Fluctuations as stochastic deformation
Kazinski, P. O.
2008-04-01
A notion of stochastic deformation is introduced and the corresponding algebraic deformation procedure is developed. This procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation parameter (the Planck constant). This method is demonstrated on diverse relativistic and nonrelativistic models with finite and infinite degrees of freedom. It is shown that under stochastic deformation the model of a nonrelativistic particle interacting with the electromagnetic field on a curved background passes into the stochastic model described by the Fokker-Planck equation with the diffusion tensor being the inverse metric tensor. The first stochastic correction to the Newton equations for this system is found. The Klein-Kramers equation is also derived as the stochastic deformation of a certain classical model. Relativistic generalizations of the Fokker-Planck and Klein-Kramers equations are obtained by applying the procedure of stochastic deformation to appropriate relativistic classical models. The analog of the Fokker-Planck equation associated with the stochastic Lorentz-Dirac equation is derived too. The stochastic deformation of the models of a free scalar field and an electromagnetic field is investigated. It turns out that in the latter case the obtained stochastic model describes a fluctuating electromagnetic field in a transparent medium.
Work fluctuations and stochastic resonance
International Nuclear Information System (INIS)
We study Brownian particle motion in a double-well potential driven by an ac force. This system exhibits the phenomenon of stochastic resonance. Distribution of work done on the system over a drive period in the time asymptotic regime has been calculated. We show that fluctuations in the input energy or work done dominate the mean value. The mean value of work done over a period as a function of noise strength can also be used to characterize stochastic resonance in the system. We also discuss the validity of steady state fluctuation theorems in this particular system
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
Marinov, Georgi K; Williams, Brian A; McCue, Ken; Schroth, Gary P; Gertz, Jason; Myers, Richard M; Wold, Barbara J
2014-03-01
Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30-100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states. PMID:24299736
Stochastic Einstein equations with fluctuating volume
Dzhunushaliev, Vladimir
2016-01-01
We develop a simple model to study classical fields on the background of a fluctuating spacetime volume. It is applied to formulate the stochastic Einstein equations with a perfect-fluid source. We investigate the particular case of a stochastic Friedmann-Lema\\^itre-Robertson-Walker cosmology, and show that the resulting field equations can lead to solutions which avoid the initial big bang singularity. By interpreting the fluctuations as the result of the presence of a quantum spacetime, we conclude that classical singularities can be avoided even within a stochastic model that include quantum effects in a very simple manner.
Density fluctuations in simple stochastic reactor models
International Nuclear Information System (INIS)
A method to study density fluctuations in a nuclear reactor simultaneously taking into account intrinsic fluctuations usually modelled by a master equation and parametric noise usually modelled by stochastic kinetic equations is presented. The mean density and density-fluctuations variance are calculated for a simple point-reactor model in the presence of Gaussian white-noise fluctuations in the fission, capture and source event rates. They are also calculated in the case of dichotomous noise fluctuations in the source event rate. 'Crossed fluctuation' contributions to the density fluctuations are found that only appear when considering simultaneously intrinsic and parametric noise. These contributions allow distinction to be made between reactivity fluctuations due to fission-rate and capture-rate fluctuations. (author)
Stochastic game dynamics under demographic fluctuations.
Huang, Weini; Hauert, Christoph; Traulsen, Arne
2015-07-21
Frequency-dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency-dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model that naturally combines these two evolutionary ingredients by assuming frequency-dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population, and thus the population size, is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by deterministic competitive Lotka-Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. Because the population size is driven by fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size the population would thrive regardless of its average payoff. PMID:26150518
Thermal diffusion by stochastic electromagnetic fluctuations
International Nuclear Information System (INIS)
A new simple systematic method has been developed to analytically evaluate the thermal diffusion coefficient of guiding center test particles brought by coexisting homogeneously stochastic electrostatic and electro-magnetic fluctuations. As a most simple case, thermal diffusion coefficients for electrons and ions are analytically obtained in a large aspect straight tokamak with a small gyro-radius and negligible magnetic shear and negligible equilibrium E vector x B vector flow shear. Those analytical formulae are applicable to the range beyond so-called quasi-linear limit: thermal diffusion coefficient are squarely (linearly) proportional to fluctuation amplitudes in the quasi-linear (beyond quasi-linear) region. It is shown that the thermal diffusion of electrons (ions) is mainly dominated by magnetic (electrostatic) fluctuations in the experimentally relevant situations, even if both magnetic and electrostatic fluctuations coexist. It is also shown that the resonant electrons do not diffuse when the electric field parallel to the unperturbed magnetic field lines is negligible, even if electrostatic and electromagnetic fluctuations coexist. (author)
Stochastically fluctuations of the modernized fast pulsed reactor IBR-2
International Nuclear Information System (INIS)
Full Text : Stochastically fluctuations of the power of the IBR-2 reactor have been quite significant (20 percent), they affect the dynamics of the reactor, the process of regulation, starting on the work of the experimental equipment, etc. On the other hand, the presence of large fluctuations in power at the IBR-2M has had its advantages. Investigation of stochastic fluctuations has allowed to estimate some physical parameters of the nuclear reactor core, for example, the mean lifetime of prompt neutrons in the reactor, source of spontaneous neutrons, and absolute power of the reactor. The main results of the investigation impulse stochastically fluctuations of the IBR-2 periodic pulsed reactor after modernization have been presented. It has been shown that the experimental results have been close to the calculated ones
Stochastic thermodynamics of macrospins with fluctuating amplitude and direction.
Bandopadhyay, Swarnali; Chaudhuri, Debasish; Jayannavar, A M
2015-09-01
We consider stochastic energy balance and entropy production (EP) in a generalized Langevin dynamics of macrospins, allowing for both amplitude and direction fluctuations, under external magnetic field. EP is calculated using a Fokker-Planck equation, distinguishing between reversible and irreversible parts of probability currents. The system entropy increases due to irreversible non-equilibrium processes, and reduces as heat dissipates to the surrounding environment. Using path probability distributions of time-forward trajectories and conjugate trajectories under time reversal, we obtain fluctuation theorems (FT) for total stochastic EP. We show that the choice of conjugate trajectories is crucial in obtaining entropy-like quantities that obey FTs. PMID:26465462
Gravitational brainwaves, quantum fluctuations and stochastic quantization
Bar, D.
2007-01-01
It is known that the biological activity of the brain involves radiation of electric waves. These waves result from ionic currents and charges traveling among the brain's neurons. But it is obvious that these ions and charges are carried by their relevant masses which should give rise, according to the gravitational theory, to extremely weak gravitational waves. We use in the following the stochastic quantization (SQ) theory to calculate the probability to find a large ensemble of brains radi...
Gravitational brainwaves, quantum fluctuations and stochastic quantization
Bar, D
2007-01-01
It is known that the biological activity of the brain involves radiation of electric waves. These waves result from ionic currents and charges traveling among the brain's neurons. But it is obvious that these ions and charges are carried by their relevant masses which should give rise, according to the gravitational theory, to extremely weak gravitational waves. We use in the following the stochastic quantization (SQ) theory to calculate the probability to find a large ensemble of brains radiating similar gravitational waves. We also use this SQ theory to derive the equilibrium state related to the known Lamb shift.
