a collection of spherical primary particles. The hydrodynamic interactions between these particles, here approximated at the Rotne-Prager-Yamakawa level, are evaluated only once to generate the body's (11 × 11) grand mobility matrix. The constancy of this matrix in the body frame, combined with the convenient properties of quaternions in rotational Brownian Dynamics, enables an efficient simulation of the body's motion. Simulations in quiescent fluids yield correct translational and rotational diffusion behaviour and sample Boltzmann's equilibrium distribution. Simulations of ellipsoids and spherical caps under shear, in the absence of thermal fluctuations, yield periodic orbits in excellent agreement with the theories by Jeffery and Dorrepaal. The time-varying stress tensors provide the Einstein coefficient and viscosity of dilute suspensions of these bodies.

Brownian gas models for extreme-value laws

International Nuclear Information System (INIS)

Eliazar, Iddo

2013-01-01

In this paper we establish one-dimensional Brownian gas models for the extreme-value laws of Gumbel, Weibull, and Fréchet. A gas model is a countable collection of independent particles governed by common diffusion dynamics. The extreme-value laws are the universal probability distributions governing the affine scaling limits of the maxima and minima of ensembles of independent and identically distributed one-dimensional random variables. Using the recently introduced concept of stationary Poissonian intensities, we construct two gas models whose global statistical structures are stationary, and yield the extreme-value laws: a linear Brownian motion gas model for the Gumbel law, and a geometric Brownian motion gas model for the Weibull and Fréchet laws. The stochastic dynamics of these gas models are studied in detail, and closed-form analytical descriptions of their temporal correlation structures, their topological phase transitions, and their intrinsic first-passage-time fluxes are presented. (paper)

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.

Static structure of active Brownian hard disks

Science.gov (United States)

de Macedo Biniossek, N.; Löwen, H.; Voigtmann, Th; Smallenburg, F.

2018-02-01

We explore the changes in static structure of a two-dimensional system of active Brownian particles (ABP) with hard-disk interactions, using event-driven Brownian dynamics simulations. In particular, the effect of the self-propulsion velocity and the rotational diffusivity on the orientationally-averaged fluid structure factor is discussed. Typically activity increases structural ordering and generates a structure factor peak at zero wave vector which is a precursor of motility-induced phase separation. Our results provide reference data to test future statistical theories for the fluid structure of active Brownian systems. This manuscript was submitted for the special issue of the Journal of Physics: Condensed Matter associated with the Liquid Matter Conference 2017.

Brownian entanglement

International Nuclear Information System (INIS)

Allahverdyan, A.E.; Khrennikov, A.; Nieuwenhuizen, Th.M.

2005-01-01

For two classical Brownian particles an analog of continuous-variable quantum entanglement is presented: The common probability distribution of the two coordinates and the corresponding coarse-grained velocities cannot always be prepared via mixing of any factorized distributions referring to the two particles separately. This is possible for particles which have interacted in the past, but do not interact at present. Three factors are crucial for the effect: (1) separation of time scales of coordinate and momentum which motivates the definition of coarse-grained velocities; (2) the resulting uncertainty relations between the coordinate of the Brownian particle and the change of its coarse-grained velocity; (3) the fact that the coarse-grained velocity, though pertaining to a single Brownian particle, is defined on a common context of two particles. The Brownian entanglement is a consequence of a coarse-grained description and disappears for a finer resolution of the Brownian motion. Analogies with the quantum situation are discussed, as well as possibilities of experimental realization of the effect in examples of macroscopic Brownian motion

Friction between Two Brownian Particles in a Lennard-Jones Solvent: A Molecular Dynamics Simulation Study

International Nuclear Information System (INIS)

Lee, Song Hi

2010-01-01

We presented a molecular dynamics (MD) simulation study of friction behavior between two very massive Brownian particles (BPs) oriented along the z axis with BP centers at -R 12 /2 and R 12 /2 in a Lennard-Jones solvent as a function of the inter-particle separation, R 12 . In order to fix the BPs in space an MD simulation method with the mass of the BP as 10 90 g/mol was employed in which the total momentum of the system was conserved. The cross friction coefficients of x- and y-components are nearly insensitive to R 12 but that of z-component varies with R 12 in good accord with the simple hydrodynamic approximation. On the other hand, the self-friction coefficients are estimated as a very small difference from the single particle friction coefficients, ξ 0 , at all inter-particle separations which agrees with the simple hydrodynamic approximation. Consequently ξ (-) xx is nearly independent of R 12 and equal to its asymptotic value of twice the single particle friction coefficient, and the other relative friction, ξ (-) zz , is in good agreement with the simple hydrodynamic approximation. Molecular theory of Brownian motion of a single heavy particle in a fluid had received a considerable attention in earlier years. After molecular dynamics (MD) simulation technique was utilized, this subject has been widely studied by a variety of MD simulation methods. The common issues here were about the long time behavior of the force and velocity autocorrelation functions, the system size dependent friction coefficient of a massive Brownian particle, and test of the Stokes-Einstein law

Hybrid finite element and Brownian dynamics method for charged particles

Energy Technology Data Exchange (ETDEWEB)

Huber, Gary A., E-mail: ghuber@ucsd.edu; Miao, Yinglong [Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365 (United States); Zhou, Shenggao [Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Suzhou, 215006 Jiangsu (China); Li, Bo [Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0112 (United States); McCammon, J. Andrew [Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093 (United States); Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365 (United States); Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States)

2016-04-28

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.

Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein.

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Anthony J Brzoska

Full Text Available Actin-like proteins (Alps are a diverse family of proteins whose genes are abundant in the chromosomes and mobile genetic elements of many bacteria. The low-copy-number staphylococcal multiresistance plasmid pSK41 encodes ParM, an Alp involved in efficient plasmid partitioning. pSK41 ParM has previously been shown to form filaments in vitro that are structurally dissimilar to those formed by other bacterial Alps. The mechanistic implications of these differences are not known. In order to gain insights into the properties and behavior of the pSK41 ParM Alp in vivo, we reconstituted the parMRC system in the ectopic rod-shaped host, E. coli, which is larger and more genetically amenable than the native host, Staphylococcus aureus. Fluorescence microscopy showed a functional fusion protein, ParM-YFP, formed straight filaments in vivo when expressed in isolation. Strikingly, however, in the presence of ParR and parC, ParM-YFP adopted a dramatically different structure, instead forming axial curved filaments. Time-lapse imaging and selective photobleaching experiments revealed that, in the presence of all components of the parMRC system, ParM-YFP filaments were dynamic in nature. Finally, molecular dissection of the parMRC operon revealed that all components of the system are essential for the generation of dynamic filaments.

Fatigue behaviour of core-spun yarns containing filament by means of cyclic dynamic loading

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Esin, S.; Osman, B.

2017-10-01

The behaviour of yarns under dynamic loading is important that leads to understand the growth characteristics which is exposed to repetitive loadings during usage of fabric made from these yarns. Fabric growth is undesirable property that originated from low resilience characteristics of fabric. In this study, the effects of the filament fineness and yarn linear density on fatigue behaviour of rigid-core spun yarns were determined. Cotton covered yarns containing different filament fineness of polyester (PET) draw textured yarns (DTY) (100d/36f, 100d/96f, 100d/144f, 100d/192f and 100d/333f) and yarn linear densities (37 tex, 30 tex, 25 tex and 21 tex) were manufactured by using a modified ring spinning system at the same spinning parameters. Repetitive loads were applied for 25 cycles at levels between 0.1 and 3 N. Dynamic modulus and dynamic strain of yarn samples were analyzed statistically. Results showed that filament fineness and yarn linear density have significance effect on dynamic modulus and dynamic strain after cyclic loading.

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

OpenAIRE

Cosseddu, Salvatore M.; Khovanov, Igor A.; 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 u...

Scaling of F-actin network rheology to probe single filament elasticity and dynamics.

Science.gov (United States)

Gardel, M L; Shin, J H; MacKintosh, F C; Mahadevan, L; Matsudaira, P A; Weitz, D A

2004-10-29

The linear and nonlinear viscoelastic response of networks of cross-linked and bundled cytoskeletal filaments demonstrates remarkable scaling with both frequency and applied prestress, which helps elucidate the origins of the viscoelasticity. The frequency dependence of the shear modulus reflects the underlying single-filament relaxation dynamics for 0.1-10 rad/sec. Moreover, the nonlinear strain stiffening of such networks exhibits a universal form as a function of prestress; this is quantitatively explained by the full force-extension relation of single semiflexible filaments.

Constructive role of Brownian motion: Brownian motors and Stochastic Resonance

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Hänggi, Peter

2005-03-01

Noise is usually thought of as the enemy of order rather as a constructive influence. For the phenomena of Stochastic Resonance [1] and Brownian motors [2], however, stochastic noise can play a beneficial role in enhancing detection and/or facilitating directed transmission of information in absence of biasing forces. Brownian motion assisted Stochastic Resonance finds useful applications in physical, technological, biological and biomedical contexts [1,3]. The basic principles that underpin Stochastic Resonance are elucidated and novel applications for nonlinear classical and quantum systems will be addressed. The presence of non-equilibrium disturbances enables to rectify Brownian motion so that quantum and classical objects can be directed around on a priori designed routes in biological and physical systems (Brownian motors). In doing so, the energy from the haphazard motion of (quantum) Brownian particles is extracted to perform useful work against an external load. This very concept together with first experimental realizations are discussed [2,4,5]. [1] L. Gammaitoni, P. Hä'nggi, P. Jung and F. Marchesoni, Stochastic Resonance, Rev. Mod. Phys. 70, 223 (1998).[2] R. D. Astumian and P. Hä'nggi, Brownian motors, Physics Today 55 (11), 33 (2002).[3] P. Hä'nggi, Stochastic Resonace in Physics and Biology, ChemPhysChem 3, 285 (2002).[4] H. Linke, editor, Special Issue on Brownian Motors, Applied Physics A 75, No. 2 (2002).[5] P. Hä'nggi, F. Marchesoni, F. Nori, Brownian motors, Ann. Physik (Leipzig) 14, xxx (2004); cond-mat/0410033.

Dynamics of fluid lines, sheets, filaments and membranes

International Nuclear Information System (INIS)

Coutris, N.

1988-01-01

We establish the dynamic equations of two types of fluid structures: 1) lines-filaments and 2) sheets-membranes. In the first part, we consider one-dimensional (line) and two-dimensional (sheet) fluid structures. The second part concerns the associated three- dimensional structures: filaments and membranes. In the third part, we establish the equations for thickened lines and thickened sheets. For that purpose, we introduce a thickness in the models of the first part. The fourth part concerns the thinning of the filament and the membrane. Then, by an asymptotic process, we deduce the corresponding equations from the equations of the second part in order to show the purely formal equivalence of the equations of the third and fourth parts. To obtain the equations, we make use of theorems whose proofs can be found in the appendices. The equations can be applied to many areas of interest: instabilities of liquid jets and liquid films, modelisation of interfaces between two different fluids as sheets or membranes, modelisation with the averaged equations over a cross section of single phase flows and two-phase flows in channels with a nonrectilinear axis such as bends or pump casings [fr

Wettability dynamics of liquid filaments on horizontal substrates

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Diez, Javier; Ravazzoli, Pablo; Cuellar, Ingrith; Gonzalez, Alejandro

2017-11-01

We study the hydrodynamic mechanisms involved in the motion of the contact line formed at the end region of a liquid filament laying on a planar and horizontal substrate. Since the flow develops under partially wetting conditions, the tip of the filament recedes and forms a bulged region (head) that subsequently develops a neck region behind it. Later the neck breaks up leading to a separated drop, while the rest of the filament restarts the sequence. One main feature of this flow is that the whole dynamics and final drop shapes are strongly influenced by the hysteresis of the contact angle typical in most of the liquid-substrate systems. The time evolution till breakup is studied experimentally and pictured in terms of a hybrid wettability theory which involves the Cox-Voinov hydrodynamic approach combined with the molecular kinetic theory developed by Blake. The parameters of this theory are determined for our liquid-substrate system (silicone oil ``coated glass). The experimental results of the retracting filament are described in terms of a simple heuristic model and compared with numerical simulations of the full Navier-Stokes equations. This study is of special interest in the context of pulsed laser-induced dewetting. The authors acknowledge support from Consejo Nacional de Investigaciones Cientficas y Tcnicas (CONICET, Argentina) with Grant PIP 844/2012 and Agencia Nacional de Promocin Cientfica y Tecnolgica (ANPCyT, Argentina) with Grant PICT 931/2012.

Brownian dynamics simulations of insulin microspheres formation

Science.gov (United States)

Li, Wei; Chakrabarti, Amit; Gunton, James

2010-03-01

Recent experiments have indicated a novel, aqueous process of microsphere insulin fabrication based on controlled phase separation of protein from water-soluble polymers. We investigate the insulin microsphere crystal formation from insulin-PEG-water systems via 3D Brownian Dynamics simulations. We use the two component Asakura-Oosawa model to simulate the kinetics of this colloid polymer mixture. We first perform a deep quench below the liquid-crystal boundary that leads to fractal formation. We next heat the system to obtain a break-up of the fractal clusters and subsequently cool the system to obtain a spherical aggregation of droplets with a relatively narrow size distribution. We analyze the structure factor S(q) to identify the cluster dimension. S(q) crosses over from a power law q dependence of 1.8 (in agreement with DLCA) to 4 as q increases, which shows the evolution from fractal to spherical clusters. By studying the bond-order parameters, we find the phase transition from liquid-like droplets to crystals which exhibit local HCP and FCC order. This work is supported by grants from the NSF and Mathers Foundation.

Large scale Brownian dynamics of confined suspensions of rigid particles

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Sprinkle, Brennan; Balboa Usabiaga, Florencio; Patankar, Neelesh A.; Donev, Aleksandar

2017-12-01

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose

Brownian Agents and Active Particles: Collective Dynamics in the Natural and Social Sciences

International Nuclear Information System (INIS)

McKane, Alan

2003-01-01

This is a book about the modelling of complex systems and, unlike many books on this subject, concentrates on the discussion of specific systems and gives practical methods for modelling and simulating them. This is not to say that the author does not devote space to the general philosophy and definition of complex systems and agent-based modelling, but the emphasis is definitely on the development of concrete methods for analysing them. This is, in my view, to be welcomed and I thoroughly recommend the book, especially to those with a theoretical physics background who will be very much at home with the language and techniques which are used. The author has developed a formalism for understanding complex systems which is based on the Langevin approach to the study of Brownian motion. This is a mesoscopic description; details of the interactions between the Brownian particle and the molecules of the surrounding fluid are replaced by a randomly fluctuating force. Thus all microscopic detail is replaced by a coarse-grained description which encapsulates the essence of the interactions at the finer level of description. In a similar way, the influences on Brownian agents in a multi-agent system are replaced by stochastic influences which sum up the effects of these interactions on a finer scale. Unlike Brownian particles, Brownian agents are not structureless particles, but instead have some internal states so that, for instance, they may react to changes in the environment or to the presence of other agents. Most of the book is concerned with developing the idea of Brownian agents using the techniques of statistical physics. This development parallels that for Brownian particles in physics, but the author then goes on to apply the technique to problems in biology, economics and the social sciences. This is a clear and well-written book which is a useful addition to the literature on complex systems. It will be interesting to see if the use of Brownian agents becomes

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.

Presentation of quantum Brownian movement in the collective coordinate method

International Nuclear Information System (INIS)

Oksak, A.I.; Sukhanov, A.D.

2003-01-01

Two explicitly solved models of quantum randomized processes described by the Langevin equation, i. e. a free quantum Brownian particle and a quantum Brownian harmonic oscillator, are considered. The Hamiltonian (string) realization of the models reveals soliton-like structure of classical solutions. Accordingly, the method of zero mode collective coordinate is an adequate means for describing the models quantum dynamics [ru

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.

From a stochastic to a macroscopic approach to brownian motion

International Nuclear Information System (INIS)

Bocquet, L.

1998-01-01

In this lecture, we examine the dynamics of suspensions of mesoscopic (Brownian) particles in a molecular fluid, starting from first principles. We introduce the technique of multiple time-scales to derive the Fokker-Planck equation for a single, or for a set of interacting Brownian particles, starting from the Liouville equation for the full system (Brownian particles and discrete bath). The limitations of the Fokker-Planck equation will then be emphasized. In particular, we shall point out that under ''standard'' experimental conditions, the Fokker-Planck description cannot be correct and that non-Markovian effects are expected. A microscopic description in the true experimental limit confirms this breakdown and leads to a ''generalized'' (non-Markovian and non-local in velocity space) Fokker-Planck equation, which describes the thermalization of the Brownian particle. (author)

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

Science.gov (United States)

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

2011-08-01

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

Analyzing animal movements using Brownian bridges.

Science.gov (United States)

Horne, Jon S; Garton, Edward O; Krone, Stephen M; Lewis, Jesse S

2007-09-01

By studying animal movements, researchers can gain insight into many of the ecological characteristics and processes important for understanding population-level dynamics. We developed a Brownian bridge movement model (BBMM) for estimating the expected movement path of an animal, using discrete location data obtained at relatively short time intervals. The BBMM is based on the properties of a conditional random walk between successive pairs of locations, dependent on the time between locations, the distance between locations, and the Brownian motion variance that is related to the animal's mobility. We describe two critical developments that enable widespread use of the BBMM, including a derivation of the model when location data are measured with error and a maximum likelihood approach for estimating the Brownian motion variance. After the BBMM is fitted to location data, an estimate of the animal's probability of occurrence can be generated for an area during the time of observation. To illustrate potential applications, we provide three examples: estimating animal home ranges, estimating animal migration routes, and evaluating the influence of fine-scale resource selection on animal movement patterns.

Dynamics of a Brownian particle in a plasma in the long-time limit

International Nuclear Information System (INIS)

Dickman, R.; Varley, R.L.

1981-01-01

The velocity autocorrelation function (VAF) of a Brownian particle in a plasma is calculated in the long-time limit. The Brownian particle VAF exhibits the same qualitative behavior as the electron VAF in a one-component plasma: oscillations at the plasma frequency and decay approx. t -3 sup(/) 2 . (orig.)

Conception of Brownian coil

OpenAIRE

Zhang, Jiayuan

2018-01-01

This article proposes a conception of Brownian coil. Brownian coil is a tiny coil with the same size of pollen. Once immersed into designed magnetic field and liquid, the coil will be moved and deformed macroscopically, due to the microscopic thermodynamic molecular collisions. Such deformation and movement will change the magnetic flux through the coil, by which an ElectroMotive Force (EMF) is produced. In this work, Brownian heat exchanger and Brownian generator are further designed to tran...

Myosin isoform determines the conformational dynamics and cooperativity of actin filaments in the strongly bound actomyosin complex

Science.gov (United States)

Prochniewicz, Ewa; Chin, Harvey F.; Henn, Arnon; Hannemann, Diane E.; Olivares, Adrian O.; Thomas, David D.; De La Cruz, Enrique M.

2010-01-01

SUMMARY We have used transient phosphorescence anisotropy (TPA) to detect the microsecond rotational dynamics of erythrosin iodoacetamide (ErIA)-labeled actin strongly bound to single-headed fragments of muscle myosin (muscle S1) and non-muscle myosin V (MV). The conformational dynamics of actin filaments in solution are markedly influenced by the isoform of bound myosin. Both myosins increase the final anisotropy of actin at sub-stoichiometric binding densities, indicating long-range, non-nearest neighbor cooperative restriction of filament rotational dynamics amplitude, but the cooperative unit is larger with MV than muscle S1. Both myosin isoforms also cooperatively affect the actin filament rotational correlation time, but with opposite effects; muscle S1 decreases rates of intrafilament torsional motion, while binding of MV increases the rates of motion. The cooperative effects on the rates of intrafilament motions correlate with the kinetics of myosin binding to actin filaments such that MV binds more rapidly, and muscle myosin more slowly, to partially decorated filaments than to bare filaments. The two isoforms also differ in their effects on the phosphorescence lifetime of the actin-bound ErIA; while muscle S1 increases the lifetime, suggesting decreased aqueous exposure of the probe, MV does not induce a significant change. We conclude that the dynamics and structure of actin in the strongly bound actomyosin complex is determined by the isoform of the bound myosin, in a manner likely to accommodate the diverse functional roles of actomyosin in muscle and non-muscle cells. PMID:19962990

Nuclear resonant scattering of synchrotron radiation from nuclei in the Brownian motion

International Nuclear Information System (INIS)

Razdan, Ashok

2003-01-01

The time evolution of the coherent forward scattering of the synchrotron radiation for resonant nuclei in Brownian motion is studied. Apart from target thickness, the appearance of the dynamical beats also depends on 'α' which is the ratio of the harmonic force constant to the damping force constant of harmonic oscillator undergoing Brownian motion

Brownian motion in short range random potentials

International Nuclear Information System (INIS)

Romero, A.H.; Romero, A.H.; Sancho, J.M.

1998-01-01

A numerical study of Brownian motion of noninteracting particles in random potentials is presented. The dynamics are modeled by Langevin equations in the high friction limit. The random potentials are Gaussian distributed and short ranged. The simulations are performed in one and two dimensions. Different dynamical regimes are found and explained. Effective subdiffusive exponents are obtained and commented on. copyright 1998 The American Physical Society

On the Brownian motion of a massive sphere suspended in a hard-sphere fluid. II. Molecular dynamics estimates of the friction coefficient

International Nuclear Information System (INIS)

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

1994-01-01

The friction coefficient γ exerted by a hard-sphere fluid on an infinitely massive Brownian sphere is calculated for several size ratios Σ/σ where Σ and σ are the diameters of the Brownian and fluid spheres, respectively. The exact microscopic expression derived in part I of this work from kinetic theory is transformed and shown to be proportional to the time integral of the autocorrelation function of the momentum transferred from the fluid to the Brownian sphere during instantaneous collisions. Three different methods are described to extract the friction coefficient from molecular dynamics simulations carried out on finite systems. The three independent methods lead to estimates of γ which agree within statistical errors (typically 5%). The results are compared to the predictions of Enskog theory and of the hydrodynamic Stokes law. The former breaks down as the size ratio and/or the packing fraction of the fluid increase. Somewhat surprisingly, Stokes' law is found to hold with stick boundary conditions, in the range 1 ≤ Σ/σ ≤ 4.5 explored in the present simulations, with a hydrodynamic diameter d=Σ. The analysis of the molecular dynamics data on the basis of Stokes' law with slip boundary conditions is less conclusive, although the right trend is found as Σ/σ increases

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

Science.gov (United States)

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

2018-02-01

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

Brownian modulated optical nanoprobes

International Nuclear Information System (INIS)

Behrend, C.J.; Anker, J.N.; Kopelman, R.

2004-01-01

Brownian modulated optical nanoprobes (Brownian MOONs) are fluorescent micro- and nanoparticles that resemble moons: one hemisphere emits a bright fluorescent signal, while an opaque metal darkens the other hemisphere. Brownian motion causes the particles to tumble and blink erratically as they rotate literally through the phases of the moon. The fluctuating probe signals are separated from optical and electronic backgrounds using principal components analysis or images analysis. Brownian MOONs enable microrheological measurements on size scales and timescales that are difficult to study with other methods. Local chemical concentrations can be measured simultaneously, using spectral characteristics of indicator dyes embedded within the MOONs

Interacting Brownian Swarms: Some Analytical Results

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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.

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores.

Science.gov (United States)

McMullen, Angus; de Haan, Hendrick W; Tang, Jay X; Stein, Derek

2018-02-16

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force. We present a scaling theory that connects the solid mechanics to the nonlinear dynamics of polyelectrolytes translocating nanopores.

The circulation dynamics associated with a northern Benguela upwelling filament during October 2010

Science.gov (United States)

Muller, Annethea A.; Mohrholz, Volker; Schmidt, Martin

2013-07-01

Upwelling filaments, a common feature in all the major upwelling systems, are also regularly observed in the Benguela upwelling system and are thought to provide an effective mechanism for the exchange of matter between the shelf and the open ocean. The mesoscale dynamics of a northern Benguela upwelling filament located at approximately 18.5°S were examined and the associated transport was quantified. The development of the filament was tracked using optimal interpolated SST satellite data and two transects were consequently sampled across the feature using a towed undulating CTD (ScanFish). Additional hydrographic, nutrient and biological parameters were investigated at several stations along each transect. Following 7 days of strong upwelling favorable winds, sampling coincided with a period of relative wind relaxation and the filament was presumably in a decaying state. The basic mesoscale structure of the investigated filament corresponded well to what had previously been described for filaments from other eastern boundary current systems. The cross-shore transport associated with the filament was found to be significantly greater than the integrated Ekman transport in the region. With the combination of the high resolution dataset and a MOM-4 ecosystem model the complex mesoscale flow field associated with the feature could be observed and the counterbalancing onshore transport, associated with subsurface dipole eddies, was revealed within the filament. The results further suggest that an interaction between the offshore bending of flow at the Angola-Benguela Front (ABF), the detachment of the strong poleward flow from the coast as the thermal front meanders and the observed dipole eddies may be driving filament occurrence in the region off Cape Frio.

Biased and flow driven Brownian motion in periodic channels

Science.gov (United States)

Martens, S.; Straube, A.; Schmid, G.; Schimansky-Geier, L.; Hänggi, P.

2012-02-01

In this talk we will present an expansion of the common Fick-Jacobs approximation to hydrodynamically as well as by external forces driven Brownian transport in two-dimensional channels exhibiting smoothly varying periodic cross-section. We employ an asymptotic analysis to the components of the flow field and to stationary probability density for finding the particles within the channel in a geometric parameter. We demonstrate that the problem of biased Brownian dynamics in a confined 2D geometry can be replaced by Brownian motion in an effective periodic one-dimensional potential ψ(x) which takes the external bias, the change of the local channel width, and the flow velocity component in longitudinal direction into account. In addition, we study the influence of the external force magnitude, respectively, the pressure drop of the fluid on the particle transport quantities like the averaged velocity and the effective diffusion coefficient. The critical ratio between the external force and pressure drop where the average velocity equals zero is identified and the dependence of the latter on the channel geometry is derived. Analytic findings are confirmed by numerical simulations of the particle dynamics in a reflection symmetric sinusoidal channel.

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Science.gov (United States)

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

2010-04-01

Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking" interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

Intrinsic and extrinsic measurement for Brownian motion

International Nuclear Information System (INIS)

Castro-Villarreal, Pavel

2014-01-01

Based upon the Smoluchowski equation on curved manifolds, three physical observables are considered for Brownian displacement, namely geodesic displacement s, Euclidean displacement δR, and projected displacement δR ⊥ . The Weingarten–Gauss equations are used to calculate the mean-square Euclidean displacements in the short-time regime. Our findings show that from an extrinsic point of view the geometry of the space affects the Brownian motion in such a way that the particle’s diffusion is decelerated, contrasting with the intrinsic point of view where dynamics is controlled by the sign of the Gaussian curvature (Castro-Villarreal, 2010 J. Stat. Mech. P08006). Furthermore, it is possible to give exact formulas for 〈δR〉 and 〈δR 2 〉 on spheres and minimal surfaces, which are valid for all values of time. In the latter case, surprisingly, Brownian motion corresponds to the usual diffusion in flat geometries, albeit minimal surfaces have non-zero Gaussian curvature. Finally, the two-dimensional case is emphasized due to its close relation to surface self-diffusion in fluid membranes. (paper)

Deterministic Brownian motion generated from differential delay equations.

Science.gov (United States)

Lei, Jinzhi; Mackey, Michael C

2011-10-01

This paper addresses the question of how Brownian-like motion can arise from the solution of a deterministic differential delay equation. To study this we analytically study the bifurcation properties of an apparently simple differential delay equation and then numerically investigate the probabilistic properties of chaotic solutions of the same equation. Our results show that solutions of the deterministic equation with randomly selected initial conditions display a Gaussian-like density for long time, but the densities are supported on an interval of finite measure. Using these chaotic solutions as velocities, we are able to produce Brownian-like motions, which show statistical properties akin to those of a classical Brownian motion over both short and long time scales. Several conjectures are formulated for the probabilistic properties of the solution of the differential delay equation. Numerical studies suggest that these conjectures could be "universal" for similar types of "chaotic" dynamics, but we have been unable to prove this.

Quantum Brownian motion model for the stock market

Science.gov (United States)

Meng, Xiangyi; Zhang, Jian-Wei; Guo, Hong

2016-06-01

It is believed by the majority today that the efficient market hypothesis is imperfect because of market irrationality. Using the physical concepts and mathematical structures of quantum mechanics, we construct an econophysical framework for the stock market, based on which we analogously map massive numbers of single stocks into a reservoir consisting of many quantum harmonic oscillators and their stock index into a typical quantum open system-a quantum Brownian particle. In particular, the irrationality of stock transactions is quantitatively considered as the Planck constant within Heisenberg's uncertainty relationship of quantum mechanics in an analogous manner. We analyze real stock data of Shanghai Stock Exchange of China and investigate fat-tail phenomena and non-Markovian behaviors of the stock index with the assistance of the quantum Brownian motion model, thereby interpreting and studying the limitations of the classical Brownian motion model for the efficient market hypothesis from a new perspective of quantum open system dynamics.

Brownian dynamics simulations of an order-disorder transition in sheared sterically stabilized colloidal suspensions

International Nuclear Information System (INIS)

Rigos, A.A.; Wilemski, G.

1992-01-01

The shear thinning behavior of a sterically stabilized nonaqueous colloidal suspension was investigated using nonequilibrium Brownian dynamics simulations of systems with 108 and 256 particles. At a volume fraction of 0.4, the suspension is thixotropic: it has a reversible shear thinning transition from a disordered state to an ordered, lamellar state with triangularly packed strings of particles. The time scale for the transition is set by the free particle diffusion constant. For the smaller system, the transition occurs gradually with increasing shear rate. For the larger system, the transition is sharp and discontinuous shear thinning is found. 34 refs., 9 figs., 1 tab

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

Science.gov (United States)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

International Nuclear Information System (INIS)

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

2010-01-01

Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking” interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon. (cross-disciplinary physics and related areas of science and technology)

Eigenfunction statistics of Wishart Brownian ensembles

International Nuclear Information System (INIS)

Shukla, Pragya

2017-01-01

We theoretically analyze the eigenfunction fluctuation measures for a Hermitian ensemble which appears as an intermediate state of the perturbation of a stationary ensemble by another stationary ensemble of Wishart (Laguerre) type. Similar to the perturbation by a Gaussian stationary ensemble, the measures undergo a diffusive dynamics in terms of the perturbation parameter but the energy-dependence of the fluctuations is different in the two cases. This may have important consequences for the eigenfunction dynamics as well as phase transition studies in many areas of complexity where Brownian ensembles appear. (paper)

On the Generalized Brownian Motion and its Applications in Finance

DEFF Research Database (Denmark)

Høg, Esben; Frederiksen, Per; Schiemert, Daniel

This paper deals with dynamic term structure models (DTSMs) and proposes a new way to handle the limitation of the classical affine models. In particular, the paper expands the exibility of the DTSMs by applying generalized Brownian motions with dependent increments as the governing force...... of the state variables instead of standard Brownian motions. This is a new direction in pricing non defaultable bonds. By extending the theory developed by Dippon & Schiemert (2006a), the paper developes a bond market with memory, and proves the absence of arbitrage. The framework is readily extendable...

Relaxation property of the fractional Brownian particle

International Nuclear Information System (INIS)

Wang Litan; Lung, C.W.

1988-08-01

Dynamic susceptibility of a diffusion system associated with the fractional Brownian motion (fBm) was examined for the fractal property of the Non-Debye relaxation process. The comparisons between fBm and other approaches were made. Anomalous diffusion and the Non-Debye relaxation processes were discussed with this approach. (author). 8 refs, 1 fig

The structure and dynamics of blob filaments in the stellarator TJ-K

Energy Technology Data Exchange (ETDEWEB)

Garland, Stephen; Ramisch, Mirko [Institut fuer Grenzflaechenverfahrenstechnik und Plasmatechnologie, Universitaet Stuttgart (Germany); Fuchert, Golo [Max-Planck-Institut fuer Plasmaphysik, Greifswald (Germany)

2016-07-01

Filamental structures with higher pressure than the background plasma are commonly observed in the scrape-off layer (SOL) of toroidal magnetic confinement devices. These structures, often referred to as blobs, propagate radially outwards and poloidally, contributing significantly to SOL transport. It is therefore important to study the properties of blobs in order to be able to predict heat loads on the plasma facing components of future reactors, as well as to better understand particle transport and plasma confinement. Detailed experiments have been carried out into blob dynamics and structure using Langmuir probes at the stellarator TJ-K. By means of the conditional averaging technique, blob dynamics in a poloidal cross section have been studied, and the influence of geodesic curvature on poloidal blob drive are shown. In addition, the result of simultaneous measurements at two toroidally separated locations is presented, providing information on the 3D structure of blob filaments and their alignment to the magnetic field as they propagate through the SOL.

Dynamics of actin cables in polarized growth of the filamentous fungus Aspergillus nidulans

Directory of Open Access Journals (Sweden)

Anna eBergs

2016-05-01

Full Text Available Highly polarized growth of filamentous fungi requires a continuous supply of proteins and lipids to the hyphal tip. This transport is managed by vesicle trafficking via the actin and microtubule cytoskeletons and their associated motor proteins. Particularly, actin cables originating from the hyphal tip are essential for hyphal growth. Although specific marker proteins to visualize actin cables have been developed in filamentous fungi, the exact organization and dynamics of actin cables has remained elusive. Here we visualized actin cables using tropomyosin (TpmA and Lifeact fused to fluorescent proteins in Aspergillus nidulans and studied the dynamics and regulation. GFP tagged TpmA visualized dynamic actin cables formed from the hyphal tip with cycles of elongation and shrinkage. The elongation and shrinkage rates of actin cables were similar and approximately 0.6 μm/s. Comparison of actin markers revealed that high concentrations of Lifeact reduced actin dynamics. Simultaneous visualization of actin cables and microtubules suggests temporally and spatially coordinated polymerization and depolymerization between the two cytoskeletons. Our results provide new insights into the molecular mechanism of ordered polarized growth regulated by actin cables and microtubules.

Achieving swift equilibration of a Brownian particle using flow-fields

Science.gov (United States)

Patra, Ayoti; Jarzynski, Christopher

Can a system be driven to a targeted equilibrium state on a timescale that is much shorter than its natural equilibration time? In a recent experiment, the swift equilibration of an overdamped Brownian particle was achieved by use of an appropriately designed, time-dependent optical trap potential. Motivated by these results, we develop a general theoretical approach for guiding an ensemble of Brownian particles to track the instantaneous equilibrium distribution of a desired potential U (q , t) . In our approach, we use flow-fields associated with the parametric evolution of the targeted equilibrium state to construct an auxiliary potential U (q , t) , such that dynamics under the composite potential U (t) + U (t) achieves the desired evolution. Our results establish a close connection between the swift equilibration of Brownian particles, quantum shortcuts to adiabaticity, and the dissipationless driving of a classical, Hamiltonian system.

Cosmophysical Factors in the Fluctuation Amplitude Spectrum of Brownian Motion

Directory of Open Access Journals (Sweden)

Kaminsky A. V.

2010-04-01

Full Text Available Phenomenon of the regular variability of the fine structure of the fluctuation in the amplitude distributions (shapes of related histograms for the case of Brownian motion was investigated. We took an advantage of the dynamic light scattering method (DLS to get a stochastically fluctuated signal determined by Brownian motion. Shape of the histograms is most likely to vary, synchronous, in two proximally located independent cells containing Brownian particles. The synchronism persists in the cells distant at 2m from each other, and positioned meridionally. With a parallel-wise positioning of the cells, high probability of the synchronous variation in the shape of the histograms by local time has been observed. This result meets the previous conclusion about the dependency of histogram shapes ("fluctuation amplitudes" of the spectra of stochastic processes upon rotation of the Earth.

Cosmophysical Factors in the Fluctuation Amplitude Spectrum of Brownian Motion

Directory of Open Access Journals (Sweden)

Kaminsky A. V.

2010-07-01

Full Text Available Phenomenon of the regular variability of the fine structure of the fluctuation in the am- plitude distributions (shapes of related histograms for the case of Brownian motion was investigated. We took an advantage of the dynamic light scattering method (DLS to get a stochastically fluctuated signal determined by Brownian motion. Shape of the histograms is most likely to vary, synchronous, in two proximally located independent cells containing Brownian particles. The synchronism persists in the cells distant at 2 m from each other, and positioned meridionally. With a parallel-wise positioning of the cells, high probability of the synchronous variation in the shape of the histograms by local time has been observed. This result meets the previous conclusion about the dependency of histogram shapes (“fluctuation amplitudes” of the spectra of stochastic processes upon rotation of the Earth.

Studying protein assembly with reversible Brownian dynamics of patchy particles

International Nuclear Information System (INIS)

Klein, Heinrich C. R.; Schwarz, Ulrich S.

2014-01-01

Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

Studying protein assembly with reversible Brownian dynamics of patchy particles

Energy Technology Data Exchange (ETDEWEB)

Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

2014-05-14

Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

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

A multiscale guide to Brownian motion

International Nuclear Information System (INIS)

Grebenkov, Denis S; Belyaev, Dmitry; Jones, Peter W

2016-01-01

We revise the Lévy construction of Brownian motion as a simple though rigorous approach to operate with various Gaussian processes. A Brownian path is explicitly constructed as a linear combination of wavelet-based ‘geometrical features’ at multiple length scales with random weights. Such a wavelet representation gives a closed formula mapping of the unit interval onto the functional space of Brownian paths. This formula elucidates many classical results about Brownian motion (e.g., non-differentiability of its path), providing an intuitive feeling for non-mathematicians. The illustrative character of the wavelet representation, along with the simple structure of the underlying probability space, is different from the usual presentation of most classical textbooks. Similar concepts are discussed for the Brownian bridge, fractional Brownian motion, the Ornstein-Uhlenbeck process, Gaussian free fields, and fractional Gaussian fields. Wavelet representations and dyadic decompositions form the basis of many highly efficient numerical methods to simulate Gaussian processes and fields, including Brownian motion and other diffusive processes in confining domains. (topical review)

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.

Multi-Dielectric Brownian Dynamics and Design-Space-Exploration Studies of Permeation in Ion Channels.

Science.gov (United States)

Siksik, May; Krishnamurthy, Vikram

2017-09-01

This paper proposes a multi-dielectric Brownian dynamics simulation framework for design-space-exploration (DSE) studies of ion-channel permeation. The goal of such DSE studies is to estimate the channel modeling-parameters that minimize the mean-squared error between the simulated and expected "permeation characteristics." To address this computational challenge, we use a methodology based on statistical inference that utilizes the knowledge of channel structure to prune the design space. We demonstrate the proposed framework and DSE methodology using a case study based on the KcsA ion channel, in which the design space is successfully reduced from a 6-D space to a 2-D space. Our results show that the channel dielectric map computed using the framework matches with that computed directly using molecular dynamics with an error of 7%. Finally, the scalability and resolution of the model used are explored, and it is shown that the memory requirements needed for DSE remain constant as the number of parameters (degree of heterogeneity) increases.

Polymer dynamics driven by a helical filament

Science.gov (United States)

Balin, Andrew; Shendruk, Tyler; Zoettl, Andreas; Yeomans, Julia

Microbial flagellates typically inhabit complex suspensions of extracellular polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better understand how the fundamental dynamics of polymers near active cells or flagella impacts these various phenomena. We study the hydrodynamic and steric influence of a rotating helical filament on suspended polymers using Stokesian Dynamics simulations. Our results show that as a stationary rotating helix pumps fluid along its long axis, nearby polymers migrate radially inwards and are elongated in the process. We observe that the actuation of the helix tends to increase the probability of finding polymeric material within its pervaded volume. At larger Weissenberg numbers, this accumulation of polymers within the vicinity of the helix is greater. Further, we have analysed the stochastic work performed by the helix on the polymers and we show that this quantity is positive on average and increases with polymer contour length. Our results provide a basis for understanding the microscopic interactions that govern cell dynamics in complex media. This work was supported through funding from the ERC Advanced Grant 291234 MiCE and we acknowledge EMBO funding to TNS (ALTF181-2013).

Biophysics of filament length regulation by molecular motors

International Nuclear Information System (INIS)

Kuan, Hui-Shun; Betterton, M D

2013-01-01

Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells. (paper)

Hydrodynamic interactions induce movement against an external load in a ratchet dimer Brownian motor.

Science.gov (United States)

Fornés, José A

2010-01-15

We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of a elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in our system were the load, the random thermal noise and an unbiased thermal fluctuation. For a given set of parameters we observe direct movement against the load force if hydrodynamic interactions were considered.

Financial Brownian Particle in the Layered Order-Book Fluid and Fluctuation-Dissipation Relations

Science.gov (United States)

Yura, Yoshihiro; Takayasu, Hideki; Sornette, Didier; Takayasu, Misako

2014-03-01

We introduce a novel description of the dynamics of the order book of financial markets as that of an effective colloidal Brownian particle embedded in fluid particles. The analysis of comprehensive market data enables us to identify all motions of the fluid particles. Correlations between the motions of the Brownian particle and its surrounding fluid particles reflect specific layering interactions; in the inner layer the correlation is strong and with short memory, while in the outer layer it is weaker and with long memory. By interpreting and estimating the contribution from the outer layer as a drag resistance, we demonstrate the validity of the fluctuation-dissipation relation in this nonmaterial Brownian motion process.

Swarming behavior of gradient-responsive Brownian particles in a porous medium

Science.gov (United States)

Grančič, Peter; Štěpánek, František

2012-07-01

Active targeting by Brownian particles in a fluid-filled porous environment is investigated by computer simulation. The random motion of the particles is enhanced by diffusiophoresis with respect to concentration gradients of chemical signals released by the particles in the proximity of a target. The mathematical model, based on a combination of the Brownian dynamics method and a diffusion problem is formulated in terms of key parameters that include the particle diffusiophoretic mobility and the signaling threshold (the distance from the target at which the particles release their chemical signals). The results demonstrate that even a relatively simple chemical signaling scheme can lead to a complex collective behavior of the particles and can be a very efficient way of guiding a swarm of Brownian particles towards a target, similarly to the way colonies of living cells communicate via secondary messengers.

O'Connell's process as a vicious Brownian motion

International Nuclear Information System (INIS)

Katori, Makoto

2011-01-01

Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of the quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.