Energy fluctuations induced by stochastic frequency changes in atom traps
International Nuclear Information System (INIS)
We study the quantum description of energy fluctuations induced by stochastic changes in the frequency of atom traps. Using the connection between classical and quantum descriptions of parametric oscillators, the classical cumulant expansion method is used to obtain quantum results beyond standard perturbation theory. Both the case of static and time-dependent traps are explicitly worked out
Extreme fluctuations in stochastic network coordination with time delays
Hunt, D.; Molnár, F.; Szymanski, B. K.; Korniss, G.
2015-12-01
We study the effects of uniform time delays on the extreme fluctuations in stochastic synchronization and coordination problems with linear couplings in complex networks. We obtain the average size of the fluctuations at the nodes from the behavior of the underlying modes of the network. We then obtain the scaling behavior of the extreme fluctuations with system size, as well as the distribution of the extremes on complex networks, and compare them to those on regular one-dimensional lattices. For large complex networks, when the delay is not too close to the critical one, fluctuations at the nodes effectively decouple, and the limit distributions converge to the Fisher-Tippett-Gumbel density. In contrast, fluctuations in low-dimensional spatial graphs are strongly correlated, and the limit distribution of the extremes is the Airy density. Finally, we also explore the effects of nonlinear couplings on the stability and on the extremes of the synchronization landscapes.
Effective cosmological constant induced by stochastic fluctuations of Newton's constant
de Cesare, Marco; Sakellariadou, Mairi
2016-01-01
We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.
Effective cosmological constant induced by stochastic fluctuations of Newton's constant
de Cesare, Marco; Lizzi, Fedele; Sakellariadou, Mairi
2016-09-01
We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.
Stochastic Amplification of Fluctuations in Cortical Up-States
Hidalgo, Jorge; Seoane, Luís F.; Cortés, Jesús M.; Muñoz, Miguel A.
2012-01-01
Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow Hz oscillations which are widely known as transitions between Up and Down States. Despite a large number of studies on Up-Down transitions, deciphering its nature, mechanisms and function are still today challenging tasks. In this paper we focus on recent experimental evidence, showing that a class of spontaneous oscillations can emerge within the Up states. In particular, a non-trivial peak around Hz appears in their associated power-spectra, what produces an enhancement of the activity power for higher frequencies (in the Hz band). Moreover, this rhythm within Ups seems to be an emergent or collective phenomenon given that individual neurons do not lock to it as they remain mostly unsynchronized. Remarkably, similar oscillations (and the concomitant peak in the spectrum) do not appear in the Down states. Here we shed light on these findings by using different computational models for the dynamics of cortical networks in presence of different levels of physiological complexity. Our conclusion, supported by both theory and simulations, is that the collective phenomenon of “stochastic amplification of fluctuations” – previously described in other contexts such as Ecology and Epidemiology – explains in an elegant and parsimonious manner, beyond model-dependent details, this extra-rhythm emerging only in the Up states but not in the Downs. PMID:22879879
Stochastic cooling of bunched beams from fluctuation and kinetic theory
Energy Technology Data Exchange (ETDEWEB)
Chattopadhyay, S.
1982-09-01
A theoretical formalism for stochastic phase-space cooling of bunched beams in storage rings is developed on the dual basis of classical fluctuation theory and kinetic theory of many-body systems in phase-space. The physics is that of a collection of three-dimensional oscillators coupled via retarded nonconservative interactions determined by an electronic feedback loop. At the heart of the formulation is the existence of several disparate time-scales characterizing the cooling process. Both theoretical approaches describe the cooling process in the form of a Fokker-Planck transport equation in phase-space valid up to second order in the strength and first order in the auto-correlation of the cooling signal. With neglect of the collective correlations induced by the feedback loop, identical expressions are obtained in both cases for the coherent damping and Schottky noise diffusion coefficients. These are expressed in terms of Fourier coefficients in a harmonic decomposition in angle of the generalized nonconservative cooling force written in canonical action-angle variables of the particles in six-dimensional phase-space. Comparison of analytic results to a numerical simulation study with 90 pseudo-particles in a model cooling system is presented.
Stochastic cooling of bunched beams from fluctuation and kinetic theory
International Nuclear Information System (INIS)
A theoretical formalism for stochastic phase-space cooling of bunched beams in storage rings is developed on the dual basis of classical fluctuation theory and kinetic theory of many-body systems in phase-space. The physics is that of a collection of three-dimensional oscillators coupled via retarded nonconservative interactions determined by an electronic feedback loop. At the heart of the formulation is the existence of several disparate time-scales characterizing the cooling process. Both theoretical approaches describe the cooling process in the form of a Fokker-Planck transport equation in phase-space valid up to second order in the strength and first order in the auto-correlation of the cooling signal. With neglect of the collective correlations induced by the feedback loop, identical expressions are obtained in both cases for the coherent damping and Schottky noise diffusion coefficients. These are expressed in terms of Fourier coefficients in a harmonic decomposition in angle of the generalized nonconservative cooling force written in canonical action-angle variables of the particles in six-dimensional phase-space. Comparison of analytic results to a numerical simulation study with 90 pseudo-particles in a model cooling system is presented
Energy Technology Data Exchange (ETDEWEB)
Li, Dongxi, E-mail: lidongxi@yahoo.cn [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an, 710072 (China); Xu, Wei; Sun, Chunyan; Wang, Liang [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an, 710072 (China)
2012-04-30
We investigate the phenomenon that stochastic fluctuation induced the competition between tumor extinction and recurrence in the model of tumor growth derived from the catalytic Michaelis–Menten reaction. We analyze the probability transitions between the extinction state and the state of the stable tumor by the Mean First Extinction Time (MFET) and Mean First Return Time (MFRT). It is found that the positional fluctuations hinder the transition, but the environmental fluctuations, to a certain level, facilitate the tumor extinction. The observed behavior could be used as prior information for the treatment of cancer. -- Highlights: ► Stochastic fluctuation induced the competition between extinction and recurrence. ► The probability transitions are investigated. ► The positional fluctuations hinder the transition. ► The environmental fluctuations, to a certain level, facilitate the tumor extinction. ► The observed behavior can be used as prior information for the treatment of cancer.
International Nuclear Information System (INIS)
We investigate the phenomenon that stochastic fluctuation induced the competition between tumor extinction and recurrence in the model of tumor growth derived from the catalytic Michaelis–Menten reaction. We analyze the probability transitions between the extinction state and the state of the stable tumor by the Mean First Extinction Time (MFET) and Mean First Return Time (MFRT). It is found that the positional fluctuations hinder the transition, but the environmental fluctuations, to a certain level, facilitate the tumor extinction. The observed behavior could be used as prior information for the treatment of cancer. -- Highlights: ► Stochastic fluctuation induced the competition between extinction and recurrence. ► The probability transitions are investigated. ► The positional fluctuations hinder the transition. ► The environmental fluctuations, to a certain level, facilitate the tumor extinction. ► The observed behavior can be used as prior information for the treatment of cancer.