Browndye: A software package for Brownian dynamics

Science.gov (United States)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

Treadmilling of actin filaments via Brownian dynamics simulations

DEFF Research Database (Denmark)

Guo, Kunkun; Shillcock, Julian C.; Lipowsky, Reinhard

2010-01-01

. For concentrations close to the critical concentration CT = CT,cr, the filaments undergo treadmilling, i.e., they grow at the barbed and shrink at the pointed end, which leads to directed translational motion of the whole filament. The corresponding nonequilibrium states are characterized by several global fluxes...

The Brownian loop soup

OpenAIRE

Lawler, Gregory F.; Werner, Wendelin

2003-01-01

We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.

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.

Quantal Brownian Motion from RPA dynamics: The master and Fokker-Planck equations

International Nuclear Information System (INIS)

Yannouleas, C.

1984-05-01

From the purely quantal RPA description of the damped harmonic oscillator and of the corresponding Brownian Motion within the full space (phonon subspace plus reservoir), a master equation (as well as a Fokker-Planck equation) for the reduced density matrix (for the reduced Wigner function, respectively) within the phonon subspace is extracted. The RPA master equation agrees with the master equation derived by the time-dependent perturbative approaches which utilize Tamm-Dancoff Hilbert spaces and invoke the rotating wave approximation. Since the RPA yields a full, as well as a contracted description, it can account for both the kinetic and the unperturbed oscillator momenta. The RPA description of the quantal Brownian Motion contrasts with the descriptions provided by the time perturbative approaches whether they invoke or not the rotating wave approximation. The RPA description also contrasts with the phenomenological phase space quantization. (orig.)

Brownian dynamics of self-regulated particles with additional degrees of freedom: Symmetry breaking and homochirality

Science.gov (United States)

Bhattacharyya, Debankur; Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

2018-04-01

We consider the Brownian motion of a collection of particles each with an additional degree of freedom. The degree of freedom of a particle (or, in general, a molecule) can assume distinct values corresponding to certain states or conformations. The time evolution of the additional degree of freedom of a particle is guided by those of its neighbors as well as the temperature of the system. We show that the local averaging over these degrees of freedom results in emergence of a collective order in the dynamics in the form of selection or dominance of one of the isomers leading to a symmetry-broken state. Our statistical model captures the basic features of homochirality, e.g., autocatalysis and chiral inhibition.

Dynamic Regulation of Sarcomeric Actin Filaments in Striated Muscle

OpenAIRE

Ono, Shoichiro

2010-01-01

In striated muscle, the actin cytoskeleton is differentiated into myofibrils. Actin and myosin filaments are organized in sarcomeres and specialized for producing contractile forces. Regular arrangement of actin filaments with uniform length and polarity is critical for the contractile function. However, the mechanisms of assembly and maintenance of sarcomeric actin filaments in striated muscle are not completely understood. Live imaging of actin in striated muscle has revealed that actin sub...

q-deformed Brownian motion

CERN Document Server

Man'ko, V I

1993-01-01

Brownian motion may be embedded in the Fock space of bosonic free field in one dimension.Extending this correspondence to a family of creation and annihilation operators satisfying a q-deformed algebra, the notion of q-deformation is carried from the algebra to the domain of stochastic processes.The properties of q-deformed Brownian motion, in particular its non-Gaussian nature and cumulant structure,are established.

The L1495-B218 filaments in Taurus seen in NH3 & CCS and Dynamical Stability of Filaments and Dense Cores

Science.gov (United States)

Seo, Youngmin

2016-01-01

We present deep NH3 map of L1495-B218 filaments and the dense cores embedded within the filaments in Taurus. The L1495-B218 filaments form an interconnected, nearby, large complex extending 8 pc. We observed the filaments in NH3 (1,1) & (2,2) and CCS 21-10 with spectral resolution of 0.038 km/s and spatial resolution of 31". The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithm, identifies 39 leaves and 16 branches in NH3 (1,1). Applying a virial analysis for the 39 NH3 leaves, we find only 9 out of 39 leaves are gravitationally bound, and 12 out of 30 gravitationally unbound leaves are pressure-confined. Our analysis suggests that a dense core may form as a pressure-confined structure, evolve to a gravitationally bound core, and then undergo collapse to form a protostar (Seo et al. 2015).We also present more realistic dynamic stability conditions for dense cores with converging motions and under the influence of radiation pressure. The critical Bonnor-Ebert sphere and the isothermal cylinder have been widely used to test stability of dense cores and filaments; however, these assume a quiescent environment while actual star forming regions are turbulent and illuminated by radiation. In a new analysis of stability conditions we account for converging motions which have been modeled toward starless cores (Seo et al. 2011) and the effect of radiation fields into account. We find that the critical size of a dense core having a homologous converging motion with its peak speed being the sound speed is roughly half of the critical size of the Bonnor-Ebert sphere (Seo et al. 2013). We also find that the critical mass/line density of a dense core/filament irradiated by radiation are considerably smaller than that of the Bonnor-Ebert sphere/isothermal cylinder when the radiation pressure is stronger than the central gas pressure of dense core/isothermal cylinder. For inner Galactic regions and regions near OB associations, the critical

Non-Markovian quantum Brownian motion in one dimension in electric fields

Science.gov (United States)

Shen, H. Z.; Su, S. L.; Zhou, Y. H.; Yi, X. X.

2018-04-01

Quantum Brownian motion is the random motion of quantum particles suspended in a field (or an effective field) resulting from their collision with fast-moving modes in the field. It provides us with a fundamental model to understand various physical features concerning open systems in chemistry, condensed-matter physics, biophysics, and optomechanics. In this paper, without either the Born-Markovian or rotating-wave approximation, we derive a master equation for a charged-Brownian particle in one dimension coupled with a thermal reservoir in electric fields. The effect of the reservoir and the electric fields is manifested as time-dependent coefficients and coherent terms, respectively, in the master equation. The two-photon correlation between the Brownian particle and the reservoir can induce nontrivial squeezing dynamics to the particle. We derive a current equation including the source from the driving fields, transient current from the system flowing into the environment, and the two-photon current caused by the non-rotating-wave term. The presented results then are compared with that given by the rotating-wave approximation in the weak-coupling limit, and these results are extended to a more general quantum network involving an arbitrary number of coupled-Brownian particles. The presented formalism might open a way to better understand exactly the non-Markovian quantum network.

[Dynamics of a vortex with the U-shaped filament in the heart of a ground squirrel].

Science.gov (United States)

Kukushkin, N I; Gorbacheva, K N; Sklifas, A N

2009-01-01

The dynamics of an electrical scroll wave with the U-shaped filament with both ends of the filament being "anchored" on the endocardial surface and the dependence of the structure of pseudoECG on the dynamics of the vortex during the development of polymorphic tachysystolia have been studied by applying premature stimuli to the "target phase" with subsequent registration of the spatial and temporal distribution of electrical potential throughout the surface (endocardial and epicardial) of a thin (approximately 1 mm) preparation. It was found that (1) the psedoECG of the polymorphic form during the tachysystolia attack can be observed in the case that the position of the filament ends on the surfaces of the preparation does not practically change from turn to turn (filament ends are "anchored"); (2) the thread of a scroll wave during this attack can twist and untwin (twisted filament), just as it was the case for scroll waves with a straight filament; (3) in the case of pseudoECG of polymorphic form, the twisting and untwining of the filament were stronger (the angle of maximal twisting was 120 degrees and more), and the angle of twisting changed by a substantially greater value from turn to turn as compared with the pseudoECG of monomorphic form; (4) in the case of pseudoECG of polymorphic form, the time interval between the appearance of waves on the surfaces of the preparation (Tepi-endo) was substantially greater and changed to a greater extent from turn to turn of the vortex; and (5) simultaneously with the appearance of pseudoECG of polymorphic form and the onset of changes in the twisting of the scroll and the Tepi-endo interval indicated in (2-4), significant changes in the patterns of coverage of the surface by excitation occurred. Based on the results obtained, an explanation of the reasons for the appearance of excitation breakdown patterns on the surface of the myocardium was proposed, which differs from the traditional viewpoint. These patterns may be

Langevin theory of anomalous Brownian motion made simple

International Nuclear Information System (INIS)

Tothova, Jana; Vasziova, Gabriela; Lisy, VladimIr; Glod, Lukas

2011-01-01

During the century from the publication of the work by Einstein (1905 Ann. Phys. 17 549) Brownian motion has become an important paradigm in many fields of modern science. An essential impulse for the development of Brownian motion theory was given by the work of Langevin (1908 C. R. Acad. Sci., Paris 146 530), in which he proposed an 'infinitely more simple' description of Brownian motion than that by Einstein. The original Langevin approach has however strong limitations, which were rigorously stated after the creation of the hydrodynamic theory of Brownian motion (1945). Hydrodynamic Brownian motion is a special case of 'anomalous Brownian motion', now intensively studied both theoretically and in experiments. We show how some general properties of anomalous Brownian motion can be easily derived using an effective method that allows one to convert the stochastic generalized Langevin equation into a deterministic Volterra-type integro-differential equation for the mean square displacement of the particle. Within the Gibbs statistics, the method is applicable to linear equations of motion with any kind of memory during the evolution of the system. We apply it to memoryless Brownian motion in a harmonic potential well and to Brownian motion in fluids, taking into account the effects of hydrodynamic memory. Exploring the mathematical analogy between Brownian motion and electric circuits, which are at nanoscales also described by the generalized Langevin equation, we calculate the fluctuations of charge and current in RLC circuits that are in contact with the thermal bath. Due to the simplicity of our approach it could be incorporated into graduate courses of statistical physics. Once the method is established, it allows bringing to the attention of students and effectively solving a number of attractive problems related to Brownian motion.

Thermodynamic and Quantum Thermodynamic Analyses of Brownian Movement

OpenAIRE

Gyftopoulos, Elias P.

2006-01-01

Thermodynamic and quantum thermodynamic analyses of Brownian movement of a solvent and a colloid passing through neutral thermodynamic equilibrium states only. It is shown that Brownian motors and E. coli do not represent Brownian movement.

Nonlinear Binormal Flow of Vortex Filaments

Science.gov (United States)

Strong, Scott; Carr, Lincoln

2015-11-01

With the current advances in vortex imaging of Bose-Einstein condensates occurring at the Universities of Arizona, São Paulo and Cambridge, interest in vortex filament dynamics is experiencing a resurgence. Recent simulations, Salman (2013), depict dissipative mechanisms resulting from vortex ring emissions and Kelvin wave generation associated with vortex self-intersections. As the local induction approximation fails to capture reconnection events, it lacks a similar dissipative mechanism. On the other hand, Strong&Carr (2012) showed that the exact representation of the velocity field induced by a curved segment of vortex contains higher-order corrections expressed in powers of curvature. This nonlinear binormal flow can be transformed, Hasimoto (1972), into a fully nonlinear equation of Schrödinger type. Continued transformation, Madelung (1926), reveals that the filament's square curvature obeys a quasilinear scalar conservation law with source term. This implies a broader range of filament dynamics than is possible with the integrable linear binormal flow. In this talk we show the affect higher-order corrections have on filament dynamics and discuss physical scales for which they may be witnessed in future experiments. Partially supported by NSF.

Dynamical 3-Space: Cosmic Filaments, Sheets and Voids

Directory of Open Access Journals (Sweden)

Cahill R. T.

2011-04-01

Full Text Available Observations of weak gravitational lensing combined with statistical tomographic techniques have revealed that galaxies have formed along filaments, essentially one- dimensional lines or strings, which form sheets and voids. These have, in the main, been interpreted as “dark matter” effects. To the contrary here we report the discovery that the dynamical 3-space theory possesses such filamentary solutions. These solutions are purely space self-interaction effects, and are attractive to matter, and as well gener- ate electromagnetic lensing. This theory of space has explained bore hole anomalies, supermassive black hole masses in spherical galaxies and globular clusters, flat rota- tion curves of spiral galaxies, and other gravitational anomalies. The theory has two constants, G and , where the bore hole experiments show that 1 = 137 is the fine structure constant.

Dynamical 3-Space: Cosmic Filaments, Sheets and Voids

Directory of Open Access Journals (Sweden)

Cahill R. T.

2011-04-01

Full Text Available Observations of weak gravitational lensing combined with statistical tomographic techniques have revealed that galaxies have formed along filaments, essentially one-dimensional lines or strings, which form sheets and voids. These have, in the main, been interpreted as "dark matter" effects. To the contrary here we report the discovery that the dynamical 3-space theory possesses such filamentary solutions. These solutions are purely space self-interaction effects, and are attractive to matter, and as well generate electromagnetic lensing. This theory of space has explained bore hole anomalies, supermassive black hole masses in spherical galaxies and globular clusters, flat rotation curves of spiral galaxies, and other gravitational anomalies. The theory has two constants, $G$ and $alpha$, where the bore hole experiments show that $alpha approx 1/137$ is the fine structure constant.

Properties of Brownian Image Models in Scale-Space

DEFF Research Database (Denmark)

Pedersen, Kim Steenstrup

2003-01-01

Brownian images) will be discussed in relation to linear scale-space theory, and it will be shown empirically that the second order statistics of natural images mapped into jet space may, within some scale interval, be modeled by the Brownian image model. This is consistent with the 1/f 2 power spectrum...... law that apparently governs natural images. Furthermore, the distribution of Brownian images mapped into jet space is Gaussian and an analytical expression can be derived for the covariance matrix of Brownian images in jet space. This matrix is also a good approximation of the covariance matrix......In this paper it is argued that the Brownian image model is the least committed, scale invariant, statistical image model which describes the second order statistics of natural images. Various properties of three different types of Gaussian image models (white noise, Brownian and fractional...

Revealing virtual processes of a quantum Brownian particle in phase space

International Nuclear Information System (INIS)

Maniscalco, S

2005-01-01

The short-time dynamics of a quantum Brownian particle in a harmonic potential is studied in phase space. An exact non-Markovian analytic approach to calculate the time evolution of the Wigner function is presented. The dynamics of the Wigner function of an initially squeezed state is analysed. It is shown that virtual exchanges of energy between the particle and the reservoir, characterizing the non-Lindblad short-time dynamics where system-reservoir correlations are not negligible, show up in phase space

Filament Activation in Response to Magnetic Flux Emergence and Cancellation in Filament Channels

Science.gov (United States)

Li, Ting; Zhang, Jun; Ji, Haisheng

2015-06-01

We conducted a comparative analysis of two filaments that showed a quite different activation in response to the flux emergence within the filament channels. The observations from the Solar Dynamics Observatory (SDO) and Global Oscillation Network Group (GONG) were made to analyze the two filaments on 2013 August 17 - 20 (SOL2013-08-17) and September 29 (SOL2013-09-29). The first event showed that the main body of the filament was separated into two parts when an active region (AR) emerged with a maximum magnetic flux of about 6.4×1021 Mx underlying the filament. The close neighborhood and common direction of the bright threads in the filament and the open AR fan loops suggest a similar magnetic connectivity of these two flux systems. The equilibrium of the filament was not destroyed three days after the start of the emergence of the AR. To our knowledge, similar observations have never been reported before. In the second event, the emerging flux occurred nearby a barb of the filament with a maximum magnetic flux of 4.2×1020 Mx, about one order of magnitude lower than that of the first event. Two patches of parasitic polarity in the vicinity of the barb merged, then cancelled with nearby network fields. About 20 hours after the onset of the emergence, the filament erupted. Our findings imply that the location of emerging flux within the filament channel is probably crucial to filament evolution. If the flux emergence appears nearby the barbs, it is highly likely that the emerging flux and the filament magnetic fields will cancel, which may lead to the eruption of the filament. The comparison of the two events shows that the emergence of a small AR may still not be enough to disrupt the stability of a filament system, and the actual eruption only occurs after the flux cancellation sets in.

Dynamical mean-field theory and weakly non-linear analysis for the phase separation of active Brownian particles

Energy Technology Data Exchange (ETDEWEB)

Speck, Thomas [Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz (Germany); Menzel, Andreas M.; Bialké, Julian; Löwen, Hartmut [Institut für Theoretische Physik II, Heinrich-Heine-Universität, D-40225 Düsseldorf (Germany)

2015-06-14

Recently, we have derived an effective Cahn-Hilliard equation for the phase separation dynamics of active Brownian particles by performing a weakly non-linear analysis of the effective hydrodynamic equations for density and polarization [Speck et al., Phys. Rev. Lett. 112, 218304 (2014)]. Here, we develop and explore this strategy in more detail and show explicitly how to get to such a large-scale, mean-field description starting from the microscopic dynamics. The effective free energy emerging from this approach has the form of a conventional Ginzburg-Landau function. On the coarsest scale, our results thus agree with the mapping of active phase separation onto that of passive fluids with attractive interactions through a global effective free energy (motility-induced phase transition). Particular attention is paid to the square-gradient term necessary for the phase separation kinetics. We finally discuss results from numerical simulations corroborating the analytical results.

Irreversible Brownian Heat Engine

Science.gov (United States)

Taye, Mesfin Asfaw

2017-10-01

We model a Brownian heat engine as a Brownian particle that hops in a periodic ratchet potential where the ratchet potential is coupled with a linearly decreasing background temperature. We show that the efficiency of such Brownian heat engine approaches the efficiency of endoreversible engine η =1-√{{Tc/Th}} [23]. On the other hand, the maximum power efficiency of the engine approaches η ^{MAX}=1-({Tc/Th})^{1\\over 4}. It is shown that the optimized efficiency always lies between the efficiency at quasistatic limit and the efficiency at maximum power while the efficiency at maximum power is always less than the optimized efficiency since the fast motion of the particle comes at the expense of the energy cost. If the heat exchange at the boundary of the heat baths is included, we show that such a Brownian heat engine has a higher performance when acting as a refrigerator than when operating as a device subjected to a piecewise constant temperature. The role of time on the performance of the motor is also explored via numerical simulations. Our numerical results depict that the time t and the external load dictate the direction of the particle velocity. Moreover, the performance of the heat engine improves with time. At large t (steady state), the velocity, the efficiency and the coefficient of performance of the refrigerator attain their maximum value. Furthermore, we study the effect of temperature by considering a viscous friction that decreases exponentially as the background temperature increases. Our result depicts that the Brownian particle exhibits a fast unidirectional motion when the viscous friction is temperature dependent than that of constant viscous friction. Moreover, the efficiency of this motor is considerably enhanced when the viscous friction is temperature dependent. On the hand, the motor exhibits a higher performance of the refrigerator when the viscous friction is taken to be constant.

Intermittency and multifractional Brownian character of geomagnetic time series

Directory of Open Access Journals (Sweden)

G. Consolini

2013-07-01

Full Text Available The Earth's magnetosphere exhibits a complex behavior in response to the solar wind conditions. This behavior, which is described in terms of mutifractional Brownian motions, could be the consequence of the occurrence of dynamical phase transitions. On the other hand, it has been shown that the dynamics of the geomagnetic signals is also characterized by intermittency at the smallest temporal scales. Here, we focus on the existence of a possible relationship in the geomagnetic time series between the multifractional Brownian motion character and the occurrence of intermittency. In detail, we investigate the multifractional nature of two long time series of the horizontal intensity of the Earth's magnetic field as measured at L'Aquila Geomagnetic Observatory during two years (2001 and 2008, which correspond to different conditions of solar activity. We propose a possible double origin of the intermittent character of the small-scale magnetic field fluctuations, which is related to both the multifractional nature of the geomagnetic field and the intermittent character of the disturbance level. Our results suggest a more complex nature of the geomagnetic response to solar wind changes than previously thought.

Brownian motion of a nano-colloidal particle: the role of the solvent.

Science.gov (United States)

Torres-Carbajal, Alexis; Herrera-Velarde, Salvador; Castañeda-Priego, Ramón

2015-07-15

Brownian motion is a feature of colloidal particles immersed in a liquid-like environment. Usually, it can be described by means of the generalised Langevin equation (GLE) within the framework of the Mori theory. In principle, all quantities that appear in the GLE can be calculated from the molecular information of the whole system, i.e., colloids and solvent molecules. In this work, by means of extensive Molecular Dynamics simulations, we study the effects of the microscopic details and the thermodynamic state of the solvent on the movement of a single nano-colloid. In particular, we consider a two-dimensional model system in which the mass and size of the colloid are two and one orders of magnitude, respectively, larger than the ones associated with the solvent molecules. The latter ones interact via a Lennard-Jones-type potential to tune the nature of the solvent, i.e., it can be either repulsive or attractive. We choose the linear momentum of the Brownian particle as the observable of interest in order to fully describe the Brownian motion within the Mori framework. We particularly focus on the colloid diffusion at different solvent densities and two temperature regimes: high and low (near the critical point) temperatures. To reach our goal, we have rewritten the GLE as a second kind Volterra integral in order to compute the memory kernel in real space. With this kernel, we evaluate the momentum-fluctuating force correlation function, which is of particular relevance since it allows us to establish when the stationarity condition has been reached. Our findings show that even at high temperatures, the details of the attractive interaction potential among solvent molecules induce important changes in the colloid dynamics. Additionally, near the critical point, the dynamical scenario becomes more complex; all the correlation functions decay slowly in an extended time window, however, the memory kernel seems to be only a function of the solvent density. Thus, the

Behavior of aerosols undergoing Brownian coagulation, Brownian diffusion and gravitational settling in a closed chamber

International Nuclear Information System (INIS)

Okuyama, Kikuo; Kousaka, Yasuo; Yoshida, Tetsuo

1976-01-01

The behavior of aerosols undergoing Brownian coagulation. Brownian diffusion and gravitational settling in a closed chamber was studied by solving the basic equation, the so-called population balance equation, numerically for a polydisperse aerosol system and analytically for a monodisperse system, and then the results were examined by experiment. In solving the basic equation, two dimensionless parameters, which are determined by the initial properties of an aerosol and the chamber dimension and also characterize the relative effects of Brownian coagulation and Brownian diffusion to gravitational settling, were introduced in order to generalize the behavior under arbitrary conditions. The calculated results, the time-dependent changes in particle number concentration and particle size distribution for a polydisperse system, were presented graphically by using the above two parameters. And further using these parameters, the domains of the three controlling factors were mapped to show the extent of each effect of these factors under various conditions for a monodisperse system. Some of the calculated results were compared with the experimental results obtained by the ultramicroscopic size analysis previously developed by the authors. (auth.)

A hydrodynamic formalism for Brownian systems

International Nuclear Information System (INIS)

Pina, E.; Rosales, M.A.

1981-01-01

A formal hydrodynamic approach to Brownian motion is presented and the corresponding equations are derived. Hydrodynamic quantities are expressed in terms of the physical variables characterizing the Brownian systems. Contact is made with the hydrodynamic model of Quantum Mechanics. (author)

Can we determine the filament chirality by the filament footpoint location or the barb-bearing?

Science.gov (United States)

Hao, Qi; Guo, Yang; Fang, Cheng; Chen, Peng-Fei; Cao, Wen-Da

2016-01-01

We attempt to propose a method for automatically detecting the solar filament chirality and barb bearing. We first introduce the concept of an unweighted undirected graph and adopt the Dijkstra shortest path algorithm to recognize the filament spine. Then, we use the polarity inversion line (PIL) shift method for measuring the polarities on both sides of the filament, and employ the connected components labeling method to identify the barbs and calculate the angle between each barb and the spine to determine the bearing of the barbs, i.e., left or right. We test the automatic detection method with Hα filtergrams from the Big Bear Solar Observatory (BBSO) Hα archive and magnetograms observed with the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). Four filaments are automatically detected and illustrated to show the results. The barbs in different parts of a filament may have opposite bearings. The filaments in the southern hemisphere (northern hemisphere) mainly have left-bearing (right-bearing) barbs and positive (negative) magnetic helicity, respectively. The tested results demonstrate that our method is efficient and effective in detecting the bearing of filament barbs. It is demonstrated that the conventionally believed one-to-one correspondence between filament chirality and barb bearing is not valid. The correct detection of the filament axis chirality should be done by combining both imaging morphology and magnetic field observations.

Can we determine the filament chirality by the filament footpoint location or the barb-bearing?

International Nuclear Information System (INIS)

Hao, Qi; Guo, Yang; Fang, Cheng; Chen, Peng-Fei; Cao, Wen-Da

2016-01-01

We attempt to propose a method for automatically detecting the solar filament chirality and barb bearing. We first introduce the concept of an unweighted undirected graph and adopt the Dijkstra shortest path algorithm to recognize the filament spine. Then, we use the polarity inversion line (PIL) shift method for measuring the polarities on both sides of the filament, and employ the connected components labeling method to identify the barbs and calculate the angle between each barb and the spine to determine the bearing of the barbs, i.e., left or right. We test the automatic detection method with Hα filtergrams from the Big Bear Solar Observatory (BBSO) Hα archive and magnetograms observed with the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). Four filaments are automatically detected and illustrated to show the results. The barbs in different parts of a filament may have opposite bearings. The filaments in the southern hemisphere (northern hemisphere) mainly have left-bearing (right-bearing) barbs and positive (negative) magnetic helicity, respectively. The tested results demonstrate that our method is efficient and effective in detecting the bearing of filament barbs. It is demonstrated that the conventionally believed one-to-one correspondence between filament chirality and barb bearing is not valid. The correct detection of the filament axis chirality should be done by combining both imaging morphology and magnetic field observations. (paper)

Focal dynamics of multiple filaments: Microscopic imaging and reconstruction

International Nuclear Information System (INIS)

Kiran, P. Prem; Bagchi, Suman; Kumar, G. Ravindra; Krishnan, Siva Rama; Arnold, C. L.; Couairon, A.

2010-01-01

We observe the complete dynamics of the propagation of very intense, femtosecond laser pulses in air under tight focusing conditions via direct imaging of the entire interaction zone. The whole life history of the focused pulses is then reconstructed by means of numerical simulations. We show that beam breakup leads to a dual-rate increase in filament numbers with laser power. Linearly and circularly polarized pulses give rise to beam breakup and fusion governed by external focusing conditions. For tight focusing conditions, intensity saturation due to plasma generation and nonlinear losses does not limit the intensity growth, thereby giving access to a new propagation regime featured by an efficient laser energy deposition in fully ionized air and intense 10 15 W/cm 2 pulses at the focus.

DNA breathing dynamics: analytic results for distribution functions of relevant Brownian functionals.

Science.gov (United States)

Bandyopadhyay, Malay; Gupta, Shamik; Segal, Dvira

2011-03-01

We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landscape. We suggest several probability distribution functions that characterize the breathing process, and adopt the recently studied backward Fokker-Planck method and the path decomposition method as elegant and flexible tools for deriving these distributions. In particular, for a bubble of an initial size x₀, we derive analytical expressions for (i) the distribution P(t{f}|x₀) of the first-passage time t{f}, characterizing the bubble lifetime, (ii) the distribution P(A|x₀) of the area A until the first-passage time, providing information about the effective reactivity of the bubble to processes within the DNA, (iii) the distribution P(M) of the maximum bubble size M attained before the first-passage time, and (iv) the joint probability distribution P(M,t{m}) of the maximum bubble size M and the time t{m} of its occurrence before the first-passage time. These distributions are analyzed in the limit of small and large bubble sizes. We supplement our analytical predictions with direct numericalsimulations of the related Langevin equation, and obtain a very good agreement in the appropriate limits. The nontrivial scaling behavior of the various quantities analyzed here can, in principle, be explored experimentally.

Operator Fractional Brownian Motion and Martingale Differences

Directory of Open Access Journals (Sweden)

Hongshuai Dai

2014-01-01

Full Text Available It is well known that martingale difference sequences are very useful in applications and theory. On the other hand, the operator fractional Brownian motion as an extension of the well-known fractional Brownian motion also plays an important role in both applications and theory. In this paper, we study the relation between them. We construct an approximation sequence of operator fractional Brownian motion based on a martingale difference sequence.

Recruitment Kinetics of Tropomyosin Tpm3.1 to Actin Filament Bundles in the Cytoskeleton Is Independent of Actin Filament Kinetics.

Science.gov (United States)

Appaduray, Mark A; Masedunskas, Andrius; Bryce, Nicole S; Lucas, Christine A; Warren, Sean C; Timpson, Paul; Stear, Jeffrey H; Gunning, Peter W; Hardeman, Edna C

2016-01-01

The actin cytoskeleton is a dynamic network of filaments that is involved in virtually every cellular process. Most actin filaments in metazoa exist as a co-polymer of actin and tropomyosin (Tpm) and the function of an actin filament is primarily defined by the specific Tpm isoform associated with it. However, there is little information on the interdependence of these co-polymers during filament assembly and disassembly. We addressed this by investigating the recovery kinetics of fluorescently tagged isoform Tpm3.1 into actin filament bundles using FRAP analysis in cell culture and in vivo in rats using intracellular intravital microscopy, in the presence or absence of the actin-targeting drug jasplakinolide. The mobile fraction of Tpm3.1 is between 50% and 70% depending on whether the tag is at the C- or N-terminus and whether the analysis is in vivo or in cultured cells. We find that the continuous dynamic exchange of Tpm3.1 is not significantly impacted by jasplakinolide, unlike tagged actin. We conclude that tagged Tpm3.1 may be able to undergo exchange in actin filament bundles largely independent of the assembly and turnover of actin.

Brownian Optimal Stopping and Random Walks

International Nuclear Information System (INIS)

Lamberton, D.

2002-01-01

One way to compute the value function of an optimal stopping problem along Brownian paths consists of approximating Brownian motion by a random walk. We derive error estimates for this type of approximation under various assumptions on the distribution of the approximating random walk

Near-Field, On-Chip Optical Brownian Ratchets.

Science.gov (United States)

Wu, Shao-Hua; Huang, Ningfeng; Jaquay, Eric; Povinelli, Michelle L

2016-08-10

Nanoparticles in aqueous solution are subject to collisions with solvent molecules, resulting in random, Brownian motion. By breaking the spatiotemporal symmetry of the system, the motion can be rectified. In nature, Brownian ratchets leverage thermal fluctuations to provide directional motion of proteins and enzymes. In man-made systems, Brownian ratchets have been used for nanoparticle sorting and manipulation. Implementations based on optical traps provide a high degree of tunability along with precise spatiotemporal control. Here, we demonstrate an optical Brownian ratchet based on the near-field traps of an asymmetrically patterned photonic crystal. The system yields over 25 times greater trap stiffness than conventional optical tweezers. Our technique opens up new possibilities for particle manipulation in a microfluidic, lab-on-chip environment.

On-chip measurements of Brownian relaxation vs. concentration of 40nm magnetic beads

DEFF Research Database (Denmark)

Østerberg, Frederik Westergaard; Rizzi, Giovanni; Hansen, Mikkel Fougt

2012-01-01

We present on-chip Brownian relaxation measurements on a logarithmic dilution series of 40 nm beads dispersed in water with bead concentrations between 16 mu g/ml and 4000 mu g/ml. The measurements are performed using a planar Hall effect bridge sensor at frequencies up to 1 MHz. No external fields...... are needed as the beads are magnetized by the field generated by the applied sensor bias current. We show that the Brownian relaxation frequency can be extracted from fitting the Cole-Cole model to measurements for bead concentrations of 64 mu g/ml or higher and that the measured dynamic magnetic response...... is proportional to the bead concentration. For bead concentrations higher than or equal to 500 mu g/ml, we extract a hydrodynamic diameter of 47(1) nm for the beads, which is close to the nominal bead size of 40 nm. Furthermore, we study the signal vs. bead concentration at a fixed frequency close to the Brownian...

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore

Science.gov (United States)

Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.

2017-08-01

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Brownian motion in complex fluids: venerable field and frontier of modern physics

International Nuclear Information System (INIS)

Vizcarra-Rendon, A.; Medina-Noyola, M.; Ruiz-Estrada, H.; Arauz-Lara, J.L.

1989-01-01

This paper reviews the current status of our understanding of tracer-diffusion phenomena in colloidal suspensions. This is the most direct observation of the Brownian motion executed by labelled Brownian particles interacting with the rest of colloidal particles in a suspension. The fundamental description of this phenomenon constitutes today one of the most relevant problems in the process of understanding the dynamic properties of this important class of complex fluids, from the experimental and theoretical perspective of physical research. This paper describes the recent developments in the extension of the classical theory of Brownian motion and its application to the description of the effects of direct and hydrodynamic interactions among colloidal particles. As a result, a coherent pictured has emerged in which the agreement between theory and experiment from nature fields of physics. The moral of the paper is that the use of well established concepts as statistical physics, assisted by modern experimental techniques, are contributing to transform complex fluids into a more amialbe class of materials from the point of view of the physicist. (Author)

Stochastic interactions of two Brownian hard spheres in the presence of depletants

International Nuclear Information System (INIS)

Karzar-Jeddi, Mehdi; Fan, Tai-Hsi; Tuinier, Remco; Taniguchi, Takashi

2014-01-01

A quantitative analysis is presented for the stochastic interactions of a pair of Brownian hard spheres in non-adsorbing polymer solutions. The hard spheres are hypothetically trapped by optical tweezers and allowed for random motion near the trapped positions. The investigation focuses on the long-time correlated Brownian motion. The mobility tensor altered by the polymer depletion effect is computed by the boundary integral method, and the corresponding random displacement is determined by the fluctuation-dissipation theorem. From our computations it follows that the presence of depletion layers around the hard spheres has a significant effect on the hydrodynamic interactions and particle dynamics as compared to pure solvent and uniform polymer solution cases. The probability distribution functions of random walks of the two interacting hard spheres that are trapped clearly shift due to the polymer depletion effect. The results show that the reduction of the viscosity in the depletion layers around the spheres and the entropic force due to the overlapping of depletion zones have a significant influence on the correlated Brownian interactions

CNT based thermal Brownian motor to pump water in nanodevices

DEFF Research Database (Denmark)

Oyarzua, Elton; Zambrano, Harvey; Walther, Jens Honore

2016-01-01

asymmetry drive the water ow in a preferential direction. We systematically modified the magnitude of the applied thermal gradient and the axial position of the fixed points. The analysis involves measurement of the vibrational modes in the CNTs using a Fast Fourier Transform (FFT) algorithm. We observed......Brownian molecular motors are nanoscale machines that exploit thermal fluctuations for directional motion by employing mechanisms such as the Feynman-Smoluchowski ratchet. In this study, using Non Equilibrium Molecular Dynamics, we propose a novel thermal Brownian motor for pumping water through...... Carbon Nanotubes (CNTs). To achieve this we impose a thermal gradient along the axis of a CNT filled with water and impose, in addition, a spatial asymmetry by flxing specific zones on the CNT in order to modify the vibrational modes of the CNT. We find that the temperature gradient and imposed spatial...

Filament structure, organization, and dynamics in MreB sheets.

Science.gov (United States)

Popp, David; Narita, Akihiro; Maeda, Kayo; Fujisawa, Tetsuro; Ghoshdastider, Umesh; Iwasa, Mitsusada; Maéda, Yuichiro; Robinson, Robert C

2010-05-21

In vivo fluorescence microscopy studies of bacterial cells have shown that the bacterial shape-determining protein and actin homolog, MreB, forms cable-like structures that spiral around the periphery of the cell. The molecular structure of these cables has yet to be established. Here we show by electron microscopy that Thermatoga maritime MreB forms complex, several mum long multilayered sheets consisting of diagonally interwoven filaments in the presence of either ATP or GTP. This architecture, in agreement with recent rheological measurements on MreB cables, may have superior mechanical properties and could be an important feature for maintaining bacterial cell shape. MreB polymers within the sheets appear to be single-stranded helical filaments rather than the linear protofilaments found in the MreB crystal structure. Sheet assembly occurs over a wide range of pH, ionic strength, and temperature. Polymerization kinetics are consistent with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation. Steady-state TIRF microscopy studies of MreB suggest filament treadmilling while high pressure small angle x-ray scattering measurements indicate that the stability of MreB polymers is similar to that of F-actin filaments. In the presence of ADP or GDP, long, thin cables formed in which MreB was arranged in parallel as linear protofilaments. This suggests that the bacterial cell may exploit various nucleotides to generate different filament structures within cables for specific MreB-based functions.

A symplectic integration method for elastic filaments

Science.gov (United States)

Ladd, Tony; Misra, Gaurav

2009-03-01

Elastic rods are a ubiquitous coarse-grained model of semi-flexible biopolymers such as DNA, actin, and microtubules. The Worm-Like Chain (WLC) is the standard numerical model for semi-flexible polymers, but it is only a linearized approximation to the dynamics of an elastic rod, valid for small deflections; typically the torsional motion is neglected as well. In the standard finite-difference and finite-element formulations of an elastic rod, the continuum equations of motion are discretized in space and time, but it is then difficult to ensure that the Hamiltonian structure of the exact equations is preserved. Here we discretize the Hamiltonian itself, expressed as a line integral over the contour of the filament. This discrete representation of the continuum filament can then be integrated by one of the explicit symplectic integrators frequently used in molecular dynamics. The model systematically approximates the continuum partial differential equations, but has the same level of computational complexity as molecular dynamics and is constraint free. Numerical tests show that the algorithm is much more stable than a finite-difference formulation and can be used for high aspect ratio filaments, such as actin. We present numerical results for the deterministic and stochastic motion of single filaments.

Linear response approach to active Brownian particles in time-varying activity fields

Science.gov (United States)

Merlitz, Holger; Vuijk, Hidde D.; Brader, Joseph; Sharma, Abhinav; Sommer, Jens-Uwe

2018-05-01

In a theoretical and simulation study, active Brownian particles (ABPs) in three-dimensional bulk systems are exposed to time-varying sinusoidal activity waves that are running through the system. A linear response (Green-Kubo) formalism is applied to derive fully analytical expressions for the torque-free polarization profiles of non-interacting particles. The activity waves induce fluxes that strongly depend on the particle size and may be employed to de-mix mixtures of ABPs or to drive the particles into selected areas of the system. Three-dimensional Langevin dynamics simulations are carried out to verify the accuracy of the linear response formalism, which is shown to work best when the particles are small (i.e., highly Brownian) or operating at low activity levels.

Experimental Studies of the Brownian Diffusion of Boomerang Colloidal Particle in a Confined Geometry

Science.gov (United States)

Chakrabarty, Ayan; Wang, Feng; Joshi, Bhuwan; Wei, Qi-Huo

2011-03-01

Recent studies shows that the boomerang shaped molecules can form various kinds of liquid crystalline phases. One debated topic related to boomerang molecules is the existence of biaxial nematic liquid crystalline phase. Developing and optical microscopic studies of colloidal systems of boomerang particles would allow us to gain better understanding of orientation ordering and dynamics at ``single molecule'' level. Here we report the fabrication and experimental studies of the Brownian motion of individual boomerang colloidal particles confined between two glass plates. We used dark-field optical microscopy to directly visualize the Brownian motion of the single colloidal particles in a quasi two dimensional geometry. An EMCCD was used to capture the motion in real time. An indigenously developed imaging processing algorithm based on MatLab program was used to precisely track the position and orientation of the particles with sub-pixel accuracy. The experimental finding of the Brownian diffusion of a single boomerang colloidal particle will be discussed.

Self-assembly of designed supramolecular magnetic filaments of different shapes

Energy Technology Data Exchange (ETDEWEB)

Novak, E.V. [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); Rozhkov, D.A., E-mail: d.a.rozhkov@gmail.com [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); Sanchez, P.A. [University of Vienna, Sensengasse 8, Vienna (Austria); Kantorovich, S.S. [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); University of Vienna, Sensengasse 8, Vienna (Austria)

2017-06-01

In the present work we study via molecular dynamics simulations filaments of ring and linear shape. Filaments are made of magnetic nanoparticles, possessing a point dipole in their centres. Particles in filaments are crosslinked in a particular way, so that the deviation of the neighbouring dipoles from the head-to-tail orientation is penalised by the bond. We show how the conformation of a single chain and ring filament changes on cooling for different lengths. We also study filament pairs, by fixing filaments at a certain distance and analysing the impact of inter-filament interaction on the equilibrium configurations. Our study opens a perspective to investigate the dispersions of filaments, both theoretically and numerically, by using effective potentials. - Highlights: • Single filament study. • Magnetic particles crosslinked in chains and rings. • Magnetic filament interactions.

Helical beating of an actuated elastic filament

International Nuclear Information System (INIS)

Coq, Nais; Roure, Olivia du; Fermigier, Marc; Bartolo, Denis

2009-01-01

We investigate the propulsive force resulting from the rotation of a flexible filament in the low Reynolds number regime. Using a simple linear model, we establish the nonlinear torque-force relations for two torque-driven actuation modes. When the rotation of the filament is induced by two perpendicular transverse oscillating torques, the propulsive force increases monotonically with the torque amplitude. Conversely, when a constant axial torque is applied, the torque-force characteristics displays an unstable branch, related to a discontinuous transition in the shape of the filament. We characterize this shape transition using two geometrical parameters, quantifying the wrapping around and the collapse on the axis of the filament. The proposed theoretical description correctly accounts for our experimental observations and reveals a strong dependence of the filament dynamics on the anchoring conditions.

Solar filament material oscillations and drainage before eruption

International Nuclear Information System (INIS)

Bi, Yi; Jiang, Yunchun; Yang, Jiayan; Hong, Junchao; Li, Haidong; Yang, Dan; Yang, Bo

2014-01-01

Both large-amplitude longitudinal (LAL) oscillations and material drainage in a solar filament are associated with the flow of material along the filament axis, often followed by an eruption. However, the relationship between these two motions and a subsequent eruption event is poorly understood. We analyze a filament eruption using EUV imaging data captured by the Atmospheric Imaging Array on board the Solar Dynamics Observatory and the Hα images from the Global Oscillation Network Group. Hours before the eruption, the filament was activated, with one of its legs undergoing a slow rising motion. The asymmetric activation inclined the filament relative to the solar surface. After the active phase, LAL oscillations were observed in the inclined filament. The oscillation period increased slightly over time, which may suggest that the magnetic fields supporting the filament evolve to be flatter during the slow rising phase. After the oscillations, a significant amount of filament material was drained toward one filament endpoint, followed immediately by the violent eruption of the filament. The material drainage may further support the change in magnetic topology prior to the eruption. Moreover, we suggest that the filament material drainage could play a role in the transition from a slow to a fast rise of the erupting filament.