Impulse power stochastically fluctuations of the modernized fast pulsed reactor IBR-2
International Nuclear Information System (INIS)
Full text : Stochastically fluctuations of the power of the IBR-2 reactor have been quite significant, they affect the dynamics of the reactor, the process of regulation, starting on the work of the experimental equipment. On the other hand, the presence of large fluctuations in power at the IBR-2M has had its advantages. Investigation of stochastic fluctuations has allowed to estimate some physical parameters of the nuclear reactor core, for example, the mean lifetime of prompt neutrons in the reactor, source of spontaneous neutrons and absolute power of the reactor. The main results of the investigation impulse power stochastically fluctuations of the IBR-2 periodic pulsed reactor after modernization have been presented. It has been shown that the experimental results have been close to the calculated ones
International Nuclear Information System (INIS)
We investigate a stochastic model of tumor growth derived from the catalytic Michaelis-Menten reaction with positional and environmental fluctuations under subthreshold periodic treatment. Firstly, the influences of environmental fluctuations on the treatable stage are analyzed numerically. Applying the standard theory of stochastic resonance derived from the two-state approach, we derive the signal-to-noise ratio (SNR) analytically, which is used to measure the stochastic resonance phenomenon. It is found that the weak environmental fluctuations could induce the extinction of tumor cells in the subthreshold periodic treatment. The positional stability is better in favor of the treatment of the tumor cells. Besides, the appropriate and feasible treatment intensity and the treatment cycle should be highlighted considered in the treatment of tumor cells.
Energy Technology Data Exchange (ETDEWEB)
Li Dongxi, E-mail: lidongxi@mail.nwpu.edu.c [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China); Xu Wei; Guo, Yongfeng; Xu Yong [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China)
2011-01-31
We investigate a stochastic model of tumor growth derived from the catalytic Michaelis-Menten reaction with positional and environmental fluctuations under subthreshold periodic treatment. Firstly, the influences of environmental fluctuations on the treatable stage are analyzed numerically. Applying the standard theory of stochastic resonance derived from the two-state approach, we derive the signal-to-noise ratio (SNR) analytically, which is used to measure the stochastic resonance phenomenon. It is found that the weak environmental fluctuations could induce the extinction of tumor cells in the subthreshold periodic treatment. The positional stability is better in favor of the treatment of the tumor cells. Besides, the appropriate and feasible treatment intensity and the treatment cycle should be highlighted considered in the treatment of tumor cells.
Optimal Stochastic Restart Renders Fluctuations in First Passage Times Universal
Reuveni, Shlomi
2016-04-01
Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT) processes seem to have very little in common but it is actually quite the other way around. Here we show that the relative standard deviation associated with the FPT of an optimally restarted process, i.e., one that is restarted at a constant (nonzero) rate which brings the mean FPT to a minimum, is always unity. We interpret, further generalize, and discuss this finding and the implications arising from it.
Environmental Fluctuations and Stochastic Resonance in Protein Folding.
Dave, Kapil; Davtyan, Aram; Papoian, Garegin A; Gruebele, Martin; Platkov, Max
2016-05-01
Stochastic resonance is a mechanism whereby a weak signal becomes detectable through the addition of noise. It is common in many macroscopic biological phenomena, but here we ask whether it can be observed in a microscopic biological phenomenon, protein folding. We investigate the folding kinetics of the protein VlsE, with a folding relaxation time of about 0.7 seconds at 38 °C in vitro. First we show that the VlsE unfolding/refolding reaction can be driven by a periodic thermal excitation above the reaction threshold. We detect the reaction by fluorescence from FRET labels on VlSE and show that accurate rate coefficients and activation barriers can be obtained from modulated kinetics. Then we weaken the periodic temperature modulation below the reaction threshold, and show that addition of artificial thermal noise speeds up the reaction from an undetectable to a detectable rate. We observe a maximum in the recovered signal as a function of thermal noise, a stochastic resonance. Simulation of a small model-protein, analysis in an accompanying theory paper, and our experimental result here all show that correlated noise is a physically and chemically plausible mechanism by which cells could modulate biomolecular dynamics during threshold processes such as signaling. PMID:26711088
A model for the optimal design of a supply chain network driven by stochastic fluctuations
Petridis, Kostas; Dey, Prasanta K
2015-01-01
Supply chain optimization schemes have more often than not underplayed the role of inherent stochastic fluctuations in the associated variables. The present article focuses on the associated reengagement and correlated renormalization of supply chain predictions now with the inclusion of stochasticity induced fluctuations in the structure. With a processing production plant in mind that involves stochastically varying production and transportation costs both from the site to the plant as well as from the plant to the customer base, this article proves that the producer may benefit through better outlay in the form of higher sale prices with lowered optimized production costs only through a suitable selective choice of producers whose production cost probability density function abides a Pareto distribution. Lower the Pareto exponent, better is the supply chain prediction for cost optimization. On the other hand, other symmetric (normal) and asymmetric (lognormal) distributions lead to upscaled costs both in t...
Black Hole Fluctuations and Backreaction in Stochastic Gravity
Sinha, S; Hu, B L; Sinha, Sukanya; Raval, Alpan
2003-01-01
We present a framework for analyzing black hole backreaction from the point of view of quantum open systems using influence functional formalism. We focus on the model of a black hole described by a radially perturbed quasi-static metric and Hawking radiation by a conformally coupled massless quantum scalar field. It is shown that the closed-time-path (CTP) effective action yields a non-local dissipation term as well as a stochastic noise term in the equation of motion, the Einstein-Langevin equation. Once the thermal Green's function in a Schwarzschild background becomes available to the required accuracy the strategy described here can be applied to obtain concrete results on backreaction. We also present an alternative derivation of the CTP effective action in terms of the Bogolyubov coefficients, thus making a connection with the interpretation of the noise term as measuring the difference in particle production in alternative histories.
Particle-density fluctuations and universality in the conserved stochastic sandpile
Dickman, Ronald; da Cunha, S. D.
2015-08-01
We examine fluctuations in particle density in the restricted-height, conserved stochastic sandpile (CSS). In this and related models, the global particle density is a temperaturelike control parameter. Thus local fluctuations in this density correspond to disorder; if this disorder is a relevant perturbation of directed percolation (DP), then the CSS should exhibit non-DP critical behavior. We analyze the scaling of the variance Vℓ of the number of particles in regions of ℓd sites in extensive simulations of the quasistationary state in one and two dimensions. Our results, combined with a Harris-like argument for the relevance of particle-density fluctuations, strongly suggest that conserved stochastic sandpiles belong to a universality class distinct from that of DP.
Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes
Kumar, Ashutosh; Nandi, Mintu; Dua, Arti
2016-01-01
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, how...
Effects of stochastic fluctuations at molecule–electrode contacts in transition voltage spectroscopy
International Nuclear Information System (INIS)
Highlights: ► Work devoted to transition voltage spectroscopy, a hot topic in molecular electronics. ► First theoretical study on the physical origin of stochastic fluctuations in TVS. ► First theoretical study that considers effects of electron correlations on TVS. ► Supporting the idea that the transition voltage is a molecular signature. ► Validation of the Newns–Anderson model for molecular junctions of interest. - Abstract: The influence of the stochastic fluctuations at contacts on the electron transport through molecular junctions based on alkanedithiols is investigated theoretically. Results are presented, which demonstrate that the transition voltage Vt is insensitive to fluctuations in the electrode–molecule hopping integrals. By contrast, reasonably large fluctuations (δJ∼2eV) in the Coulomb contact interaction J, included via an extended Newns–Anderson model, lead to fluctuations in the molecular orbital energetic alignment ε0, which are consistent with the fluctuations in Vt observed experimentally. The impact of these J- (or ε0-) fluctuations on the conductance G is considerably stronger than on Vt. The G-fluctuations driven by δJ represent a substantial fraction of the fluctuations displayed by experimental conductance histograms. The electron system for J≠0 is correlated, i.e., it cannot be described within a single-particle (Landauer-based) picture. However, in the J-range of interest, the ratio Vt/ε0 turns out to be only weakly dependent on J. The weak impact of J on the ratio Vt/ε0 is important because it suggests that, even in the presence of realistically strong electron correlations, transition voltage spectroscopy can be a useful tool of investigation.
Altaner, Bernhard; Wachtel, Artur; Vollmer, Jürgen
2015-10-01
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational states of these biological macromolecules. A recently developed theoretical framework [A. Wachtel, J. Vollmer, and B. Altaner, Phys. Rev. E 92, 042132 (2015), 10.1103/PhysRevE.92.042132] provides a simple algorithm for the determination of macroscopic currents and correlation integrals of arbitrary fluctuating currents. Here we use it to discuss energy conversion and nonequilibrium response in different models for the molecular motor kinesin. Methodologically, our results demonstrate the effectiveness of the algorithm in dealing with parameter-dependent stochastic models. For the concrete biophysical problem our results reveal two interesting features in experimentally accessible parameter regions: the validity of a nonequilibrium Green-Kubo relation at mechanical stalling as well as a negative differential mobility for superstalling forces.
Space-time fluctuations and a stochastic Schr\\"odinger-Newton equation
Bera, Sayantani; Singh, Tejinder P
2016-01-01
We propose a stochastic modification of the Schr\\"{o}dinger-Newton equation which takes into account the effect of extrinsic spacetime fluctuations. We use this equation to demonstrate gravitationally induced decoherence of two gaussian wave-packets, and obtain a decoherence criterion similar to those obtained in the earlier literature in the context of effects of gravity on the Schr\\"{o}dinger equation.
A Stochastic Approach to Thermal Fluctuations during a First Order Electroweak Phase Transition
Illuminati, F.; Riotto, A.
1995-01-01
We investigate the role played by subcritical bubbles at the onset of the electroweak phase transition. Treating the configuration modelling the thermal fluctuations around the homogeneous zero configuration of the Higgs field as a stochastic variable, we describe its dynamics by a phenomenological Langevin equation. This approach allows to properly take into account both the effects of the thermal bath on the system: a systematic dyssipative force, which tends to erase out any initial subcri...
Rocha, Paulo; Raischel, Frank; Boto, João P.; Lind, Pedro G.
2016-05-01
We present a framework for describing the evolution of stochastic observables having a nonstationary distribution of values. The framework is applied to empirical volume-prices from assets traded at the New York Stock Exchange, about which several remarks are pointed out from our analysis. Using Kullback-Leibler divergence we evaluate the best model out of four biparametric models commonly used in the context of financial data analysis. In our present data sets we conclude that the inverse Γ distribution is a good model, particularly for the distribution tail of the largest volume-price fluctuations. Extracting the time series of the corresponding parameter values we show that they evolve in time as stochastic variables themselves. For the particular case of the parameter controlling the volume-price distribution tail we are able to extract an Ornstein-Uhlenbeck equation which describes the fluctuations of the highest volume-prices observed in the data. Finally, we discuss how to bridge the gap from the stochastic evolution of the distribution parameters to the stochastic evolution of the (nonstationary) observable and put our conclusions into perspective for other applications in geophysics and biology.
A stochastic approach to thermal fluctuations during a first order electroweak phase transition
Illuminati, F
1995-01-01
We investigate the role played by subcritical bubbles at the onset of the electroweak phase transition. Treating the configuration modelling the thermal fluctuations around the homogeneous zero configuration of the Higgs field as a stochastic variable, we describe its dynamics by a phenomenological Langevin equation. This approach allows to properly take into account both the effects of the thermal bath on the system: a systematic dyssipative force, which tends to erase out any initial subcritical configuration, and a random stochastic force responsible for the fluctuations. We show that the contribution to the variance \\lgh\\phi^2(t)\\rg_V in a given volume V from any initial subcritical configuration is quickly damped away and that, in the limit of long times, \\lgh\\phi^2(t)\\rg_V approaches its equilibrium value provided by the stochastic force and independent from the viscosity coefficient, as predicted by the fluctuation-dissipation theorem. In agreement with some recent claims, we conclude that thermal fluc...
Fluctuations of large-scale jets in the stochastic 2D Euler equation
Nardini, Cesare
2016-01-01
Two-dimensional turbulence in a rectangular domain self-organises into large-scale unidirectional jets. While several results are present to characterize the mean jets velocity profile, much less is known about the fluctuations. We study jets dynamics in the stochastically forced two-dimensional Euler equations. In the limit where the average jets velocity profile evolves slowly with respect to turbulent fluctuations, we employ a multi-scale (kinetic theory) approach, which relates jet dynamics to the statistics of Reynolds stresses. We study analytically the Gaussian fluctuations of Reynolds stresses and predict the spatial structure of the jets velocity covariance. Our results agree qualitatively well with direct numerical simulations, clearly showing that the jets velocity profile are enhanced away from the stationary points of the average velocity profile. A numerical test of our predictions at quantitative level seems out of reach at the present day.
Jansen, TL; Hayashi, T; Zhuang, W; Mukamel, S
2005-01-01
The effects of hydrogen-bond forming and breaking kinetics on the linear and coherent third-order infrared spectra of the OH stretch of HOD in D2O are described by Markovian, not necessarily Gaussian, fluctuations and simulated using the stochastic Liouville equations. Slow (0.5 ps) fluctuations are
QB1 - Stochastic Gene Regulation
Energy Technology Data Exchange (ETDEWEB)
Munsky, Brian [Los Alamos National Laboratory
2012-07-23
Summaries of this presentation are: (1) Stochastic fluctuations or 'noise' is present in the cell - Random motion and competition between reactants, Low copy, quantization of reactants, Upstream processes; (2) Fluctuations may be very important - Cell-to-cell variability, Cell fate decisions (switches), Signal amplification or damping, stochastic resonances; and (3) Some tools are available to mode these - Kinetic Monte Carlo simulations (SSA and variants), Moment approximation methods, Finite State Projection. We will see how modeling these reactions can tell us more about the underlying processes of gene regulation.
Petrosyan, K G
2014-01-01
We present a statistical physics framework for description of nonlinear non-equilibrium stochastic processes, modeled via chemical master equation, in the weak-noise limit. Using the Poisson representation approach and applying the large-deviation principle we first solve the master equation. Then we use the notion of the non-equilibrium free energy to derive an integral fluctuation relation for nonlinear non-equilibrium systems under feedback control. We point out that the free energy as well as some functionals can serve as non-equilibrium Lyapunov function which has an important property to decay to its minimal value monotonously at all times. The Poisson representation technique is illustrated via exact stochastic treatment of biophysical processes, such as bacterial chemosensing and molecular evolution.
Stochastic volatility of financial markets as the fluctuating rate of trading: an empirical study
Silva, A C; Yakovenko, Victor M.
2006-01-01
We present an empirical study of the subordination hypothesis for a stochastic time series of a stock price. The fluctuating rate of trading is identified with the stochastic variance of the stock price, as in the continuous-time random walk (CTRW) framework. The probability distribution of the stock price changes (log-returns) for a given number of trades N is found to be approximately Gaussian. The probability distribution of N for a given time interval Dt is non-Poissonian and has an exponential tail for large N and a sharp cutoff for small N. Combining these two distributions produces a nontrivial distribution of log-returns for a given time interval Dt, which has exponential tails and a Gaussian central part, in agreement with empirical observations.