Conformal correlation functions in the Brownian loop soup

Science.gov (United States)

Camia, Federico; Gandolfi, Alberto; Kleban, Matthew

2016-01-01

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Conformal correlation functions in the Brownian loop soup

Energy Technology Data Exchange (ETDEWEB)

Camia, Federico, E-mail: federico.camia@nyu.edu [New York University Abu Dhabi (United Arab Emirates); VU University, Amsterdam (Netherlands); Gandolfi, Alberto, E-mail: albertogandolfi@nyu.edu [New York University Abu Dhabi (United Arab Emirates); Università di Firenze (Italy); Kleban, Matthew, E-mail: kleban@nyu.edu [New York University Abu Dhabi (United Arab Emirates); Center for Cosmology and Particle Physics, Department of Physics, New York University (United States)

2016-01-15

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Conformal correlation functions in the Brownian loop soup

Directory of Open Access Journals (Sweden)

Federico Camia

2016-01-01

Full Text Available We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

On the Humble Origins of the Brownian Entropic Force

OpenAIRE

Neumann, Richard M.

2015-01-01

Recognition that certain forces arising from the averaging of the multiple impacts of a solute particle by the surrounding solvent particles undergoing random thermal motion can be of an entropic nature has led to the incorporation of these forces and their related entropies into theoretical protocols ranging from molecular-dynamics simulations to the modeling of quarkonium suppression in particle physics. Here we present a rigorous derivation of this Brownian entropic force by means of the c...

More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

Science.gov (United States)

Chen, How-Huan; Goodman, Alyssa

2018-01-01

In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

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.

High-resolution Observations of Sympathetic Filament Eruptions by NVST

Energy Technology Data Exchange (ETDEWEB)

Li, Shangwei; Su, Yingna; Zhou, Tuanhui; Ji, Haisheng [Key Laboratory for Dark Matter and Space Science, Purple Mountain Observatory, CAS, Nanjing 210008 (China); Van Ballegooijen, Adriaan [5001 Riverwood Avenue, Sarasota, FL 34231 (United States); Sun, Xudong, E-mail: ynsu@pmo.ac.cn [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States)

2017-07-20

We investigate two sympathetic filament eruptions observed by the New Vacuum Solar Telescope on 2015 October 15. The full picture of the eruptions is obtained from the corresponding Solar Dynamics Observatory ( SDO )/Atmospheric Imaging Assembly (AIA) observations. The two filaments start from active region NOAA 12434 in the north and end in one large quiescent filament channel in the south. The left filament erupts first, followed by the right filament eruption about 10 minutes later. Clear twist structure and rotating motion are observed in both filaments during the eruption. Both eruptions failed, since the filaments first rise up, then flow toward the south and merge into the southern large quiescent filament. We also observe repeated activations of mini filaments below the right filament after its eruption. Using magnetic field models constructed based on SDO /HMI magnetograms via the flux rope insertion method, we find that the left filament eruption is likely to be triggered by kink instability, while the weakening of overlying magnetic fields due to magnetic reconnection at an X-point between the two filament systems might play an important role in the onset of the right filament eruption.

Morphological indictors of the chirality of solar filaments

Science.gov (United States)

Filippov, B. P.

2017-10-01

There is no doubt that the structural features of filaments reflect properties of their magnetic fields, such as chirality and helicity. However, the interpretation of some morphological features can lead to incorrect conclusions when the observing time is limited and the spatial resolution is insufficiently high. In spite of the relative constancy of their overall shapes, filaments are dynamical formations with inhomogeneities moving along the threads making them up. Therefore, it is possible to observe material concentrated not only in magnetic traps, but also along curved arcs. Difficulties often arise in determining the chirality of filaments with anomalous "barbs"; i.e., those whose jagged side is located on the opposite side of the axis compared to most ("normal") filaments. A simple model is used to show that anomalous barbs can exist in an ordinary magnetic flux rope, with the threads of its fine structure oriented nearly perpendicular to its length. A careful analysis of images with the maximum available spatial resolution and with information about temporal dynamics, together with comparisons with observations in various spectral lines, can enable a correct determination of the chirality of filaments.

Generalized Arcsine Laws for Fractional Brownian Motion.

Science.gov (United States)

Sadhu, Tridib; Delorme, Mathieu; Wiese, Kay Jörg

2018-01-26

The three arcsine laws for Brownian motion are a cornerstone of extreme-value statistics. For a Brownian B_{t} starting from the origin, and evolving during time T, one considers the following three observables: (i) the duration t_{+} the process is positive, (ii) the time t_{last} the process last visits the origin, and (iii) the time t_{max} when it achieves its maximum (or minimum). All three observables have the same cumulative probability distribution expressed as an arcsine function, thus the name arcsine laws. We show how these laws change for fractional Brownian motion X_{t}, a non-Markovian Gaussian process indexed by the Hurst exponent H. It generalizes standard Brownian motion (i.e., H=1/2). We obtain the three probabilities using a perturbative expansion in ϵ=H-1/2. While all three probabilities are different, this distinction can only be made at second order in ϵ. Our results are confirmed to high precision by extensive numerical simulations.

Dynamical stability of the one-dimensional rigid Brownian rotator: the role of the rotator’s spatial size and shape

Science.gov (United States)

Jeknić-Dugić, Jasmina; Petrović, Igor; Arsenijević, Momir; Dugić, Miroljub

2018-05-01

We investigate dynamical stability of a single propeller-like shaped molecular cogwheel modelled as the fixed-axis rigid rotator. In the realistic situations, rotation of the finite-size cogwheel is subject to the environmentally-induced Brownian-motion effect that we describe by utilizing the quantum Caldeira-Leggett master equation. Assuming the initially narrow (classical-like) standard deviations for the angle and the angular momentum of the rotator, we investigate the dynamics of the first and second moments depending on the size, i.e. on the number of blades of both the free rotator as well as of the rotator in the external harmonic field. The larger the standard deviations, the less stable (i.e. less predictable) rotation. We detect the absence of the simple and straightforward rules for utilizing the rotator’s stability. Instead, a number of the size-related criteria appear whose combinations may provide the optimal rules for the rotator dynamical stability and possibly control. In the realistic situations, the quantum-mechanical corrections, albeit individually small, may effectively prove non-negligible, and also revealing subtlety of the transition from the quantum to the classical dynamics of the rotator. As to the latter, we detect a strong size-dependence of the transition to the classical dynamics beyond the quantum decoherence process.

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

Science.gov (United States)

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

Science.gov (United States)

Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

Directory of Open Access Journals (Sweden)

Alexandra B Wolf

Full Text Available The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus and a motile rod-shaped bacterium (Bacillus weihenstephanensis to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions. These data, combined with information on bacterial motility (expansion potential across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Decay ratio for third order Brownian oscillators

International Nuclear Information System (INIS)

Konno, H.; Kanemoto, S.

1998-01-01

We have obtained the analytical expressions of the decay ratios for two types of third order Brownian oscillators which are generalizations of the second order Brownian oscillator driven by the Gaussian-white noise. The resulting expressions will provide us useful baseline information for more complicated practical problems and their applications

Dissipation and decoherence in Brownian motion

Energy Technology Data Exchange (ETDEWEB)

Bellomo, Bruno [Dipartimento di Scienze Fisiche ed Astronomiche dell' Universita di Palermo, Via Archirafi, 36, 90123 Palermo (Italy); Barnett, Stephen M [Department of Physics, University of Strathclyde, Glasgow G4 0NG (United Kingdom); Jeffers, John [Department of Physics, University of Strathclyde, Glasgow G4 0NG (United Kingdom)

2007-05-15

We consider the evolution of a Brownian particle described by a measurement-based master equation. We derive the solution to this equation for general initial conditions and apply it to a Gaussian initial state. We analyse the effects of the diffusive terms, present in the master equation, and describe how these modify uncertainties and coherence length. This allows us to model dissipation and decoherence in quantum Brownian motion.

Brownian movement and molecular reality

CERN Document Server

Perrin, Jean

2005-01-01

How do we know that molecules really exist? An important clue came from Brownian movement, a concept developed in 1827 by botanist Robert Brown, who noticed that tiny objects like pollen grains shook and moved erratically when viewed under a microscope. Nearly 80 years later, in 1905, Albert Einstein explained this ""Brownian motion"" as the result of bombardment by molecules. Einstein offered a quantitative explanation by mathematically estimating the average distance covered by the particles over time as a result of molecular bombardment. Four years later, Jean Baptiste Perrin wrote Brownia

Bundling of elastic filaments induced by hydrodynamic interactions

Science.gov (United States)

Man, Yi; Page, William; Poole, Robert J.; Lauga, Eric

2017-12-01

Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a tight helical bundle. When the bacterium changes its direction, the flagellar filaments unbundle and randomly reorient the cell for a short period of time before returning to their bundled state and resuming swimming. This rapid bundling and unbundling is, at its heart, a mechanical process whereby hydrodynamic interactions balance with elasticity to determine the time-varying deformation of the filaments. Inspired by this biophysical problem, we present in this paper what is perhaps the simplest model of bundling whereby two or more straight elastic filaments immersed in a viscous fluid rotate about their centerline, inducing rotational flows which tend to bend the filaments around each other. We derive an integrodifferential equation governing the shape of the filaments resulting from mechanical balance in a viscous fluid at low Reynolds number. We show that such equation may be evaluated asymptotically analytically in the long-wavelength limit, leading to a local partial differential equation governed by a single dimensionless bundling number. A numerical study of the dynamics predicted by the model reveals the presence of two configuration instabilities with increasing bundling numbers: first to a crossing state where filaments touch at one point and then to a bundled state where filaments wrap along each other in a helical fashion. We also consider the case of multiple filaments and the unbundling dynamics. We next provide an intuitive physical model for the crossing instability and show that it may be used to predict analytically its threshold and adapted to address the transition to a bundling state. We then use a macroscale experimental implementation of the two-filament configuration in order to validate our theoretical predictions and obtain excellent agreement. This long

Hydrodynamic interaction induced spontaneous rotation of coupled active filaments.

Science.gov (United States)

Jiang, Huijun; Hou, Zhonghuai

2014-12-14

We investigate the coupled dynamics of active filaments with long range hydrodynamic interactions (HI). Remarkably, we find that filaments can rotate spontaneously under the same conditions in which a single filament alone can only move in translation. Detailed analysis reveals that the emergence of coupled rotation originates from an asymmetric flow field associated with HI which breaks the symmetry of translational motion when filaments approach. The breaking is then further stabilized by HI to form self-sustained coupled rotation. Intensive simulations show that coupled rotation forms easily when one filament tends to collide with the front-half of the other. For head-to-tail approaching, we observe another interesting HI-induced coupled motion, where filaments move together in the form of one following the other. Moreover, the radius of coupled rotation increases exponentially as the rigidity of the filament increases, which suggests that HI are also important for the alignment of rigid-rod-like filaments which has been assumed to be solely a consequence of direct collisions.

Gyrofluid computations of filament dynamics in tokamak scrape-off layers

International Nuclear Information System (INIS)

Wiesenberger, M.

2014-01-01

-dimensional and three-dimensional gyrofluid model. To the knowledge of the author we are the first to achieve this. The models are used to investigate blob dynamics of seeded blobs in the tokamak scrape-off-layer. In two dimensions we identifie two regimes of blob convection. Blobs, defined as the vicinity of the maximal amplitude position, quickly loose mass in the first and retain their mass in the second regime as they propagate radially. Our simulations indicate that over a wide range of parameters, namely ion temperature, initial blob width, and initial blob amplitude, these two regimes are characterised by the ratio of ion gyroradius to the initial gradient scale length. This ratio is interpreted as a measure for the strength of FLR effects. Blobs with a low ratio belong to the first, blobs with strong FLR effects belong to the second regime. Three-dimensional effects enter the filament dynamics in two regimes, namely the interchange and the Boltzmann regime. These regimes are characterized by the collisionality, the parallel gradient length scale and the perpendicular blob size. Our initial blob simulations confirm that for high collisionality the blob dynamics is essentially two-dimensional at least in the initial blob phase. The interchange motion is shown to break the field-alignment. This effect pushes the filament into the Boltzmann regime in which potential and density align. (author) [de

Brownian diode: Molecular motor based on a semi-permeable Brownian particle with internal potential drop

International Nuclear Information System (INIS)

Plyukhin, A.V.

2013-01-01

A model of an autonomous isothermal Brownian motor with an internal propulsion mechanism is considered. The motor is a Brownian particle which is semi-transparent for molecules of surrounding ideal gas. Molecular passage through the particle is controlled by a potential similar to that in the transition rate theory, i.e. characterized by two stationary states with a finite energy difference separated by a potential barrier. The internal potential drop maintains the diode-like asymmetry of molecular fluxes through the particle, which results in the particle's stationary drift.

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

International Nuclear Information System (INIS)

Greczylo, Tomasz; Debowska, Ewa

2007-01-01

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)

Bundling Actin Filaments From Membranes: Some Novel Players

Directory of Open Access Journals (Sweden)

Clément eThomas

2012-08-01

Full Text Available Progress in live-cell imaging of the cytoskeleton has significantly extended our knowledge about the organization and dynamics of actin filaments near the plasma membrane of plant cells. Noticeably, two populations of filamentous structures can be distinguished. On the one hand, fine actin filaments which exhibit an extremely dynamic behavior basically characterized by fast polymerization and prolific severing events, a process referred to as actin stochastic dynamics. On the other hand, thick actin bundles which are composed of several filaments and which are comparatively more stable although they constantly remodel as well. There is evidence that the actin cytoskeleton plays critical roles in trafficking and signaling at both the cell cortex and organelle periphery but the exact contribution of actin bundles remains unclear. A common view is that actin bundles provide the long-distance tracks used by myosin motors to deliver their cargo to growing regions and accordingly play a particularly important role in cell polarization. However, several studies support that actin bundles are more than simple passive highways and display multiple and dynamic roles in the regulation of many processes, such as cell elongation, polar auxin transport, stomatal and chloroplast movement, and defense against pathogens. The list of identified plant actin-bundling proteins is ever expanding, supporting that plant cells shape structurally and functionally different actin bundles. Here I review the most recently characterized actin-bundling proteins, with a particular focus on those potentially relevant to membrane trafficking and/or signaling.

Brownian quasi-particles in statistical physics

International Nuclear Information System (INIS)

Tellez-Arenas, A.; Fronteau, J.; Combis, P.

1979-01-01

The idea of a Brownian quasi-particle and the associated differentiable flow (with nonselfadjoint forces) are used here in the context of a stochastic description of the approach towards statistical equilibrium. We show that this quasi-particle flow acquires, at equilibrium, the principal properties of a conservative Hamiltonian flow. Thus the model of Brownian quasi-particles permits us to establish a link between the stochastic description and the Gibbs description of statistical equilibrium

Stock price prediction using geometric Brownian motion

Science.gov (United States)

Farida Agustini, W.; Restu Affianti, Ika; Putri, Endah RM

2018-03-01

Geometric Brownian motion is a mathematical model for predicting the future price of stock. The phase that done before stock price prediction is determine stock expected price formulation and determine the confidence level of 95%. On stock price prediction using geometric Brownian Motion model, the algorithm starts from calculating the value of return, followed by estimating value of volatility and drift, obtain the stock price forecast, calculating the forecast MAPE, calculating the stock expected price and calculating the confidence level of 95%. Based on the research, the output analysis shows that geometric Brownian motion model is the prediction technique with high rate of accuracy. It is proven with forecast MAPE value ≤ 20%.

Reflection Negative Kernels and Fractional Brownian Motion

Directory of Open Access Journals (Sweden)

Palle E. T. Jorgensen

2018-06-01

Full Text Available In this article we study the connection of fractional Brownian motion, representation theory and reflection positivity in quantum physics. We introduce and study reflection positivity for affine isometric actions of a Lie group on a Hilbert space E and show in particular that fractional Brownian motion for Hurst index 0 < H ≤ 1 / 2 is reflection positive and leads via reflection positivity to an infinite dimensional Hilbert space if 0 < H < 1 / 2 . We also study projective invariance of fractional Brownian motion and relate this to the complementary series representations of GL 2 ( R . We relate this to a measure preserving action on a Gaussian L 2 -Hilbert space L 2 ( E .

Spherical particle Brownian motion in viscous medium as non-Markovian random process

International Nuclear Information System (INIS)

Morozov, Andrey N.; Skripkin, Alexey V.

2011-01-01

The Brownian motion of a spherical particle in an infinite medium is described by the conventional methods and integral transforms considering the entrainment of surrounding particles of the medium by the Brownian particle. It is demonstrated that fluctuations of the Brownian particle velocity represent a non-Markovian random process. The features of Brownian motion in short time intervals and in small displacements are considered. -- Highlights: → Description of Brownian motion considering the entrainment of medium is developed. → We find the equations for statistical characteristics of impulse fluctuations. → Brownian motion at small time intervals is considered. → Theoretical results and experimental data are compared.

Density profiles in the Scrape-Off Layer interpreted through filament dynamics

Science.gov (United States)

Militello, Fulvio

2017-10-01

We developed a new theoretical framework to clarify the relation between radial Scrape-Off Layer density profiles and the fluctuations that generate them. The framework provides an interpretation of the experimental features of the profiles and of the turbulence statistics on the basis of simple properties of the filaments, such as their radial motion and their draining towards the divertor. L-mode and inter-ELM filaments are described as a Poisson process in which each event is independent and modelled with a wave function of amplitude and width statistically distributed according to experimental observations and evolving according to fluid equations. We will rigorously show that radially accelerating filaments, less efficient parallel exhaust and also a statistical distribution of their radial velocity can contribute to induce flatter profiles in the far SOL and therefore enhance plasma-wall interactions. A quite general result of our analysis is the resiliency of this non-exponential nature of the profiles and the increase of the relative fluctuation amplitude towards the wall, as experimentally observed. According to the framework, profile broadening at high fueling rates can be caused by interactions with neutrals (e.g. charge exchange) in the divertor or by a significant radial acceleration of the filaments. The framework assumptions were tested with 3D numerical simulations of seeded SOL filaments based on a two fluid model. In particular, filaments interact through the electrostatic field they generate only when they are in close proximity (separation comparable to their width in the drift plane), thus justifying our independence hypothesis. In addition, we will discuss how isolated filament motion responds to variations in the plasma conditions, and specifically divertor conditions. Finally, using the theoretical framework we will reproduce and interpret experimental results obtained on JET, MAST and HL-2A.

Striation and convection in penumbral filaments

Science.gov (United States)

Spruit, H. C.; Scharmer, G. B.; Löfdahl, M. G.

2010-10-01

Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward propagating striations with inclination angles suggesting that they are aligned with the local magnetic field. We interpret it as the equivalent of the striations seen in the walls of small isolated magnetic structures. Their origin is then a corrugation of the boundary between an overturning convective flow inside the filament and the magnetic field wrapping around it. The outward propagation is a combination of a pattern motion due to the downflow observed along the sides of bright filaments, and the Evershed flow. The observed short wavelength of the striation argues against the existence of a dynamically significant horizontal field inside the bright filaments. Its intensity contrast is explained by the same physical effect that causes the dark cores of filaments, light bridges and “canals”. In this way striation represents an important clue to the physics of penumbral structure and its relation with other magnetic structures on the solar surface. We put this in perspective with results from the recent 3-D radiative hydrodynamic simulations. 4 movies are only available in electronic form at http://www.aanda.org

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

Science.gov (United States)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

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. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

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.

Optical spectroscopy using gas-phase femtosecond laser filamentation.

Science.gov (United States)

Odhner, Johanan; Levis, Robert

2014-01-01

Femtosecond laser filamentation occurs as a dynamic balance between the self-focusing and plasma defocusing of a laser pulse to produce ultrashort radiation as brief as a few optical cycles. This unique source has many properties that make it attractive as a nonlinear optical tool for spectroscopy, such as propagation at high intensities over extended distances, self-shortening, white-light generation, and the formation of an underdense plasma. The plasma channel that constitutes a single filament and whose position in space can be controlled by its input parameters can span meters-long distances, whereas multifilamentation of a laser beam can be sustained up to hundreds of meters in the atmosphere. In this review, we briefly summarize the current understanding and use of laser filaments for spectroscopic investigations of molecules. A theoretical framework of filamentation is presented, along with recent experimental evidence supporting the established understanding of filamentation. Investigations carried out on vibrational and rotational spectroscopy, filament-induced breakdown, fluorescence spectroscopy, and backward lasing are discussed.

Brownian motion probe for water-ethanol inhomogeneous mixtures

Science.gov (United States)

Furukawa, Kazuki; Judai, Ken

2017-12-01

Brownian motion provides information regarding the microscopic geometry and motion of molecules, insofar as it occurs as a result of molecular collisions with a colloid particle. We found that the mobility of polystyrene beads from the Brownian motion in a water-ethanol mixture is larger than that predicted from the liquid shear viscosity. This indicates that mixing water and ethanol is inhomogeneous in micron-sized probe beads. The discrepancy between the mobility of Brownian motion and liquid mobility can be explained by the way the rotation of the beads in an inhomogeneous viscous solvent converts the translational movement.

On the fragmentation of filaments in a molecular cloud simulation

Science.gov (United States)

Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.

2018-03-01

increases far more quickly than those identified in two-dimensional column density maps. Conclusions: Our results suggest that hydrostatic or dynamic compression from the surrounding cloud has a significant impact on the early dynamical evolution of filaments. A simple model of an isolated, isothermal cylinder may not provide a good approach for fragmentation analysis. Caution must be exercised in interpreting distributions of properties of filaments identified in column density maps, especially in the case of low-mass filaments. Comparing or combining results from studies that use different filament finding techniques is strongly discouraged.

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

KAUST Repository

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

2015-01-01

© 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.

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.

On some generalization of fractional Brownian motions

International Nuclear Information System (INIS)

Wang Xiaotian; Liang Xiangqian; Ren Fuyao; Zhang Shiying

2006-01-01

The multifractional Brownian motion (mBm) is a continuous Gaussian process that extends the classical fractional Brownian motion (fBm) defined by Barton and Vincent Poor [Barton RJ, Vincent Poor H. IEEE Trans Inform 1988;34(5):943] and Decreusefond and Ustuenel [Decreusefond L, Ustuenel AS. Potential Anal 1999;10:177]. In addition, an innovational representation of fBm is given

Bivariate Gaussian bridges: directional factorization of diffusion in Brownian bridge models.

Science.gov (United States)

Kranstauber, Bart; Safi, Kamran; Bartumeus, Frederic

2014-01-01

In recent years high resolution animal tracking data has become the standard in movement ecology. The Brownian Bridge Movement Model (BBMM) is a widely adopted approach to describe animal space use from such high resolution tracks. One of the underlying assumptions of the BBMM is isotropic diffusive motion between consecutive locations, i.e. invariant with respect to the direction. Here we propose to relax this often unrealistic assumption by separating the Brownian motion variance into two directional components, one parallel and one orthogonal to the direction of the motion. Our new model, the Bivariate Gaussian bridge (BGB), tracks movement heterogeneity across time. Using the BGB and identifying directed and non-directed movement within a trajectory resulted in more accurate utilisation distributions compared to dynamic Brownian bridges, especially for trajectories with a non-isotropic diffusion, such as directed movement or Lévy like movements. We evaluated our model with simulated trajectories and observed tracks, demonstrating that the improvement of our model scales with the directional correlation of a correlated random walk. We find that many of the animal trajectories do not adhere to the assumptions of the BBMM. The proposed model improves accuracy when describing the space use both in simulated correlated random walks as well as observed animal tracks. Our novel approach is implemented and available within the "move" package for R.

Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling.

Science.gov (United States)

Hammond, Nathan A; Kamm, Roger D

2008-07-01

The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long beta-sheets that pair together to form filaments; filaments form bundles approximately 30-60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two beta-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials.

Plasma Brightenings in a Failed Solar Filament Eruption

Energy Technology Data Exchange (ETDEWEB)

Li, Y.; Ding, M. D., E-mail: yingli@nju.edu.cn [School of Astronomy and Space Science, Nanjing University, Nanjing 210023 (China)

2017-03-20

Failed filament eruptions are solar eruptions that are not associated with coronal mass ejections. In a failed filament eruption, the filament materials usually show some ascending and falling motions as well as generating bright EUV emissions. Here we report a failed filament eruption (SOL2016-07-22) that occurred in a quiet-Sun region observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory . In this event, the filament spreads out but gets confined by the surrounding magnetic field. When interacting with the ambient magnetic field, the filament material brightens up and flows along the magnetic field lines through the corona to the chromosphere. We find that some materials slide down along the lifting magnetic structure containing the filament and impact the chromosphere, and through kinetic energy dissipation, cause two ribbon-like brightenings in a wide temperature range. There is evidence suggesting that magnetic reconnection occurs between the filament magnetic structure and the surrounding magnetic fields where filament plasma is heated to coronal temperatures. In addition, thread-like brightenings show up on top of the erupting magnetic fields at low temperatures, which might be produced by an energy imbalance from a fast drop of radiative cooling due to plasma rarefaction. Thus, this single event of a failed filament eruption shows the existence of a variety of plasma brightenings that may be caused by completely different heating mechanisms.

A multiscale approach to Brownian motors

International Nuclear Information System (INIS)

Pavliotis, G.A.

2005-01-01

The problem of Brownian motion in a periodic potential, under the influence of external forcing, which is either random or periodic in time, is studied in this Letter. Multiscale techniques are used to derive general formulae for the steady state particle current and the effective diffusion tensor. These formulae are then applied to calculate the effective diffusion coefficient for a Brownian particle in a periodic potential driven simultaneously by additive Gaussian white and colored noise. Our theoretical findings are supported by numerical simulations

Filament heater current modulation for increased filament lifetime

International Nuclear Information System (INIS)

Paul, J.D.; Williams, H.E. III.

1996-01-01

The surface conversion H-minus ion source employs two 60 mil tungsten filaments which are approximately 17 centimeters in length. These filaments are heated to approximately 2,800 degrees centigrade by 95--100 amperes of DC heater current. The arc is struck at a 120 hertz rate, for 800 microseconds and is generally run at 30 amperes peak current. Although sputtering is considered a contributing factor in the demise of the filament, evaporation is of greater concern. If the peak arc current can be maintained with less average heater current, the filament evaporation rate for this arc current will diminish. In the vacuum of an ion source, the authors expect the filaments to retain much of their heat throughout a 1 millisecond (12% duty) loss of heater current. A circuit to eliminate 100 ampere heater currents from filaments during the arc pulse was developed. The magnetic field due to the 100 ampere current tends to hold electrons to the filament, decreasing the arc current. By eliminating this magnetic field, the arc should be more efficient, allowing the filaments to run at a lower average heater current. This should extend the filament lifetime. The circuit development and preliminary filament results are discussed

Random motion and Brownian rotation

International Nuclear Information System (INIS)

Wyllie, G.

1980-01-01

The course is centred on the Brownian motion - the random movement of molecules arising from thermal fluctuations of the surrounding medium - and starts with the classical theory of A. Einstein, M.v. Smoluchowski and P. Langevin. The first part of this article is quite elementary, and several of the questions raised in it have been instructively treated in a much more sophisticated way in recent reviews by Pomeau and Resibois and by Fox. This simple material may nevertheless be helpful to some readers whose main interest lies in approaching the work on Brownian rotation reviewed in the latter part of the present article. The simplest, and most brutally idealised, problem in our field of interest is that of the random walk in one dimension of space. Its solution leads on, through the diffusivity-mobility relation of Einstein, to Langevin's treatment of the Brownian motion. The application of these ideas to the movement of a molecule in a medium of similar molecules is clearly unrealistic, and much energy has been devoted to finding a suitable generalisation. We shall discuss in particular ideas due to Green, Zwanzig and Mori. (orig./WL)

A dynamic Brownian bridge movement model to estimate utilization distributions for heterogeneous animal movement.

Science.gov (United States)

Kranstauber, Bart; Kays, Roland; Lapoint, Scott D; Wikelski, Martin; Safi, Kamran

2012-07-01

1. The recently developed Brownian bridge movement model (BBMM) has advantages over traditional methods because it quantifies the utilization distribution of an animal based on its movement path rather than individual points and accounts for temporal autocorrelation and high data volumes. However, the BBMM assumes unrealistic homogeneous movement behaviour across all data. 2. Accurate quantification of the utilization distribution is important for identifying the way animals use the landscape. 3. We improve the BBMM by allowing for changes in behaviour, using likelihood statistics to determine change points along the animal's movement path. 4. This novel extension, outperforms the current BBMM as indicated by simulations and examples of a territorial mammal and a migratory bird. The unique ability of our model to work with tracks that are not sampled regularly is especially important for GPS tags that have frequent failed fixes or dynamic sampling schedules. Moreover, our model extension provides a useful one-dimensional measure of behavioural change along animal tracks. 5. This new method provides a more accurate utilization distribution that better describes the space use of realistic, behaviourally heterogeneous tracks. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Fractional Brownian motion and long term clinical trial recruitment.

Science.gov (United States)

Zhang, Qiang; Lai, Dejian

2011-05-01

Prediction of recruitment in clinical trials has been a challenging task. Many methods have been studied, including models based on Poisson process and its large sample approximation by Brownian motion (BM), however, when the independent incremental structure is violated for BM model, we could use fractional Brownian motion to model and approximate the underlying Poisson processes with random rates. In this paper, fractional Brownian motion (FBM) is considered for such conditions and compared to BM model with illustrated examples from different trials and simulations.

Dynamical correlations for circular ensembles of random matrices

International Nuclear Information System (INIS)

Nagao, Taro; Forrester, Peter

2003-01-01

Circular Brownian motion models of random matrices were introduced by Dyson and describe the parametric eigenparameter correlations of unitary random matrices. For symmetric unitary, self-dual quaternion unitary and an analogue of antisymmetric Hermitian matrix initial conditions, Brownian dynamics toward the unitary symmetry is analyzed. The dynamical correlation functions of arbitrary number of Brownian particles at arbitrary number of times are shown to be written in the forms of quaternion determinants, similarly as in the case of Hermitian random matrix models

The mode coupling theory in the FDR-preserving field theory of interacting Brownian particles

International Nuclear Information System (INIS)

Kim, Bongsoo; Kawasaki, Kyozi

2007-01-01

We develop a renormalized perturbation theory for the dynamics of interacting Brownian particles, which preserves the fluctuation-dissipation relation order by order. We then show that the resulting one-loop theory gives a closed equation for the density correlation function, which is identical with that in the standard mode coupling theory. (fast track communication)

Post-filament self-trapping of ultrashort laser pulses.

Science.gov (United States)

Mitrofanov, A V; Voronin, A A; Sidorov-Biryukov, D A; Andriukaitis, G; Flöry, T; Pugžlys, A; Fedotov, A B; Mikhailova, J M; Panchenko, V Ya; Baltuška, A; Zheltikov, A M

2014-08-15

Laser filamentation is understood to be self-channeling of intense ultrashort laser pulses achieved when the self-focusing because of the Kerr nonlinearity is balanced by ionization-induced defocusing. Here, we show that, right behind the ionized region of a laser filament, ultrashort laser pulses can couple into a much longer light channel, where a stable self-guiding spatial mode is sustained by the saturable self-focusing nonlinearity. In the limiting regime of negligibly low ionization, this post-filamentation beam dynamics converges to a large-scale beam self-trapping scenario known since the pioneering work on saturable self-focusing nonlinearities.

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.

Axon initial segment cytoskeleton comprises a multiprotein submembranous coat containing sparse actin filaments

Science.gov (United States)

Jones, Steven L.; Korobova, Farida

2014-01-01

The axon initial segment (AIS) of differentiated neurons regulates action potential initiation and axon–dendritic polarity. The latter function depends on actin dynamics, but actin structure and functions at the AIS remain unclear. Using platinum replica electron microscopy (PREM), we have characterized the architecture of the AIS cytoskeleton in mature and developing hippocampal neurons. The AIS cytoskeleton assembly begins with bundling of microtubules and culminates in formation of a dense, fibrillar–globular coat over microtubule bundles. Immunogold PREM revealed that the coat contains a network of known AIS proteins, including ankyrin G, spectrin βIV, neurofascin, neuronal cell adhesion molecule, voltage-gated sodium channels, and actin filaments. Contrary to existing models, we find neither polarized actin arrays, nor dense actin meshworks in the AIS. Instead, the AIS contains two populations of sparse actin filaments: short, stable filaments and slightly longer dynamic filaments. We propose that stable actin filaments play a structural role for formation of the AIS diffusion barrier, whereas dynamic actin may promote AIS coat remodeling. PMID:24711503

Manipulation and controlled amplification of Brownian motion of microcantilever sensors

International Nuclear Information System (INIS)

Mehta, Adosh; Cherian, Suman; Hedden, David; Thundat, Thomas

2001-01-01

Microcantilevers, such as those used in atomic force microscopy, undergo Brownian motion due to mechanical thermal noise. The root mean square amplitude of the Brownian motion of a cantilever typically ranges from 0.01--0.1 nm, which limits its use in practical applications. Here we describe a technique by which the Brownian amplitude and the Q factor in air and water can be amplified by three and two orders of magnitude, respectively. This technique is similar to a positive feedback oscillator, wherein the Brownian motion of the vibrating cantilever controls the frequency output of the oscillator. This technique can be exploited to improve sensitivity of microcantilever-based chemical and biological sensors, especially for sensors in liquid environments

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

International Nuclear Information System (INIS)

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

2004-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2004-05-15

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

Intermediate Filaments at the Junction of Mechanotransduction, Migration, and Development

Directory of Open Access Journals (Sweden)

Rucha Sanghvi-Shah

2017-09-01

Full Text Available Mechanically induced signal transduction has an essential role in development. Cells actively transduce and respond to mechanical signals and their internal architecture must manage the associated forces while also being dynamically responsive. With unique assembly-disassembly dynamics and physical properties, cytoplasmic intermediate filaments play an important role in regulating cell shape and mechanical integrity. While this function has been recognized and appreciated for more than 30 years, continually emerging data also demonstrate important roles of intermediate filaments in cell signal transduction. In this review, with a particular focus on keratins and vimentin, the relationship between the physical state of intermediate filaments and their role in mechanotransduction signaling is illustrated through a survey of current literature. Association with adhesion receptors such as cadherins and integrins provides a critical interface through which intermediate filaments are exposed to forces from a cell's environment. As a consequence, these cytoskeletal networks are posttranslationally modified, remodeled and reorganized with direct impacts on local signal transduction events and cell migratory behaviors important to development. We propose that intermediate filaments provide an opportune platform for cells to both cope with mechanical forces and modulate signal transduction.

Chip-Based Measurements of Brownian Relaxation of Magnetic Beads Using a Planar Hall Effect Magnetic Field Sensor

DEFF Research Database (Denmark)

Østerberg, Frederik Westergaard; Dalslet, Bjarke Thomas; Snakenborg, Detlef

2010-01-01

using only the self-field arising from the bias current applied to the sensors as excitation field. We present measurements on a suspension of magnetic beads with a nominal diameter of 250 nm vs. temperature and find that the observations are consistent with the Cole-Cole model for Brownian relaxation...... with a constant hydrodynamic bead diameter when the temperature dependence of the viscosity of water is taken into account. These measurements demonstrate the feasibility of performing measurements of the Brownian relaxation response in a lab-on-a-chip system and constitute the first step towards an integrated...... biosensor based on the detection of the dynamic response of magnetic beads....

Quantum harmonic Brownian motion in a general environment: A modified phase-space approach

International Nuclear Information System (INIS)

Yeh, L.

1993-01-01

After extensive investigations over three decades, the linear-coupling model and its equivalents have become the standard microscopic models for quantum harmonic Brownian motion, in which a harmonically bound Brownian particle is coupled to a quantum dissipative heat bath of general type modeled by infinitely many harmonic oscillators. The dynamics of these models have been studied by many authors using the quantum Langevin equation, the path-integral approach, quasi-probability distribution functions (e.g., the Wigner function), etc. However, the quantum Langevin equation is only applicable to some special problems, while other approaches all involve complicated calculations due to the inevitable reduction (i.e., contraction) operation for ignoring/eliminating the degrees of freedom of the heat bath. In this dissertation, the author proposes an improved methodology via a modified phase-space approach which employs the characteristic function (the symplectic Fourier transform of the Wigner function) as the representative of the density operator. This representative is claimed to be the most natural one for performing the reduction, not only because of its simplicity but also because of its manifestation of geometric meaning. Accordingly, it is particularly convenient for studying the time evolution of the Brownian particle with an arbitrary initial state. The power of this characteristic function is illuminated through a detailed study of several physically interesting problems, including the environment-induced damping of quantum interference, the exact quantum Fokker-Planck equations, and the relaxation of non-factorizable initial states. All derivations and calculations axe shown to be much simplified in comparison with other approaches. In addition to dynamical problems, a novel derivation of the fluctuation-dissipation theorem which is valid for all quantum linear systems is presented

Slow kinetics of Brownian maxima.

Science.gov (United States)

Ben-Naim, E; Krapivsky, P L

2014-07-18

We study extreme-value statistics of Brownian trajectories in one dimension. We define the maximum as the largest position to date and compare maxima of two particles undergoing independent Brownian motion. We focus on the probability P(t) that the two maxima remain ordered up to time t and find the algebraic decay P ∼ t(-β) with exponent β = 1/4. When the two particles have diffusion constants D(1) and D(2), the exponent depends on the mobilities, β = (1/π) arctan sqrt[D(2)/D(1)]. We also use numerical simulations to investigate maxima of multiple particles in one dimension and the largest extension of particles in higher dimensions.

Optimum analysis of a Brownian refrigerator.

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Luo, X G; Liu, N; He, J Z

2013-02-01

A Brownian refrigerator with the cold and hot reservoirs alternating along a space coordinate is established. The heat flux couples with the movement of the Brownian particles due to an external force in the spatially asymmetric but periodic potential. After using the Arrhenius factor to describe the behaviors of the forward and backward jumps of the particles, the expressions for coefficient of performance (COP) and cooling rate are derived analytically. Then, through maximizing the product of conversion efficiency and heat flux flowing out, a new upper bound only depending on the temperature ratio of the cold and hot reservoirs is found numerically in the reversible situation, and it is a little larger than the so-called Curzon and Ahlborn COP ε(CA)=(1/√[1-τ])-1. After considering the irreversible factor owing to the kinetic energy change of the moving particles, we find the optimized COP is smaller than ε(CA) and the external force even does negative work on the Brownian particles when they jump from a cold to hot reservoir.

Time rescaling and Gaussian properties of the fractional Brownian motions

International Nuclear Information System (INIS)

Maccone, C.

1981-01-01

The fractional Brownian motions are proved to be a class of Gaussian (normal) stochastic processes suitably rescaled in time. Some consequences affecting their eigenfunction expansion (Karhunen-Loeve expansion) are inferred. A known formula of Cameron and Martin is generalized. The first-passage time probability density is found. The partial differential equation of the fractional Brownian diffusion is obtained. And finally the increments of the fractional Brownian motions are proved to be independent for nonoverlapping time intervals. (author)

How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement

Science.gov (United States)

de Jager, Monique; Bartumeus, Frederic; Kölzsch, Andrea; Weissing, Franz J.; Hengeveld, Geerten M.; Nolet, Bart A.; Herman, Peter M. J.; van de Koppel, Johan

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein's original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern. PMID:24225464

How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement.

Science.gov (United States)

de Jager, Monique; Bartumeus, Frederic; Kölzsch, Andrea; Weissing, Franz J; Hengeveld, Geerten M; Nolet, Bart A; Herman, Peter M J; van de Koppel, Johan

2014-01-07

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein's original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern.

Conformal geometry and invariants of 3-strand Brownian braids

International Nuclear Information System (INIS)

Nechaev, Sergei; Voituriez, Raphael

2005-01-01

We propose a simple geometrical construction of topological invariants of 3-strand Brownian braids viewed as world lines of 3 particles performing independent Brownian motions in the complex plane z. Our construction is based on the properties of conformal maps of doubly-punctured plane z to the universal covering surface. The special attention is paid to the case of indistinguishable particles. Our method of conformal maps allows us to investigate the statistical properties of the topological complexity of a bunch of 3-strand Brownian braids and to compute the expectation value of the irreducible braid length in the non-Abelian case

Area distribution of an elastic Brownian motion

International Nuclear Information System (INIS)

Rajabpour, M A

2009-01-01

We calculate the excursion and meander area distributions of the elastic Brownian motion by using the self-adjoint extension of the Hamiltonian of the free quantum particle on the half line. We also give some comments on the area of the Brownian motion bridge on the real line with the origin removed. We will focus on the power of self-adjoint extension to investigate different possible boundary conditions for the stochastic processes. We also discuss some possible physical applications.

Eigenfunction expansion for fractional Brownian motions

International Nuclear Information System (INIS)

Maccone, C.

1981-01-01

The fractional Brownian motions, a class of nonstationary stochastic processes defined as the Riemann-Liouville fractional integral/derivative of the Brownian motion, are studied. It is shown that these processes can be regarded as the output of a suitable linear system of which the input is the white noise. Their autocorrelation is then derived with a study of their standard-deviation curves. Their power spectra are found by resorting to the nonstationary spectral theory. And finally their eigenfunction expansion (Karhunen-Loeve expansion) is obtained: the eigenfunctions are proved to be suitable Bessel functions and the eigenvalues zeros of the Bessel functions. (author)

Drop dynamics on a stretched viscoelastic filament: An experimental study

Science.gov (United States)

Peixinho, Jorge; Renoult, Marie-Charlotte; Crumeyrolle, Olivier; Mutabazi, Innocent

2016-11-01

Capillary pressure can destabilize a thin liquid filament during breakup into a succession of drops. Besides, the addition of a linear, high molecular weight, flexible and soluble polymer is enough to modify the morphology of this instability. In the time period preceding the breakup, the development of beads-on-a-string structures where drops are connected by thin threads is monitored. The drops dynamics involve drop formation, drop migration and drop coalescence. Experiments using a high-speed camera on stretched bridges of viscoelastic polymeric solutions were conducted for a range of viscosities and polymer concentrations. The rheological properties of the solutions are also quantified through conventional shear rheology and normal stress difference. The overall goal of this experimental investigation is to gain more insight into the formation and time evolution of the drops. The project BIOENGINE is co-financed by the European Union with the European regional development fund and by the Normandie Regional Council.