International Nuclear Information System (INIS)
We investigate a stochastic heat engine based on an over-damped particle diffusing on the positive real axis in an externally driven time-periodic log-harmonic potential. The periodic driving is composed of two isothermal and two adiabatic branches. Within our specific setting we verify the recent universal results regarding efficiency at maximum power and discuss properties of the optimal protocol. Namely, we show that for certain fixed parameters the optimal protocol maximizes not only the output power but also the efficiency. Moreover, we calculate the variance of the output work and discuss the possibility of minimizing fluctuations of the output power. (paper)
Stochastic resonance in a groundwater-dependent plant ecosystem with fluctuations and time delay
International Nuclear Information System (INIS)
We numerically investigate the stochastic resonance (SR) pheno menon in a groundwater-dependent plant ecosystem under the combined influence of environmental fluctuations, seasonal rainfall oscillation, and time delay. The effects of time delay and intrinsic and extrinsic fluctuations on the output signal-to-noise ratio (SNR) of the system are analyzed. The results indicate that the SNR exhibits a maximum as a function of the intensities of the intrinsic and extrinsic noises, identifying the occurrence of the SR effect. An increase of the delay time always suppresses the SR effect, while an increase of correlation strength between noises may suppress or enhance it. The SNR also shows a resonant behavior as a function of the correlation strength between noises, and it can be weakened by the time delay. (paper)
Charmet, Jérôme; Michaels, Thomas C. T.; Daly, Ronan; Prasad, Abhinav; Thiruvenkathanathan, Pradyumna; Langley, Robin S.; Knowles, Tuomas P. J.; Seshia, Ashwin A.
2016-06-01
Recent advances in micro- and nanotechnology have enabled the development of ultrasensitive sensors capable of detecting small numbers of species. In general, however, the response induced by the random adsorption of a small number of objects onto the surface of such sensors results in significant fluctuations due to the heterogeneous sensitivity inherent to many such sensors coupled to statistical fluctuations in the particle number. At present, this issue is addressed by considering either the limit of very large numbers of analytes, where fluctuations vanish, or the converse limit, where the sensor response is governed by individual analytes. Many cases of practical interest, however, fall between these two limits and remain challenging to analyze. Here, we address this limitation by deriving a general theoretical framework for quantifying measurement variations on mechanical resonators resulting from statistical-number fluctuations of analyte species. Our results provide insights into the stochastic processes in the sensing environment and offer opportunities to improve the performance of mechanical-resonator-based sensors. This metric can be used, among others, to aid in the design of robust sensor platforms to reach ultrahigh-resolution measurements using an array of sensors. These concepts, illustrated here in the context of biosensing, are general and can therefore be adapted and extended to other sensors with heterogeneous sensitivity.
International Nuclear Information System (INIS)
We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications
Energy Technology Data Exchange (ETDEWEB)
Leonard, T.; Lander, B.; Seifert, U. [II. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Speck, T. [Institut für Theoretische Physik II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany)
2013-11-28
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for the work still hold albeit for a different, apparent, change of free energy.
A simple stochastic model for dipole moment fluctuations in numerical dynamo simulations
Directory of Open Access Journals (Sweden)
Domenico G. eMeduri
2016-04-01
Full Text Available Earth's axial dipole field changes in a complex fashion on many differenttime scales ranging from less than a year to tens of million years.Documenting, analysing, and replicating this intricate signalis a challenge for data acquisition, theoretical interpretation,and dynamo modelling alike. Here we explore whether axial dipole variationscan be described by the superposition of a slow deterministic driftand fast stochastic fluctuations, i.e. by a Langevin-type system.The drift term describes the time averaged behaviour of the axial dipole variations,whereas the stochastic part mimics complex flow interactions over convective time scales.The statistical behaviour of the system is described by a Fokker-Planck equation whichallows useful predictions, including the average rates of dipole reversals and excursions.We analyse several numerical dynamo simulations, most of which havebeen integrated particularly long in time, and also the palaeomagneticmodel PADM2M which covers the past 2 Myr.The results show that the Langevin description provides a viable statistical modelof the axial dipole variations on time scales longer than about 1 kyr.For example, the axial dipole probability distribution and the average reversalrate are successfully predicted.The exception is PADM2M where the stochastic model reversal rate seems too low.The dependence of the drift on the axial dipolemoment reveals the nonlinear interactions that establish thedynamo balance. A separate analysis of inductive and diffusive magnetic effectsin three dynamo simulations suggests that the classical quadraticquenching of induction predicted by mean-field theory seems at work.
Out-of-equilibrium fluctuations in stochastic long-range interacting systems
Gupta, Shamik; Dauxois, Thierry; Ruffo, Stefano
2016-03-01
For a many-particle system with long-range interactions and evolving under stochastic dynamics, we study for the first time the out-of-equilibrium fluctuations of the work done on the system by a time-dependent external force. For equilibrium initial conditions, the work distributions for a given protocol of variation of the force in time and the corresponding time-reversed protocol exhibit a remarkable scaling and a symmetry when expressed in terms of the average and the standard deviation of the work. The distributions of the work per particle predict, by virtue of the Crooks fluctuation theorem, the equilibrium free-energy density of the system. For a large number N of particles, the latter is in excellent agreement with the value computed by considering the Langevin dynamics of a single particle in a self-consistent mean field generated by its interaction with other particles. The agreement highlights the effective mean-field nature of the original many-particle dynamics for large N. For initial conditions in non-equilibrium stationary states (NESSs), we study the distribution of a quantity similar to dissipated work that satisfies the non-equilibrium generalization of the Clausius inequality, namely, the Hatano-Sasa equality, for transitions between NESSs. Besides illustrating the validity of the equality, we show that the distribution has exponential tails that decay differently on the left and on the right.
Schunck, M.; Hegmann, M.; Sedlmayr, E.
2007-01-01
We investigate the effects of stochastic density fluctuations on the dust temperatures and the resulting infrared (IR) emission spectra of interstellar clouds as an extension of preceding investigations by Hegmann & Kegel. We consider absorption and scattering by dust grains in spherical clouds which are, on average, homogeneous but have a fluctuating density. The spatial variation of the density is described by means of a Markov process. This clump model introduces two parameters: the correlation length ln and the Gaussian width σn of the density fluctuations. As the intensity Iλ,n inherits the randomness of the density n, the ordinary radiative transfer equation has to be replaced by a generalized transfer equation of Fokker-Planck type. In the first part, we investigate the influence of our model parameters on the radiative transport in the ultraviolet (UV) and use the results to calculate the dust temperature in radiative equilibrium. Afterwards, the IR emission of the dust is modelled for the same set of clump parameters. We find that the presence of clumps decreases the effective extinction and therefore leads to substantial differences in UV illumination and dust temperatures, compared with the homogeneous case. Because of the distribution of dust temperatures, the presence of clumps also affects the IR emission and thus possible observations. In the second part, we use a fit with two blackbody spectra to determine the cloud dust mass from our synthetic IR fluxes. It is shown that in a clumpy environment the overall dust mass is generally underestimated. This effect correlates with the degree of cloud fragmentation.
Listening to the noise: random fluctuations reveal gene network parameters
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2009-01-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations show cell-to-cell variability that can manifest significant phenotypic differences. Noise-induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far...
International Nuclear Information System (INIS)
Highlights: ► Solar radiation data for European cities follow the Extreme Value or Weibull distribution. ► Simulation model for the sizing of SAPV systems based on energy balance and stochastic analysis. ► Simulation of PV Generator-Loads-Battery Storage System performance for all months. ► Minimum peak power and battery capacity required for reliable SAPV sizing for various European cities. ► Peak power and battery capacity reduced by more than 30% for operation 95% success rate. -- Abstract: The large fluctuations observed in the daily solar radiation profiles affect highly the reliability of the PV system sizing. Increasing the reliability of the PV system requires higher installed peak power (Pm) and larger battery storage capacity (CL). This leads to increased costs, and makes PV technology less competitive. This research paper presents a new stochastic simulation model for stand-alone PV systems, developed to determine the minimum installed Pm and CL for the PV system to be energy independent. The stochastic simulation model developed, makes use of knowledge acquired from an in-depth statistical analysis of the solar radiation data for the site, and simulates the energy delivered, the excess energy burnt, the load profiles and the state of charge of the battery system for the month the sizing is applied, and the PV system performance for the entire year. The simulation model provides the user with values for the autonomy factor d, simulating PV performance in order to determine the minimum Pm and CL depending on the requirements of the application, i.e. operation with critical or non-critical loads. The model makes use of NASA’s Surface meteorology and Solar Energy database for the years 1990–2004 for various cities in Europe with a different climate. The results obtained with this new methodology indicate a substantial reduction in installed peak power and battery capacity, both for critical and non-critical operation, when compared to
Colucci, Paul John
A methodology termed the "filtered density function" (FDF) is developed and implemented for large eddy simulation (LES) of chemically reacting turbulent flows. In this methodology, the effects of the unresolved scalar fluctuations are taken into account by considering the probability density function (PDF) of the subgrid scale (SGS) scalar quantities. The transport equation governing the evolution of the FDF is derived in which the effect of chemical reaction appears in a closed form. The influences of scalar mixing and convection within the subgrid are modeled. The generalization to variable density flows is made through consideration of the filtered mass density function (FMDF). The FDF and FMDF transport equations are solved numerically via a Lagrangian Monte Carlo scheme in which the solutions of equivalent stochastic differential equations (SDEs) are obtained. The consistency of the approach, the convergence of the Monte Carlo solution, and the performance of the closures employed in the FDF and FMDF transport equations are assessed by comparisons with results obtained by direct numerical simulation (DNS) and by conventional LES procedures in which the first two SGS scalar moments are obtained by a finite difference method (LES-FD). In non-reacting flows, the Monte Carlo solution yields results similar to those via LES-FD for the first two SGS moments. The advantage of the methodology is demonstrated by its use in LES of reacting flows. In the absence of a closure for the SGS scalar fluctuations, the LES-FD results are significantly different from those based on DNS. Comparatively, the FDF and FMDF yield much better agreement with filtered DNS results. The methodology is also tested by comparative assessments against experimental data for a heat releasing hydrogen-fluorine reacting mixing layer.
Zhang, Yue; Zhang, Qingling; Yan, Xing-Gang
2014-06-01
In this paper, a class of singular Leslie-Gower predator-prey bioeconomic models with environment fluctuations and time delays is investigated. Local stability analysis of the model reveals that there is a phenomenon of singularity induced bifurcation due to variation of economic interest of harvesting. By choosing the delay as a bifurcation parameter, it is shown that the Hopf bifurcations can occur as the delay crosses some critical values. Then, the effect of a fluctuating environment on the singular stochastic delayed predator-prey bioeconomic model is discussed. Finally numerical simulations demonstrate that the amplitude of oscillation for population is enhanced when compared with the oscillation observed in the deterministic environment.
Hong, Dawei; Man, Shushuang; Martin, Joseph V
2016-01-21
There are two functionally important factors in signal propagation in a brain structural network: the very first synaptic delay-a time delay about 1ms-from the moment when signals originate to the moment when observation on the signal propagation can begin; and rapid random fluctuations in membrane potentials of every individual neuron in the network at a timescale of microseconds. We provide a stochastic analysis of signal propagation in a general setting. The analysis shows that the two factors together result in a stochastic mechanism for the signal propagation as described below. A brain structural network is not a rigid circuit rather a very flexible framework that guides signals to propagate but does not guarantee success of the signal propagation. In such a framework, with the very first synaptic delay, rapid random fluctuations in every individual neuron in the network cause an "alter-and-concentrate effect" that almost surely forces signals to successfully propagate. By the stochastic mechanism we provide analytic evidence for the existence of a force behind signal propagation in a brain structural network caused by rapid random fluctuations in every individual neuron in the network at a timescale of microseconds with a time delay of 1ms. PMID:26555846
Rocha, Paulo; Boto, João P; Lind, Pedro G
2015-01-01
We present a framework for describing the evolution of stochastic observables having a non-stationary distribution of values. The framework is applied to empirical volume-prices from assets traded at the New York stock exchange. Using Kullback-Leibler divergence we evaluate the best model out from four biparametric models standardly used in the context of financial data analysis. In our present data sets we conclude that the inverse $\\Gamma$-distribution is a good model, particularly for the distribution tail of the largest volume-price fluctuations. Extracting the time-series of the corresponding parameter values we show that they evolve in time as stochastic variables themselves. For the particular case of the parameter controlling the volume-price distribution tail we are able to extract an Ornstein-Uhlenbeck equation which describes the fluctuations of the largest volume-prices observed in the data. Finally, we discuss how to bridge from the stochastic evolution of the distribution parameters to the stoch...
Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver
2013-01-01
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulatio...
Kim, Won Kyu; 10.1063/1.4746118
2012-01-01
Within the cell, biopolymers are often situated in constrained, fluid environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is of paramount importance to understand quantitatively how they, utilizing their flexibility, optimally respond to a minute signal, which is, in general, temporally fluctuating far away from equilibrium. To this end, we analytically study viscoelastic response and associated stochastic resonance in a stretched single semi-flexible chain to an oscillatory force or electric field. Including hydrodynamic interactions between chain segments, we evaluate dynamics of the polymer extension in coherent response to the force or field. We find power amplification factor of the response at a noise-strength (temperature) can attain the maximum that grows as the chain length increases, indicative of an entropic stochastic resonance (ESR). In particular for a charged chain under an electric field, we find that the maximum also occurs at an optimal chain length, a new feature of E...
Garcia, O. E.; Kube, R.; Theodorsen, A.; Pécseli, H. L.
2016-05-01
A stochastic model is presented for intermittent fluctuations in the scrape-off layer of magnetically confined plasmas. The fluctuations in the plasma density are modeled by a super-position of uncorrelated pulses with fixed shape and duration, describing radial motion of blob-like structures. In the case of an exponential pulse shape and exponentially distributed pulse amplitudes, predictions are given for the lowest order moments, probability density function, auto-correlation function, level crossings, and average times for periods spent above and below a given threshold level. Also, the mean squared errors on estimators of sample mean and variance for realizations of the process by finite time series are obtained. These results are discussed in the context of single-point measurements of fluctuations in the scrape-off layer, broad density profiles, and implications for plasma-wall interactions due to the transient transport events in fusion grade plasmas. The results may also have wide applications for modelling fluctuations in other magnetized plasmas such as basic laboratory experiments and ionospheric irregularities.