The open quantum Brownian motions

International Nuclear Information System (INIS)

Bauer, Michel; Bernard, Denis; Tilloy, Antoine

2014-01-01

Using quantum parallelism on random walks as the original seed, we introduce new quantum stochastic processes, the open quantum Brownian motions. They describe the behaviors of quantum walkers—with internal degrees of freedom which serve as random gyroscopes—interacting with a series of probes which serve as quantum coins. These processes may also be viewed as the scaling limit of open quantum random walks and we develop this approach along three different lines: the quantum trajectory, the quantum dynamical map and the quantum stochastic differential equation. We also present a study of the simplest case, with a two level system as an internal gyroscope, illustrating the interplay between the ballistic and diffusive behaviors at work in these processes. Notation H z : orbital (walker) Hilbert space, C Z in the discrete, L 2 (R) in the continuum H c : internal spin (or gyroscope) Hilbert space H sys =H z ⊗H c : system Hilbert space H p : probe (or quantum coin) Hilbert space, H p =C 2 ρ t tot : density matrix for the total system (walker + internal spin + quantum coins) ρ-bar t : reduced density matrix on H sys : ρ-bar t =∫dxdy ρ-bar t (x,y)⊗|x〉 z 〈y| ρ-hat t : system density matrix in a quantum trajectory: ρ-hat t =∫dxdy ρ-hat t (x,y)⊗|x〉 z 〈y|. If diagonal and localized in position: ρ-hat t =ρ t ⊗|X t 〉 z 〈X t | ρ t : internal density matrix in a simple quantum trajectory X t : walker position in a simple quantum trajectory B t : normalized Brownian motion ξ t , ξ t † : quantum noises (paper)

Elastic moduli of a Brownian colloidal glass former

Science.gov (United States)

Fritschi, S.; Fuchs, M.

2018-01-01

The static, dynamic and flow-dependent shear moduli of a binary mixture of Brownian hard disks are studied by an event-driven molecular dynamics simulation. Thereby, the emergence of rigidity close to the glass transition encoded in the static shear modulus G_∞ is accessed by three methods. Results from shear stress auto-correlation functions, elastic dispersion relations, and the elastic response to strain deformations upon the start-up of shear flow are compared. This enables one to sample the time-dependent shear modulus G(t) consistently over several decades in time. By that a very precise specification of the glass transition point and of G_∞ is feasible. Predictions by mode coupling theory of a finite shear modulus at the glass transition, of α-scaling in fluid states close to the transition, and of shear induced decay in yielding glass states are tested and broadly verified.

Deep inelastic collisions viewed as Brownian motion

International Nuclear Information System (INIS)

Gross, D.H.E.; Freie Univ. Berlin

1980-01-01

Non-equilibrium transport processes like Brownian motion, are studied since perhaps 100 years and one should ask why does one not use these theories to explain deep inelastic collision data. These theories have reached a high standard of sophistication, experience, and precision that I believe them to be very usefull for our problem. I will try to sketch a possible form of an advanced theory of Brownian motion that seems to be suitable for low energy heavy ion collisions. (orig./FKS)

Nonparametric Regression with Subfractional Brownian Motion via Malliavin Calculus

Directory of Open Access Journals (Sweden)

Yuquan Cang

2014-01-01

Full Text Available We study the asymptotic behavior of the sequence Sn=∑i=0n-1K(nαSiH1(Si+1H2-SiH2, as n tends to infinity, where SH1 and SH2 are two independent subfractional Brownian motions with indices H1 and H2, respectively. K is a kernel function and the bandwidth parameter α satisfies some hypotheses in terms of H1 and H2. Its limiting distribution is a mixed normal law involving the local time of the sub-fractional Brownian motion SH1. We mainly use the techniques of Malliavin calculus with respect to sub-fractional Brownian motion.

Maximum Principle for General Controlled Systems Driven by Fractional Brownian Motions

International Nuclear Information System (INIS)

Han Yuecai; Hu Yaozhong; Song Jian

2013-01-01

We obtain a maximum principle for stochastic control problem of general controlled stochastic differential systems driven by fractional Brownian motions (of Hurst parameter H>1/2). This maximum principle specifies a system of equations that the optimal control must satisfy (necessary condition for the optimal control). This system of equations consists of a backward stochastic differential equation driven by both fractional Brownian motions and the corresponding underlying standard Brownian motions. In addition to this backward equation, the maximum principle also involves the Malliavin derivatives. Our approach is to use conditioning and Malliavin calculus. To arrive at our maximum principle we need to develop some new results of stochastic analysis of the controlled systems driven by fractional Brownian motions via fractional calculus. Our approach of conditioning and Malliavin calculus is also applied to classical system driven by standard Brownian motions while the controller has only partial information. As a straightforward consequence, the classical maximum principle is also deduced in this more natural and simpler way.

Prokaryotic DNA segregation by an actin-like filament

DEFF Research Database (Denmark)

Møller-Jensen, Jakob; Bugge Jensen, Rasmus; Löwe, Jan

2002-01-01

The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments with prop...... point for ParM polymerization. Hence, we provide evidence for a simple prokaryotic analogue of the eukaryotic mitotic spindle apparatus.......The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments...

On the motion of a Brownian particle with an asymmetric bias

International Nuclear Information System (INIS)

Kim, K.S.

1981-01-01

On the infinite three dimensional cubic lattice, the transport process of a Brownian particle biased on the direction (in the case of nearest-neighbor jumping) is discussed. The Brownian particle is considered as a walker of the random process. By introducing the theorem that the probability density P(l,t) becomes Gaussian for large t, P(l,t) is completely specified when the first and second moments of P(l,t) become known. The respective values for the transprot averaged velocity and dispersion of a biased Brownian particle are obtained. Finally as t becomes large we find Gaussian packets of a biased Brownian particle which propagate with a constant velocity and have a dispersion proportional to time t. (KAERI)

Topology of interaction between titin and myosin thick filaments.

Science.gov (United States)

Kellermayer, Miklós; Sziklai, Dominik; Papp, Zsombor; Decker, Brennan; Lakatos, Eszter; Mártonfalvi, Zsolt

2018-05-05

Titin is a giant protein spanning between the Z- and M-lines of the sarcomere. In the A-band titin is associated with the myosin thick filament. It has been speculated that titin may serve as a blueprint for thick-filament formation due to the super-repeat structure of its A-band domains. Accordingly, titin might provide a template that determines the length and structural periodicity of the thick filament. Here we tested the titin ruler hypothesis by mixing titin and myosin at in situ stoichiometric ratios (300 myosins per 12 titins) in buffers of different ionic strength (KCl concentration range 100-300 mM). The topology of the filamentous complexes was investigated with atomic force microscopy. We found that the samples contained distinct, segregated populations of titin molecules and myosin thick filaments. We were unable to identify complexes in which myosin molecules were regularly associated to either mono- or oligomeric titin in either relaxed or stretched states of the titin filaments. Thus, the electrostatically driven self-association is stronger in both myosin and titin than their binding to each other, and it is unlikely that titin functions as a geometrical template for thick-filament formation. However, when allowed to equilibrate configurationally, long myosin thick filaments appeared with titin oligomers attached to their surface. The titin meshwork formed on the thick-filament surface may play a role in controlling thick-filament length by regulating the structural dynamics of myosin molecules and placing a mechanical limit on the filament length. Copyright © 2018 Elsevier Inc. All rights reserved.

Laser-induced filaments in the mid-infrared

International Nuclear Information System (INIS)

Zheltikov, A M

2017-01-01

Laser-induced filamentation in the mid-infrared gives rise to unique regimes of nonlinear wave dynamics and reveals in many ways unusual nonlinear-optical properties of materials in this frequency range. The λ 2 scaling of the self-focusing threshold P cr , with radiation wavelength λ , allows the laser powers transmitted by single mid-IR filaments to be drastically increased without the loss of beam continuity and spatial coherence. When extended to the mid-infrared, laser filamentation enables new methods of pulse compression. Often working around the universal physical limitations, it helps generate few-cycle and subcycle field waveforms within an extraordinarily broad range of peak powers, from just a few up to hundreds of P cr . As a part of a bigger picture, laser-induced filamentation in the mid-infrared offers important physical insights into the general properties of the nonlinear-optical response of matter as a function of the wavelength. Unlike their near-infrared counterparts, which can be accurately described within the framework of perturbative nonlinear optics, mid-infrared filaments often entangle perturbative and nonperturbative nonlinear-optical effects, showing clear signatures of strong-field optical physics. With the role of nonperturbative nonlinear-optical phenomena growing, as a general tendency, with the field intensity and the driver wavelength, extension of laser filamentation to even longer driver wavelengths, toward the long-wavelength infrared, promises a hic sunt dracones land. (topical review)

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.

Science.gov (United States)

Cheng, Mary Hongying; Coalson, Rob D; Tang, Pei

2010-11-24

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.

Fast orthogonal transforms and generation of Brownian paths.

Science.gov (United States)

Leobacher, Gunther

2012-04-01

We present a number of fast constructions of discrete Brownian paths that can be used as alternatives to principal component analysis and Brownian bridge for stratified Monte Carlo and quasi-Monte Carlo. By fast we mean that a path of length [Formula: see text] can be generated in [Formula: see text] floating point operations. We highlight some of the connections between the different constructions and we provide some numerical examples.

Intermediate Filaments as Organizers of Cellular Space: How They Affect Mitochondrial Structure and Function.

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Schwarz, Nicole; Leube, Rudolf E

2016-07-05

Intermediate filaments together with actin filaments and microtubules form the cytoskeleton, which is a complex and highly dynamic 3D network. Intermediate filaments are the major mechanical stress protectors but also affect cell growth, differentiation, signal transduction, and migration. Using intermediate filament-mitochondrial crosstalk as a prominent example, this review emphasizes the importance of intermediate filaments as crucial organizers of cytoplasmic space to support these functions. We summarize observations in different mammalian cell types which demonstrate how intermediate filaments influence mitochondrial morphology, subcellular localization, and function through direct and indirect interactions and how perturbations of these interactions may lead to human diseases.

Superresolution imaging of dynamic MreB filaments in B. subtilis--a multiple-motor-driven transport?

Science.gov (United States)

Olshausen, Philipp V; Defeu Soufo, Hervé Joël; Wicker, Kai; Heintzmann, Rainer; Graumann, Peter L; Rohrbach, Alexander

2013-09-03

The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillus subtilis cells, MreB forms filamentous structures of variable lengths, typically not longer than 1 μm. These filaments move along their orientation and mainly perpendicular to the long bacterial axis, revealing a maximal velocity at an intermediate length and a decreasing velocity with increasing filament length. Filaments move along straight trajectories but can reverse or alter their direction of propagation. Based on our measurements, we provide a mechanistic model that is consistent with all observations. In this model, MreB filaments mechanically couple several motors that putatively synthesize the cell wall, whereas the filaments' traces mirror the trajectories of the motors. On the basis of our mechanistic model, we developed a mathematical model that can explain the nonlinear velocity length dependence. We deduce that the coupling of cell wall synthesis motors determines the MreB filament transport velocity, and the filament mechanically controls a concerted synthesis of parallel peptidoglycan strands to improve cell wall stability. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Directed motion of a Brownian motor in a temperature gradient

Science.gov (United States)

Liu, Yibing; Nie, Wenjie; Lan, Yueheng

2017-05-01

Directed motion of mesoscopic systems in a non-equilibrium environment is of great interest to both scientists and engineers. Here, the translation and rotation of a Brownian motor is investigated under non-equilibrium conditions. An anomalous directed translation is found if the two heads of the Brownian motor are immersed in baths with different particle masses, which is hinted in the analytic computation and confirmed by the numerical simulation. Similar consideration is also used to find the directed movement in the single rotational and translational degree of freedom of the Brownian motor when residing in one thermal bath with a temperature gradient.

Subarcsecond bright points and quasi-periodic upflows below a quiescent filament observed by IRIS

Science.gov (United States)

Li, T.; Zhang, J.

2016-05-01

Context. The new Interface Region Imaging Spectrograph (IRIS) mission provides high-resolution observations of UV spectra and slit-jaw images (SJIs). These data have become available for investigating the dynamic features in the transition region (TR) below the on-disk filaments. Aims: The driver of "counter-streaming" flows along the filament spine is still unknown yet. The magnetic structures and the upflows at the footpoints of the filaments and their relations with the filament mainbody have not been well understood. We study the dynamic evolution at the footpoints of filaments in order to find some clues for solving these questions. Methods: Using UV spectra and SJIs from the IRIS, along with coronal images and magnetograms from the Solar Dynamics Observatory (SDO), we present the new features in a quiescent filament channel: subarcsecond bright points (BPs) and quasi-periodic upflows. Results: The BPs in the TR have a spatial scale of about 350-580 km and lifetimes of more than several tens of minutes. They are located at stronger magnetic structures in the filament channel with a magnetic flux of about 1017-1018 Mx. Quasi-periodic brightenings and upflows are observed in the BPs, and the period is about 4-5 min. The BP and the associated jet-like upflow comprise a "tadpole-shaped" structure. The upflows move along bright filament threads, and their directions are almost parallel to the spine of the filament. The upflows initiated from the BPs with opposite polarity magnetic fields have opposite directions. The velocity of the upflows in the plane of sky is about 5-50 km s-1. The emission line of Si IV 1402.77 Å at the locations of upflows exhibits obvious blueshifts of about 5-30 km s-1, and the line profile is broadened with the width of more than 20 km s-1. Conclusions: The BPs seem to be the bases of filament threads, and the upflows are able to convey mass for the dynamic balance of the filament. The "counter-streaming" flows in previous observations

Mathematical interpretation of Brownian motor model: Limit cycles and directed transport phenomena

Science.gov (United States)

Yang, Jianqiang; Ma, Hong; Zhong, Suchuang

2018-03-01

In this article, we first suggest that the attractor of Brownian motor model is one of the reasons for the directed transport phenomenon of Brownian particle. We take the classical Smoluchowski-Feynman (SF) ratchet model as an example to investigate the relationship between limit cycles and directed transport phenomenon of the Brownian particle. We study the existence and variation rule of limit cycles of SF ratchet model at changing parameters through mathematical methods. The influences of these parameters on the directed transport phenomenon of a Brownian particle are then analyzed through numerical simulations. Reasonable mathematical explanations for the directed transport phenomenon of Brownian particle in SF ratchet model are also formulated on the basis of the existence and variation rule of the limit cycles and numerical simulations. These mathematical explanations provide a theoretical basis for applying these theories in physics, biology, chemistry, and engineering.

Stochastic calculus of protein filament formation under spatial confinement

Science.gov (United States)

Michaels, Thomas C. T.; Dear, Alexander J.; Knowles, Tuomas P. J.

2018-05-01

The growth of filamentous aggregates from precursor proteins is a process of central importance to both normal and aberrant biology, for instance as the driver of devastating human disorders such as Alzheimer's and Parkinson's diseases. The conventional theoretical framework for describing this class of phenomena in bulk is based upon the mean-field limit of the law of mass action, which implicitly assumes deterministic dynamics. However, protein filament formation processes under spatial confinement, such as in microdroplets or in the cellular environment, show intrinsic variability due to the molecular noise associated with small-volume effects. To account for this effect, in this paper we introduce a stochastic differential equation approach for investigating protein filament formation processes under spatial confinement. Using this framework, we study the statistical properties of stochastic aggregation curves, as well as the distribution of reaction lag-times. Moreover, we establish the gradual breakdown of the correlation between lag-time and normalized growth rate under spatial confinement. Our results establish the key role of spatial confinement in determining the onset of stochasticity in protein filament formation and offer a formalism for studying protein aggregation kinetics in small volumes in terms of the kinetic parameters describing the aggregation dynamics in bulk.

Comparisons of actin filament disruptors and Rho kinase inhibitors as potential antiglaucoma medications

OpenAIRE

Tian, Baohe; Kaufman, Paul L

2012-01-01

Dynamics of the actin cytoskeleton in the trabecular meshwork play a crucial role in the regulation of trabecular outflow resistance. The actin filament disruptors and Rho kinase inhibitors affect the dynamics of the actomyosin system by either disrupting the actin filaments or inhibiting the Rho kinase-activated cellular contractility. Both approaches induce similar morphological changes and resistance decreases in the trabecular outflow pathway, and thus both have potential as antiglaucoma ...

Flux Cancellation Leading to CME Filament Eruptions

Science.gov (United States)

Popescu, Roxana M.; Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L.

2016-01-01

Solar filaments are strands of relatively cool, dense plasma magnetically suspended in the lower density hotter solar corona. They trace magnetic polarity inversion lines (PILs) in the photosphere below, and are supported against gravity at heights of up to approx.100 Mm above the chromosphere by the magnetic field in and around them. This field erupts when it is rendered unstable, often by magnetic flux cancellation or emergence at or near the PIL. We have studied the evolution of photospheric magnetic flux leading to ten observed filament eruptions. Specifically, we look for gradual magnetic changes in the neighborhood of the PIL prior to and during eruption. We use Extreme Ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA), and magnetograms from the Helioseismic and Magnetic Imager (HMI), both on board the Solar Dynamics Observatory (SDO), to study filament eruptions and their photospheric magnetic fields. We examine whether flux cancellation or/and emergence leads to filament eruptions. We find that continuous flux cancellation was present at the PIL for many hours prior to each eruption. We present two CME-producing eruptions in detail and find the following: (a) the pre-eruption filament-holding core field is highly sheared and appears in the shape of a sigmoid above the PIL; (b) at the start of the eruption the opposite arms of the sigmoid reconnect in the middle above the site of (tether-cutting) flux cancellation at the PIL; (c) the filaments first show a slow-rise, followed by a fast-rise as they erupt. We conclude that these two filament eruptions result from flux cancellation in the middle of the sheared field, and thereafter evolve in agreement with the standard model for a CME/flare filament eruption from a closed bipolar magnetic field [flux cancellation (van Ballegooijen and Martens 1989 and Moore and Roumelrotis 1992) and runaway tether-cutting (Moore et. al 2001)].

Profilin-Dependent Nucleation and Assembly of Actin Filaments Controls Cell Elongation in Arabidopsis1[OPEN

Science.gov (United States)

Cao, Lingyan; Blanchoin, Laurent; Staiger, Christopher J.

2016-01-01

Actin filaments in plant cells are incredibly dynamic; they undergo incessant remodeling and assembly or disassembly within seconds. These dynamic events are choreographed by a plethora of actin-binding proteins, but the exact mechanisms are poorly understood. Here, we dissect the contribution of Arabidopsis (Arabidopsis thaliana) PROFILIN1 (PRF1), a conserved actin monomer-binding protein, to actin organization and single filament dynamics during axial cell expansion of living epidermal cells. We found that reduced PRF1 levels enhanced cell and organ growth. Surprisingly, we observed that the overall frequency of nucleation events in prf1 mutants was dramatically decreased and that a subpopulation of actin filaments that assemble at high rates was reduced. To test whether profilin cooperates with plant formin proteins to execute actin nucleation and rapid filament elongation in cells, we used a pharmacological approach. Here, we used Small Molecule Inhibitor of Formin FH2 (SMIFH2), after validating its mode of action on a plant formin in vitro, and observed a reduced nucleation frequency of actin filaments in live cells. Treatment of wild-type epidermal cells with SMIFH2 mimicked the phenotype of prf1 mutants, and the nucleation frequency in prf1-2 mutant was completely insensitive to these treatments. Our data provide compelling evidence that PRF1 coordinates the stochastic dynamic properties of actin filaments by modulating formin-mediated actin nucleation and assembly during plant cell expansion. PMID:26574597

Non-colliding Brownian Motions and the Extended Tacnode Process

Science.gov (United States)

Johansson, Kurt

2013-04-01

We consider non-colliding Brownian motions with two starting points and two endpoints. The points are chosen so that the two groups of Brownian motions just touch each other, a situation that is referred to as a tacnode. The extended kernel for the determinantal point process at the tacnode point is computed using new methods and given in a different form from that obtained for a single time in previous work by Delvaux, Kuijlaars and Zhang. The form of the extended kernel is also different from that obtained for the extended tacnode kernel in another model by Adler, Ferrari and van Moerbeke. We also obtain the correlation kernel for a finite number of non-colliding Brownian motions starting at two points and ending at arbitrary points.

Biased Brownian motion mechanism for processivity and directionality of single-headed myosin-VI.

Science.gov (United States)

Iwaki, Mitsuhiro; Iwane, Atsuko Hikikoshi; Ikebe, Mitsuo; Yanagida, Toshio

2008-01-01

Conventional form to function as a vesicle transporter is not a 'single molecule' but a coordinated 'two molecules'. The coordinated two molecules make it complicated to reveal its mechanism. To overcome the difficulty, we adopted a single-headed myosin-VI as a model protein. Myosin-VI is an intracellular vesicle and organelle transporter that moves along actin filaments in a direction opposite to most other known myosin classes. The myosin-VI was expected to form a dimer to move processively along actin filaments with a hand-over-hand mechanism like other myosin organelle transporters. However, wild-type myosin-VI was demonstrated to be monomer and single-headed, casting doubt on its processivity. Using single molecule techniques, we show that green fluorescent protein (GFP)-fused single-headed myosin-VI does not move processively. However, when coupled to a 200 nm polystyrene bead (comparable to an intracellular vesicle in size) at a ratio of one head per bead, single-headed myosin-VI moves processively with large (40 nm) steps. Furthermore, we found that a single-headed myosin-VI-bead complex moved more processively in a high-viscous solution (40-fold higher than water) similar to cellular environment. Because diffusion of the bead is 60-fold slower than myosin-VI heads alone in water, we propose a model in which the bead acts as a diffusional anchor for the myosin-VI, enhancing the head's rebinding following detachment and supporting processive movement of the bead-monomer complex. This investigation will help us understand how molecular motors utilize Brownian motion in cells.

Entropic Approach to Brownian Movement.

Science.gov (United States)

Neumann, Richard M.

1980-01-01

A diffusional driving force, called the radial force, which is responsible for the increase with time of the scalar separation between a fixed point and a particle undergoing three-dimensional Brownian motion, is derived using Boltzmann's equation. (Author/HM)

Exponential functionals of Brownian motion, I: Probability laws at fixed time

OpenAIRE

Matsumoto, Hiroyuki; Yor, Marc

2005-01-01

This paper is the first part of our survey on various results about the distribution of exponential type Brownian functionals defined as an integral over time of geometric Brownian motion. Several related topics are also mentioned.

Rapid Formation and Disappearance of a Filament Barb

Science.gov (United States)

Joshi, Anand D.; Srivastava, Nandita; Mathew, Shibu K.; Martin, Sara F.

2013-11-01

We present observations of an activated quiescent filament obtained in Hα from the high-resolution Dutch Open Telescope (DOT) on 20 August 2010. The filament developed a barb in 10 min, which disappeared within the next 35 min. A data set from the DOT spanning 2 h was used to analyse this event. Line-of-sight velocity maps were constructed from the Doppler images, which reveal flows in filament spine during this period. Photospheric magnetograms were used from the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) to determine the changes in magnetic flux in the region surrounding the barb location. The analysis shows flows in the filament spine towards the barb location preceding its formation, and flows in the barb towards the spine during its disappearance. Magnetograms reveal patches of minority polarity flux close to the end of the barb at its greatest elongation. The flows in the spine and barbs are along numerous threads that compose these typical filament structures. The flows are consistent with field-aligned threads and demonstrate that the replacement time of the mass in barbs, and by inference, in the spine is very rapid.

Mutation-specific effects on thin filament length in thin filament myopathy.

Science.gov (United States)

Winter, Josine M de; Joureau, Barbara; Lee, Eun-Jeong; Kiss, Balázs; Yuen, Michaela; Gupta, Vandana A; Pappas, Christopher T; Gregorio, Carol C; Stienen, Ger J M; Edvardson, Simon; Wallgren-Pettersson, Carina; Lehtokari, Vilma-Lotta; Pelin, Katarina; Malfatti, Edoardo; Romero, Norma B; Engelen, Baziel G van; Voermans, Nicol C; Donkervoort, Sandra; Bönnemann, C G; Clarke, Nigel F; Beggs, Alan H; Granzier, Henk; Ottenheijm, Coen A C

2016-06-01

Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force-sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin-thick filament overlap. These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. Ann Neurol 2016;79:959-969. © 2016 American Neurological Association.

Breaking the symmetry of a Brownian motor with symmetric potentials

International Nuclear Information System (INIS)

Hagman, H; Zelan, M; Dion, C M

2011-01-01

The directed transport of Brownian particles requires a system with an asymmetry and with non-equilibrium noise. Here we investigate numerically alternative ways of fulfilling these requirements for a two-state Brownian motor, realized with Brownian particles alternating between two phase-shifted, symmetric potentials. We show that, besides the previously known spatio-temporal asymmetry based on unequal transfer rates between the potentials, inequalities in the potential depths, the frictions, or the equilibrium temperatures of the two potentials also generate the required asymmetry. We also show that the effects of the thermal noise and the noise of the transfer's randomness depend on the way the asymmetry is induced.

Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.

Directory of Open Access Journals (Sweden)

Chen Song

Full Text Available The macroscopic Nernst-Planck (NP theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.

Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.

Science.gov (United States)

Song, Chen; Corry, Ben

2011-01-01

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.

Diffusion in one dimensional random medium and hyperbolic Brownian motion

International Nuclear Information System (INIS)

Comtet, A.; Monthus, C.; Paris-6 Univ., 75

1995-03-01

Classical diffusion in a random medium involves an exponential functional of Brownian motion. This functional also appears in the study of Brownian diffusion on a Riemann surface of constant negative curvature. This relationship is analyzed in detail and various distributions are studied using stochastic calculus and functional integration. (author) 17 refs

Simple Brownian diffusion an introduction to the standard theoretical models

CERN Document Server

Gillespie, Daniel T

2013-01-01

Brownian diffusion, the motion of large molecules in a sea of very many much smaller molecules, is topical because it is one of the ways in which biologically important molecules move about inside living cells. This book presents the mathematical physics that underlies the four simplest models of Brownian diffusion.

Brownian dynamics simulations with stiff finitely extensible nonlinear elastic-Fraenkel springs as approximations to rods in bead-rod models.

Science.gov (United States)

Hsieh, Chih-Chen; Jain, Semant; Larson, Ronald G

2006-01-28

A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations.

Type III intermediate filaments desmin, glial fibrillary acidic protein (GFAP), vimentin, and peripherin

NARCIS (Netherlands)

Hol, Elly M.; Capetanaki, Yassemi

2017-01-01

Type III intermediate filament (IF) proteins assemble into cytoplasmic homopolymeric and heteropolymeric filaments with other type III and some type IV IFs. These highly dynamic structures form an integral component of the cytoskeleton of muscle, brain, and mesenchymal cells. Here, we review the

Type III Intermediate Filaments Desmin, Glial Fibrillary Acidic Protein (GFAP), Vimentin, and Peripherin

NARCIS (Netherlands)

Hol, Elly M; Capetanaki, Yassemi

2017-01-01

SummaryType III intermediate filament (IF) proteins assemble into cytoplasmic homopolymeric and heteropolymeric filaments with other type III and some type IV IFs. These highly dynamic structures form an integral component of the cytoskeleton of muscle, brain, and mesenchymal cells. Here, we review

Meandering Brownian Donkeys

Science.gov (United States)

Eichhorn, R.; Reimann, P.

2004-04-01

We consider a Brownian particle whose motion is confined to a ``meandering'' pathway and which is driven away from thermal equilibrium by an alternating external force. This system exhibits absolute negative mobility, i.e. when an external static force is applied the particle moves in the direction opposite to that force. We reveal the physical mechanism behind this ``donkey-like'' behavior, and derive analytical approximations that are in excellent agreement with numerical results.

Meandering Brownian Donkeys

International Nuclear Information System (INIS)

Eichhorn, R.; Reimann, P.

2004-01-01

We consider a Brownian particle whose motion is confined to a ''meandering'' pathway and which is driven away from thermal equilibrium by an alternating external force. This system exhibits absolute negative mobility, i.e. when an external static force is applied the particle moves in the direction opposite to that force. We reveal the physical mechanism behind this ''donkey-like'' behavior, and derive analytical approximations that are in excellent agreement with numerical results. (author)

Stochastic flows in the Brownian web and net

Czech Academy of Sciences Publication Activity Database

Schertzer, E.; Sun, R.; Swart, Jan M.

2014-01-01

Roč. 227, č. 1065 (2014), s. 1-160 ISSN 0065-9266 R&D Projects: GA ČR GA201/07/0237; GA ČR GA201/09/1931 Institutional support: RVO:67985556 Keywords : Brownian web * Brownian net * stochastic flow of kernels * measure-valued process * Howitt-Warren flow * linear system * random walk in random environment * finite graph representation Subject RIV: BA - General Mathematics Impact factor: 1.727, year: 2014 http://library.utia.cas.cz/separaty/2013/SI/swart-0396636.pdf

The Intersection Probability of Brownian Motion and SLEκ

Directory of Open Access Journals (Sweden)

Shizhong Zhou

2015-01-01

Full Text Available By using excursion measure Poisson kernel method, we obtain a second-order differential equation of the intersection probability of Brownian motion and SLEκ. Moreover, we find a transformation such that the second-order differential equation transforms into a hypergeometric differential equation. Then, by solving the hypergeometric differential equation, we obtain the explicit formula of the intersection probability for the trace of the chordal SLEκ and planar Brownian motion started from distinct points in an upper half-plane H-.

A one-dimensional gravitationally interacting gas and the convex minorant of Brownian motion

International Nuclear Information System (INIS)

Suidan, T M

2001-01-01

The surprising connection between a one-dimensional gravitationally interacting gas of sticky particles and the convex minorant process generated by Brownian motion on [0,1] is studied. A study is made of the dynamics of this 1-D gas system by identifying three distinct clustering regimes and the time scales at which they occur. At the critical moment of time the mass distribution of the gas can be computed in terms of functionals of the convex minorant process

Active Brownian particles with velocity-alignment and active fluctuations

International Nuclear Information System (INIS)

Großmann, R; Schimansky-Geier, L; Romanczuk, P

2012-01-01

We consider a model of active Brownian particles (ABPs) with velocity alignment in two spatial dimensions with passive and active fluctuations. Here, active fluctuations refers to purely non-equilibrium stochastic forces correlated with the heading of an individual active particle. In the simplest case studied here, they are assumed to be independent stochastic forces parallel (speed noise) and perpendicular (angular noise) to the velocity of the particle. On the other hand, passive fluctuations are defined by a noise vector independent of the direction of motion of a particle, and may account, for example, for thermal fluctuations. We derive a macroscopic description of the ABP gas with velocity-alignment interaction. Here, we start from the individual-based description in terms of stochastic differential equations (Langevin equations) and derive equations of motion for the coarse-grained kinetic variables (density, velocity and temperature) via a moment expansion of the corresponding probability density function. We focus here on the different impact of active and passive fluctuations on onset of collective motion and show how active fluctuations in the active Brownian dynamics can change the phase-transition behaviour of the system. In particular, we show that active angular fluctuations lead to an earlier breakdown of collective motion and to the emergence of a new bistable regime in the mean-field case. (paper)

Quantum description of the Brownian movement in an external field

International Nuclear Information System (INIS)

Svin'in, I.R.

1976-01-01

The Schroedinger equation for brownian motion in an external field is obtained on the basis of the classical Langevin equation. The specific features of the approach proposed are illustrated by the example of the brownian motion of the quantum oscillator. The influence of the fluctuations on the various physical quantities is considered

Reflected Brownian motions in the KPZ universality class

CERN Document Server

Weiss, Thomas; Spohn, Herbert

2017-01-01

This book presents a detailed study of a system of interacting Brownian motions in one dimension. The interaction is point-like such that the n-th Brownian motion is reflected from the Brownian motion with label n-1. This model belongs to the Kardar-Parisi-Zhang (KPZ) universality class. In fact, because of the singular interaction, many universal properties can be established with rigor. They depend on the choice of initial conditions. Discussion addresses packed and periodic initial conditions (Chapter 5), stationary initial conditions (Chapter 6), and mixtures thereof (Chapter 7). The suitably scaled spatial process will be proven to converge to an Airy process in the long time limit. A chapter on determinantal random fields and another one on Airy processes are added to have the notes self-contained. These notes serve as an introduction to the KPZ universality class, illustrating the main concepts by means of a single model only. The notes will be of interest to readers from interacting diffusion processe...

Electromechanical vortex filaments during cardiac fibrillation

Science.gov (United States)

Christoph, J.; Chebbok, M.; Richter, C.; Schröder-Schetelig, J.; Bittihn, P.; Stein, S.; Uzelac, I.; Fenton, F. H.; Hasenfuß, G.; Gilmour, R. F., Jr.; Luther, S.

2018-03-01

The self-organized dynamics of vortex-like rotating waves, which are also known as scroll waves, are the basis of the formation of complex spatiotemporal patterns in many excitable chemical and biological systems. In the heart, filament-like phase singularities that are associated with three-dimensional scroll waves are considered to be the organizing centres of life-threatening cardiac arrhythmias. The mechanisms that underlie the onset, maintenance and control of electromechanical turbulence in the heart are inherently three-dimensional phenomena. However, it has not previously been possible to visualize the three-dimensional spatiotemporal dynamics of scroll waves inside cardiac tissues. Here we show that three-dimensional mechanical scroll waves and filament-like phase singularities can be observed deep inside the contracting heart wall using high-resolution four-dimensional ultrasound-based strain imaging. We found that mechanical phase singularities co-exist with electrical phase singularities during cardiac fibrillation. We investigated the dynamics of electrical and mechanical phase singularities by simultaneously measuring the membrane potential, intracellular calcium concentration and mechanical contractions of the heart. We show that cardiac fibrillation can be characterized using the three-dimensional spatiotemporal dynamics of mechanical phase singularities, which arise inside the fibrillating contracting ventricular wall. We demonstrate that electrical and mechanical phase singularities show complex interactions and we characterize their dynamics in terms of trajectories, topological charge and lifetime. We anticipate that our findings will provide novel perspectives for non-invasive diagnostic imaging and therapeutic applications.

Survival probabilities for branching Brownian motion with absorption

OpenAIRE

Harris, John; Harris, Simon

2007-01-01

We study a branching Brownian motion (BBM) with absorption, in which particles move as Brownian motions with drift $-\\rho$, undergo dyadic branching at rate $\\beta>0$, and are killed on hitting the origin. In the case $\\rho>\\sqrt{2\\beta}$ the extinction time for this process, $\\zeta$, is known to be finite almost surely. The main result of this article is a large-time asymptotic formula for the survival probability $P^x(\\zeta>t)$ in the case $\\rho>\\sqrt{2\\beta}$, where $P^x$ is...

MATERIAL SUPPLY AND MAGNETIC CONFIGURATION OF AN ACTIVE REGION FILAMENT

Energy Technology Data Exchange (ETDEWEB)

Zou, P.; Fang, C.; Chen, P. F.; Yang, K.; Hao, Q. [School of Astronomy and Space Science, Nanjing University, Nanjing 210023 (China); Cao, Wenda, E-mail: fangc@nju.edu.cn [Big Bear Solar Observatory, New Jersey Institute of Technology, 40386 North Shore Lane, Big Bear City, CA 92314 (United States)

2016-11-10

It is important to study the fine structures of solar filaments with high-resolution observations, since it can help us understand the magnetic and thermal structures of the filaments and their dynamics. In this paper, we study a newly formed filament located inside the active region NOAA 11762, which was observed by the 1.6 m New Solar Telescope at Big Bear Solar Observatory from 16:40:19 UT to 17:07:58 UT on 2013 June 5. As revealed by the H α filtergrams, cool material is seen to be injected into the filament spine with a speed of 5–10 km s{sup -1}. At the source of the injection, brightenings are identified in the chromosphere, which are accompanied by magnetic cancellation in the photosphere, implying the importance of magnetic reconnection in replenishing the filament with plasmas from the lower atmosphere. Counter-streamings are detected near one endpoint of the filament, with the plane-of-the-sky speed being 7–9 km s{sup -1} in the H α red-wing filtergrams and 9–25 km s{sup -1} in the blue-wing filtergrams. The observations are indicative that this active region filament is supported by a sheared arcade without magnetic dips, and the counter-streamings are due to unidirectional flows with alternative directions, rather than due to the longitudinal oscillations of filament threads as in many other filaments.

Filamentation and networking of electric currents in dense Z-pinch plasmas

International Nuclear Information System (INIS)

Kukushkin, A.B.; Rantsev-Kartinov, V.A.

2001-01-01

The results of high-resolution processing using the multilevel dynamical contrasting method of earlier experiments on linear Z-pinches are presented which illustrate formation of a dynamical percolating network woven by long-living filaments of electric current. A qualitative approach is outlined which treats long-living filaments as a classical plasma formation governed by the long-range quantum bonds provided, at the microscopical level, by nanotubes of elements of optimal valence. The self-similarity of structuring in laboratory and cosmic plasmas is shown, and examples are found of nanotube-like and/or fullerene-like structures of cosmic length scales. (author)

Filamentation and networking of electric currents in dense Z-pinch plasmas

International Nuclear Information System (INIS)

Kukushkin, A.B.; Rantsev-Kartinov, V.A.

1999-01-01

The results of high-resolution processing using the multilevel dynamical contrasting method of earlier experiments on linear Z-pinches are presented which illustrate formation of a dynamical percolating network woven by long-living filaments of electric current. A qualitative approach is outlined which treats long-living filaments as a classical plasma formation governed by the long-range quantum bonds provided, at the micro-scopical level, by nanotubes of elements of optimal valence. The self-similarity of structuring in laboratory and cosmic plasmas is shown, and examples are found of nanotube-like and/or fullerene-like structures of cosmic length scales. (author)

Phase transition for absorbed Brownian motion with drift

International Nuclear Information System (INIS)

Ferrari, P.A.; Martinez, S.; San Martin, J.

1997-01-01

We study one-dimensional Brownian motion with constant drift toward the origin and initial distribution concentrated in the strictly positive real line. We say that at the first time the process hits the origin, it is absorbed. We study the asymptotic behavior, as t → ∞, of m t , the conditional distribution at time zero of the process conditioned on survival up to time t and on the process having a fixed value at time t. We find that there is a phase transition in the decay rate of the initial condition. For fast decay rate (subcritical case) m t is localized, in the critical case m t is located around √t, and for slow rates (supercritical case) m, is located around t. The critical rate is given by the decay of the minimal quasistationary distribution of this process. We also study in each case the asymptotic distribution of the process, scaled by √t, conditioned as before. We prove that in the subcritical case this distribution is a Brownian excursion. In the critical case it is a Brownian bridge attaining 0 for the first time at time 1, with some initial distribution. In the supercritical case, after centering around the expected value-which is of the order of t we show that this process converges to a Brownian bridge arriving at 0 at time 1 and with a Gaussian initial distribution

Algorithm for generating a Brownian motion on a sphere

International Nuclear Information System (INIS)

Carlsson, Tobias; Elvingson, Christer; Ekholm, Tobias

2010-01-01

We present a new algorithm for generation of a random walk on a two-dimensional sphere. The algorithm is obtained by viewing the 2-sphere as the equator in the 3-sphere surrounded by an infinitesimally thin band with boundary which reflects Brownian particles and then applying known effective methods for generating Brownian motion on the 3-sphere. To test the method, the diffusion coefficient was calculated in computer simulations using the new algorithm and, for comparison, also using a commonly used method in which the particle takes a Brownian step in the tangent plane to the 2-sphere and is then projected back to the spherical surface. The two methods are in good agreement for short time steps, while the method presented in this paper continues to give good results also for larger time steps, when the alternative method becomes unstable.

Diffusion limit of Lévy-Lorentz gas is Brownian motion

Science.gov (United States)

Magdziarz, Marcin; Szczotka, Wladyslaw

2018-07-01

In this paper we analyze asymptotic behaviour of a stochastic process called Lévy-Lorentz gas. This process is aspecial kind of continuous-time random walk in which walker moves in the fixed environment composed of scattering points. Upon each collision the walker performs a flight to the nearest scattering point. This type of dynamics is observed in Lévy glasses or long quenched polymers. We show that the diffusion limit of Lévy-Lorentz gas with finite mean distance between scattering centers is the standard Brownian motion. Thus, for long times the behaviour of the Lévy-Lorentz gas is close to the diffusive regime.

Directed Transport of Brownian Particles in a Periodic Channel

International Nuclear Information System (INIS)

Jiang Jie; Ai Bao-Quan; Wu Jian-Chun

2015-01-01

The transport of Brownian particles in the infinite channel within an external force along the axis of the channel has been studied. In this paper, we study the transport of Brownian particle in the infinite channel within an external force along the axis of the channel and an external force in the transversal direction. In this more sophisticated situation, some property is similar to the simple situation, but some interesting property also appears. (paper)

Brownian motion and stochastic calculus

CERN Document Server

Karatzas, Ioannis

1998-01-01

This book is designed as a text for graduate courses in stochastic processes. It is written for readers familiar with measure-theoretic probability and discrete-time processes who wish to explore stochastic processes in continuous time. The vehicle chosen for this exposition is Brownian motion, which is presented as the canonical example of both a martingale and a Markov process with continuous paths. In this context, the theory of stochastic integration and stochastic calculus is developed. The power of this calculus is illustrated by results concerning representations of martingales and change of measure on Wiener space, and these in turn permit a presentation of recent advances in financial economics (option pricing and consumption/investment optimization). This book contains a detailed discussion of weak and strong solutions of stochastic differential equations and a study of local time for semimartingales, with special emphasis on the theory of Brownian local time. The text is complemented by a large num...

Under which conditions is quantum Brownian motion observable in a microscope?

International Nuclear Information System (INIS)

Helseth, L.E.

2010-01-01

We investigate under which conditions we can expect to observe quantum Brownian motion in a microscope. Using the fluctuation-dissipation theorem, we investigate quantum Brownian motion in an ohmic bath, and estimate temporal and spatial accuracy required to observe a crossover from classical to quantum behavior.

Interaction of Two Active Region Filaments Observed by NVST and SDO

Energy Technology Data Exchange (ETDEWEB)

Yang, Liheng; Yan, Xiaoli; Xue, Zhike; Xiang, Yongyuan [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650216 (China); Li, Ting, E-mail: yangliheng@ynao.ac.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

2017-04-01

Using high spatial and temporal resolution H α data from the New Vacuum Solar Telescope (NVST) and simultaneous observations from the Solar Dynamics Observatory , we present the rare event of the interaction between two filaments (F1 and F2) in AR 11967 on 2014 January 31. The adjacent two filaments were almost perpendicular to each other. Their interaction was driven by the movement of F1 and started when the two filaments collided with each other. During the interaction, the threads of F1 continuously slipped from the northeast to the southwest, and were accompanied by the brightenings at the junction of two filaments and the northeast footpoint of F2. Part of F1 and the main body of F2 became invisible in H α wavelength due to the heating and the motion of F2. At the same time, bright material initiated from the junction of two filaments were observed to move along F1. The magnetic connectivities of F1 were found to be changed after their interaction. These observations suggest that magnetic reconnection was involved in the interaction of two filaments and resulted in the eruption of one filament.

The single- and double-particle properties and the current reversal of coupled Brownian motors

International Nuclear Information System (INIS)

Li, Chen-Pu; Chen, Hong-Bin; Zheng, Zhi-Gang; Fan, Hong; Shen, Wen-Mei

2017-01-01

In this paper, we investigate the directed transport of coupled Brownian motors composed of two identical particles which is individually subject to a time-symmetric rocking force in spatially-symmetric periodic potentials. We find that both the coupling free length and the coupling strength can induce the reversed motion of the coupled Brownian motors, the essence of which is the coupled Brownian motors can exhibit completely different single- or double-particle properties under certain conditions. Namely, the current reversal is the result of the mutual conversion between the single- and double-particle properties of the coupled Brownian motors. Moreover, the directed current of coupled Brownian motors can be optimized and manipulated by adjusting the strength, the period, the phase difference of the rocking forces, and the noise intensity. (paper)

FILAMENT INTERACTION MODELED BY FLUX ROPE RECONNECTION

International Nuclear Information System (INIS)

Toeroek, T.; Chandra, R.; Pariat, E.; Demoulin, P.; Schmieder, B.; Aulanier, G.; Linton, M. G.; Mandrini, C. H.

2011-01-01

Hα observations of solar active region NOAA 10501 on 2003 November 20 revealed a very uncommon dynamic process: during the development of a nearby flare, two adjacent elongated filaments approached each other, merged at their middle sections, and separated again, thereby forming stable configurations with new footpoint connections. The observed dynamic pattern is indicative of 'slingshot' reconnection between two magnetic flux ropes. We test this scenario by means of a three-dimensional zero β magnetohydrodynamic simulation, using a modified version of the coronal flux rope model by Titov and Demoulin as the initial condition for the magnetic field. To this end, a configuration is constructed that contains two flux ropes which are oriented side-by-side and are embedded in an ambient potential field. The choice of the magnetic orientation of the flux ropes and of the topology of the potential field is guided by the observations. Quasi-static boundary flows are then imposed to bring the middle sections of the flux ropes into contact. After sufficient driving, the ropes reconnect and two new flux ropes are formed, which now connect the former adjacent flux rope footpoints of opposite polarity. The corresponding evolution of filament material is modeled by calculating the positions of field line dips at all times. The dips follow the morphological evolution of the flux ropes, in qualitative agreement with the observed filaments.

Adiabatic Processes Realized with a Trapped Brownian Particle

Science.gov (United States)

Martínez, Ignacio A.; Roldán, Édgar; Dinis, Luis; Petrov, Dmitri; Rica, Raúl A.

2015-03-01

The ability to implement adiabatic processes in the mesoscale is of key importance in the study of artificial or biological micro- and nanoengines. Microadiabatic processes have been elusive to experimental implementation due to the difficulty in isolating Brownian particles from their fluctuating environment. Here we report on the experimental realization of a microscopic quasistatic adiabatic process employing a trapped Brownian particle. We circumvent the complete isolation of the Brownian particle by designing a protocol where both characteristic volume and temperature of the system are changed in such a way that the entropy of the system is conserved along the process. We compare the protocols that follow from either the overdamped or underdamped descriptions, demonstrating that the latter is mandatory in order to obtain a vanishing average heat flux to the particle. We provide analytical expressions for the distributions of the fluctuating heat and entropy and verify them experimentally. Our protocols could serve to implement the first microscopic engine that is able to attain the fundamental limit for the efficiency set by Carnot.

Stochastic calculus for fractional Brownian motion and related processes

CERN Document Server

Mishura, Yuliya S

2008-01-01

The theory of fractional Brownian motion and other long-memory processes are addressed in this volume. Interesting topics for PhD students and specialists in probability theory, stochastic analysis and financial mathematics demonstrate the modern level of this field. Among these are results about Levy characterization of fractional Brownian motion, maximal moment inequalities for Wiener integrals including the values 0Brownian SDE. The author develops optimal filtering of mixed models including linear case, and studies financial applications and statistical inference with hypotheses testing and parameter estimation. She proves that the market with stock guided by the mixed model is arbitrage-free without any restriction on the dependence of the components and deduces different forms of the Black-Scholes equation for fractional mark...

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

Science.gov (United States)

Hoda, Nazish; Kumar, Satish

2007-12-01

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 N1/3Wi2/3 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-1/2κ-3(lB∣σq∣)3/2, where κ is the inverse screening length, lB is the Bjerrum length, σ 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.

Entropy production of a Brownian ellipsoid in the overdamped limit.

Science.gov (United States)

Marino, Raffaele; Eichhorn, Ralf; Aurell, Erik

2016-01-01

We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called "anomalous" contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the "anomalous" entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the "anomalous entropy" for prolate and oblate spheroids and for near-spherical Brownian particles.

Brownian dynamics simulation of a polymer chain in a solid-state nanopore attached to a molecular stop

Science.gov (United States)

Wells, Craig; Hulings, Zachery; Melnikov, Dmitriy; Gracheva, Maria

We study a nanopore inside a silicon dioxide membrane submerged in a KCl solution with a negatively charged polymer chain of varying lengths whose movement is described using Brownian dynamics. The polymer is attached to a molecule with a radius larger than that of the nanopore's which acts as a molecular stop, allowing the chain to thread the nanopore but preventing it from translocating. We found that the polymer chain's variation of movement along the nanopore decreased when increasing applied biases and chain lengths for portions of the chain closest to the molecular stop. The chain displacement within the pore is also compared to a freely translocating polymer where preliminary results show the free polymer having a greater variation in the radial direction. Overall, our preliminary results indicate that the radial direction of the polymer chain is dominated by the confinement in the narrow nanopore with restrictions imposed by the molecular stop and bias playing a lesser role. Understanding the interaction behavior of the polymer chain-stop molecule may lead to methods that decrease movement variation, facilitating an improvement on characterizing and identification of molecules. NSF DMR and CBET Grant No. 1352218.

Superresolution Imaging of Dynamic MreB Filaments in B. subtilis—A Multiple-Motor-Driven Transport?

Science.gov (United States)

Olshausen, Philipp v.; Defeu Soufo, Hervé Joël; Wicker, Kai; Heintzmann, Rainer; Graumann, Peter L.; Rohrbach, Alexander

2013-01-01

The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillus subtilis cells, MreB forms filamentous structures of variable lengths, typically not longer than 1 μm. These filaments move along their orientation and mainly perpendicular to the long bacterial axis, revealing a maximal velocity at an intermediate length and a decreasing velocity with increasing filament length. Filaments move along straight trajectories but can reverse or alter their direction of propagation. Based on our measurements, we provide a mechanistic model that is consistent with all observations. In this model, MreB filaments mechanically couple several motors that putatively synthesize the cell wall, whereas the filaments’ traces mirror the trajectories of the motors. On the basis of our mechanistic model, we developed a mathematical model that can explain the nonlinear velocity length dependence. We deduce that the coupling of cell wall synthesis motors determines the MreB filament transport velocity, and the filament mechanically controls a concerted synthesis of parallel peptidoglycan strands to improve cell wall stability. PMID:24010660

Communication: Memory effects and active Brownian diffusion

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Pulak K. [Department of Chemistry, Presidency University, Kolkata 700073 (India); Li, Yunyun, E-mail: yunyunli@tongji.edu.cn [Center for Phononics and Thermal Energy Science, Tongji University, Shanghai 200092 (China); Marchegiani, Giampiero [Dipartimento di Fisica, Università di Camerino, I-62032 Camerino (Italy); Marchesoni, Fabio [Center for Phononics and Thermal Energy Science, Tongji University, Shanghai 200092 (China); Dipartimento di Fisica, Università di Camerino, I-62032 Camerino (Italy)

2015-12-07

A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer’s diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer’s propulsion are exponentially correlated in time, whereas in the second one, we account for possible damped fluctuations of the propulsion velocity around the swimmer’s axis. The corresponding swimmer’s diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed.

Dissipative light-bullets in the filamentation of femtosecond pulses

International Nuclear Information System (INIS)

Porras, M.A.; Gonzalo, I.

2010-01-01

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

Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling.

Science.gov (United States)

Zheng, Wenjun

2017-01-10

Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions.

Single-molecule dynamics in nanofabricated traps

Science.gov (United States)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

On the validity of Brownian assumptions in the spin van der Waals model

International Nuclear Information System (INIS)

Oh, Suhk Kun

1985-01-01

A simple Brownian motion theory of the spin van der Waals model, which can be stationary, Markoffian or Gaussian, is studied. By comparing the Brownian motion theory with an exact theory called the generalized Langevin equation theory, the validity of the Brownian assumptions is tested. Thereby, it is shown explicitly how the Markoffian and Gaussian properties are modified in the spin van der Waals model under the influence of quantum fluctuations and long range ordering. (Author)

Two Types of Long-duration Quasi-static Evolution of Solar Filaments

Science.gov (United States)

Xing, C.; Li, H. C.; Jiang, B.; Cheng, X.; Ding, M. D.

2018-04-01

In this Letter, we investigate the long-duration quasi-static evolution of 12 pre-eruptive filaments (four active region (AR) and eight quiescent filaments), mainly focusing on the evolution of the filament height in 3D and the decay index of the background magnetic field. The filament height in 3D is derived through two-perspective observations of Solar Dynamics Observatory (SDO) and Solar TErrestrial RElations Observatory (STEREO). The coronal magnetic field is reconstructed using the potential field source surface model. A new finding is that the filaments we studied show two types of long-duration evolution: one type comprises a long-duration static phase and a short, slow rise phase with a duration of less than 12 hr and a speed of 0.1–0.7 km s‑1, while the other one only presents a slow rise phase but with an extremely long duration of more than 60 hr and a smaller speed of 0.01–0.2 km s‑1. At the moment approaching the eruption, the decay index of the background magnetic field at the filament height is similar for both AR and quiescent filaments. The average value and upper limit are ∼0.9 and ∼1.4, close to the critical index of torus instability. Moreover, the filament height and background magnetic field strength are also found to be linearly and exponentially related with the filament length, respectively.

Research on bimodal particle extinction coefficient during Brownian coagulation and condensation for the entire particle size regime

International Nuclear Information System (INIS)

Tang Hong; Lin Jianzhong

2011-01-01

The extinction coefficient of atmospheric aerosol particles influences the earth’s radiation balance directly or indirectly, and it can be determined by the scattering and absorption characteristics of aerosol particles. The problem of estimating the change of extinction coefficient due to time evolution of bimodal particle size distribution is studied, and two improved methods for calculating the Brownian coagulation coefficient and the condensation growth rate are proposed, respectively. Through the improved method based on Otto kernel, the Brownian coagulation coefficient can be expressed simply in powers of particle volume for the entire particle size regime based on the fitted polynomials of the mean enhancement function. Meanwhile, the improved method based on Fuchs–Sutugin kernel is developed to obtain the condensation growth rate for the entire particle size regime. And then, the change of the overall extinction coefficient of bimodal distributions undergoing Brownian coagulation and condensation can be estimated comprehensively for the entire particle size regime. Simulation experiments indicate that the extinction coefficients obtained with the improved methods coincide fairly well with the true values, which provide a simple, reliable, and general method to estimate the change of extinction coefficient for the entire particle size regime during the bimodal particle dynamic processes.

Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

Science.gov (United States)

Defeu Soufo, Hervé Joël; Reimold, Christian; Breddermann, Hannes; Mannherz, Hans G; Graumann, Peter L

2015-04-24

EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds after addition of magnesium. Purified EF-Tu enhanced the amount of MreB filaments, as seen by sedimentation assays, the speed of filament formation and the length of MreB filaments in vitro. EF-Tu had the strongest impact on MreB filaments in a 1:1 ratio, and EF-Tu co-sedimented with MreB filaments, revealing a stoichiometric interaction between both proteins. This was supported by cross-linking assays where 1:1 species were well detectable. When expressed in E. coli cells, B. subtilis MreB formed filaments and induced the formation of co-localizing B. subtilis EF-Tu structures, indicating that MreB can direct the positioning of EF-Tu structures in a heterologous cell system. Fluorescence recovery after photobleaching analysis showed that MreB filaments have a higher turnover in B. subtilis cells than in E. coli cells, indicating different filament kinetics in homologous or heterologous cell systems. The data show that MreB can direct the localization of EF-Tu in vivo, which in turn positively affects the formation and dynamics of MreB filaments. Thus, EF-Tu is a modulator of the activity of a bacterial actin-like protein. Copyright © 2015. Published by Elsevier Ltd.

On the definition of an admitted Lie group for stochastic differential equations with multi-Brownian motion

International Nuclear Information System (INIS)

Srihirun, B; Meleshko, S V; Schulz, E

2006-01-01

The definition of an admitted Lie group of transformations for stochastic differential equations has been already presented for equations with one-dimensional Brownian motion. The transformation of the dependent variables involves time as well, and it has been proven that Brownian motion is transformed to Brownian motion. In this paper, we will discuss this concept for stochastic differential equations involving multi-dimensional Brownian motion and present applications to a variety of stochastic differential equations

How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement

OpenAIRE

de Jager, Monique; Bartumeus, Frederic; Kölzsch, Andrea; Weissing, Franz J.; Hengeveld, Geerten M.; Nolet, Bart A.; Herman, Peter M. J.; van de Koppel, Johan

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein’s original theory ...

Volume of the domain visited by N spherical Brownian particles

International Nuclear Information System (INIS)

Berezhkovskii, A.M.

1994-01-01

The average value and variance of the volume of the domain visited in time t by N spherical Brownian particles starting initially at the same point are presented as quadratures of the solutions of simple diffusion problems of the survival of a point Brownian particle in the presence of one and two spherical traps. As an illustration, explicit time dependences are obtained for the average volume in one and three dimensions

Filamentary structures in dense plasma focus: Current filaments or vortex filaments?

Energy Technology Data Exchange (ETDEWEB)

Soto, Leopoldo, E-mail: lsoto@cchen.cl; Pavez, Cristian; Moreno, José [Comisión Chilena de Energía Nuclear, CCHEN, Casilla 188-D, Santiago (Chile); Center for Research and Applications in Plasma Physics and Pulsed Power, P4, Departamento de Ciencias Físicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, República 220, Santiago (Chile); Castillo, Fermin [Universidad Nacional Autónoma de México, Cuernavaca, México (Mexico); Veloso, Felipe [Instituto de Física, Pontificia Universidad Católica de Chile, 7820436 Santiago (Chile); Auluck, S. K. H. [Bhabha Atomic Research Center, Mumbai 400 085 (India)

2014-07-15

Recent observations of an azimuthally distributed array of sub-millimeter size sources of fusion protons and correlation between extreme ultraviolet (XUV) images of filaments with neutron yield in PF-1000 plasma focus have re-kindled interest in their significance. These filaments have been described variously in literature as current filaments and vortex filaments, with very little experimental evidence in support of either nomenclature. This paper provides, for the first time, experimental observations of filaments on a table-top plasma focus device using three techniques: framing photography of visible self-luminosity from the plasma, schlieren photography, and interferometry. Quantitative evaluation of density profile of filaments from interferometry reveals that their radius closely agrees with the collision-less ion skin depth. This is a signature of relaxed state of a Hall fluid, which has significant mass flow with equipartition between kinetic and magnetic energy, supporting the “vortex filament” description. This interpretation is consistent with empirical evidence of an efficient energy concentration mechanism inferred from nuclear reaction yields.

Population study of the filamentous sulfur bacteria Thioploca spp. off the Bay of Concepcion, Chile

DEFF Research Database (Denmark)

Schulz, HN; Strotmann, B.; Gallardo, VA

2000-01-01

A population of filamentous sulfur bacteria Thioploca spp. living in the Bay of Concepcion, Chile, and the adjoining shelf area was sampled for 14 mo at 4 to 6 wk intervals to investigate the influence of seasonal variations in upwelling intensity and oxygen concentrations on the population dynam......, filaments with short cells in sheaths, populating the upper 7 cm of the sediment, and filaments without sheaths living at the sediment surface....

Fractional Brownian motion with a reflecting wall

Science.gov (United States)

Wada, Alexander H. O.; Vojta, Thomas

2018-02-01

Fractional Brownian motion, a stochastic process with long-time correlations between its increments, is a prototypical model for anomalous diffusion. We analyze fractional Brownian motion in the presence of a reflecting wall by means of Monte Carlo simulations. Whereas the mean-square displacement of the particle shows the expected anomalous diffusion behavior ˜tα , the interplay between the geometric confinement and the long-time memory leads to a highly non-Gaussian probability density function with a power-law singularity at the barrier. In the superdiffusive case α >1 , the particles accumulate at the barrier leading to a divergence of the probability density. For subdiffusion α implications of these findings, in particular, for applications that are dominated by rare events.

EVIDENCE OF FILAMENT UPFLOWS ORIGINATING FROM INTENSITY OSCILLATIONS ON THE SOLAR SURFACE

International Nuclear Information System (INIS)

Cao, Wenda; Goode, Philip R.; Ning, Zongjun; Yurchyshyn, Vasyl; Ji Haisheng

2010-01-01

A filament footpoint rooted in an active region (NOAA 11032) was well observed for about 78 minutes with the 1.6 m New Solar Telescope at the Big Bear Solar Observatory on 2009 November 18 in Hα ±0.75 A. This data set had high cadence (∼15 s) and high spatial resolution (∼0.''1) and offered a unique opportunity to study filament dynamics. As in previous findings from space observations, several dark intermittent upflows were identified, and they behave in groups at isolated locations along the filament. However, we have two new findings. First, we find that the dark upflows propagating along the filament channel are strongly associated with the intensity oscillations on the solar surface around the filament footpoints. The upflows start at the same time as the peak in the oscillations, illustrating that the upflow velocities are well correlated with the oscillations. Second, the intensity of one of the seven upflows detected in our data set exhibits a clear periodicity when the upflow propagates along the filament. The periods gradually vary from ∼10 to ∼5 minutes. Our results give observational clues on the driving mechanism of the upflows in the filament.

Brownian motion of tethered nanowires.

Science.gov (United States)

Ota, Sadao; Li, Tongcang; Li, Yimin; Ye, Ziliang; Labno, Anna; Yin, Xiaobo; Alam, Mohammad-Reza; Zhang, Xiang

2014-05-01

Brownian motion of slender particles near a boundary is ubiquitous in biological systems and in nanomaterial assembly, but the complex hydrodynamic interaction in those systems is still poorly understood. Here, we report experimental and computational studies of the Brownian motion of silicon nanowires tethered on a substrate. An optical interference method enabled direct observation of microscopic rotations of the slender bodies in three dimensions with high angular and temporal resolutions. This quantitative observation revealed anisotropic and angle-dependent hydrodynamic wall effects: rotational diffusivity in inclined and azimuth directions follows different power laws as a function of the length, ∼ L(-2.5) and ∼ L(-3), respectively, and is more hindered for smaller inclined angles. In parallel, we developed an implicit simulation technique that takes the complex wire-wall hydrodynamic interactions into account efficiently, the result of which agreed well with the experimentally observed angle-dependent diffusion. The demonstrated techniques provide a platform for studying the microrheology of soft condensed matters, such as colloidal and biological systems near interfaces, and exploring the optimal self-assembly conditions of nanostructures.

Dynamical Timescale of Pre-collapse Evolution Inferred from Chemical Distribution in the Taurus Molecular Cloud-1 (TMC-1) Filament

Energy Technology Data Exchange (ETDEWEB)

Choi, Yunhee; Lee, Jeong-Eun [School of Space Research, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 (Korea, Republic of); Bourke, Tyler L. [Square Kilometre Array Organisation, Jodrell Bank Observatory, Lower Withington, Cheshire SK11 9DL (United Kingdom); II, Neal J. Evans, E-mail: yunhee.choi@khu.ac.kr, E-mail: jeongeun.lee@khu.ac.kr [Department of Astronomy, University of Texas at Austin, 2515 Speedway, Stop C1400, Austin, TX 78712-1205 (United States)

2017-04-01

We present observations and analyses of the low-mass star-forming region, Taurus Molecular Cloud-1 (TMC-1). CS ( J = 2–1)/N{sub 2}H{sup +} ( J = 1–0) and C{sup 17}O ( J = 2–1)/C{sup 18}O ( J = 2–1) were observed with the Five College Radio Astronomy Observatory and the Seoul Radio Astronomy Observatory, respectively. In addition, Spitzer infrared data and 1.2 mm continuum data observed with Max-Planck Millimetre Bolometer are used. We also perform chemical modeling to investigate the relative molecular distributions of the TMC-1 filament. Based on Spitzer observations, there is no young stellar object along the TMC-1 filament, while five Class II and one Class I young stellar objects are identified outside the filament. The comparison between column densities calculated from dust continuum and C{sup 17}O 2–1 line emission shows that CO is depleted much more significantly in the ammonia peak than in the cyanopolyyne peak, while the column densities calculated from the dust continuum are similar at the two peaks. N{sub 2}H{sup +} is not depleted much in either peak. According to our chemical calculation, the differential chemical distribution in the two peaks can be explained by different timescales required to reach the same density, i.e., by different dynamical processes.

Decidable and undecidable arithmetic functions in actin filament networks

Science.gov (United States)

Schumann, Andrew

2018-01-01

The plasmodium of Physarum polycephalum is very sensitive to its environment, and reacts to stimuli with appropriate motions. Both the sensory and motor stages of these reactions are explained by hydrodynamic processes, based on fluid dynamics, with the participation of actin filament networks. This paper is devoted to actin filament networks as a computational medium. The point is that actin filaments, with contributions from many other proteins like myosin, are sensitive to extracellular stimuli (attractants as well as repellents), and appear and disappear at different places in the cell to change aspects of the cell structure—e.g. its shape. By assembling and disassembling actin filaments, some unicellular organisms, like Amoeba proteus, can move in response to various stimuli. As a result, these organisms can be considered a simple reversible logic gate—extracellular signals being its inputs and motions its outputs. In this way, we can implement various logic gates on amoeboid behaviours. These networks can embody arithmetic functions within p-adic valued logic. Furthermore, within these networks we can define the so-called diagonalization for deducing undecidable arithmetic functions.

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

Science.gov (United States)

Bharat, Tanmay A M; Murshudov, Garib N; Sachse, Carsten; Löwe, Jan

2015-07-02

Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

Brownian motion, martingales, and stochastic calculus

CERN Document Server

Le Gall, Jean-François

2016-01-01

This book offers a rigorous and self-contained presentation of stochastic integration and stochastic calculus within the general framework of continuous semimartingales. The main tools of stochastic calculus, including Itô’s formula, the optional stopping theorem and Girsanov’s theorem, are treated in detail alongside many illustrative examples. The book also contains an introduction to Markov processes, with applications to solutions of stochastic differential equations and to connections between Brownian motion and partial differential equations. The theory of local times of semimartingales is discussed in the last chapter. Since its invention by Itô, stochastic calculus has proven to be one of the most important techniques of modern probability theory, and has been used in the most recent theoretical advances as well as in applications to other fields such as mathematical finance. Brownian Motion, Martingales, and Stochastic Calculus provides a strong theoretical background to the reader interested i...

On modeling animal movements using Brownian motion with measurement error.

Science.gov (United States)

Pozdnyakov, Vladimir; Meyer, Thomas; Wang, Yu-Bo; Yan, Jun

2014-02-01

Modeling animal movements with Brownian motion (or more generally by a Gaussian process) has a long tradition in ecological studies. The recent Brownian bridge movement model (BBMM), which incorporates measurement errors, has been quickly adopted by ecologists because of its simplicity and tractability. We discuss some nontrivial properties of the discrete-time stochastic process that results from observing a Brownian motion with added normal noise at discrete times. In particular, we demonstrate that the observed sequence of random variables is not Markov. Consequently the expected occupation time between two successively observed locations does not depend on just those two observations; the whole path must be taken into account. Nonetheless, the exact likelihood function of the observed time series remains tractable; it requires only sparse matrix computations. The likelihood-based estimation procedure is described in detail and compared to the BBMM estimation.

High-Resolution Observations of a Filament showing Activated Barb

Science.gov (United States)

Joshi, Anand; Martin, Sara F.; Mathew, Shibu; Srivastava, Nandita

2012-07-01

Analysis of a filament showing an activated barb using observations from the Dutch Open Telescope (DOT) on 2010 August 20 are presented. The DOT takes Doppler images in Hα, among other wavelengths, in a region about 110 × 110 arcsec^{2} in area, at a cadence of 30~seconds. The offline image restoration technique of speckle reconstruction is applied to obtain diffraction limited images. The filament developed a new barb in 10~minutes, which disappeared within the next 35~minutes. Such a rapid formation and disappearance of a filament barb is unusual, and has not been reported earlier. Line-of-sight velocity maps were constructed from the Doppler images of the target filament. We observe flows in the filament spine towards the barb location prior to its formation, and flows in the barb towards the spine during its disappearance. Photospheric magnetograms from Heliospheric Magnetic Imager on board the Solar Dynamics Observatory, at a cadence of 45~seconds, were used to determine the changes in magnetic flux in the region surrounding the barb location. The variation of magnetic flux in this duration supports the view that barbs are rooted in minor magnetic polarity. Our analysis shows that barbs can be short-lived and formation and disappearance of the barb was associated with cancellation of magnetic flux.

The colour of thermal noise in classical Brownian motion: a feasibility study of direct experimental observation

International Nuclear Information System (INIS)

Berg-Soerensen, Kirstine; Flyvbjerg, Henrik

2005-01-01

One hundred years after Einstein modelled Brownian motion, a central aspect of this motion in incompressible fluids has not been verified experimentally: the thermal noise that drives the Brownian particle, is not white, as in Einstein's simple theory. It is slightly coloured, due to hydrodynamics and the fluctuation-dissipation theorem. This theoretical result from the 1970s was prompted by computer simulation results in apparent violation of Einstein's theory. We discuss how a direct experimental observation of this colour might be carried out by using optical tweezers to separate the thermal noise from the particle's dynamic response to it. Since the thermal noise is almost white, very good statistics is necessary to resolve its colour. That requires stable equipment and long recording times, possibly making this experiment one for the future only. We give results for experimental requirements and for stochastic errors as functions of experimental window and measurement time, and discuss some potential sources of systematic errors

Brownian coagulation at high particle concentrations

NARCIS (Netherlands)

Trzeciak, T.M.

2012-01-01

The process of Brownian coagulation, whereby particles are brought together by thermal motion and grow by collisions, is one of the most fundamental processes influencing the final properties of particulate matter in a variety of technically important systems. It is of importance in colloids,

Unconventional actin conformations localize on intermediate filaments in mitosis

International Nuclear Information System (INIS)

Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan

2011-01-01

Research highlights: → Unconventional actin conformations colocalize with vimentin on a cage-like structure in metaphase HEK 293T cells. → These conformations are detected with the anti-actin antibodies 1C7 ('lower dimer') and 2G2 ('nuclear actin'), but not C4 (monomeric actin). → Mitotic unconventional actin cables are independent of filamentous actin or microtubules. → Unconventional actin colocalizes with vimentin on a nocodazole-induced perinuclear dense mass of cables. -- Abstract: Different structural conformations of actin have been identified in cells and shown to reside in distinct subcellular locations of cells. In this report, we describe the localization of actin on a cage-like structure in metaphase HEK 293T cells. Actin was detected with the anti-actin antibodies 1C7 and 2G2, but not with the anti-actin antibody C4. Actin contained in this structure is independent of microtubules and actin filaments, and colocalizes with vimentin. Taking advantage of intermediate filament collapse into a perinuclear dense mass of cables when microtubules are depolymerized, we were able to relocalize actin to such structures. We hypothesize that phosphorylation of intermediate filaments at mitosis entry triggers the recruitment of different actin conformations to mitotic intermediate filaments. Storage and partition of the nuclear actin and antiparallel 'lower dimer' actin conformations between daughter cells possibly contribute to gene transcription and transient actin filament dynamics at G1 entry.

Actin filaments as tension sensors.

Science.gov (United States)

Galkin, Vitold E; Orlova, Albina; Egelman, Edward H

2012-02-07

The field of mechanobiology has witnessed an explosive growth over the past several years as interest has greatly increased in understanding how mechanical forces are transduced by cells and how cells migrate, adhere and generate traction. Actin, a highly abundant and anomalously conserved protein, plays a large role in forming the dynamic cytoskeleton that is so essential for cell form, motility and mechanosensitivity. While the actin filament (F-actin) has been viewed as dynamic in terms of polymerization and depolymerization, new results suggest that F-actin itself may function as a highly dynamic tension sensor. This property may help explain the unusual conservation of actin's sequence, as well as shed further light on actin's essential role in structures from sarcomeres to stress fibers. Copyright © 2012 Elsevier Ltd. All rights reserved.

How superdiffusion gets arrested: ecological encounters explain shift from Levy to Brownian movement

NARCIS (Netherlands)

de Jager, M.; Bartumeus, F.; Kölzsch, A.; Weissing, F.J.; Hengeveld, G.M.; Nolet, B.A.; Herman, P.M.J.; de Koppel, J.

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when

How superdiffusion gets arrested : ecological encounters explain shift from Levy to Brownian movement

NARCIS (Netherlands)

de Jager, Monique; Bartumeus, Frederic; Kolzsch, Andrea; Weissing, Franz J.; Hengeveld, Geerten M.; Nolet, Bart A.; Herman, Peter M. J.; de Koppel, Johan van

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when

How superdiffusion gets arrested : Ecological encounters explain shift from Levy to Brownian movement

NARCIS (Netherlands)

de Jager, Monique; Bartumeus, Frederic; Kölzsch, Andrea; Weissing, Franz J.; Hengeveld, Geerten M.; Nolet, Bart A.; Herman, Peter M.J.; van de Koppel, Johan

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when

Estimation of the global regularity of a multifractional Brownian motion

DEFF Research Database (Denmark)

Lebovits, Joachim; Podolskij, Mark

This paper presents a new estimator of the global regularity index of a multifractional Brownian motion. Our estimation method is based upon a ratio statistic, which compares the realized global quadratic variation of a multifractional Brownian motion at two different frequencies. We show that a ...... that a logarithmic transformation of this statistic converges in probability to the minimum of the Hurst functional parameter, which is, under weak assumptions, identical to the global regularity index of the path....

Self-Intersection Local Times of Generalized Mixed Fractional Brownian Motion as White Noise Distributions

International Nuclear Information System (INIS)

Suryawan, Herry P.; Gunarso, Boby

2017-01-01

The generalized mixed fractional Brownian motion is defined by taking linear combinations of a finite number of independent fractional Brownian motions with different Hurst parameters. It is a Gaussian process with stationary increments, posseses self-similarity property, and, in general, is neither a Markov process nor a martingale. In this paper we study the generalized mixed fractional Brownian motion within white noise analysis framework. As a main result, we prove that for any spatial dimension and for arbitrary Hurst parameter the self-intersection local times of the generalized mixed fractional Brownian motions, after a suitable renormalization, are well-defined as Hida white noise distributions. The chaos expansions of the self-intersection local times in the terms of Wick powers of white noises are also presented. (paper)

Whole life cycle of femtosecond ultraviolet filaments in water

Science.gov (United States)

Jarnac, Amélie; Tamosauskas, Gintaras; Majus, Donatas; Houard, Aurélien; Mysyrowicz, André; Couairon, Arnaud; Dubietis, Audrius

2014-03-01

We present measurements fully characterizing the whole life cycle of femtosecond pulses undergoing filamentation in water at 400 nm. The complete pulse dynamics is monitored by means of a four-dimensional mapping technique for the intensity distribution I (x,y,z,t) during the nonlinear interaction. Measured events (focusing or defocusing cycles, pulse splitting and replenishment, supercontinuum generation, conical emission, nonlinear absorption peaks) are mutually connected.The filament evolution from laser energy deposition in water, which is of paramount importance for a wide range of technological and medical applications, is interpreted in light of simulation results.

Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

Science.gov (United States)

Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo; Minteer, Shelley D; McCammon, J Andrew

2018-02-01

Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another. © 2017 The Protein Society.

Impact of Matric Potential and Pore Size Distribution on Growth Dynamics of Filamentous and Non-Filamentous Soil Bacteria

NARCIS (Netherlands)

Wolf, A.B.; Vos, de M.; Boer, de W.; Kowalchuk, G.A.

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria

NARCIS (Netherlands)

Wolf, A.B.; Vos, M.; De Boer, W.; Kowalchuk, G.A.

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to

Asian Option Pricing with Monotonous Transaction Costs under Fractional Brownian Motion

Directory of Open Access Journals (Sweden)

Di Pan

2013-01-01

Full Text Available Geometric-average Asian option pricing model with monotonous transaction cost rate under fractional Brownian motion was established. The method of partial differential equations was used to solve this model and the analytical expressions of the Asian option value were obtained. The numerical experiments show that Hurst exponent of the fractional Brownian motion and transaction cost rate have a significant impact on the option value.

Filament Substructures and their Interrelation

Science.gov (United States)

Lin, Y.; Martin, S. F.; Engvold, O.

The main structural components of solar filaments, their spines, barbs, and legs at the extreme ends of the spine, are illustrated from recent high-resolution observations. The thread-like structures appear to be present in filaments everywhere and at all times. They are the fundamental elements of solar filaments. The interrelation of the spines, barbs and legs are discussed. From observations, we present a conceptual model of the magnetic field of a filament. We suggest that only a single physical model is needed to explain filaments in a continuous spectrum represented by active region filaments at one end and quiescent filaments at the other end.

Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.

Science.gov (United States)

Chung, Shin-Ho; Corry, Ben

2007-07-01

In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.

Biosensor based on measurements of the clustering dynamics of magnetic particles

DEFF Research Database (Denmark)

2014-01-01

Disclosed herein is a biosensor for optical detection of Brownian relaxation dynamics of magnetic particles measured by light transmission. The magnetic particles can be functionalized with biological ligands for the detection of target analytes in a sample.......Disclosed herein is a biosensor for optical detection of Brownian relaxation dynamics of magnetic particles measured by light transmission. The magnetic particles can be functionalized with biological ligands for the detection of target analytes in a sample....

Exact master equation for a noncommutative Brownian particle

International Nuclear Information System (INIS)

Costa Dias, Nuno; Nuno Prata, Joao

2009-01-01

We derive the Hu-Paz-Zhang master equation for a Brownian particle linearly coupled to a bath of harmonic oscillators on the plane with spatial noncommutativity. The results obtained are exact to all orders in the noncommutative parameter. As a by-product we derive some miscellaneous results such as the equilibrium Wigner distribution for the reservoir of noncommutative oscillators, the weak coupling limit of the master equation and a set of sufficient conditions for strict purity decrease of the Brownian particle. Finally, we consider a high-temperature Ohmic model and obtain an estimate for the time scale of the transition from noncommutative to ordinary quantum mechanics. This scale is considerably smaller than the decoherence scale

Flapping modes of three filaments placed side by side in a free stream

Science.gov (United States)

Tian, Fang-Bao; Luo, Haoxiang; Zhu, Luoding; Lu, Xi-Yun

2010-11-01

Flexible filaments flapping in a surrounding flow are useful models for understanding the flow-induced vibration and mimicking the schooling behavior of fish. In the present work, the coupled modes of three identical filaments in a side-by- side arrangement are studied using the linear stability analysis and also an immersed boundary--lattice Boltzmann method for low Reynolds numbers (Re on order of 100). The numerical simulations show that the system dynamics exhibits several patterns that depend on the spacing between the filaments. Among these patterns, three can be predicted by the linear analysis and have been reported before. These modes are: (1) the three filaments all flap in phase; (2) the two outer filaments are out of phase while the middle one is stable; (3) the two outer filaments are in phase while the middle one is out of phase. The simulations also identified two additional modes: (1) the outer two filaments are out of phase while the middle one flaps at a frequency reduced by half; (2) the outer two filaments are out of phase while the middle one flaps at a slightly different frequency. In addition to the vibratory modes, the drag force and the flapping amplitude are also computed, and the implication of the result will be discussed.

The Onsager reciprocity relation and generalized efficiency of a thermal Brownian motor

International Nuclear Information System (INIS)

Tian-Fu, Gao; Jin-Can, Chen; Yue, Zhang

2009-01-01

Based on a general model of Brownian motors, the Onsager coefficients and generalized efficiency of a thermal Brownian motor are calculated analytically. It is found that the Onsager reciprocity relation holds and the Onsager coefficients are not affected by the kinetic energy change due to the particle's motion. Only when the heat leak in the system is negligible can the determinant of the Onsager matrix vanish. Moreover, the influence of the main parameters characterizing the model on the generalized efficiency of the Brownian motor is discussed in detail. The characteristic curves of the generalized efficiency varying with these parameters are presented, and the maximum generalized efficiency and the corresponding optimum parameters are determined. The results obtained here are of general significance. They are used to analyze the performance characteristics of the Brownian motors operating in the three interesting cases with zero heat leak, zero average drift velocity or a linear response relation, so that some important conclusions in current references are directly included in some limit cases of the present paper. (general)

Brownian ratchets from statistical physics to bio and nano-motors

CERN Document Server

Cubero, David

2016-01-01

Illustrating the development of Brownian ratchets, from their foundations, to their role in the description of life at the molecular scale and in the design of artificial nano-machinery, this text will appeal to both advanced graduates and researchers entering the field. Providing a self-contained introduction to Brownian ratchets, devices which rectify microscopic fluctuations, Part I avoids technicalities and sets out the broad range of physical systems where the concept of ratchets is relevant. Part II supplies a single source for a complete and modern theoretical analysis of ratchets in regimes such as classical vs quantum and stochastic vs deterministic, and in Part III readers are guided through experimental developments in different physical systems, each highlighting a specific unique feature of ratchets. The thorough and systematic approach to the topic ensures that this book provides a complete guide to Brownian ratchets for newcomers and established researchers in physics, biology and biochemistry.

Dual-frequency magnetic particle imaging of the Brownian particle contribution

Energy Technology Data Exchange (ETDEWEB)

Viereck, Thilo, E-mail: t.viereck@tu-bs.de; Kuhlmann, Christian; Draack, Sebastian; Schilling, Meinhard; Ludwig, Frank

2017-04-01

Magnetic particle imaging (MPI) is an emerging medical imaging modality based on the non-linear response of magnetic nanoparticles to an exciting magnetic field. MPI has been recognized as a fast imaging technique with high spatial resolution in the mm range. For some applications of MPI, especially in the field of functional imaging, the determination of the particle mobility (Brownian rotation) is of great interest, as it enables binding detection in MPI. It also enables quantitative imaging in the presence of Brownian-dominated particles, which is otherwise implausible. Discrimination of different particle responses in MPI is possible via the joint reconstruction approach. In this contribution, we propose a dual-frequency acquisition scheme to enhance sensitivity and contrast in the detection of different particle mobilities compared to a standard single-frequency MPI protocol. The method takes advantage of the fact, that the magnetization response of the tracer is strongly frequency-dependent, i.e. for low excitation frequencies a stronger Brownian contribution is observed.

Brownian motion in Robertson-Walker spacetimes from electromagnetic vacuum fluctuations

International Nuclear Information System (INIS)

Bessa, Carlos H. G.; Bezerra, V. B.; Ford, L. H.

2009-01-01

We consider the effects of the vacuum fluctuations of a quantized electromagnetic field on particles in an expanding universe. We find that these particles typically undergo Brownian motion and acquire a nonzero mean squared velocity that depends on the scale factor of the universe. This Brownian motion can be interpreted as due to noncancellation of anticorrelated vacuum fluctuations in the time-dependent background spacetime. Alternatively, one can interpret this effect as the particles acquiring energy from the background spacetime geometry, a phenomenon that cannot occur in a static spacetime. We treat several types of coupling between the electromagnetic field and the particles and several model universes. We also consider both free particles, which, on the average, move on geodesics, and particles in bound systems. There are significant differences between these two cases, which illustrates that nongeodesic motion alters the effects of the vacuum fluctuations. We discuss the possible applications of this Brownian motion effect to cosmological scenarios.

Brownian motion in a flowing fluid revisited

International Nuclear Information System (INIS)

Ramshaw, J.D.

1981-01-01

It is shown how the phenomenon of osmosis may be treated using the phenomenological theory of Brownian motion in a flowing fluid. The theory is also generalized to include viscous stresses in the particle and mixture momentum equations

Quantum equations from Brownian motions

International Nuclear Information System (INIS)

Rajput, B.S.

2011-01-01

Classical Schrodinger and Dirac equations have been derived from Brownian motions of a particle, it has been shown that the classical Schrodinger equation can be transformed to usual Schrodinger Quantum equation on applying Heisenberg uncertainty principle between position and momentum while Dirac Quantum equation follows it's classical counter part on applying Heisenberg uncertainly principle between energy and time without applying any analytical continuation. (author)

Bidirectional Interplay between Vimentin Intermediate Filaments and Contractile Actin Stress Fibers

Directory of Open Access Journals (Sweden)

Yaming Jiu

2015-06-01

Full Text Available The actin cytoskeleton and cytoplasmic intermediate filaments contribute to cell migration and morphogenesis, but the interplay between these two central cytoskeletal elements has remained elusive. Here, we find that specific actin stress fiber structures, transverse arcs, interact with vimentin intermediate filaments and promote their retrograde flow. Consequently, myosin-II-containing arcs are important for perinuclear localization of the vimentin network in cells. The vimentin network reciprocally restricts retrograde movement of arcs and hence controls the width of flat lamellum at the leading edge of the cell. Depletion of plectin recapitulates the vimentin organization phenotype of arc-deficient cells without affecting the integrity of vimentin filaments or stress fibers, demonstrating that this cytoskeletal cross-linker is required for productive interactions between vimentin and arcs. Collectively, our results reveal that plectin-mediated interplay between contractile actomyosin arcs and vimentin intermediate filaments controls the localization and dynamics of these two cytoskeletal systems and is consequently important for cell morphogenesis.