International Nuclear Information System (INIS)
Considering a damped linear oscillator model subjected to a white noise with an inherent angular frequency and a periodic external driving force, we derive the analytic expression of the first moment of output response, and study the stochastic resonance phenomenon in a system. The results show that the output response of this system behaves as a simple harmonic vibration, of which the frequency is the same as the external driving frequency, and the variations of amplitude with the driving frequency and the inherent frequency present a bona fide stochastic resonance. (general)
Institute of Scientific and Technical Information of China (English)
Zhang Ling-Ying; Jin Guo-Xiang; Cao Li; Wang Zhi-Yun
2012-01-01
Considering a damped linear oscillator model subjected to a white noise with an inherent angular frequency and a periodic external driving force,we derive the analytic expression of the first moment of output response,and study the stochastic resonance phenomenon in a system.The results show that the output response of this system behaves as a simple harmonic vibration,of which the frequency is the same as the external driving frequency,and the variations of amplitude with the driving frequency and the inherent frequency present a bona fide stochastic resonance.
Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver
2013-10-22
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host-parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5 °C) and permissive (23 °C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645
Duncan, Alison B.; Gonzalez, Andrew; Kaltz, Oliver
2013-01-01
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645
EFT Beyond the Horizon: Stochastic Inflation and How Primordial Quantum Fluctuations Go Classical
Burgess, C P; Tasinato, G; Williams, M
2015-01-01
We identify the effective theory describing inflationary super-Hubble scales and show it to be a special case of effective field theories appropriate to open systems. Open systems allow information to be exchanged between the degrees of freedom of interest and those that are integrated out, such as for particles moving through a fluid. Strictly speaking they cannot in general be described by an effective lagrangian; rather the appropriate `low-energy' limit is instead a Lindblad equation describing the evolution of the density matrix of the slow degrees of freedom. We derive the equation relevant to super-Hubble modes of quantum fields in near-de Sitter spacetimes and derive two implications. We show the evolution of the diagonal density-matrix elements quickly approaches the Fokker-Planck equation of Starobinsky's stochastic inflationary picture. This provides an alternative first-principles derivation of this picture's stochastic noise and drift, as well as its leading corrections. (An application computes ...
Determinants of Cell-to-Cell Variability in Protein Kinase Signaling
Matthias Jeschke; Stephan Baumgärtner; Stefan Legewie
2013-01-01
Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds ('pathway sensitivity') and the maximal act...
Wen, Xing-Chun; He, Ling-Yun
2015-08-01
There is a bitter controversy over what drives the housing price in China in the existing literature. In this paper, we investigate the underlying driving force behind housing price fluctuations in China, especially focusing on the role of housing demand shock with that of money supply shock in explaining housing price movements, by a new Keynesian dynamic stochastic general equilibrium model. Empirical results suggest that it is housing demand, instead of money supply, that mainly drives China's housing price movements. Relevant policy implication is further discussed, namely, whether to consider the housing price fluctuations in the conduct of monetary policy. By means of the policy simulations, we find that a real house price-augmented money supply rule is a better monetary policy for China's economy stabilization. 1. Investment refers to fixed capital investment. 2. Housing price refers to national average housing price. Quarterly data on housing price during the period of our work are not directly available. However, monthly data of the value of sales on housing and sale volume on housing can be directly obtained from National Bureau of Statistics of China. We add up the monthly data and calculate one quarter's housing price by dividing the value of housing sales by its sale volume in one quarter. 3. M2 means the broad money supply in China.
Bouzat, Sebastián
2016-01-01
One-dimensional models coupling a Langevin equation for the cargo position to stochastic stepping dynamics for the motors constitute a relevant framework for analyzing multiple-motor microtubule transport. In this work we explore the consistence of these models focusing on the effects of the thermal noise. We study how to define consistent stepping and detachment rates for the motors as functions of the local forces acting on them in such a way that the cargo velocity and run-time match previously specified functions of the external load, which are set on the base of experimental results. We show that due to the influence of the thermal fluctuations this is not a trivial problem, even for the single-motor case. As a solution, we propose a motor stepping dynamics which considers memory on the motor force. This model leads to better results for single-motor transport than the approaches previously considered in the literature. Moreover, it gives a much better prediction for the stall force of the two-motor case, highly compatible with the experimental findings. We also analyze the fast fluctuations of the cargo position and the influence of the viscosity, comparing the proposed model to the standard one, and we show how the differences on the single-motor dynamics propagate to the multiple motor situations. Finally, we find that the one-dimensional character of the models impede an appropriate description of the fast fluctuations of the cargo position at small loads. We show how this problem can be solved by considering two-dimensional models. PMID:26871095
Absorptive and dispersive optical profiles in fluctuating environments: A stochastic model
International Nuclear Information System (INIS)
In this study, we determined the absorptive and dispersive optical profiles of a molecular system coupled with a thermal bath. Solvent effects were explicitly considered by modelling the non-radiative interaction with the solute as a random variable. The optical stochastical Bloch equations (OSBE) were solved using a time-ordered cumulant expansion with white noise as a correlation function. We found a solution for the Fourier component of coherence at the third order of perturbation for the nonlinear Four-wave mixing signal and produced analytical expressions for the optical responses of the system. Finally, we examined the behaviour of these properties with respect to the noise parameter, frequency detuning of the dynamic perturbation, and relaxation times.
Fluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics
Wachtel, Artur; Vollmer, Jürgen; Altaner, Bernhard
2015-10-01
Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication.
Stochasticity in the yeast mating pathway
International Nuclear Information System (INIS)
We report stochastic simulations of the yeast mating signal transduction pathway. The effects of intrinsic and external noise, the influence of cell-to-cell difference in the pathway capacity, and noise propagation in the pathway have been examined. The stochastic temporal behaviour of the pathway is found to be robust to the influence of inherent fluctuations, and intrinsic noise propagates in the pathway in a uniform pattern when the yeasts are treated with pheromones of different stimulus strengths and of varied fluctuations. In agreement with recent experimental findings, extrinsic noise is found to play a more prominent role than intrinsic noise in the variability of proteins. The occurrence frequency for the reactions in the pathway are also examined and a more compact network is obtained by dropping most of the reactions of least occurrence
Stochastic fluctuations and distributed control of gene expression impact cellular memory.
Directory of Open Access Journals (Sweden)
Guillaume Corre
Full Text Available Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.
Conformally-related Einstein-Langevin equations for metric fluctuations in stochastic gravity
Satin, Seema; Hu, Bei Lok
2016-01-01
For a conformally-coupled scalar field we obtain the conformally-related Einstein-Langevin equations, using appropriate transformations for all the quantities in the equations between two conformally-related spacetimes. In particular, we analyze the transformations of the influence action, the stress energy tensor, the noise kernel and the dissipation kernel. In due course the fluctuation-dissipation relation is also discussed. The analysis in this paper thereby facilitates a general solution to the Einstein-Langevin equation once the solution of the equation in a simpler, conformally-related spacetime is known. For example, from the Minkowski solution of Martin and Verdaguer, those of the Einstein-Langevin equations in conformally-flat spacetimes, especially for spatially-flat Friedmann-Robertson-Walker models, can be readily obtained.
Wetland Ecohydrology: stochastic description of water level fluctuations across the soil surface
Tamea, S.; Muneepeerakul, R.; Laio, F.; Ridolfi, L.; Rodriguez-Iturbe, I.