Drift bifurcation detection for dissipative solitons

International Nuclear Information System (INIS)

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

2003-01-01

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

Fractionalization of the complex-valued Brownian motion of order n using Riemann-Liouville derivative. Applications to mathematical finance and stochastic mechanics

International Nuclear Information System (INIS)

Jumarie, Guy

2006-01-01

The (complex-valued) Brownian motion of order n is defined as the limit of a random walk on the complex roots of the unity. Real-valued fractional noises are obtained as fractional derivatives of the Gaussian white noise (or order two). Here one combines these two approaches and one considers the new class of fractional noises obtained as fractional derivative of the complex-valued Brownian motion of order n. The key of the approach is the relation between differential and fractional differential provided by the fractional Taylor's series of analytic function f(z+h)=E α (h α D z α ).f(z), where E α is the Mittag-Leffler function on the one hand, and the generalized Maruyama's notation, on the other hand. Some questions are revisited such as the definition of fractional Brownian motion as integral w.r.t. (dt) α , and the exponential growth equation driven by fractional Brownian motion, to which a new solution is proposed. As a first illustrative example of application, in mathematical finance, one proposes a new approach to the optimal management of a stochastic portfolio of fractional order via the Lagrange variational technique applied to the state moment dynamical equations. In the second example, one deals with non-random Lagrangian mechanics of fractional order. The last example proposes a new approach to fractional stochastic mechanics, and the solution so obtained gives rise to the question as to whether physical systems would not have their own internal random times

SYMPATHETIC SOLAR FILAMENT ERUPTIONS

Energy Technology Data Exchange (ETDEWEB)

Wang, Rui; Liu, Ying D.; Zimovets, Ivan; Hu, Huidong; Yang, Zhongwei [State Key Laboratory of Space Weather, National Space Science Center, Chinese Academy of Sciences, Beijing 100190 (China); Dai, Xinghua, E-mail: liuxying@spaceweather.ac.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

2016-08-10

The 2015 March 15 coronal mass ejection as one of the two that together drove the largest geomagnetic storm of solar cycle 24 so far was associated with sympathetic filament eruptions. We investigate the relations between the different filaments involved in the eruption. A surge-like small-scale filament motion is confirmed as the trigger that initiated the erupting filament with multi-wavelength observations and using a forced magnetic field extrapolation method. When the erupting filament moved to an open magnetic field region, it experienced an obvious acceleration process and was accompanied by a C-class flare and the rise of another larger filament that eventually failed to erupt. We measure the decay index of the background magnetic field, which presents a critical height of 118 Mm. Combining with a potential field source surface extrapolation method, we analyze the distributions of the large-scale magnetic field, which indicates that the open magnetic field region may provide a favorable condition for F2 rapid acceleration and have some relation with the largest solar storm. The comparison between the successful and failed filament eruptions suggests that the confining magnetic field plays an important role in the preconditions for an eruption.

Modern filaments for composite materials

International Nuclear Information System (INIS)

Krivelli-Viskonti, I.

1982-01-01

Analysis of modern state and ways to improve properties of different filaments for the forecast of the filament application in composite materials has been conducted. In the near future as before the greatest attention will be paid to fibre glass, as this material is widely used in the reinforcing of organic matrices. Carbon and kevlar filaments are the most prospective ones. For the service at medium, high or superhigh temperatures selection of matrix material is more significant than selection of filament. Organic matrices can not be used at temperatures > 250 deg C: this is already the range of metal matrix application. Though at temperatures above room one many filaments can be used, boron filaments and metal wire are the only reinforcing materials, inspite of the fact that carbon filaments are successfully used for metal matrix reinforcing. At very high temperatures only carbon filaments or silicon carbide ones can be used, but their cost is very high and besides economical problems there are many difficulties of technical character

Spindles and active vortices in a model of confined filament-motor mixtures.

Science.gov (United States)

Head, David A; Briels, Wj; Gompper, Gerhard

2011-11-16

Robust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of microtubules, motor proteins and the confining cell walls, and asters and vortices have been observed to self-assemble in quasi-two dimensional microtubule-kinesin assays. There is no clear microscopic picture of the role of the active motors driving this pattern formation, and the relevance of continuum modeling to filament-scale structures remains uncertain. Here we present results of numerical simulations of a discrete filament-motor protein model confined to a pressurised cylindrical box. Stable spindles, nematic configurations, asters and high-density semi-asters spontaneously emerge, the latter pair having also been observed in cytosol confined within emulsion droplets. State diagrams are presented delineating each stationary state as the pressure, motor speed and motor density are varied. We further highlight a parameter regime where vortices form exhibiting collective rotation of all filaments, but have a finite life-time before contracting to a semi-aster. Quantifying the distribution of life-times suggests this contraction is a Poisson process. Equivalent systems with fixed volume exhibit persistent vortices with stochastic switching in the direction of rotation, with switching times obeying similar statistics to contraction times in pressurised systems. Furthermore, we show that increasing the detachment rate of motors from filament plus-ends can both destroy vortices and turn some asters into vortices. We have shown that discrete filament-motor protein models provide new insights into the stationary and dynamical behavior of active gels and subcellular structures, because many phenomena occur on the length-scale of single filaments. Based on our findings, we argue the need for a deeper understanding of the microscopic

How superdiffusion gets arrested: Ecological encounters explain shift from Lévy to Brownian movement

NARCIS (Netherlands)

De Jager, M.; Bartumeus, F.; Kölzsch, A.; Weissing, F.J.; Hengeveld, G.M.; Nolet, B.A.; Herman, P.M.J.; Van de Koppel, J.

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when

How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement

NARCIS (Netherlands)

Jager, de M.; Bartumeus, F.; Kölzsch, A.; Weissing, F.J.; Hengeveld, G.M.; Nolet, B.A.; Herman, P.M.J.; Koppel, van de J.

2014-01-01

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when

Regime of aggregate structures and magneto-rheological characteristics of a magnetic rod-like particle suspension: Monte Carlo and Brownian dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Okada, Kazuya [School of Akita Prefectural University, Yurihonjo (Japan); Satoh, Akira, E-mail: asatoh@akita-pu.ac.jp [Department of Machine Intelligence and System Engineering, Akita Prefectural University, Yurihonjo (Japan)

2017-09-01

Highlights: • Monte Carlo simulations have been employed for the aggregate structures. • Brownian dynamics simulations have been employed for the magneto-rheology. • Even a weak shear flow induces a significant regime change in the aggregates. • A strong external magnetic field drastically changes the aggregates. • The dependence of the viscosity on these factors is governed in a complex manner. - Abstract: 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

Single-particle tracking: applications to membrane dynamics.

Science.gov (United States)

Saxton, M J; Jacobson, K

1997-01-01

Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

The Diffusion Process in Small Particles and Brownian Motion

Science.gov (United States)

Khoshnevisan, M.

Albert Einstein in 1926 published his book entitled ''INVESTIGATIONS ON THE THEORY OF THE BROWNIAN MOVEMENT''. He investigated the process of diffusion in an undissociated dilute solution. The diffusion process is subject to Brownian motion. Furthermore, he elucidated the fact that the heat content of a substance will change the position of the single molecules in an irregular fashion. In this paper, I have shown that in order for the displacement of the single molecules to be proportional to the square root of the time, and for v/2 - v 1 Δ =dv/dx , (where v1 and v2 are the concentrations in two cross sections that are separated by a very small distance), ∫ - ∞ ∞ Φ (Δ) dΔ = I and I/τ ∫ - ∞ ∞Δ2/2 Φ (Δ) dΔ = D conditions to hold, then equation (7a) D =√{ 2 D }√{ τ} must be changed to Δ =√{ 2 D }√{ τ} . I have concluded that D =√{ 2 D }√{ τ} is an unintended error, and it has not been amended for almost 90 years in INVESTIGATIONS ON THE THEORY OF THE BROWNIAN MOVEMENT, 1926 publication.

Regulation of Contraction by the Thick Filaments in Skeletal Muscle.

Science.gov (United States)

Irving, Malcolm

2017-12-19

Contraction of skeletal muscle cells is initiated by a well-known signaling pathway. An action potential in a motor nerve triggers an action potential in a muscle cell membrane, a transient increase of intracellular calcium concentration, binding of calcium to troponin in the actin-containing thin filaments, and a structural change in the thin filaments that allows myosin motors from the thick filaments to bind to actin and generate force. This calcium/thin filament mediated pathway provides the "START" signal for contraction, but it is argued that the functional response of the muscle cell, including the speed of its contraction and relaxation, adaptation to the external load, and the metabolic cost of contraction is largely determined by additional mechanisms. This review considers the role of the thick filaments in those mechanisms, and puts forward a paradigm for the control of contraction in skeletal muscle in which both the thick and thin filaments have a regulatory function. The OFF state of the thick filament is characterized by helical packing of most of the myosin head or motor domains on the thick filament surface in a conformation that makes them unavailable for actin binding or ATP hydrolysis, although a small fraction of the myosin heads are constitutively ON. The availability of the majority fraction of the myosin heads for contraction is controlled in part by the external load on the muscle, so that these heads only attach to actin and hydrolyze ATP when they are required. This phenomenon seems to be the major determinant of the well-known force-velocity relationship of muscle, and controls the metabolic cost of contraction. The regulatory state of the thick filament also seems to control the dynamics of both muscle activation and relaxation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Brownian motion of solitons in a Bose-Einstein condensate.

Science.gov (United States)

Aycock, Lauren M; Hurst, Hilary M; Efimkin, Dmitry K; Genkina, Dina; Lu, Hsin-I; Galitski, Victor M; Spielman, I B

2017-03-07

We observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated [Formula: see text] Bose-Einstein condensates (BECs) and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one dimension (1D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton's diffusive behavior using a quasi-1D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment.

A CIRCULAR-RIBBON SOLAR FLARE FOLLOWING AN ASYMMETRIC FILAMENT ERUPTION

Energy Technology Data Exchange (ETDEWEB)

Liu, Chang; Deng, Na; Lee, Jeongwoo; Wang, Haimin [Space Weather Research Laboratory, New Jersey Institute of Technology, University Heights, Newark, NJ 07102-1982 (United States); Liu, Rui [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Sciences, University of Science and Technology of China, Hefei 230026 (China); Pariat, Étienne [LESIA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Universits, UPMC Univ. Paris 06, Univ. Paris Diderot, Sorbonne Paris Cité, F-92190 Meudon (France); Wiegelmann, Thomas [Max-Planck-Institut für Sonnensystemforschung, Justus-von-Liebig Weg 3, D-37077 Göttingen (Germany); Liu, Yang [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305-4085 (United States); Kleint, Lucia, E-mail: chang.liu@njit.edu [University of Applied Sciences and Arts Northwestern Switzerland, Bahnhofstrasse 6, 5210 Windisch (Switzerland)

2015-10-20

The dynamic properties of flare ribbons and the often associated filament eruptions can provide crucial information on the flaring coronal magnetic field. This Letter analyzes the GOES-class X1.0 flare on 2014 March 29 (SOL2014-03-29T17:48), in which we found an asymmetric eruption of a sigmoidal filament and an ensuing circular flare ribbon. Initially both EUV images and a preflare nonlinear force-free field model show that the filament is embedded in magnetic fields with a fan-spine-like structure. In the first phase, which is defined by a weak but still increasing X-ray emission, the western portion of the sigmoidal filament arches upward and then remains quasi-static for about five minutes. The western fan-like and the outer spine-like fields display an ascending motion, and several associated ribbons begin to brighten. Also found is a bright EUV flow that streams down along the eastern fan-like field. In the second phase that includes the main peak of hard X-ray (HXR) emission, the filament erupts, leaving behind two major HXR sources formed around its central dip portion and a circular ribbon brightened sequentially. The expanding western fan-like field interacts intensively with the outer spine-like field, as clearly seen in running difference EUV images. We discuss these observations in favor of a scenario where the asymmetric eruption of the sigmoidal filament is initiated due to an MHD instability and further facilitated by reconnection at a quasi-null in corona; the latter is in turn enhanced by the filament eruption and subsequently produces the circular flare ribbon.

Magnetic tension and instabilities in the Orion A integral-shaped filament

Science.gov (United States)

Schleicher, Dominik R. G.; Stutz, Amelia

2018-03-01

The Orion nebula is a prime example of a massive star-forming region in our galaxy. Observations have shown that gravitational and magnetic energy are comparable in its integral-shaped filament on a scale of ˜1 pc, and that the population of pre-main sequence stars appears dynamically heated compared to the protostars. These results have been attributed to a slingshot mechanism resulting from the oscillation of the filament by Stutz & Gould. In this paper, we show that radially contracting filaments naturally evolve towards a state where gravitational, magnetic, and rotational energy are comparable. While the contraction of the filament will preferentially amplify the axial component of the magnetic field, the presence of rotation leads to a helical field structure. We show how magnetic tension can give rise to a filament oscillation, and estimate a typical time-scale of 0.7 Myr for the motion of the filament to the position of maximum displacement, consistent with the characteristic time-scale of the ejected stars. Furthermore, the presence of helical magnetic fields is expected to give rise to magneto-hydrodynamical instabilities. We show here that the presence of a magnetic field significantly enhances the overall instability, which operates on a characteristic scale of about 1 pc. We expect the physics discussed here to be generally relevant in massive star-forming regions, and encourage further investigations in the future.

Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits

Science.gov (United States)

2016-01-01

Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the “stiffness site” affects filament mechanical properties. Incorporating a magnesium ion in the “polymerization site” does not seem to require any large-scale change to an actin subunit’s conformation. Binding of a magnesium ion in the “stiffness site” adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids. PMID:27146246

Actin filaments growing against an elastic membrane: Effect of membrane tension

Science.gov (United States)

Sadhu, Raj Kumar; Chatterjee, Sakuntala

2018-03-01

We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to protrusive polymerization force exerted by the filaments, costs energy. We study two lattice models to describe the membrane dynamics. In one case, the energy cost is assumed to be proportional to the absolute magnitude of the height gradient (gradient model) and in the other case it is proportional to the square of the height gradient (Gaussian model). For the gradient model we find that the membrane velocity is a nonmonotonic function of the elastic constant μ and reaches a peak at μ =μ* . For μ membrane energy keeps increasing with time. For the Gaussian model, the system always reaches a steady state and the membrane velocity decreases monotonically with the elastic constant ν for all nonzero values of ν . Multiple filaments give rise to protrusions at different regions of the membrane and the elasticity of the membrane induces an effective attraction between the two protrusions in the Gaussian model which causes the protrusions to merge and a single wide protrusion is present in the system. In both the models, the relative time scale between the membrane and filament dynamics plays an important role in deciding whether the shape of elasticity-velocity curve is concave or convex. Our numerical simulations agree reasonably well with our analytical calculations.

Nonlinear-drifted Brownian motion with multiple hidden states for remaining useful life prediction of rechargeable batteries

Science.gov (United States)

Wang, Dong; Zhao, Yang; Yang, Fangfang; Tsui, Kwok-Leung

2017-09-01

Brownian motion with adaptive drift has attracted much attention in prognostics because its first hitting time is highly relevant to remaining useful life prediction and it follows the inverse Gaussian distribution. Besides linear degradation modeling, nonlinear-drifted Brownian motion has been developed to model nonlinear degradation. Moreover, the first hitting time distribution of the nonlinear-drifted Brownian motion has been approximated by time-space transformation. In the previous studies, the drift coefficient is the only hidden state used in state space modeling of the nonlinear-drifted Brownian motion. Besides the drift coefficient, parameters of a nonlinear function used in the nonlinear-drifted Brownian motion should be treated as additional hidden states of state space modeling to make the nonlinear-drifted Brownian motion more flexible. In this paper, a prognostic method based on nonlinear-drifted Brownian motion with multiple hidden states is proposed and then it is applied to predict remaining useful life of rechargeable batteries. 26 sets of rechargeable battery degradation samples are analyzed to validate the effectiveness of the proposed prognostic method. Moreover, some comparisons with a standard particle filter based prognostic method, a spherical cubature particle filter based prognostic method and two classic Bayesian prognostic methods are conducted to highlight the superiority of the proposed prognostic method. Results show that the proposed prognostic method has lower average prediction errors than the particle filter based prognostic methods and the classic Bayesian prognostic methods for battery remaining useful life prediction.

The probability of an encounter of two Brownian particles before escape

International Nuclear Information System (INIS)

Holcman, D; Kupka, I

2009-01-01

We study the probability of meeting of two Brownian particles before one of them exits a finite interval. We obtain an explicit expression for the probability as a function of the initial distance between the two particles using the Weierstrass elliptic function. We also find the law of the meeting location. Brownian simulations show the accuracy of our analysis. Finally, we discuss some applications to the probability that a double-strand DNA break repairs in confined environments.

The Pricing of Vulnerable Options in a Fractional Brownian Motion Environment

Directory of Open Access Journals (Sweden)

Chao Wang

2015-01-01

Full Text Available Under the assumption of the stock price, interest rate, and default intensity obeying the stochastic differential equation driven by fractional Brownian motion, the jump-diffusion model is established for the financial market in fractional Brownian motion setting. With the changes of measures, the traditional pricing method is simplified and the general pricing formula is obtained for the European vulnerable option with stochastic interest rate. At the same time, the explicit expression for it comes into being.

Bacillus subtilis MreB orthologs self-organize into filamentous structures underneath the cell membrane in a heterologous cell system.

Directory of Open Access Journals (Sweden)

Felix Dempwolff

Full Text Available Actin-like bacterial cytoskeletal element MreB has been shown to be essential for the maintenance of rod cell shape in many bacteria. MreB forms rapidly remodelling helical filaments underneath the cell membrane in Bacillus subtilis and in other bacterial cells, and co-localizes with its two paralogs, Mbl and MreBH. We show that MreB localizes as dynamic bundles of filaments underneath the cell membrane in Drosophila S2 Schneider cells, which become highly stable when the ATPase motif in MreB is modified. In agreement with ATP-dependent filament formation, the depletion of ATP in the cells lead to rapid dissociation of MreB filaments. Extended induction of MreB resulted in the formation of membrane protrusions, showing that like actin, MreB can exert force against the cell membrane. Mbl also formed membrane associated filaments, while MreBH formed filaments within the cytosol. When co-expressed, MreB, Mbl and MreBH built up mixed filaments underneath the cell membrane. Membrane protein RodZ localized to endosomes in S2 cells, but localized to the cell membrane when co-expressed with Mbl, showing that bacterial MreB/Mbl structures can recruit a protein to the cell membrane. Thus, MreB paralogs form a self-organizing and dynamic filamentous scaffold underneath the membrane that is able to recruit other proteins to the cell surface.

Bacillus subtilis MreB orthologs self-organize into filamentous structures underneath the cell membrane in a heterologous cell system.

Science.gov (United States)

Dempwolff, Felix; Reimold, Christian; Reth, Michael; Graumann, Peter L

2011-01-01

Actin-like bacterial cytoskeletal element MreB has been shown to be essential for the maintenance of rod cell shape in many bacteria. MreB forms rapidly remodelling helical filaments underneath the cell membrane in Bacillus subtilis and in other bacterial cells, and co-localizes with its two paralogs, Mbl and MreBH. We show that MreB localizes as dynamic bundles of filaments underneath the cell membrane in Drosophila S2 Schneider cells, which become highly stable when the ATPase motif in MreB is modified. In agreement with ATP-dependent filament formation, the depletion of ATP in the cells lead to rapid dissociation of MreB filaments. Extended induction of MreB resulted in the formation of membrane protrusions, showing that like actin, MreB can exert force against the cell membrane. Mbl also formed membrane associated filaments, while MreBH formed filaments within the cytosol. When co-expressed, MreB, Mbl and MreBH built up mixed filaments underneath the cell membrane. Membrane protein RodZ localized to endosomes in S2 cells, but localized to the cell membrane when co-expressed with Mbl, showing that bacterial MreB/Mbl structures can recruit a protein to the cell membrane. Thus, MreB paralogs form a self-organizing and dynamic filamentous scaffold underneath the membrane that is able to recruit other proteins to the cell surface.

On correlations between certain random variables associated with first passage Brownian motion

International Nuclear Information System (INIS)

Kearney, Michael J; Pye, Andrew J; Martin, Richard J

2014-01-01

We analyse how the area swept out by a Brownian motion up to its first passage time correlates with the first passage time itself, obtaining several exact results in the process. Additionally, we analyse the relationship between the time average of a Brownian motion during a first passage and the maximum value attained. The results, which find various applications, are in excellent agreement with simulations. (paper)

Dynamics of unwinding of a simple entaglement

NARCIS (Netherlands)

Wiegel, F.W.; Michels, J.P.J.

1987-01-01

The dynamics of unwinding of a simple entanglement is studied in two ways, firstly using an optimal path approximation in the Rouse model and secondly by simulating the movement of a more realistic model using Brownian molecular dynamics

THE CONTRACTION OF OVERLYING CORONAL LOOP AND THE ROTATING MOTION OF A SIGMOID FILAMENT DURING ITS ERUPTION

Energy Technology Data Exchange (ETDEWEB)

Yan, X. L.; Qu, Z. Q.; Xue, Z. K.; Deng, L. H.; Ma, L.; Kong, D. F. [National Astronomical Observatories/Yunnan Astronomical Observatory, Chinese Academy of Sciences, Kunming 650011 (China); Pan, G. M. [College of Mathematics Physics and Information Engineering, Jiaxing University, Jiaxing 314001 (China); Liu, J. H. [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

2013-06-15

We present an observation of overlying coronal loop contraction and rotating motion of the sigmoid filament during its eruption on 2012 May 22 observed by the Solar Dynamics Observatory (SDO). Our results show that the twist can be transported into the filament from the lower atmosphere to the higher atmosphere. The successive contraction of the coronal loops was due to a suddenly reduced magnetic pressure underneath the filament, which was caused by the rising of the filament. Before the sigmoid filament eruption, there was a counterclockwise flow in the photosphere at the right feet of the filament and the contraction loops and a convergence flow at the left foot of the filament. The hot and cool materials have inverse motion along the filament before the filament eruption. Moreover, two coronal loops overlying the filament first experienced brightening, expansion, and contraction successively. At the beginning of the rising and rotation of the left part of the filament, the second coronal loop exhibited rapid contraction. The top of the second coronal loop also showed counterclockwise rotation during the contraction process. After the contraction of the second loop, the left part of the filament rotated counterclockwise and expanded toward the right of NOAA AR 11485. During the filament expansion, the right part of the filament also exhibited counterclockwise rotation like a tornado.

From Levy to Brownian: a computational model based on biological fluctuation.

Directory of Open Access Journals (Sweden)

Surya G Nurzaman

Full Text Available BACKGROUND: Theoretical studies predict that Lévy walks maximizes the chance of encountering randomly distributed targets with a low density, but Brownian walks is favorable inside a patch of targets with high density. Recently, experimental data reports that some animals indeed show a Lévy and Brownian walk movement patterns when forage for foods in areas with low and high density. This paper presents a simple, Gaussian-noise utilizing computational model that can realize such behavior. METHODOLOGY/PRINCIPAL FINDINGS: We extend Lévy walks model of one of the simplest creature, Escherichia coli, based on biological fluctuation framework. We build a simulation of a simple, generic animal to observe whether Lévy or Brownian walks will be performed properly depends on the target density, and investigate the emergent behavior in a commonly faced patchy environment where the density alternates. CONCLUSIONS/SIGNIFICANCE: Based on the model, animal behavior of choosing Lévy or Brownian walk movement patterns based on the target density is able to be generated, without changing the essence of the stochastic property in Escherichia coli physiological mechanism as explained by related researches. The emergent behavior and its benefits in a patchy environment are also discussed. The model provides a framework for further investigation on the role of internal noise in realizing adaptive and efficient foraging behavior.

Non-intersecting Brownian walkers and Yang-Mills theory on the sphere

International Nuclear Information System (INIS)

Forrester, Peter J.; Majumdar, Satya N.; Schehr, Gregory

2011-01-01

We study a system of N non-intersecting Brownian motions on a line segment [0,L] with periodic, absorbing and reflecting boundary conditions. We show that the normalized reunion probabilities of these Brownian motions in the three models can be mapped to the partition function of two-dimensional continuum Yang-Mills theory on a sphere respectively with gauge groups U(N), Sp(2N) and SO(2N). Consequently, we show that in each of these Brownian motion models, as one varies the system size L, a third order phase transition occurs at a critical value L=L c (N)∼√(N) in the large N limit. Close to the critical point, the reunion probability, properly centered and scaled, is identical to the Tracy-Widom distribution describing the probability distribution of the largest eigenvalue of a random matrix. For the periodic case we obtain the Tracy-Widom distribution corresponding to the GUE random matrices, while for the absorbing and reflecting cases we get the Tracy-Widom distribution corresponding to GOE random matrices. In the absorbing case, the reunion probability is also identified as the maximal height of N non-intersecting Brownian excursions ('watermelons' with a wall) whose distribution in the asymptotic scaling limit is then described by GOE Tracy-Widom law. In addition, large deviation formulas for the maximum height are also computed.

Negative mobility of a Brownian particle: Strong damping regime

Science.gov (United States)

Słapik, A.; Łuczka, J.; Spiechowicz, J.

2018-02-01

We study impact of inertia on directed transport of a Brownian particle under non-equilibrium conditions: the particle moves in a one-dimensional periodic and symmetric potential, is driven by both an unbiased time-periodic force and a constant force, and is coupled to a thermostat of temperature T. Within selected parameter regimes this system exhibits negative mobility, which means that the particle moves in the direction opposite to the direction of the constant force. It is known that in such a setup the inertial term is essential for the emergence of negative mobility and it cannot be detected in the limiting case of overdamped dynamics. We analyse inertial effects and show that negative mobility can be observed even in the strong damping regime. We determine the optimal dimensionless mass for the presence of negative mobility and reveal three mechanisms standing behind this anomaly: deterministic chaotic, thermal noise induced and deterministic non-chaotic. The last origin has never been reported. It may provide guidance to the possibility of observation of negative mobility for strongly damped dynamics which is of fundamental importance from the point of view of biological systems, all of which in situ operate in fluctuating environments.

Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes.

Science.gov (United States)

Xie, Ping

2009-09-16

A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes

International Nuclear Information System (INIS)

Xie Ping

2009-01-01

A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

Dynamic tracking of a nano-particle in fluids under Brownian motions

International Nuclear Information System (INIS)

Wu, X C; Zhang, W J; Sammynaiken, R

2008-01-01

Most previous studies on H 2 S were devoted to its toxic effects. However, recently there have been increasing evidences which show that endogenously generated H 2 S in specific mammalian tissues has certain significant positive physiological effects such as a neuromodulator and vasorelaxant in a membrane receptor-independent manner. In order to know the functions of endogenous H 2 S, low concentration and high accuracy measurement of H 2 S is a must. Furthermore, this measurement is desired to be real-time and non-invasive. It is reported that low concentration and nano quantity of H 2 S can be detected in water solutions and sera using carbon nanotubes with the fluorescence by confocal laser scanning microscopy. However, because of the Brownian motion of the small particle (carbon nanotube), a control system must be developed to track the movement of the particle in fluids. In this paper, we present a study to track a carbon nanotube which absorbs H 2 S in water or serum using a Raman microscope or confocal laser scanning microscope. In particular, we developed a novel control system for this task. Simulation has shown that our system works very well.

Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

Science.gov (United States)

Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

2012-02-01

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

On the distribution of estimators of diffusion constants for Brownian motion

International Nuclear Information System (INIS)

Boyer, Denis; Dean, David S

2011-01-01

We discuss the distribution of various estimators for extracting the diffusion constant of single Brownian trajectories obtained by fitting the squared displacement of the trajectory. The analysis of the problem can be framed in terms of quadratic functionals of Brownian motion that correspond to the Euclidean path integral for simple Harmonic oscillators with time dependent frequencies. Explicit analytical results are given for the distribution of the diffusion constant estimator in a number of cases and our results are confirmed by numerical simulations.

Solar Filament Extraction and Characterizing

Science.gov (United States)

Yuan, Yuan; Shih, F. Y.; Jing, J.; Wang, H.

2010-05-01

This paper presents a new method to extract and characterize solar filaments from H-alpha full-disk images produced by Big Bear Solar Observatory. A cascading Hough Transform method is designed to identify solar disk center location and radius. Solar disks are segmented from the background, and unbalanced illumination on the surface of solar disks is removed using polynomial surface fitting. And then a localized adaptive thresholding is employed to extract solar filament candidates. After the removal of small solar filament candidates, the remaining larger candidates are used as the seeds of region growing. The procedure of region growing not only connects broken filaments but also generate complete shape for each filament. Mathematical morphology thinning is adopted to produce the skeleton of each filament, and graph theory is used to prune branches and barbs to get the main skeleton. The length and the location of the main skeleton is characterized. The proposed method can help scientists and researches study the evolution of solar filament, for instance, to detect solar filament eruption. The presented method has already been used by Space Weather Research Lab of New Jersey Institute of Technology (http://swrl.njit.edu) to generate the solar filament online catalog using H-alpha full-disk images of Global H-alpha Network (http://swrl.njit.edu/ghn_web/).

Modulation of terahertz generation in dual-color filaments by an external electric field and preformed plasma

International Nuclear Information System (INIS)

Li Min; Li An-Yuan; Yuan Shuai; Zeng He-Ping; He Bo-Qu

2016-01-01

Terahertz generation driven by dual-color filaments in air is demonstrated to be remarkably enhanced by applying an external electric field to the filaments. As terahertz generation is sensitive to the dual-color phase difference, a preformed plasma is verified efficiently in modulating terahertz radiation from linear to elliptical polarization. In the presence of preformed plasma, a dual-color filament generates terahertz pulses of elliptical polarization and the corresponding ellipse rotates regularly with the change of the preformed plasma density. The observed terahertz modulation with the external electric field and the preformed plasma provides a simple way to estimate the plasma density and evaluate the photocurrent dynamics of the dual-color filaments. It provides further experimental evidence of the photo-current model in governing the dual-color filament driven terahertz generation processes. (paper)

Temporal symmetry of individual filaments in different spatial symmetry filaments pattern in a dielectric barrier discharge

International Nuclear Information System (INIS)

Dong, L. F.; Xiao, H.; Fan, W. L.; Yin, Z. Q.; Zhao, H. T.

2010-01-01

The temporal behavior of individual filament in different spatial symmetry filaments patterns in dielectric barrier discharge is investigated by using an optical method. A series of return maps of the discharge moments of individual filaments is given. It is found that the temporal symmetry of individual filament changes with the change of the spatial symmetry of filaments pattern as the applied voltage increases. The role of wall charges for this phenomenon is analyzed.

3-d brownian motion simulator for high-sensitivity nanobiotechnological applications.

Science.gov (United States)

Toth, Arpád; Banky, Dániel; Grolmusz, Vince

2011-12-01

A wide variety of nanobiotechnologic applications are being developed for nanoparticle based in vitro diagnostic and imaging systems. Some of these systems make possible highly sensitive detection of molecular biomarkers. Frequently, the very low concentration of the biomarkers makes impossible the classical, partial differential equation-based mathematical simulation of the motion of the nanoparticles involved. We present a three-dimensional Brownian motion simulation tool for the prediction of the movement of nanoparticles in various thermal, viscosity, and geometric settings in a rectangular cuvette. For nonprofit users the server is freely available at the site http://brownian.pitgroup.org.

Magnetic helicity and active filament configuration

Science.gov (United States)

Romano, P.; Zuccarello, F.; Poedts, S.; Soenen, A.; Zuccarello, F. P.

2009-11-01

Context: The role of magnetic helicity in active filament formation and destabilization is still under debate. Aims: Although active filaments usually show a sigmoid shape and a twisted configuration before and during their eruption, it is unclear which mechanism leads to these topologies. In order to provide an observational contribution to clarify these issues, we describe a filament evolution whose characteristics seem to be directly linked to the magnetic helicity transport in corona. Methods: We applied different methods to determine the helicity sign and the chirality of the filament magnetic field. We also computed the magnetic helicity transport rate at the filament footpoints. Results: All the observational signatures provided information on the positive helicity and sinistral chirality of the flux rope containing the filament material: its forward S shape, the orientation of its barbs, the bright and dark threads at 195 Å. Moreover, the magnetic helicity transport rate at the filament footpoints showed a clear accumulation of positive helicity. Conclusions: The study of this event showed a correspondence between several signatures of the sinistral chirality of the filament and several evidences of the positive magnetic helicity of the filament magnetic field. We also found that the magnetic helicity transported along the filament footpoints showed an increase just before the change of the filament shape observed in Hα images. We argued that the photospheric regions where the filament was rooted might be the preferential ways where the magnetic helicity was injected along the filament itself and where the conditions to trigger the eruption were yielded.

Bidirectional Interplay between Vimentin Intermediate Filaments and Contractile Actin Stress Fibers.

Science.gov (United States)

Jiu, Yaming; Lehtimäki, Jaakko; Tojkander, Sari; Cheng, Fang; Jäälinoja, Harri; Liu, Xiaonan; Varjosalo, Markku; Eriksson, John E; Lappalainen, Pekka

2015-06-16

The actin cytoskeleton and cytoplasmic intermediate filaments contribute to cell migration and morphogenesis, but the interplay between these two central cytoskeletal elements has remained elusive. Here, we find that specific actin stress fiber structures, transverse arcs, interact with vimentin intermediate filaments and promote their retrograde flow. Consequently, myosin-II-containing arcs are important for perinuclear localization of the vimentin network in cells. The vimentin network reciprocally restricts retrograde movement of arcs and hence controls the width of flat lamellum at the leading edge of the cell. Depletion of plectin recapitulates the vimentin organization phenotype of arc-deficient cells without affecting the integrity of vimentin filaments or stress fibers, demonstrating that this cytoskeletal cross-linker is required for productive interactions between vimentin and arcs. Collectively, our results reveal that plectin-mediated interplay between contractile actomyosin arcs and vimentin intermediate filaments controls the localization and dynamics of these two cytoskeletal systems and is consequently important for cell morphogenesis. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Femtosecond Laser Filamentation

CERN Document Server

Chin, See Leang

2010-01-01

Femtosecond Laser Filamentation gives a comprehensive review of the physics of propagation of intense femtosecond laser pulses in optical media (principally air) and the applications and challenges of this new technique. This book presents the modern understanding of the physics of femtosecond laser pulse propagation, including unusual new effects such as the self-transformation of the pulse into a white light laser pulse, intensity clamping, the physics of multiple filamentation and competition, and how filaments’ ability to melt glass leads to wave guide writing. The potential applications of laser filamentation in atmospheric sensing and the generation of other electromagnetic pulses from the UV to the radio frequency are treated, together with possible future challenges in the excitation of super-excited states of molecules. Exciting new phenomena such as filament induced ultrafast birefringence and the excitation of molecular rotational wave packets and their multiple revivals in air (gases) will also ...

Modeling single-file diffusion with step fractional Brownian motion and a generalized fractional Langevin equation

International Nuclear Information System (INIS)

Lim, S C; Teo, L P

2009-01-01

Single-file diffusion behaves as normal diffusion at small time and as subdiffusion at large time. These properties can be described in terms of fractional Brownian motion with variable Hurst exponent or multifractional Brownian motion. We introduce a new stochastic process called Riemann–Liouville step fractional Brownian motion which can be regarded as a special case of multifractional Brownian motion with a step function type of Hurst exponent tailored for single-file diffusion. Such a step fractional Brownian motion can be obtained as a solution of the fractional Langevin equation with zero damping. Various kinds of fractional Langevin equations and their generalizations are then considered in order to decide whether their solutions provide the correct description of the long and short time behaviors of single-file diffusion. The cases where the dissipative memory kernel is a Dirac delta function, a power-law function and a combination of these functions are studied in detail. In addition to the case where the short time behavior of single-file diffusion behaves as normal diffusion, we also consider the possibility of a process that begins as ballistic motion

Helical filaments

Energy Technology Data Exchange (ETDEWEB)

Barbieri, Nicholas; Lim, Khan; Durand, Magali; Baudelet, Matthieu; Richardson, Martin [Townes Laser Institute, CREOL—The College of Optics and Photonics, University of Central Florida, Orlando, Florida 32816 (United States); Hosseinimakarem, Zahra; Johnson, Eric [Micro-Photonics Laboratory – Center for Optical Material Science, Clemson, Anderson, South Carolina 29634 (United States)

2014-06-30

The shaping of laser-induced filamenting plasma channels into helical structures by guiding the process with a non-diffracting beam is demonstrated. This was achieved using a Bessel beam superposition to control the phase of an ultrafast laser beam possessing intensities sufficient to induce Kerr effect driven non-linear self-focusing. Several experimental methods were used to characterize the resulting beams and confirm the observed structures are laser air filaments.

F-actin-like filaments formed by plasmid segregation protein ParM

DEFF Research Database (Denmark)

van den Ent, Fusinita; Møller-Jensen, Jakob; Amos, Linda A.

2002-01-01

It was the general belief that DNA partitioning in prokaryotes is independent of a cytoskeletal structure, which in eukaryotic cells is indispensable for DNA segregation. Recently, however, immunofluorescence microscopy revealed highly dynamic, filamentous structures along the longitudinal axis...

From Lévy to Brownian: a computational model based on biological fluctuation.

Science.gov (United States)

Nurzaman, Surya G; Matsumoto, Yoshio; Nakamura, Yutaka; Shirai, Kazumichi; Koizumi, Satoshi; Ishiguro, Hiroshi

2011-02-03

Theoretical studies predict that Lévy walks maximizes the chance of encountering randomly distributed targets with a low density, but Brownian walks is favorable inside a patch of targets with high density. Recently, experimental data reports that some animals indeed show a Lévy and Brownian walk movement patterns when forage for foods in areas with low and high density. This paper presents a simple, Gaussian-noise utilizing computational model that can realize such behavior. We extend Lévy walks model of one of the simplest creature, Escherichia coli, based on biological fluctuation framework. We build a simulation of a simple, generic animal to observe whether Lévy or Brownian walks will be performed properly depends on the target density, and investigate the emergent behavior in a commonly faced patchy environment where the density alternates. Based on the model, animal behavior of choosing Lévy or Brownian walk movement patterns based on the target density is able to be generated, without changing the essence of the stochastic property in Escherichia coli physiological mechanism as explained by related researches. The emergent behavior and its benefits in a patchy environment are also discussed. The model provides a framework for further investigation on the role of internal noise in realizing adaptive and efficient foraging behavior.

Feedback control of two-headed Brownian motors in flashing ratchet potential

International Nuclear Information System (INIS)

Zhao A-Ke; Zhang Hong-Wei; Li Yu-Xiao

2010-01-01

We presented a detailed investigation on the movement of two-headed Brownian motors in an asymmetric potential under a feedback control. By numerical simulations the direct current is obtained. The current is periodic in the initial length of spring. There is an optimal value of the spring constant. And the dependence of the current on the opposing force is reversed. Then we found that when the change of the temperature and the opposing force have optimal values, the Brownian motors can also obtain the optimal efficiency

Filament poisoning at typical carbon nanotube deposition conditions by hot-filament CVD

CSIR Research Space (South Africa)

Oliphant, CJ

2009-05-01

Full Text Available extensively used for the deposition of various materials, including diamond [1], polymers [2], silicon thin films [3], boron-carbon-nitride layers [4] and carbon nanotubes (CNTs) [5]. The process relies on the catalytic decomposition of precursor gases... (Ho) twice as efficient as a W filament during the deposition of microcrystalline silicon thin films [6]. Reactions between the precursor gases and the heated filament result in changes of the structural properties of the filaments; a process...

Filament wound structure and method

International Nuclear Information System (INIS)

Dritt, W.S.; Gerth, H.L.; Knight, C.E. Jr.; Pardue, R.M.

1977-01-01

A filament wound spherical structure is described comprising a plurality of filament band sets disposed about the surface of a mandrel with each band of each set formed of a continuous filament circumferentially wound about the mandrel a selected number of circuits and with each circuit of filament being wound parallel to and contiguous with an immediate previously wound circuit. Each filament band in each band set is wound at the same helix angle from the axis of revolution of the mandrel and all of the bands of each set are uniformly distributed about the mandrel circumference. The pole-to-equator wall thickness taper associated with each band set, as several contiguous band sets are wound about the mandrel starting at the poles, is accumulative as the band sets are nested to provide a complete filament wound sphere of essentially uniform thickness

Brownian relaxation of an inelastic sphere in air

Energy Technology Data Exchange (ETDEWEB)

Bird, G. A., E-mail: gab@gab.com.au [University of Sydney, Sydney, NSW 2006 (Australia)

2016-06-15

The procedures that are used to calculate the forces and moments on an aerodynamic body in the rarefied gas of the upper atmosphere are applied to a small sphere of the size of an aerosol particle at sea level. While the gas-surface interaction model that provides accurate results for macroscopic bodies may not be appropriate for bodies that are comprised of only about a thousand atoms, it provides a limiting case that is more realistic than the elastic model. The paper concentrates on the transfer of energy from the air to an initially stationary sphere as it acquires Brownian motion. Individual particle trajectories vary wildly, but a clear relaxation process emerges from an ensemble average over tens of thousands of trajectories. The translational and rotational energies in equilibrium Brownian motion are determined. Empirical relationships are obtained for the mean translational and rotational relaxation times, the mean initial power input to the particle, the mean rates of energy transfer between the particle and air, and the diffusivity. These relationships are functions of the ratio of the particle mass to an average air molecule mass and the Knudsen number, which is the ratio of the mean free path in the air to the particle diameter. The ratio of the molecular radius to the particle radius also enters as a correction factor. The implications of Brownian relaxation for the second law of thermodynamics are discussed.

Spindles and active vortices in a model of confined filament-motor mixtures

Directory of Open Access Journals (Sweden)

Head David A

2011-11-01

Full Text Available Abstract Background Robust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of microtubules, motor proteins and the confining cell walls, and asters and vortices have been observed to self-assemble in quasi-two dimensional microtubule-kinesin assays. There is no clear microscopic picture of the role of the active motors driving this pattern formation, and the relevance of continuum modeling to filament-scale structures remains uncertain. Results Here we present results of numerical simulations of a discrete filament-motor protein model confined to a pressurised cylindrical box. Stable spindles, nematic configurations, asters and high-density semi-asters spontaneously emerge, the latter pair having also been observed in cytosol confined within emulsion droplets. State diagrams are presented delineating each stationary state as the pressure, motor speed and motor density are varied. We further highlight a parameter regime where vortices form exhibiting collective rotation of all filaments, but have a finite life-time before contracting to a semi-aster. Quantifying the distribution of life-times suggests this contraction is a Poisson process. Equivalent systems with fixed volume exhibit persistent vortices with stochastic switching in the direction of rotation, with switching times obeying similar statistics to contraction times in pressurised systems. Furthermore, we show that increasing the detachment rate of motors from filament plus-ends can both destroy vortices and turn some asters into vortices. Conclusions We have shown that discrete filament-motor protein models provide new insights into the stationary and dynamical behavior of active gels and subcellular structures, because many phenomena occur on the length-scale of single filaments. Based on our findings, we argue

Using dynamic Brownian bridge movement modelling to measure temporal patterns of habitat selection.

Science.gov (United States)

Byrne, Michael E; Clint McCoy, J; Hinton, Joseph W; Chamberlain, Michael J; Collier, Bret A

2014-09-01

Accurately describing animal space use is vital to understanding how wildlife use habitat. Improvements in GPS technology continue to facilitate collection of telemetry data at high spatial and temporal resolutions. Application of the recently introduced dynamic Brownian bridge movement model (dBBMM) to such data is promising as the method explicitly incorporates the behavioural heterogeneity of a movement path into the estimated utilization distribution (UD). Utilization distributions defining space use are normally estimated for time-scales ranging from weeks to months, obscuring much of the fine-scale information available from high-volume GPS data sets. By accounting for movement heterogeneity, the dBBMM provides a rigorous, behaviourally based estimate of space use between each set of relocations. Focusing on UDs generated between individual sets of locations allows us to quantify fine-scale circadian variation in habitat use. We used the dBBMM to estimate UDs bounding individual time steps for three terrestrial species with different life histories to illustrate how the method can be used to identify fine-scale variations in habitat use. We also demonstrate how dBBMMs can be used to characterize circadian patterns of habitat selection and link fine-scale patterns of habitat use to behaviour. We observed circadian patterns of habitat use that varied seasonally for a white-tailed deer (Odocoileus virginianus) and coyote (Canis latrans). We found seasonal patterns in selection by the white-tailed deer and were able to link use of conifer forests and agricultural fields to behavioural state of the coyote. Additionally, we were able to quantify the date in which a Rio Grande wild turkey (Meleagris gallopavo intermedia) initiated laying as well as when during the day, she was most likely to visit the nest site to deposit eggs. The ability to quantify circadian patterns of habitat use may have important implications for research and management of wildlife

Non-intersecting Brownian motions leaving from and going to several points

Science.gov (United States)

Adler, Mark; van Moerbeke, Pierre; Vanderstichelen, Didier

2012-03-01

Consider n non-intersecting Brownian motions on R, depending on time t∈[0,1], with mi particles forced to leave from ai at time t=0, 1≤i≤q, and nj particles forced to end up at bj at time t=1, 1≤j≤p. For arbitrary p and q, it is not known if the distribution of the positions of the non-intersecting Brownian particles at a given time 0miracle! Unfortunately we were unable to find its explicit expression. The case p=q=2 will be discussed in the last section.

A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments

Directory of Open Access Journals (Sweden)

James M. Wagstaff

2017-05-01

Full Text Available Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus FtsZ (SaFtsZ, we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of Escherichia coli FtsZ as deduced by electron cryomicroscopy. The closed form is found within several crystal forms of two nonpolymerizing SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ’s conformational switch is polymerization-associated, driven by the formation of the longitudinal intersubunit interfaces along the filament. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament and why filament assembly is cooperative.

Brownian motion model with stochastic parameters for asset prices

Science.gov (United States)

Ching, Soo Huei; Hin, Pooi Ah

2013-09-01

The Brownian motion model may not be a completely realistic model for asset prices because in real asset prices the drift μ and volatility σ may change over time. Presently we consider a model in which the parameter x = (μ,σ) is such that its value x (t + Δt) at a short time Δt ahead of the present time t depends on the value of the asset price at time t + Δt as well as the present parameter value x(t) and m-1 other parameter values before time t via a conditional distribution. The Malaysian stock prices are used to compare the performance of the Brownian motion model with fixed parameter with that of the model with stochastic parameter.

Microwave processing of ceramic oxide filaments

Energy Technology Data Exchange (ETDEWEB)

Vogt, G.J.; Katz, J.D. [Los Alamos National Laboratory, NM (United States)

1995-05-01

The objective of the microwave filament processing project is to develop microwave techniques at 2.45 GHZ to manufacture continuous ceramic oxide filaments. Microwave processing uses the volumetric absorption of microwave power in oxide filament tows to drive off process solvents, to burn out organic binders, and to sinter the dried fibers to produce flexible, high-strength ceramic filaments. The technical goal is to advance filament processing technology by microwave heating more rapidly with less energy and at a lower cost than conventional processing, but with the same quality as conventional processing. The manufacturing goal is to collaborate with the 3M Company, a US manufacturer of ceramic oxide filaments, to evaluate the technology using a prototype filament system and to transfer the microwave technology to the 3M Company.

Finding viscosity of liquids from Brownian motion at students' laboratory

International Nuclear Information System (INIS)

Greczylo, Tomasz; Debowska, Ewa

2005-01-01

Brownian motion appears to be a good subject for investigation at advanced students' laboratory [1]. The paper presents such an investigation carried out in Physics Laboratory II at the Institute of Experimental Physics of Wroclaw University. The experiment has been designed to find viscosity of liquids from Brownian motion phenomenon. Authors use modern technology that helps to proceed with measurements and makes the procedure less time and effort consuming. Discussion of the process of setting up the experiment and the results obtained for three different solutions of glycerin in water are presented. Advantages and disadvantages of the apparatus are pointed out along with descriptions of possible future uses

Isotope ratio measurements of pg-size plutonium samples using TIMS in combination with the 'Multiple Ion Counting' and filament carburization

Energy Technology Data Exchange (ETDEWEB)

Jakopic, Rozle; Richter, Stephan; Kuehn, Heinz; Aregbe, Yetunde [European Commission, Directorate General Joint Research Centre Institute for Reference Materials and Measurements, IRMM Retieseweg 111, B-2440 Geel (Belgium)

2008-07-01

A new sample preparation procedure for isotopic measurements using the Triton TIMS (Thermal Ionization Mass Spectrometer) was developed which employed the technique of carburization of rhenium filaments. Carburized filaments were prepared in a special vacuum chamber in which the filaments were heated and exposed to benzene vapor. Ionization efficiency was improved by an order of magnitude. Additionally, a new 'multi-dynamic' measurement technique was developed for Pu isotope ratio measurements using the 'multiple ion counting' (MIC) system. This technique was further combined with the filament carburization technique and applied to the NBL-137 isotopic standard and samples of the NUSIMEP 5 inter-laboratory comparison campaign. The results clearly show an improved precision and accuracy for the 'multi-dynamic' measurement procedure, compared to measurements carried out either in peak-jumping or in static mode using the MIC system with non-carburized filaments. (authors)

Solar Features - Prominences and Filaments - Filaments

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Filaments are formed in magnetic loops that hold relatively cool, dense gas suspended above the surface of the Sun (David Hathaway/NASA)

PARTIAL ERUPTION OF A FILAMENT WITH TWISTING NON-UNIFORM FIELDS

International Nuclear Information System (INIS)

Bi, Yi; Jiang, Yunchun; Yang, Jiayan; Xiang, Yongyuan; Cai, Yunfang; Liu, Weiwei

2015-01-01

The eruption of a filament in a kinklike fashion is often regarded as a signature of kink instability. However, the kink instability threshold for the filament’s magnetic structure is not widely understood. Using Hα observations from the New Vacuum Solar Telescope, we present a partial eruptive filament. During the eruption, the filament thread appeared to split from its middle and to break out in a kinklike fashion. In this period, the remaining filament material stayed below and erupted without the kinking motion later on. The coronal magnetic field lines associated with the filament are obtained from nonlinear force-free field extrapolations using the twelve-minute-cadence vector magnetograms of the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamic Observatory. We studied the extrapolated field lines passing through the magnetic dips which are in good agreement with the observed filament. The field lines are non-uniformly twisted and appear to be composed of two twisted flux ropes winding around each other. One of them has a higher twist than the other, and the flux rope with the higher twist has its dips aligned with the kinking eruptive thread at the beginning of its eruption. Before the eruption, moreover, the flux rope with the higher twist was found to expand with an approximately constant field twist. In addition, the helicity flux maps deduced from the HMI magnetograms show that some helicity is injected into the overlying magnetic arcade, but no significant helicity is injected into the flux ropes. Accordingly, we suggest that the highly twisted flux rope became kink unstable when the instability threshold declined with the expansion of the flux rope

Tungsten Filament Fire

Science.gov (United States)

Ruiz, Michael J.; Perkins, James

2016-01-01

We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent…

Brownian Movement and Avogadro's Number: A Laboratory Experiment.

Science.gov (United States)

Kruglak, Haym

1988-01-01

Reports an experimental procedure for studying Einstein's theory of Brownian movement using commercially available latex microspheres and a video camera. Describes how students can monitor sphere motions and determine Avogadro's number. Uses a black and white video camera, microscope, and TV. (ML)

Collective motion of active Brownian particles with polar alignment.

Science.gov (United States)

Martín-Gómez, Aitor; Levis, Demian; Díaz-Guilera, Albert; Pagonabarraga, Ignacio

2018-04-04

We present a comprehensive computational study of the collective behavior emerging from the competition between self-propulsion, excluded volume interactions and velocity-alignment in a two-dimensional model of active particles. We consider an extension of the active brownian particles model where the self-propulsion direction of the particles aligns with the one of their neighbors. We analyze the onset of collective motion (flocking) in a low-density regime (10% surface area) and show that it is mainly controlled by the strength of velocity-alignment interactions: the competition between self-propulsion and crowding effects plays a minor role in the emergence of flocking. However, above the flocking threshold, the system presents a richer pattern formation scenario than analogous models without alignment interactions (active brownian particles) or excluded volume effects (Vicsek-like models). Depending on the parameter regime, the structure of the system is characterized by either a broad distribution of finite-sized polar clusters or the presence of an amorphous, highly fluctuating, large-scale traveling structure which can take a lane-like or band-like form (and usually a hybrid structure which is halfway in between both). We establish a phase diagram that summarizes collective behavior of polar active brownian particles and propose a generic mechanism to describe the complexity of the large-scale structures observed in systems of repulsive self-propelled particles.

Coupling between myosin head conformation and the thick filament backbone structure.

Science.gov (United States)

Hu, Zhongjun; Taylor, Dianne W; Edwards, Robert J; Taylor, Kenneth A

2017-12-01

The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force. Here we show the first structural evidence that the arrangement of myosin heads within the interacting heads motif is coupled to the structure of the thick filament backbone. We find that a change in helical angle of 0.16° disorders the blocked head preferentially within the Lethocerus interacting heads motif. This observation suggests a mechanism for how tension affects the dynamics of the myosin heads leading to a detailed hypothesis for stretch activation and shortening deactivation, in which the blocked head preferentially binds the thin filament followed by the free head when force production occurs. Copyright © 2017 Elsevier Inc. All rights reserved.

Fine filament NbTi superconductive composite

International Nuclear Information System (INIS)

Hong, S.; Grabinsky, G.; Marancik, W.; Pattanayak, D.

1986-01-01

The large superconducting magnet for the high energy physics accelerator requires fine filament composite to minimize the field error due to the persistent current in the filaments. New concepts toward the fine filament composite and its cable fabrication are discussed. Two-stage cables of fine wire with intermediate number of filaments were introduced. The first stage was six wires cables around one and in the second stage this was used to produce a Rutherford cable. The advantage of this process is in the ease of billet fabrication since the number of filaments in a single wire is within the range of easy billet fabrication. The disadvantage is in the cable fabrication. One of the major concerns in the fabrication of fine NbTi filaments composite in a copper matrix is the intermetallic compound formation during the extrusion and heat treatment steps. The hard intermetallic particles degrade the uniformity of the filaments and reduce the critical current density. The process of using Nb barrier between the filaments and copper matrix in order to prevent this CuTi intermetallic particle formation is described

Stability of two-dimensional vorticity filaments

International Nuclear Information System (INIS)

Elhmaidi, D.; Provenzale, A.; Lili, T.; Babiano, A.

2004-01-01

We discuss the results of a numerical study on the stability of two-dimensional vorticity filaments around a circular vortex. We illustrate how the stability of the filaments depends on the balance between the strain associated with the far field of the vortex and the local vorticity of the filament, and we discuss an empirical criterion for filament stability

Bose polaron as an instance of quantum Brownian motion

Directory of Open Access Journals (Sweden)

Aniello Lampo

2017-09-01

Full Text Available We study the dynamics of a quantum impurity immersed in a Bose-Einstein condensate as an open quantum system in the framework of the quantum Brownian motion model. We derive a generalized Langevin equation for the position of the impurity. The Langevin equation is an integrodifferential equation that contains a memory kernel and is driven by a colored noise. These result from considering the environment as given by the degrees of freedom of the quantum gas, and thus depend on its parameters, e.g. interaction strength between the bosons, temperature, etc. We study the role of the memory on the dynamics of the impurity. When the impurity is untrapped, we find that it exhibits a super-diffusive behavior at long times. We find that back-flow in energy between the environment and the impurity occurs during evolution. When the particle is trapped, we calculate the variance of the position and momentum to determine how they compare with the Heisenberg limit. One important result of this paper is that we find position squeezing for the trapped impurity at long times. We determine the regime of validity of our model and the parameters in which these effects can be observed in realistic experiments.

Three dimensional simulations of plasma filaments in the scrape off layer

DEFF Research Database (Denmark)

Easy, L.; Militello, F.; Omotani, J.

2014-01-01

closure was found to not replicate the 3D perpendicular dynamics and overestimated the initial radial acceleration of all the filaments studied. In contrast, a more satisfactory comparison with the sheath dissipation closure was obtained, even in the presence of significant parallel gradients, where...

Unwinding motion of a twisted active region filament

Energy Technology Data Exchange (ETDEWEB)

Yan, X. L.; Xue, Z. K.; Kong, D. F. [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China); Liu, J. H. [Department of Physics, Shijiazhuang University, Shijiazhuang 050035 (China); Xu, C. L. [Yunnan Normal University, Kunming 650092 (China)

2014-12-10

To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament, we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.

Dynamical correlations for vicious random walk with a wall

International Nuclear Information System (INIS)

Nagao, Taro

2003-01-01

A one-dimensional system of nonintersecting Brownian particles is constructed as the diffusion scaling limit of Fisher's vicious random walk model. N Brownian particles start from the origin at time t=0 and undergo mutually avoiding motion until a finite time t=T. Dynamical correlation functions among the walkers are exactly evaluated in the case with a wall at the origin. Taking an asymptotic limit N→∞, we observe discontinuous transitions in the dynamical correlations. It is further shown that the vicious walk model with a wall is equivalent to a parametric random matrix model describing the crossover between the Bogoliubov-deGennes universality classes

Filaments and clusters of galaxies

International Nuclear Information System (INIS)

Soltan, A.

1987-01-01

A statistical test to investigate filaments of galaxies is performed. Only particular form of filaments is considered, viz. filaments connecting Abell clusters of galaxies. Relative position of triplets ''cluster - field object - cluster'' is analysed. Though neither cluster sample nor field object sample are homogeneous and complete only peculiar form of selection effects could affect the present statistics. Comparison of observational data with simulations shows that less than 15 per cent of all field galaxies is concentrated in filaments connecting rich clusters. Most of the field objects used in the analysis are not normal galaxies and it is possible that this conclusion is not in conflict with apparent filaments seen in the Lick counts and in some nearby 3D maps of the galaxy distribution. 26 refs., 2 figs. (author)

Electromagnetic effects on plasma blob-filament transport

Energy Technology Data Exchange (ETDEWEB)

Lee, Wonjae, E-mail: wol023@ucsd.edu [University of California, San Diego, La Jolla, CA (United States); Angus, J.R. [Naval Research Laboratory, Washington, DC (United States); Umansky, Maxim V. [Lawrence Livermore National Laboratory, Livermore, CA (United States); Krasheninnikov, Sergei I. [University of California, San Diego, La Jolla, CA (United States); Nuclear Research National University MEPhI, Moscow 115409 (Russian Federation)

2015-08-15

Both microscopic and macroscopic impacts of the electromagnetic effects on blob dynamics are considered. Linear stability analysis and nonlinear BOUT++ simulations demonstrate that electromagnetic effects in high temperature or high beta plasmas suppress the resistive drift wave turbulence in the blob when resistivity drops below a certain value. In the course of blob’s motion in the SOL its temperature is reduced, which leads to enhancement of resistive effects, so the blob can switch from electromagnetic to electrostatic regime, where resistive drift wave turbulence become important. It is found that inhomogeneity of magnetic curvature or plasma pressure along the filament length leads to bending of the high-beta blob filaments. This is caused by the increase of the propagation time of plasma current (Alfvén time) in higher-density plasma. The effects of sheath boundary conditions on the part of the blob away from the boundary are also diminished by the increased Alfvén time.

Anomalous Brownian motion of colloidal particle in a nematic environment: effect of the director fluctuations

Directory of Open Access Journals (Sweden)

T. Turiv

2015-06-01

Full Text Available As recently reported [Turiv T. et al., Science, 2013, Vol. 342, 1351], fluctuations in the orientation of the liquid crystal (LC director can transfer momentum from the LC to a colloid, such that the diffusion of the colloid becomes anomalous on a short time scale. Using video microscopy and single particle tracking, we investigate random thermal motion of colloidal particles in a nematic liquid crystal for the time scales shorter than the expected time of director fluctuations. At long times, compared to the characteristic time of the nematic director relaxation we observe typical anisotropic Brownian motion with the mean square displacement (MSD linear in time τ and inversly proportional to the effective viscosity of the nematic medium. At shorter times, however, the dynamics is markedly nonlinear with MSD growing more slowly (subdiffusion or faster (superdiffusion than τ. These results are discussed in the context of coupling of colloidal particle's dynamics to the director fluctuation dynamics.

High-energy-throughput pulse compression by off-axis group-delay compensation in a laser-induced filament

International Nuclear Information System (INIS)

Voronin, A. A.; Alisauskas, S.; Muecke, O. D.; Pugzlys, A.; Baltuska, A.; Zheltikov, A. M.

2011-01-01

Off-axial beam dynamics of ultrashort laser pulses in a filament enable a radical energy-throughput improvement for filamentation-assisted pulse compression. We identify regimes where a weakly diverging wave, produced on the trailing edge of the pulse, catches up with a strongly diverging component, arising in the central part of the pulse, allowing sub-100-fs millijoule infrared laser pulses to be compressed to 20-25-fs pulse widths with energy throughputs in excess of 70%. Theoretical predictions have been verified by experimental results on filamentation-assisted compression of 70-fs, 1.5-μm laser pulses in high-pressure argon.

Brownian Motion of 2D Vacancy Islands by Adatom Terrace Diffusion

International Nuclear Information System (INIS)

Morgenstern, Karina; Laegsgaard, Erik; Besenbacher, Flemming

2001-01-01

We have studied the Brownian motion of two-dimensional (2D) vacancy islands on Ag(110) at temperatures between 175 and 215K. While the detachment of adatoms from the island and their diffusion on the terrace are permitted in this temperature range, the periphery diffusion of single adatoms is prohibited. The present scanning tunneling microscopy results provide the first direct experimental proof that the Brownian motion of the islands follows a simple scaling law with terrace diffusion being the rate limiting process. The activation energy of the vacancy island motion is determined to 0.41eV

Analytical Solutions of a Model for Brownian Motion in the Double Well Potential

International Nuclear Information System (INIS)

Liu Ai-Jie; Zheng Lian-Cun; Zhang Xin-Xin; Ma Lian-Xi

2015-01-01

In this paper, the analytical solutions of Schrödinger equation for Brownian motion in a double well potential are acquired by the homotopy analysis method and the Adomian decomposition method. Double well potential for Brownian motion is always used to obtain the solutions of Fokker—Planck equation known as the Klein—Kramers equation, which is suitable for separation and additive Hamiltonians. In essence, we could study the random motion of Brownian particles by solving Schrödinger equation. The analytical results obtained from the two different methods agree with each other well. The double well potential is affected by two parameters, which are analyzed and discussed in details with the aid of graphical illustrations. According to the final results, the shapes of the double well potential have significant influence on the probability density function. (general)

Multi-code analysis of scrape-off layer filament dynamics in MAST

DEFF Research Database (Denmark)

Militello, F.; Walkden, N. R.; Farley, T.

2016-01-01

velocities of the order of 1 km s(-1), a perpendicular diameter of around 2-3 cm and a density amplitude 2-3.5 times the background plasma. 3D and 2D numerical codes (the STORM module of BOUT++, GBS, HESEL and TOKAM3X) are used to reproduce the motion of the observed filaments with the purpose of validating...

Evolution of Filament Barbs

OpenAIRE

Liu, Rui; Xu, Yan; Wang, Haimin

2010-01-01

We present a selected few cases in which the sense of chirality of filament barbs changed within as short as hours. We investigate in detail a quiescent filament on 2003 September 10 and 11. Of its four barbs displaying such changes only one overlay a small polarity inversion line inside the EUV filament channel (EFC). No magnetic elements with magnitude above the noise level were detected at the endpoints of all barbs. In particular, a pair of barbs first approached toward and then departed ...

Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells.

Science.gov (United States)

Kampourakis, Thomas; Yan, Ziqian; Gautel, Mathias; Sun, Yin-Biao; Irving, Malcolm

2014-12-30

Myosin binding protein-C (MyBP-C) is a key regulatory protein in heart muscle, and mutations in the MYBPC3 gene are frequently associated with cardiomyopathy. However, the mechanism of action of MyBP-C remains poorly understood, and both activating and inhibitory effects of MyBP-C on contractility have been reported. To clarify the function of the regulatory N-terminal domains of MyBP-C, we determined their effects on the structure of thick (myosin-containing) and thin (actin-containing) filaments in intact sarcomeres of heart muscle. We used fluorescent probes on troponin C in the thin filaments and on myosin regulatory light chain in the thick filaments to monitor structural changes associated with activation of demembranated trabeculae from rat ventricle by the C1mC2 region of rat MyBP-C. C1mC2 induced larger structural changes in thin filaments than calcium activation, and these were still present when active force was blocked with blebbistatin, showing that C1mC2 directly activates the thin filaments. In contrast, structural changes in thick filaments induced by C1mC2 were smaller than those associated with calcium activation and were abolished or reversed by blebbistatin. Low concentrations of C1mC2 did not affect resting force but increased calcium sensitivity and reduced cooperativity of force and structural changes in both thin and thick filaments. These results show that the N-terminal region of MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments and lead to a novel hypothesis for the physiological role of MyBP-C in the regulation of cardiac contractility.

Fractional Langevin Equation Model for Characterization of Anomalous Brownian Motion from NMR Signals

Science.gov (United States)

Lisý, Vladimír; Tóthová, Jana

2018-02-01

Nuclear magnetic resonance is often used to study random motion of spins in different systems. In the long-time limit the current mathematical description of the experiments allows proper interpretation of measurements of normal and anomalous diffusion. The shorter-time dynamics is however correctly considered only in a few works that do not go beyond the standard Langevin theory of the Brownian motion (BM). In the present work, the attenuation function S (t) for an ensemble of spins in a magnetic-field gradient, expressed in a form applicable for any kind of stationary stochastic dynamics of spins with or without a memory, is calculated in the frame of the model of fractional BM. The solution of the model for particles trapped in a harmonic potential is obtained in a simple way and used for the calculation of S (t). In the limit of free particles coupled to a fractal heat bath, the results compare favorably with experiments acquired in human neuronal tissues.

Nonisothermal Brownian motion: Thermophoresis as the macroscopic manifestation of thermally biased molecular motion.

Science.gov (United States)

Brenner, Howard

2005-12-01

A quiescent single-component gravity-free gas subject to a small steady uniform temperature gradient T, despite being at rest, is shown to experience a drift velocity UD=-D* gradient ln T, where D* is the gas's nonisothermal self-diffusion coefficient. D* is identified as being the gas's thermometric diffusivity alpha. The latter differs from the gas's isothermal isotopic self-diffusion coefficient D, albeit only slightly. Two independent derivations are given of this drift velocity formula, one kinematical and the other dynamical, both derivations being strictly macroscopic in nature. Within modest experimental and theoretical uncertainties, this virtual drift velocity UD=-alpha gradient ln T is shown to be constitutively and phenomenologically indistinguishable from the well-known experimental and theoretical formulas for the thermophoretic velocity U of a macroscopic (i.e., non-Brownian) non-heat-conducting particle moving under the influence of a uniform temperature gradient through an otherwise quiescent single-component rarefied gas continuum at small Knudsen numbers. Coupled with the size independence of the particle's thermophoretic velocity, the empirically observed equality, U=UD, leads naturally to the hypothesis that these two velocities, the former real and the latter virtual, are, in fact, simply manifestations of the same underlying molecular phenomenon, namely the gas's Brownian movement, albeit biased by the temperature gradient. This purely hydrodynamic continuum-mechanical equality is confirmed by theoretical calculations effected at the kinetic-molecular level on the basis of an existing solution of the Boltzmann equation for a quasi-Lorentzian gas, modulo small uncertainties pertaining to the choice of collision model. Explicitly, this asymptotically valid molecular model allows the virtual drift velocity UD of the light gas and the thermophoretic velocity U of the massive, effectively non-Brownian, particle, now regarded as the tracer particle

The escape of brownian particle over potential barriers

International Nuclear Information System (INIS)

Zhong Yunxiao

1985-01-01

A convenient method is introduced to calculate the rate of escape of Brownian particle over potential barriers by exact solution of Smoluchowskian equation. This method is applied to calculate the nuclear fission probabilities. The results for four different cases are compared with the results of other theories

Thick filament length and isoform composition determine self-organized contractile units in actomyosin bundles.

Science.gov (United States)

Thoresen, Todd; Lenz, Martin; Gardel, Margaret L

2013-02-05

Diverse myosin II isoforms regulate contractility of actomyosin bundles in disparate physiological processes by variations in both motor mechanochemistry and the extent to which motors are clustered into thick filaments. Although the role of mechanochemistry is well appreciated, the extent to which thick filament length regulates actomyosin contractility is unknown. Here, we study the contractility of minimal actomyosin bundles formed in vitro by mixtures of F-actin and thick filaments of nonmuscle, smooth, and skeletal muscle myosin isoforms with varied length. Diverse myosin II isoforms guide the self-organization of distinct contractile units within in vitro bundles with shortening rates similar to those of in vivo myofibrils and stress fibers. The tendency to form contractile units increases with the thick filament length, resulting in a bundle shortening rate proportional to the length of constituent myosin thick filament. We develop a model that describes our data, providing a framework in which to understand how diverse myosin II isoforms regulate the contractile behaviors of disordered actomyosin bundles found in muscle and nonmuscle cells. These experiments provide insight into physiological processes that use dynamic regulation of thick filament length, such as smooth muscle contraction. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Functional characterisation of filamentous actin probe expression in neuronal cells.

Directory of Open Access Journals (Sweden)

Shrujna Patel

Full Text Available Genetically encoded filamentous actin probes, Lifeact, Utrophin and F-tractin, are used as tools to label the actin cytoskeleton. Recent evidence in several different cell types indicates that these probes can cause changes in filamentous actin dynamics, altering cell morphology and function. Although these probes are commonly used to visualise actin dynamics in neurons, their effects on axonal and dendritic morphology has not been systematically characterised. In this study, we quantitatively analysed the effect of Lifeact, Utrophin and F-tractin on neuronal morphogenesis in primary hippocampal neurons. Our data show that the expression of actin-tracking probes significantly impacts on axonal and dendrite growth these neurons. Lifeact-GFP expression, under the control of a pBABE promoter, caused a significant decrease in total axon length, while another Lifeact-GFP expression, under the control of a CAG promoter, decreased the length and complexity of dendritic trees. Utr261-EGFP resulted in increased dendritic branching but Utr230-EGFP only accumulated in cell soma, without labelling any neurites. Lifeact-7-mEGFP and F-tractin-EGFP in a pEGFP-C1 vector, under the control of a CMV promoter, caused only minor changes in neuronal morphology as detected by Sholl analysis. The results of this study demonstrate the effects that filamentous actin tracking probes can have on the axonal and dendritic compartments of neuronal cells and emphasise the care that must be taken when interpreting data from experiments using these probes.

Functionals of Brownian motion, localization and metric graphs

International Nuclear Information System (INIS)

Comtet, Alain; Desbois, Jean; Texier, Christophe

2005-01-01

We review several results related to the problem of a quantum particle in a random environment. In an introductory part, we recall how several functionals of Brownian motion arise in the study of electronic transport in weakly disordered metals (weak localization). Two aspects of the physics of the one-dimensional strong localization are reviewed: some properties of the scattering by a random potential (time delay distribution) and a study of the spectrum of a random potential on a bounded domain (the extreme value statistics of the eigenvalues). Then we mention several results concerning the diffusion on graphs, and more generally the spectral properties of the Schroedinger operator on graphs. The interest of spectral determinants as generating functions characterizing the diffusion on graphs is illustrated. Finally, we consider a two-dimensional model of a charged particle coupled to the random magnetic field due to magnetic vortices. We recall the connection between spectral properties of this model and winding functionals of planar Brownian motion. (topical review)

Experimental study and numerical simulation of the propulsion of microbeads by femtosecond laser filament

International Nuclear Information System (INIS)

Zhang Nan; Liu Weiwei; Xu Zhijun; Wang Mingwei; Zhu Xiaonong

2008-01-01

The light filament formed by intense femtosecond laser pulses in air can be used to generate the effective impulse to propel a micro glass bead. In this report, through both experimental studies and the corresponding numerical simulations that involve the dynamics of the nonlinear propagation of light and the laser ablation mechanism, we confirm that this propulsion scheme is based on the laser ablation of the target material. The fundamental characteristics of laser propulsion using a single ultrafast laser filament is also revealed

Electron emitting filaments for electron discharge devices

International Nuclear Information System (INIS)

Leung, K.N.; Pincosy, P.A.; Ehlers, K.W.

1988-01-01

This patent describes an electron emitting device for use in an electron discharge system. It comprises: a filament having a pair of terminal ends, electrical supply means for supplying electrical power to the terminal ends of the filament for directly heating the filament by the passage of an electrical current along the filament between the terminal ends, the filament being substantially tapered in cross section continuously in one direction from one of its pair of terminal ends to another of its pair of terminal ends to achieve uniform heating of the filament along the length thereof by compensating for the nonuniform current along the filament due to the emission of electrons therefrom

Time-averaged MSD of Brownian motion

OpenAIRE

Andreanov, Alexei; Grebenkov, Denis

2012-01-01

We study the statistical properties of the time-averaged mean-square displacements (TAMSD). This is a standard non-local quadratic functional for inferring the diffusion coefficient from an individual random trajectory of a diffusing tracer in single-particle tracking experiments. For Brownian motion, we derive an exact formula for the Laplace transform of the probability density of the TAMSD by mapping the original problem onto chains of coupled harmonic oscillators. From this formula, we de...

Rotational and translational Brownian motion

International Nuclear Information System (INIS)

Coffey, W.T.; Salford Univ.

1980-01-01

In this review it is proposed to summarise the work on the theory of the translational and rotational Brownian movement which has been carried on over roughly the past 30 years. The review is intended to take the form of a tutorial paper rather than a list of the results obtained by the various investigators over the period in question. In this vein then it seems appropriate to firstly give a brief account of those parts of the theory of probability which are relevant to the problems under discussion. (orig.)

Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus.

Science.gov (United States)

Kim, So Yeon; Gitai, Zemer; Kinkhabwala, Anika; Shapiro, Lucy; Moerner, W E

2006-07-18

The actin cytoskeleton represents a key regulator of multiple essential cellular functions in both eukaryotes and prokaryotes. In eukaryotes, these functions depend on the orchestrated dynamics of actin filament assembly and disassembly. However, the dynamics of the bacterial actin homolog MreB have yet to be examined in vivo. In this study, we observed the motion of single fluorescent MreB-yellow fluorescent protein fusions in living Caulobacter cells in a background of unlabeled MreB. With time-lapse imaging, polymerized MreB [filamentous MreB (fMreB)] and unpolymerized MreB [globular MreB (gMreB)] monomers could be distinguished: gMreB showed fast motion that was characteristic of Brownian diffusion, whereas the labeled molecules in fMreB displayed slow, directed motion. This directional movement of labeled MreB in the growing polymer provides an indication that, like actin, MreB monomers treadmill through MreB filaments by preferential polymerization at one filament end and depolymerization at the other filament end. From these data, we extract several characteristics of single MreB filaments, including that they are, on average, much shorter than the cell length and that the direction of their polarized assembly seems to be independent of the overall cellular polarity. Thus, MreB, like actin, exhibits treadmilling behavior in vivo, and the long MreB structures that have been visualized in multiple bacterial species seem to represent bundles of short filaments that lack a uniform global polarity.

Analysis of a filament stretching rheometer

DEFF Research Database (Denmark)

Kolte, Mette Irene; Rasmussen, Henrik K.; Hassager, Ole

1996-01-01

A finite element analysis of the stretching filament rheometer of Tirtaadmadja and Sridhar (1993) is presenetd. Simulations of the stretching of a filament of the polymet test solution, fluid A, between two plates are shown.......A finite element analysis of the stretching filament rheometer of Tirtaadmadja and Sridhar (1993) is presenetd. Simulations of the stretching of a filament of the polymet test solution, fluid A, between two plates are shown....

Motion of isolated open vortex filaments evolving under the truncated local induction approximation

Science.gov (United States)

Van Gorder, Robert A.

2017-11-01

The study of nonlinear waves along open vortex filaments continues to be an area of active research. While the local induction approximation (LIA) is attractive due to locality compared with the non-local Biot-Savart formulation, it has been argued that LIA appears too simple to model some relevant features of Kelvin wave dynamics, such as Kelvin wave energy transfer. Such transfer of energy is not feasible under the LIA due to integrability, so in order to obtain a non-integrable model, a truncated LIA, which breaks the integrability of the classical LIA, has been proposed as a candidate model with which to study such dynamics. Recently Laurie et al. ["Interaction of Kelvin waves and nonlocality of energy transfer in superfluids," Phys. Rev. B 81, 104526 (2010)] derived truncated LIA systematically from Biot-Savart dynamics. The focus of the present paper is to study the dynamics of a section of common open vortex filaments under the truncated LIA dynamics. We obtain the analog of helical, planar, and more general filaments which rotate without a change in form in the classical LIA, demonstrating that while quantitative differences do exist, qualitatively such solutions still exist under the truncated LIA. Conversely, solitons and breather solutions found under the LIA should not be expected under the truncated LIA, as the existence of such solutions relies on the existence of an infinite number of conservation laws which is violated due to loss of integrability. On the other hand, similarity solutions under the truncated LIA can be quite different to their counterparts found for the classical LIA, as they must obey a t1/3 type scaling rather than the t1/2 type scaling commonly found in the LIA and Biot-Savart dynamics. This change in similarity scaling means that Kelvin waves are radiated at a slower rate from vortex kinks formed after reconnection events. The loss of soliton solutions and the difference in similarity scaling indicate that dynamics emergent under

Proteomics of Filamentous Fungi

NARCIS (Netherlands)

Passel, van M.W.J.; Schaap, P.J.; Graaff, de L.H.

2013-01-01

Filamentous fungi, such as Aspergillus niger and Aspergillus oryzae traditionally have had an important role in providing enzymes and enzyme cocktails that are used in food industry. In recent years the genome sequences of many filamentous fungi have become available. This combined with

Double-temperature ratchet model and current reversal of coupled Brownian motors

Science.gov (United States)

Li, Chen-Pu; Chen, Hong-Bin; Zheng, Zhi-Gang

2017-12-01

On the basis of the transport features and experimental phenomena observed in studies of molecular motors, we propose a double-temperature ratchet model of coupled motors to reveal the dynamical mechanism of cooperative transport of motors with two heads, where the interactions and asynchrony between two motor heads are taken into account. We investigate the collective unidirectional transport of coupled system and find that the direction of motion can be reversed under certain conditions. Reverse motion can be achieved by modulating the coupling strength, coupling free length, and asymmetric coefficient of the periodic potential, which is understood in terms of the effective potential theory. The dependence of the directed current on various parameters is studied systematically. Directed transport of coupled Brownian motors can be manipulated and optimized by adjusting the pulsation period or the phase shift of the pulsation temperature.

The Mysterious Case of the Missing Filaments

Science.gov (United States)

Alden, C. R.

2016-12-01

Coronal Mass Ejections, or CMEs, are large solar eruptions that can have major debilitating impacts on society. Typically, these eruptions have the three following key structures: the leading edge, the empty chamber known as the cavity, and the filament which often is the brightest part of the CME. When we can see all three structures clearly with a coronagraph, it is called a classic three-part CME, also referred to as a 'lightbulb' CME. According to current knowledge, when a CME erupts, a filament should also erupt or lift off the Sun in order to have the bright center within the CME. However, we do not always see a filament erupt at the surface, and yet we still get a 'filament' within the coronagraph CME. To better understand what might be occurring with these missing filaments, we looked at three-part CMEs using the SOHO LASCO CME Catalog and filaments from the SDO AIA Filament Catalog in order to create a list of 50 CMEs without a listed filament erupting at the surface. For those CMEs without filaments in the list we closely inspected the AIA images for evidence of filament eruption. To ensure that there were no filaments past the limb of the Sun, we used data from the STEREO-A and STEREO-B spacecraft's to look at the Sun from other angles. We have found numerous events where no filament erupts from the surface, but we still see the classic three-part CME. We believe this may be due to an optical illusion occurring from the twisting of the flux rope.

Tracking Filament Evolution in the Low Solar Corona Using Remote Sensing and In Situ Observations

Science.gov (United States)

Kocher, Manan; Landi, Enrico; Lepri, Susan. T.

2018-06-01

In the present work, we analyze a filament eruption associated with an interplanetary coronal mass ejection that arrived at L1 on 2011 August 5. In multiwavelength Solar Dynamic Observatory/Advanced Imaging Assembly (AIA) images, three plasma parcels within the filament were tracked at high cadence along the solar corona. A novel absorption diagnostic technique was applied to the filament material traveling along the three chosen trajectories to compute the column density and temperature evolution in time. Kinematics of the filamentary material were estimated using STEREO/Extreme Ultraviolet Imager and STEREO/COR1 observations. The Michigan Ionization Code used inputs of these density, temperature, and speed profiles for the computation of ionization profiles of the filament plasma. Based on these measurements, we conclude that the core plasma was in near ionization equilibrium, and the ionization states were still evolving at the altitudes where they were visible in absorption in AIA images. Additionally, we report that the filament plasma was heterogeneous, and the filamentary material was continuously heated as it expanded in the low solar corona.

A Dynamical Theory of Markovian Diffusion

OpenAIRE

Davidson, Mark

2001-01-01

A dynamical treatment of Markovian diffusion is presented and several applications discussed. The stochastic interpretation of quantum mechanics is considered within this framework. A model for Brownian movement which includes second order quantum effects is derived.

Actin-interacting Protein 1 Promotes Disassembly of Actin-depolymerizing Factor/Cofilin-bound Actin Filaments in a pH-dependent Manner.

Science.gov (United States)

Nomura, Kazumi; Hayakawa, Kimihide; Tatsumi, Hitoshi; Ono, Shoichiro

2016-03-04

Actin-interacting protein 1 (AIP1) is a conserved WD repeat protein that promotes disassembly of actin filaments when actin-depolymerizing factor (ADF)/cofilin is present. Although AIP1 is known to be essential for a number of cellular events involving dynamic rearrangement of the actin cytoskeleton, the regulatory mechanism of the function of AIP1 is unknown. In this study, we report that two AIP1 isoforms from the nematode Caenorhabditis elegans, known as UNC-78 and AIPL-1, are pH-sensitive in enhancement of actin filament disassembly. Both AIP1 isoforms only weakly enhance disassembly of ADF/cofilin-bound actin filaments at an acidic pH but show stronger disassembly activity at neutral and basic pH values. However, a severing-defective mutant of UNC-78 shows pH-insensitive binding to ADF/cofilin-decorated actin filaments, suggesting that the process of filament severing or disassembly, but not filament binding, is pH-dependent. His-60 of AIP1 is located near the predicted binding surface for the ADF/cofilin-actin complex, and an H60K mutation of AIP1 partially impairs its pH sensitivity, suggesting that His-60 is involved in the pH sensor for AIP1. These biochemical results suggest that pH-dependent changes in AIP1 activity might be a novel regulatory mechanism of actin filament dynamics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

The verification of the Taylor-expansion moment method for the nanoparticle coagulation in the entire size regime due to Brownian motion

International Nuclear Information System (INIS)

Yu Mingzhou; Lin Jianzhong; Jin Hanhui; Jiang Ying

2011-01-01

The closure of moment equations for nanoparticle coagulation due to Brownian motion in the entire size regime is performed using a newly proposed method of moments. The equations in the free molecular size regime and the continuum plus near-continuum regime are derived separately in which the fractal moments are approximated by three-order Taylor-expansion series. The moment equations for coagulation in the entire size regime are achieved by the harmonic mean solution and the Dahneke’s solution. The results produced by the quadrature method of moments (QMOM), the Pratsinis’s log-normal moment method (PMM), the sectional method (SM), and the newly derived Taylor-expansion moment method (TEMOM) are presented and compared in accuracy and efficiency. The TEMOM method with Dahneke’s solution produces the most accurate results with a high efficiency than other existing moment models in the entire size regime, and thus it is recommended to be used in the following studies on nanoparticle dynamics due to Brownian motion.

Localized nonlinear waves on quantized superfluid vortex filaments in the presence of mutual friction and a driving normal fluid flow.

Science.gov (United States)

Shah, Rehan; Van Gorder, Robert A

2016-03-01

We demonstrate the existence of localized structures along quantized vortex filaments in superfluid helium under the quantum form of the local induction approximation (LIA), which includes mutual friction and normal fluid effects. For small magnitude normal fluid velocities, the dynamics are dissipative under mutual friction. On the other hand, when normal fluid velocities are sufficiently large, we observe parametric amplification of the localized disturbances along quantized vortex filaments, akin to the Donnelly-Glaberson instability for regular Kelvin waves. As the waves amplify they will eventually cause breakdown of the LIA assumption (and perhaps the vortex filament itself), and we derive a characteristic time for which this breakdown occurs under our model. More complicated localized waves are shown to occur, and we study these asymptotically and through numerical simulations. Such solutions still exhibit parametric amplification for large enough normal fluid velocities, although this amplification may be less uniform than would be seen for more regular filaments such as those corresponding to helical curves. We find that large rotational velocities or large wave speeds of nonlinear waves along the filaments will result in more regular and stable structures, while small rotational velocities and wave speeds will permit far less regular dynamics.

Analysis of filament statistics in fast camera data on MAST

Science.gov (United States)

Farley, Tom; Militello, Fulvio; Walkden, Nick; Harrison, James; Silburn, Scott; Bradley, James

2017-10-01

Coherent filamentary structures have been shown to play a dominant role in turbulent cross-field particle transport [D'Ippolito 2011]. An improved understanding of filaments is vital in order to control scrape off layer (SOL) density profiles and thus control first wall erosion, impurity flushing and coupling of radio frequency heating in future devices. The Elzar code [T. Farley, 2017 in prep.] is applied to MAST data. The code uses information about the magnetic equilibrium to calculate the intensity of light emission along field lines as seen in the camera images, as a function of the field lines' radial and toroidal locations at the mid-plane. In this way a `pseudo-inversion' of the intensity profiles in the camera images is achieved from which filaments can be identified and measured. In this work, a statistical analysis of the intensity fluctuations along field lines in the camera field of view is performed using techniques similar to those typically applied in standard Langmuir probe analyses. These filament statistics are interpreted in terms of the theoretical ergodic framework presented by F. Militello & J.T. Omotani, 2016, in order to better understand how time averaged filament dynamics produce the more familiar SOL density profiles. This work has received funding from the RCUK Energy programme (Grant Number EP/P012450/1), from Euratom (Grant Agreement No. 633053) and from the EUROfusion consortium.

Role of Intermediate Filaments in Vesicular Traffic

Directory of Open Access Journals (Sweden)

Azzurra Margiotta

2016-04-01

Full Text Available Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

Soliton on thin vortex filament

International Nuclear Information System (INIS)

Konno, Kimiaki; Mituhashi, Masahiko; Ichikawa, Y.H.

1990-12-01

Showing that one of the equations found by Wadati, Konno and Ichikawa is equivalent to the equation of motion of a thin vortex filament, we investigate solitons on the vortex filament. N vortex soliton solution is given in terms of the inverse scattering method. We examine two soliton collision processes on the filament. Our analysis provides the theoretical foundation of two soliton collision processes observed numerically by Aref and Flinchem. (author)

Striation and convection in penumbral filaments

NARCIS (Netherlands)

Spruit, H.C.; Scharmer, G.B.; Löfdahl, M.G.

2010-01-01

Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward

Boolean gates on actin filaments

International Nuclear Information System (INIS)

Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

2016-01-01

Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications. - Highlights: • We simulate interaction between voltage pulses using on actin filaments. • We use a coupled nonlinear transmission line model. • We design Boolean logical gates via interactions between the voltage pulses. • We construct one-bit half-adder with interacting voltage pulses.

Boolean gates on actin filaments

Energy Technology Data Exchange (ETDEWEB)

Siccardi, Stefano, E-mail: ssiccardi@2ssas.it [The Unconventional Computing Centre, University of the West of England, Bristol (United Kingdom); Tuszynski, Jack A., E-mail: jackt@ualberta.ca [Department of Oncology, University of Alberta, Edmonton, Alberta (Canada); Adamatzky, Andrew, E-mail: andrew.adamatzky@uwe.ac.uk [The Unconventional Computing Centre, University of the West of England, Bristol (United Kingdom)

2016-01-08

Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications. - Highlights: • We simulate interaction between voltage pulses using on actin filaments. • We use a coupled nonlinear transmission line model. • We design Boolean logical gates via interactions between the voltage pulses. • We construct one-bit half-adder with interacting voltage pulses.

Statistics of the first passage time of Brownian motion conditioned by maximum value or area

International Nuclear Information System (INIS)

Kearney, Michael J; Majumdar, Satya N

2014-01-01

We derive the moments of the first passage time for Brownian motion conditioned by either the maximum value or the area swept out by the motion. These quantities are the natural counterparts to the moments of the maximum value and area of Brownian excursions of fixed duration, which we also derive for completeness within the same mathematical framework. Various applications are indicated. (paper)

NMR signals within the generalized Langevin model for fractional Brownian motion

Science.gov (United States)

Lisý, Vladimír; Tóthová, Jana

2018-03-01

The methods of Nuclear Magnetic Resonance belong to the best developed and often used tools for studying random motion of particles in different systems, including soft biological tissues. In the long-time limit the current mathematical description of the experiments allows proper interpretation of measurements of normal and anomalous diffusion. The shorter-time dynamics is however correctly considered only in a few works that do not go beyond the standard memoryless Langevin description of the Brownian motion (BM). In the present work, the attenuation function S (t) for an ensemble of spin-bearing particles in a magnetic-field gradient, expressed in a form applicable for any kind of stationary stochastic dynamics of spins with or without a memory, is calculated in the frame of the model of fractional BM. The solution of the model for particles trapped in a harmonic potential is obtained in an exceedingly simple way and used for the calculation of S (t). In the limit of free particles coupled to a fractal heat bath, the results compare favorably with experiments acquired in human neuronal tissues. The effect of the trap is demonstrated by introducing a simple model for the generalized diffusion coefficient of the particle.

Langevin formulation of quantum dynamics

International Nuclear Information System (INIS)

Roncadelli, M.

1989-03-01

We first show that nonrelativistic quantum mechanics formulated at imaginary-(h/2 π) can formally be viewed as the Fokker-Planck description of a frictionless brownian motion, which occurs (in general) in an absorbing medium. We next offer a new formulation of quantum mechanics, which is basically the Langevin treatment of this brownian motion. Explicitly, we derive a noise-average representation for the transition probability W(X'',t''|X',t'), in terms of the solutions to a Langevin equation with a Gaussian white-noise. Upon analytic continuation back to real-(h/2 π),W(X'',t''|X',t') becomes the propagator of the original Schroedinger equation. Our approach allows for a straightforward application to quantum dynamical problems of the mathematical techniques of classical stochastic processes. Moreover, computer simulations of quantum mechanical systems can be carried out by using numerical programs based on the Langevin dynamics. (author). 19 refs, 1 tab

Natural convection in nano-fluids: Are the thermophoresis and Brownian motion effects significant in nano-fluid heat transfer enhancement?

International Nuclear Information System (INIS)

Haddad, Zoubida; Abu-Nada, Eiyad; Oztop, Hakan F.; Mataoui, Amina

2012-01-01

Natural convection heat transfer and fluid flow of CuO-Water nano-fluids is studied using the Rayleigh-Benard problem. A two component non-homogenous equilibrium model is used for the nano-fluid that incorporates the effects of Brownian motion and thermophoresis. Variable thermal conductivity and variable viscosity are taken into account in this work. Finite volume method is used to solve governing equations. Results are presented by streamlines, isotherms, nano-particle distribution, local and mean Nusselt numbers and nano-particle profiles at top and bottom side. Comparison of two cases as absence of Brownian and thermophoresis effects and presence of Brownian and thermophoresis effects showed that higher heat transfer is formed with the presence of Brownian and thermophoresis effect. In general, by considering the role of thermophoresis and Brownian motion, an enhancement in heat transfer is observed at any volume fraction of nano-particles. However, the enhancement is more pronounced at low volume fraction of nano-particles and the heat transfer decreases by increasing nano-particle volume fraction. On the other hand, by neglecting the role of thermophoresis and Brownian motion, deterioration in heat transfer is observed and this deterioration elevates by increasing the volume fraction of nano-particles. (authors)

Mass motions in a quiescent filament

International Nuclear Information System (INIS)

Malherbe, J.M.; Mein, P.; Schmieder, B.

1982-01-01

Observations are presented of the sudden disappearance of a filament (N2O, E35) above an active region with the Multichannel Substractive Double Pass Spectrograph operating on the Meudon Solar Tower, France, from 10:45 UT to 13:30 UT on June 22, 1981. Measurements of the velocity fields and intensity fluctuations were obtained. It was found that the sudden disappearance did not take place simultaneously in all parts of the filament: thin threads with upward radial velocities reaching about 50 km/s were successively observed inside the prominence from the south to north regions. It is suggested that these motions corresponded to the rise of material along magnetic loops closely related to the prominence structure. An investigation of the dynamics inside such a magnetic loop shows a strongly accelerated high speed flow and a deformation of the flux tube, probably due to the centrifugal forces exerted by the flow on the magnetic lines. In addition, it is shown that the present theoretical models cannot account for the prominence structure as a cold H-alpha loop system and the acceleration process of material inside such loops

Modeling collective emotions: a stochastic approach based on Brownian agents

International Nuclear Information System (INIS)

Schweitzer, F.

2010-01-01

We develop a agent-based framework to model the emergence of collective emotions, which is applied to online communities. Agents individual emotions are described by their valence and arousal. Using the concept of Brownian agents, these variables change according to a stochastic dynamics, which also considers the feedback from online communication. Agents generate emotional information, which is stored and distributed in a field modeling the online medium. This field affects the emotional states of agents in a non-linear manner. We derive conditions for the emergence of collective emotions, observable in a bimodal valence distribution. Dependent on a saturated or a super linear feedback between the information field and the agent's arousal, we further identify scenarios where collective emotions only appear once or in a repeated manner. The analytical results are illustrated by agent-based computer simulations. Our framework provides testable hypotheses about the emergence of collective emotions, which can be verified by data from online communities. (author)

Prediction of Solar Eruptions Using Filament Metadata

Science.gov (United States)

Aggarwal, Ashna; Schanche, Nicole; Reeves, Katharine K.; Kempton, Dustin; Angryk, Rafal

2018-05-01

We perform a statistical analysis of erupting and non-erupting solar filaments to determine the properties related to the eruption potential. In order to perform this study, we correlate filament eruptions documented in the Heliophysics Event Knowledgebase (HEK) with HEK filaments that have been grouped together using a spatiotemporal tracking algorithm. The HEK provides metadata about each filament instance, including values for length, area, tilt, and chirality. We add additional metadata properties such as the distance from the nearest active region and the magnetic field decay index. We compare trends in the metadata from erupting and non-erupting filament tracks to discover which properties present signs of an eruption. We find that a change in filament length over time is the most important factor in discriminating between erupting and non-erupting filament tracks, with erupting tracks being more likely to have decreasing length. We attempt to find an ensemble of predictive filament metadata using a Random Forest Classifier approach, but find the probability of correctly predicting an eruption with the current metadata is only slightly better than chance.

High-resolution Observations of Downflows at One End of a Pre-eruption Filament

Energy Technology Data Exchange (ETDEWEB)

Li, Qin; Deng, Na; Jing, Ju; Wang, Haimin, E-mail: ql47@njit.edu [Space Weather Research Laboratory, New Jersey Institute of Technology, University Heights, Newark, NJ 07102-1982 (United States)

2017-06-01

Studying the dynamics of filaments at the pre-eruption phase can shed light on the precursor of eruptive events. Such high-resolution studies (of the order of 0.″1) are highly desirable yet very rare. In this work, we present a detailed observation of a pre-eruption evolution of a filament obtained by the 1.6 m New Solar Telescope (NST) at the Big Bear Solar Observatory (BBSO). One end of the filament is anchored at the sunspot in the NOAA active region (AR) 11515, which is well observed by NST H α off-bands from four hours before to one hour after the filament eruption. A M1.6 flare is associated with the eruption. We observed persistent downflowing materials along the H α multi-threaded component of the loop toward the AR end during the pre-eruption phase. We traced the trajectories of plasma blobs along the H α threads and obtained a plane-of-sky velocity of 45 km s{sup −1} on average. Furthermore, we estimated the real velocities of the downflows and the altitude of the filament by matching the observed H α threads with magnetic field lines extrapolated from a nonlinear force-free field model. Observations of chromospheric brightenings at the footpoints of the falling plasma blobs are also presented. The lower limit of the kinetic energy per second of the downflows through the brightenings is found to be ∼10{sup 21} erg. Larger FOV observations from BBSO full-disk H α images show that the AR end of the filament started ascending four hours before the flare. We attribute the observed downflows at the AR end of the filament to the draining effect of the filament rising prior to its eruption. During the slow-rise phase, the downflows continuously drained away ∼10{sup 15}g mass from the filament over a few hours, which is believed to be essential for the instability, and could be an important precursor of eruptive events.

An explicit local uniform large deviation bound for Brownian bridges

NARCIS (Netherlands)

Wittich, O.

2005-01-01

By comparing curve length in a manifold and a standard sphere, we prove a local uniform bound for the exponent in the Large Deviation formula that describes the concentration of Brownian bridges to geodesics.

Analytical Solutions for Multi-Time Scale Fractional Stochastic Differential Equations Driven by Fractional Brownian Motion and Their Applications

Directory of Open Access Journals (Sweden)

Xiao-Li Ding

2018-01-01

Full Text Available In this paper, we investigate analytical solutions of multi-time scale fractional stochastic differential equations driven by fractional Brownian motions. We firstly decompose homogeneous multi-time scale fractional stochastic differential equations driven by fractional Brownian motions into independent differential subequations, and give their analytical solutions. Then, we use the variation of constant parameters to obtain the solutions of nonhomogeneous multi-time scale fractional stochastic differential equations driven by fractional Brownian motions. Finally, we give three examples to demonstrate the applicability of our obtained results.

Temperature distributions of a conductively heated filament

International Nuclear Information System (INIS)

Tamura, Koji; Ohba, Hironori; Shibata, Takemasa

1999-07-01

Temperature distributions of a heated filament were measured. A W-Re(5%) filament (0.25 mm in diameter, 24.7 mm in length) was conductively heated by currents between 5A and 7A with a DC power supply, and the surface of the filament was imaged with a charge coupled device (CCD) camera through a monochromatic filter. The spectral radiation intensity at the filament center region was almost uniform. Since the temperature distribution was also uniform and the energy loss by thermal conduction was negligible, temperature in this region was determined from the energy balance between applied power and radiation loss. Temperature distribution of the filament was determined based on the Planck's law of radiation from the spectral radiation intensity ratio of the filament surface using obtained temperature as a reference. It was found that temperature distribution of a filament was easily measured by this method. (author)

ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.

Directory of Open Access Journals (Sweden)

Johannes Schöneberg

Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.

Measuring Filament Orientation: A New Quantitative, Local Approach

Energy Technology Data Exchange (ETDEWEB)

Green, C.-E.; Cunningham, M. R.; Jones, P. A. [School of Physics, University of New South Wales, Sydney, NSW, 2052 (Australia); Dawson, J. R. [CSIRO Astronomy and Space Science, Australia Telescope National Facility, P.O. Box 76, Epping, NSW 1710 (Australia); Novak, G. [Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Fissel, L. M. [National Radio Astronomy Observatory (NRAO), 520 Edgemont Road, Charlottesville, VA, 22903 (United States)

2017-09-01

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”.

Measuring Filament Orientation: A New Quantitative, Local Approach

Science.gov (United States)

Green, C.-E.; Dawson, J. R.; Cunningham, M. R.; Jones, P. A.; Novak, G.; Fissel, L. M.

2017-09-01

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”

Measuring Filament Orientation: A New Quantitative, Local Approach

International Nuclear Information System (INIS)

Green, C.-E.; Cunningham, M. R.; Jones, P. A.; Dawson, J. R.; Novak, G.; Fissel, L. M.

2017-01-01

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”

Curcumin Inhibits Tau Aggregation and Disintegrates Preformed Tau Filaments in vitro.

Science.gov (United States)

Rane, Jitendra Subhash; Bhaumik, Prasenjit; Panda, Dulal

2017-01-01

The pathological aggregation of tau is a common feature of most of the neuronal disorders including frontotemporal dementia, Parkinson's disease, and Alzheimer's disease. The inhibition of tau aggregation is considered to be one of the important strategies for treating these neurodegenerative diseases. Curcumin, a natural polyphenolic molecule, has been reported to have neuroprotective ability. In this work, curcumin was found to bind to adult tau and fetal tau with a dissociation constant of 3.3±0.4 and 8±1 μM, respectively. Molecular docking studies indicated a putative binding site of curcumin in the microtubule-binding region of tau. Using several complementary techniques, including dynamic light scattering, thioflavin S fluorescence, 90° light scattering, electron microscopy, and atomic force microscopy, curcumin was found to inhibit the aggregation of tau. The dynamic light scattering analysis and atomic force microscopic images revealed that curcumin inhibits the oligomerization of tau. Curcumin also disintegrated preformed tau oligomers. Using Far-UV circular dichroism, curcumin was found to inhibit the β-sheets formation in tau indicating that curcumin inhibits an initial step of tau aggregation. In addition, curcumin inhibited tau fibril formation. Furthermore, the effect of curcumin on the preformed tau filaments was analyzed by atomic force microscopy, transmission electron microscopy, and 90° light scattering. Curcumin treatment disintegrated preformed tau filaments. The results indicated that curcumin inhibited the oligomerization of tau and could disaggregate tau filaments.

Brownian motion, Minkowski space and principle of special relativity

International Nuclear Information System (INIS)

Caubet, J.-P.

1977-01-01

From the assumption that the brownian diffusion locally behaves like an ideal gas (pressure being inversely proportional to volume according to Boyle's law) one can deduce the signature +++- of the Minkowski space, the Lorentz addition of velocities, and the principle of special relativity [fr

Solar Features - Prominences and Filaments

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Prominences and filaments are two manifestations of the same phenomenon. Both prominences and filaments are features formed above the chromosphere by cool dense...

Frustrated Brownian Motion of Nonlocal Solitary Waves

International Nuclear Information System (INIS)

Folli, V.; Conti, C.

2010-01-01

We investigate the evolution of solitary waves in a nonlocal medium in the presence of disorder. By using a perturbational approach, we show that an increasing degree of nonlocality may largely hamper the Brownian motion of self-trapped wave packets. The result is valid for any kind of nonlocality and in the presence of nonparaxial effects. Analytical predictions are compared with numerical simulations based on stochastic partial differential equations.

The quantum brownian particle and memory effects

International Nuclear Information System (INIS)

Britani, J.R.; Mizrahi, S.S.; Pimentel, B.M.

1991-01-01

The Quantum Brownian particle, immersed in a heat bath, is described by a statistical operator whose evolution is ruled by a Generalized Master Equation (GME). The heat bath degrees of freedom are considered to be either white noise or coloured noise correlated,while the GME is considered under either the Markov or Non-Markov approaches. The comparison between these considerations are fully developed and their physical meaning is discussed. (author)

THE EVOLUTION OF THE ELECTRIC CURRENT DURING THE FORMATION AND ERUPTION OF ACTIVE-REGION FILAMENTS

Energy Technology Data Exchange (ETDEWEB)

Wang, Jincheng; Yan, Xiaoli; Qu, Zhongquan; Xue, Zhike; Xiang, Yongyuan; Li, Hao, E-mail: egnever@ynao.ac.cn [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China)

2016-02-01

We present a comprehensive study of the electric current related to the formation and eruption of active region filaments in NOAA AR 11884. The vertical current on the solar surface was investigated by using vector magnetograms (VMs) observed by HMI on board the Solar Dynamics Observatory. To obtain the electric current along the filament's axis, we reconstructed the magnetic fields above the photosphere by using nonlinear force-free field extrapolation based on photospheric VMs. Spatio-temporal evolutions of the vertical current on the photospheric surface and the horizontal current along the filament's axis were studied during the long-term evolution and eruption-related period, respectively. The results show that the vertical currents of the entire active region behaved with a decreasing trend and the magnetic fields also kept decreasing during the long-term evolution. For the eruption-related evolution, the mean transverse field strengths decreased before two eruptions and increased sharply after two eruptions in the vicinity of the polarity inversion lines underneath the filament. The related vertical current showed different behaviors in two of the eruptions. On the other hand, a very interesting feature was found: opposite horizontal currents with respect to the current of the filament's axis appeared and increased under the filament before the eruptions and disappeared after the eruptions. We suggest that these opposite currents were carried by the new flux emerging from the photosphere bottom and might be the trigger mechanism for these filament eruptions.

Asset pricing puzzles explained by incomplete Brownian equilibria

DEFF Research Database (Denmark)

Christensen, Peter Ove; Larsen, Kasper

We examine a class of Brownian based models which produce tractable incomplete equilibria. The models are based on finitely many investors with heterogeneous exponential utilities over intermediate consumption who receive partially unspanned income. The investors can trade continuously on a finit...... markets. Consequently, our model can simultaneously help explaining the risk-free rate and equity premium puzzles....

Analytical Core Mass Function (CMF) from Filaments: Under Which Circumstances Can Filament Fragmentation Reproduce the CMF?

Energy Technology Data Exchange (ETDEWEB)

Lee, Yueh-Ning; Hennebelle, Patrick [IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette (France); Chabrier, Gilles, E-mail: yueh-ning.lee@cea.fr [École normale supérieure de Lyon, CRAL, UMR CNRS 5574, Université de Lyon, F-69364 Lyon Cedex 07 (France)

2017-10-01

Observations suggest that star formation in filamentary molecular clouds occurs in a two-step process, with the formation of filaments preceding that of prestellar cores and stars. Here, we apply the gravoturbulent fragmentation theory of Hennebelle and Chabrier to a filamentary environment, taking into account magnetic support. We discuss the induced geometrical effect on the cores, with a transition from 3D geometry at small scales to 1D at large ones. The model predicts the fragmentation behavior of a filament for a given mass per unit length (MpL) and level of magnetization. This core mass function (CMF) for individual filaments is then convolved with the distribution of filaments to obtain the final system CMF. The model yields two major results. (i) The filamentary geometry naturally induces a hierarchical fragmentation process, first into groups of cores, separated by a length equal to a few filament Jeans lengths, i.e., a few times the filament width. These groups then fragment into individual cores. (ii) Non-magnetized filaments with high MpL are found to fragment excessively, at odds with observations. This is resolved by taking into account the magnetic field (treated simply as additional pressure support). The present theory suggests two complementary modes of star formation: although small (spherical or filamentary) structures will collapse directly into prestellar cores, according to the standard Hennebelle–Chabrier theory, the large (filamentary) ones, the dominant population according to observations, will follow the aforedescribed two-step process.

Automatic Detect and Trace of Solar Filaments

Science.gov (United States)

Fang, Cheng; Chen, P. F.; Tang, Yu-hua; Hao, Qi; Guo, Yang

We developed a series of methods to automatically detect and trace solar filaments in solar Hα images. The programs are able to not only recognize filaments and determine their properties, such as the position, the area and other relevant parameters, but also to trace the daily evolution of the filaments. For solar full disk Hα images, the method consists of three parts: first, preprocessing is applied to correct the original images; second, the Canny edge-detection method is used to detect the filaments; third, filament properties are recognized through the morphological operators. For each Hα filament and its barb features, we introduced the unweighted undirected graph concept and adopted Dijkstra shortest-path algorithm to recognize the filament spine; then, using polarity inversion line shift method for measuring the polarities in both sides of the filament to determine the filament axis chirality; finally, employing connected components labeling method to identify the barbs and calculating the angle between each barb and spine to indicate the barb chirality. Our algorithms are applied to the observations from varied observatories, including the Optical & Near Infrared Solar Eruption Tracer (ONSET) in Nanjing University, Mauna Loa Solar Observatory (MLSO) and Big Bear Solar Observatory (BBSO). The programs are demonstrated to be effective and efficient. We used our method to automatically process and analyze 3470 images obtained by MLSO from January 1998 to December 2009, and a butterfly diagram of filaments is obtained. It shows that the latitudinal migration of solar filaments has three trends in the Solar Cycle 23: The drift velocity was fast from 1998 to the solar maximum; after the solar maximum, it became relatively slow and after 2006, the migration became divergent, signifying the solar minimum. About 60% filaments with the latitudes larger than 50 degree migrate towards the Polar Regions with relatively high velocities, and the latitudinal migrating

Filamentation and light bullet formation dynamics in solid-state dielectric media with weak, moderate and strong anomalous group velocity dispersion

International Nuclear Information System (INIS)

Gražulevičiūtė, I; Garejev, N; Majus, D; Tamošauskas, G; A Dubietis; Jukna, V

2016-01-01

We present a series of measurements, which characterize filamentation dynamics of intense ultrashort laser pulses in the space–time domain, as captured by means of three-dimensional imaging technique in sapphire and fused silica, in the wavelength range of 1.45–2.25 μm, accessing the regimes of weak, moderate and strong anomalous group velocity dispersion (GVD). In the regime of weak anomalous GVD (at 1.45 μm), pulse splitting into two sub-pulses producing a pair of light bullets with spectrally shifted carrier frequencies in both nonlinear media is observed. In contrast, in the regimes of moderate (at 1.8 μm) and strong (at 2.25 μm) anomalous GVD we observe notably different transient dynamics, which however lead to the formation of a single self-compressed quasistationary light bullet with an universal spatiotemporal shape comprised of an extended ring-shaped periphery and a localized intense core that carries the self-compressed pulse. (paper)

Filamentation and light bullet formation dynamics in solid-state dielectric media with weak, moderate and strong anomalous group velocity dispersion

Science.gov (United States)

Gražulevičiūtė, I.; Garejev, N.; Majus, D.; Jukna, V.; Tamošauskas, G.; Dubietis, A.

2016-02-01

We present a series of measurements, which characterize filamentation dynamics of intense ultrashort laser pulses in the space-time domain, as captured by means of three-dimensional imaging technique in sapphire and fused silica, in the wavelength range of 1.45-2.25 μm, accessing the regimes of weak, moderate and strong anomalous group velocity dispersion (GVD). In the regime of weak anomalous GVD (at 1.45 μm), pulse splitting into two sub-pulses producing a pair of light bullets with spectrally shifted carrier frequencies in both nonlinear media is observed. In contrast, in the regimes of moderate (at 1.8 μm) and strong (at 2.25 μm) anomalous GVD we observe notably different transient dynamics, which however lead to the formation of a single self-compressed quasistationary light bullet with an universal spatiotemporal shape comprised of an extended ring-shaped periphery and a localized intense core that carries the self-compressed pulse.

Synchronization and collective motion of globally coupled Brownian particles

International Nuclear Information System (INIS)

Sevilla, Francisco J; Heiblum-Robles, Alexandro; Dossetti, Victor

2014-01-01

In this work, we study a system of passive Brownian (non-self-propelled) particles in two dimensions, interacting only through a social-like force (velocity alignment in this case) that resembles Kuramoto's coupling among phase oscillators. We show that the kinematical stationary states of the system go from a phase in thermal equilibrium with no net flux of particles, to far-from-equilibrium phases exhibiting collective motion by increasing the coupling among particles. The mechanism that leads to the instability of the equilibrium phase relies on the competition between two time scales, namely, the mean collision time of the Brownian particles in a thermal bath and the time it takes for a particle to orient its direction of motion along the direction of motion of the group. Our results show a clear connection between collective motion and the Kuramoto model for synchronization, in our case, for the direction of motion of the particles. (paper)

Laser light scattering in Brownian medium

International Nuclear Information System (INIS)

Suwono; Santoso, Budi; Baiquni, A.

1983-01-01

The principle of laser light scattering in Brownian medium and photon correlation spectroscopy are described in detail. Their application to the study of the behaviour of a polystyrene latex solution are discussed. The auto-correlation function of light scattered by the polystyrene latex solution in various angle, various temperature and in various sample times, have been measured. Information on the translation diffusion coefficient and size on the particle can be obtained from the auto-correlation function. Good agreement between the available data and experiment is shown. (author)

NLTE modeling of a small active region filament observed with the VTT

Czech Academy of Sciences Publication Activity Database

Schwartz, P.; Balthasar, H.; Kuckein, C.; Koza, J.; Gömöry, P.; Rybák, J.; Heinzel, Petr; Kučera, A.

2016-01-01

Roč. 337, č. 10 (2016), s. 1045-1049 ISSN 0004-6337. [Dynamic Sun - Exploring the Many Facets of Solar Eruptive Events. Potsdam, 26.10.2015-29.10.2015] Institutional support: RVO:67985815 Keywords : Sun * filaments * prominences Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 0.916, year: 2016

Spectropolarimetric observations of an arch filament system with the GREGOR solar telescope

Czech Academy of Sciences Publication Activity Database

Balthasar, H.; Gömöry, P.; Gonzalez Manrique, S. J.; Kuckein, C.; Kavka, J.; Kučera, A.; Schwartz, P.; Vašková, R.; Berkefeld, T.; Collados Vera, M.; Denker, C.; Feller, A.; Hofmann, A.; Lagg, A.; Nicklas, H.; Orozco Suárez, D.; Pastor Yabar, A.; Schlichenmaier, R.; Schmidt, D.; Schmidt, W.; Sigwarth, M.; Sobotka, Michal; Solanki, S.K.; Soltau, D.; Staude, J.; Strassmeier, K.G.; Volkmer, R.; von der Lühe, O.; Waldmann, T.A.

2016-01-01

Roč. 337, č. 10 (2016), s. 1050-1056 ISSN 0004-6337. [Dynamic Sun - Exploring the Many Facets of Solar Eruptive Events. Potsdam, 26.10.2015-29.10.2015] Institutional support: RVO:67985815 Keywords : Sun * filaments * photosphere Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 0.916, year: 2016

On the biased motion of a brownian particle for the pausing time behavior of the CTRW

International Nuclear Information System (INIS)

Kim, K.S.

1982-01-01

The purpose of this paper is to discuss the biased Brownian motion with the absorbing barrier for the pausing time behavior of the CTRW (continuous-time random walk method), regarding a Brownian particle as a walker. For two pausing time density functions, the respective values for the transport averaged velocity and the dispersion are calculated as the time t becomes large. (KAERI)

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders

Science.gov (United States)

Kanazawa, Kiyoshi; Sueshige, Takumi; Takayasu, Hideki; Takayasu, Misako

2018-03-01

A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models. We next introduce the corresponding microscopic model of HFTs and present its theoretical solution paralleling molecular kinetic theory: Boltzmann-like and Langevin-like equations are derived from the microscopic dynamics via the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy. Our model is the first microscopic model that has been directly validated through data analysis of the microscopic dynamics, exhibiting quantitative agreements with mesoscopic and macroscopic empirical results.

Algorithms for Brownian first-passage-time estimation

Science.gov (United States)

Adib, Artur B.

2009-09-01

A class of algorithms in discrete space and continuous time for Brownian first-passage-time estimation is considered. A simple algorithm is derived that yields exact mean first-passage times (MFPTs) for linear potentials in one dimension, regardless of the lattice spacing. When applied to nonlinear potentials and/or higher spatial dimensions, numerical evidence suggests that this algorithm yields MFPT estimates that either outperform or rival Langevin-based (discrete time and continuous space) estimates.

Current fluctuations of interacting active Brownian particles

OpenAIRE

Pre, Trevor Grand; Limmer, David T.

2018-01-01

We derive the distribution function for particle currents for a system of interacting active Brownian particles in the long time limit using large deviation theory and a weighted many body expansion. We find the distribution is non-Gaussian, except in the limit of passive particles. The non-Gaussian fluctuations can be understood from the effective potential the particles experience when conditioned on a given current. This potential suppresses fluctuations of the particle's orientation, and ...

Evolution of filament barbs.

Science.gov (United States)

Liu, R.; Xu, Y.; Wang, H.

We present a selected few cases in which the sense of chirality of filament barbs changed within periods as short as hours. We investigate in detail a quiescent filament on 2003 September 10 and 11. Of its four barbs displaying such changes, only one overlays a small polarity inversion line inside the EUV filament channel (EFC). No magnetic elements with magnitude above the noise level were detected at the endpoints of all barbs. In particular, a pair of barbs first approached toward, and then departed from, each other in Halpha , with the barb endpoints migrating as far as ˜ 10 arcsec. We conclude that the evolution of the barbs was driven by flux emergence and cancellation of small bipolar units at the EFC border.

Fractional Brownian motion and motion governed by the fractional Langevin equation in confined geometries.

Science.gov (United States)

Jeon, Jae-Hyung; Metzler, Ralf

2010-02-01

Motivated by subdiffusive motion of biomolecules observed in living cells, we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and restricted to a finite domain. We investigate by analytic calculations and simulations how time-averaged observables (e.g., the time-averaged mean-squared displacement and displacement correlation) are affected by spatial confinement and dimensionality. In particular, we study the degree of weak ergodicity breaking and scatter between different single trajectories for this confined motion in the subdiffusive domain. The general trend is that deviations from ergodicity are decreased with decreasing size of the movement volume and with increasing dimensionality. We define the displacement correlation function and find that this quantity shows distinct features for fractional Brownian motion, fractional Langevin equation, and continuous time subdiffusion, such that it appears an efficient measure to distinguish these different processes based on single-particle trajectory data.

Occupation times distribution for Brownian motion on graphs

CERN Document Server

Desbois, J

2002-01-01

Considering a Brownian motion on a general graph, we study the joint law for the occupation times on all the bonds. In particular, we show that the Laplace transform of this distribution can be expressed as the ratio of two determinants. We give two formulations, with arc or vertex matrices, for this result and discuss a simple example. (letter to the editor)

[Application of Brownian dynamics to the description of transmembrane ion flow as exemplified by the chloride channel of glycine receptor].

Science.gov (United States)

Boronovskiĭ, S E; Nartsissov, Ia R

2009-01-01

Using the Brownian dynamics of the movement of hydrated ion in a viscous water solution, a mathematical model has been built, which describes the transport of charged particles through a single protein pore in a lipid membrane. The dependences of transmembrane ion currents on ion concentrations in solution have been obtained. It was shown that, if the geometry of a membrane pore is identical to that of the inner part of the glycine receptor channel and there is no ion selectivity, then the values of both chloride and sodium currents are not greater than 0.5 pA at the physiological concentrations of these ions. If local charge heterogeneity caused by charged amino acid residues of transmembrane protein segments is included into the model calculations, the chloride current increases to about 3.7 pA, which exceeds more than seven times the value for sodium ions under the conditions of the complex channel geometry in the range of physiological concentrations of ions in the solution. The model takes changes in the density of charge distribution both inside the channel and near the protein surface into account. The alteration of pore geometry can be also considered as a parameter at the researcher's option. Thus, the model appears as an effective tool for the description of transmembrane currents for other types of membrane channels.

Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem.

Science.gov (United States)

Benson, Christopher R; Maffeo, Christopher; Fatila, Elisabeth M; Liu, Yun; Sheetz, Edward G; Aksimentiev, Aleksei; Singharoy, Abhishek; Flood, Amar H

2018-05-07

The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the "three-body problem." Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring-thread interactions for kinetics, and ring-ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.

A Nonthermal Radio Filament Connected to the Galactic Black Hole?

Science.gov (United States)

Morris, Mark R.; Zhao, Jun-Hui; Goss, W. M.

2017-12-01

Using the Very Large Array, we have investigated a nonthermal radio filament (NTF) recently found very near the Galactic black hole and its radio counterpart, Sgr A*. While this NTF—the Sgr A West Filament (SgrAWF)—shares many characteristics with the population of NTFs occupying the central few hundred parsecs of the Galaxy, the SgrAWF has the distinction of having an orientation and sky location that suggest an intimate physical connection to Sgr A*. We present 3.3 and 5.5 cm images constructed using an innovative methodology that yields a very high dynamic range, providing an unprecedentedly clear picture of the SgrAWF. While the physical association of the SgrAWF with Sgr A* is not unambiguous, the images decidedly evoke this interesting possibility. Assuming that the SgrAWF bears a physical relationship to Sgr A*, we examine the potential implications. One is that Sgr A* is a source of relativistic particles constrained to diffuse along ordered local field lines. The relativistic particles could also be fed into the local field by a collimated outflow from Sgr A*, perhaps driven by the Poynting flux accompanying the black hole spin in the presence of a magnetic field threading the event horizon. Second, we consider the possibility that the SgrAWF is the manifestation of a low-mass-density cosmic string that has become anchored to the black hole. The simplest form of these hypotheses would predict that the filament be bi-directional, whereas the SgrAWF is only seen on one side of Sgr A*, perhaps because of the dynamics of the local medium.

Filamentation of Campylobacter in broth cultures

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Nacheervan M Ghaffar

2015-06-01

Full Text Available The transition from rod to filamentous cell morphology has been identified as a response to stressful conditions in many bacterial species and has been ascribed to confer certain survival advantages. Filamentation of Campylobacter jejuni was demonstrated to occur spontaneously on entry in to stationary phase distinguishing it from many other bacteria where a reduction in size is more common. The aim of this study was to investigate the cues that give rise to filamentation of C. jejuni and C. coli and gain insights into the process. Using minimal medium, augmentation of filamentation occurred and it was observed that this morphological change was wide spread amongst C. jejuni strains tested but was not universal in C. coli strains. Filamentation did not appear to be due to release of diffusible molecules, toxic metabolites, or be in response to oxidative stress in the medium. Separated filaments exhibited greater intracellular ATP contents (2.66 to 17.4 fg than spiral forms (0.99 to 1.7 fg and showed enhanced survival in water at 4oC and 37oC compared to spiral cells. These observations support the conclusion that the filaments are adapted to survive extra-intestinal environments. Differences in cell morphology and physiology need to be considered in the context of the design of experimental studies and the methods adopted for the isolation of campylobacters from food, clinical and environmental sources.

The physical structure of a cold filament in a Chilean upwelling zone (Península de Mejillones, Chile, 23°S)

Science.gov (United States)

Sobarzo, Marcus; Figueroa, Dante

2001-12-01

Cold filaments associated with Eastern Boundary Currents are typically narrower than 100 km but can be several hundred kilometers long, extending from the coast to the open ocean in upwelling areas. One such structure, observed off Península de Mejillones (23°S, Chile), was studied with both satellite images and two 5-days hydrographic cruises carried out during January 1997. The study used a coastal grid of 31 stations in an area of 165 ×155 km 2, approximately. The spatial distribution of the filament and its change between cruises are described from the horizontal distributions of dynamic height, temperature, salinity and dissolved oxygen. The filament was a shallow feature (thickness zone show the ascent of the shallow salinity minimum (SSM), and its extension toward the ocean, bound to the filament. It is concluded that Subantarctic Water ((SAAW) distinguish by low salinity, high dissolved oxygen) and Equatorial Subsurface Water ((ESSW) high salinity, low dissolved oxygen, high nutrient content) form this filament, and that their relative proportions depend on the strength of the coastal upwelling. Thus, the knowledge of the dynamics of these structures is fundamental to better understanding of the spatial distribution of important biological variables, such as nutrients and chlorophyll, in the coastal ecosystem.

Active Brownian motion models and applications to ratchets

Science.gov (United States)

Fiasconaro, A.; Ebeling, W.; Gudowska-Nowak, E.

2008-10-01

We give an overview over recent studies on the model of Active Brownian Motion (ABM) coupled to reservoirs providing free energy which may be converted into kinetic energy of motion. First, we present an introduction to a general concept of active Brownian particles which are capable to take up energy from the source and transform part of it in order to perform various activities. In the second part of our presentation we consider applications of ABM to ratchet systems with different forms of differentiable potentials. Both analytical and numerical evaluations are discussed for three cases of sinusoidal, staircaselike and Mateos ratchet potentials, also with the additional loads modelled by tilted potential structure. In addition, stochastic character of the kinetics is investigated by considering perturbation by Gaussian white noise which is shown to be responsible for driving the directionality of the asymptotic flux in the ratchet. This stochastically driven directionality effect is visualized as a strong nonmonotonic dependence of the statistics of the right versus left trajectories of motion leading to a net current of particles. Possible applications of the ratchet systems to molecular motors are also briefly discussed.

“Dandelion” Filament Eruption and Coronal Waves Associated with a Solar Flare on 2011 February 16

International Nuclear Information System (INIS)

Cabezas, Denis P.; Ishitsuka, Mutsumi; Ishitsuka, José K.; Martínez, Lurdes M.; Buleje, Yovanny J.; Morita, Satoshi; Asai, Ayumi; UeNo, Satoru; Ishii, Takako T.; Kitai, Reizaburo; Takasao, Shinsuke; Yoshinaga, Yusuke; Otsuji, Kenichi; Shibata, Kazunari

2017-01-01

Coronal disturbances associated with solar flares, such as H α Moreton waves, X-ray waves, and extreme ultraviolet (EUV) coronal waves, are discussed herein in relation to magnetohydrodynamic fast-mode waves or shocks in the corona. To understand the mechanism of coronal disturbances, full-disk solar observations with high spatial and temporal resolution over multiple wavelengths are of crucial importance. We observed a filament eruption, whose shape is like a “dandelion,” associated with the M1.6 flare that occurred on 2011 February 16 in H α images taken by the Flare Monitoring Telescope at Ica University, Peru. We derive the three-dimensional velocity field of the erupting filament. We also identify winking filaments that are located far from the flare site in the H α images, whereas no Moreton wave is observed. By comparing the temporal evolution of the winking filaments with those of the coronal wave seen in the EUV images data taken by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory and by the Extreme Ultraviolet Imager on board the Solar Terrestrial Relations Observatory-Ahead , we confirm that the winking filaments were activated by the EUV coronal wave.

“Dandelion” Filament Eruption and Coronal Waves Associated with a Solar Flare on 2011 February 16

Energy Technology Data Exchange (ETDEWEB)

Cabezas, Denis P.; Ishitsuka, Mutsumi; Ishitsuka, José K. [Geophysical Institute of Peru, Calle Badajoz 169, Mayorazgo IV Etapa, Ate Vitarte, Lima (Peru); Martínez, Lurdes M.; Buleje, Yovanny J. [Centro de Investigación del Estudio de la Actividad Solar y sus Efectos Sobre la Tierra, Facultad de Ciencias, Universidad Nacional San Luis Gonzaga de Ica, Av. Los Maestros S/N, Ica (Peru); Morita, Satoshi [National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo, 181-8588 (Japan); Asai, Ayumi [Unit of Synergetic Studies for Space, Kyoto University, Sakyo, Kyoto, 606-8502 (Japan); UeNo, Satoru; Ishii, Takako T.; Kitai, Reizaburo; Takasao, Shinsuke; Yoshinaga, Yusuke; Otsuji, Kenichi; Shibata, Kazunari, E-mail: denis@kwasan.kyoto-u.ac.jp [Kwasan and Hida Observatories, Kyoto University, Yamashina, Kyoto, 607-8471 (Japan)

2017-02-10