2009-12-01
Wetlands provide a suite of social and ecological critical functions such as being habitats of disease-carrying vectors, providing buffer zones against hurricanes, controlling sediment transport, filtering nutrients and contaminants, and a repository of great biological diversity. More recently, wetlands have also been recognized as crucial for carbon storage in the context of global climate change. Despite such importance, quantitative approaches to many aspects of wetlands are far from adequate. Therefore, improving our quantitative understanding of wetlands is necessary to our ability to maintain, manage, and restore these invaluable environments. In wetlands, hydrologic factors and ecosystem processes interplay and generate unique characteristics and a delicate balance between biotic and abiotic elements. The main hydrologic driver of wetland ecosystems is the position of the water level that, being above or below ground, determines the submergence or exposure of soil. When the water level is above the soil surface, soil saturation and lack of oxygen causes hypoxia, anaerobic functioning of microorganisms and anoxic stress in plants, that might lead to the death of non-adapted organisms. When the water level lies below the soil surface, the ecosystem becomes groundwater-dependent, and pedological and physiological aspects play their role in the soil water balance. We propose here a quantitative description of wetland ecohydrology, through a stochastic process-based water balance, driven by a marked compound Poisson noise representing rainfall events. The model includes processes such as rainfall infiltration, evapotranspiration, capillary rise, and the contribution of external water bodies, which are quantified in a simple yet realistic way. The semi-analytical steady-state probability distributions of water level spanning across the soil surface are validated with data from the Everglades (Florida, USA). The model and its results allow for a quantitative
Directory of Open Access Journals (Sweden)
Shnoll S. E.
2006-04-01
Full Text Available This is a survey of the fine structure stochastic distributions in measurements obtained by me over 50 years. It is shown: (1 The forms of the histograms obtained at each geographic point (at each given moment of time are similar with high probability, even if we register phenomena of completely different nature — from biochemical reactions to the noise in a gravitational antenna, or α-decay. (2 The forms of the histograms change with time. The iterations of the same form have the periods of the stellar day (1.436 min, the solar day (1.440 min, the calendar year (365 solar days, and the sidereal year (365 solar days plus 6 hours and 9 min. (3 At the same instants of the local time, at different geographic points, the forms of the histograms are the same, with high probability. (4 The forms of the histograms depend on the locations of the Moon and the Sun with respect to the horizon. (5 All the facts are proof of the dependance of the form of the histograms on the location of the measured objects with respect to stars, the Sun, and the Moon. (6 At the instants of New Moon and the maxima of solar eclipses there are specific forms of the histograms. (7 It is probable that the observed correlations are not connected to flow power changes (the changes of the gravity force — we did not find the appropriate periods in changes in histogram form. (8 A sharp anisotropy of space was discovered, registered by α-decay detectors armed with collimators. Observations at 54◦ North (the collimator was pointed at the Pole Star showed no day-long periods, as was also the case for observations at 82◦ North, near the Pole. Histograms obtained by observations with an Easterly-directed collimator were determined every 718 minutes (half stellar day and with observations using a Westerly-directed collimator. (9 Collimators rotating counter-clockwise, in parallel with the celestial equator, gave the probability of changes in histograms as the number of the
Directory of Open Access Journals (Sweden)
Shnoll S. E.
2006-04-01
Full Text Available This is a survey of the fine structure stochastic distributions in measurements obtained by me over 50 years. It is shown: (1 The forms of the histograms obtained at each geographic point (at each given moment of time are similar with high probability, even if we register phenomena of completely different nature --- from biochemical reactions to the noise in a gravitational antenna, or alpha-decay. (2 The forms of the histograms change with time. The iterations of the same form have the periods of the stellar day (1.436 min, the solar day (1.440 min, the calendar year (365 solar days, and the sidereal year (365 solar days plus 6 hours and 9 min. (3 At the same instants of the local time, at different geographic points, the forms of the histograms are the same, with high probability. (4 The forms of the histograms depend on the locations of the Moon and the Sun with respect to the horizon. (5 All the facts are proof of the dependance of the form of the histograms on the location of the measured objects with respect to stars, the Sun, and the Moon. (6 At the instants of New Moon and the maxima of solar eclipses there are specific forms of the histograms. (7 It is probable that the observed correlations are not connected to flow power changes (the changes of the gravity force --- we did not find the appropriate periods in changes in histogram form. (8 A sharp anisotropy of space was discovered, registered by alpha-decay detectors armed with collimators. Observations at 54 North (the collimator was pointed at the Pole Star showed no day-long periods, as was also the case for observations at 82 North, near the Pole. Histograms obtained by observations with an Easterly-directed collimator were determined every 718 minutes (half stellar day and with observations using a Westerly-directed collimator. (9 Collimators rotating counter-clockwise, in parallel with the celestial equator, gave the probability of changes in histograms as the number of the
Reyes, Luz Marina; Aguilar, Jose Edgar Madriz; Bellini, Mauricio
2010-01-01
We develop a stochastic approach to study scalar field fluctuations of the inflaton field in an early inflationary universe with a black-hole (BH), which is described by an effective 4D SdS metric. Considering a 5D Ricci-flat SdS static metric, we implement a planar coordinate transformation, in order to obtain a 5D cosmological metric, from which the effective 4D SdS metric can be induced on a 4D hypersurface. We found that at the end of inflation, the squared fluctuations of the inflaton fi...
Hu, B. L. (Bei-Lok)
1999-01-01
We give a summary of the status of current research in stochastic semiclassical gravity and suggest directions for further investigations. This theory generalizes the semiclassical Einstein equation to an Einstein-Langevin equation with a stochastic source term arising from the fluctuations of the energy-momentum tensor of quantum fields. We mention recent efforts in applying this theory to the study of black hole fluctuations and backreaction problems, linear response of hot flat space, and ...
Modulating cell-to-cell variability and sensitivity to death ligands by co-drugging
Flusberg, Deborah A.; Sorger, Peter K.
2013-06-01
TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) holds promise as an anti-cancer therapeutic but efficiently induces apoptosis in only a subset of tumor cell lines. Moreover, even in clonal populations of responsive lines, only a fraction of cells dies in response to TRAIL and individual cells exhibit cell-to-cell variability in the timing of cell death. Fractional killing in these cell populations appears to arise not from genetic differences among cells but rather from differences in gene expression states, fluctuations in protein levels and the extent to which TRAIL-induced death or survival pathways become activated. In this study, we ask how cell-to-cell variability manifests in cell types with different sensitivities to TRAIL, as well as how it changes when cells are exposed to combinations of drugs. We show that individual cells that survive treatment with TRAIL can regenerate the sensitivity and death-time distribution of the parental population, demonstrating that fractional killing is a stable property of cell populations. We also show that cell-to-cell variability in the timing and probability of apoptosis in response to treatment can be tuned using combinations of drugs that together increase apoptotic sensitivity compared to treatment with one drug alone. In the case of TRAIL, modulation of cell-to-cell variability by co-drugging appears to involve a reduction in the threshold for mitochondrial outer membrane permeabilization.
Cell-to-cell movement of mitochondria in plants
Gurdon, Csanad; Svab, Zora; Feng, Yaping; Kumar, Dibyendu; Maliga, Pal
2016-01-01
We report cell-to-cell movement of mitochondria through a graft junction of two tobacco species, Nicotiana tabacum and Nicotiana sylvestris. The flowers of the N. tabacum line we used are male sterile due to a sterility-causing mitochondrial genome, whereas the N. sylvestris flowers are fertile. Grafting created an opportunity for organelle movement during the healing process when cell-to-cell connections at the graft junction were restored. We recognized N. sylvestris mitochondrial DNA trans...
Determinants of cell-to-cell variability in protein kinase signaling.
Directory of Open Access Journals (Sweden)
Matthias Jeschke
Full Text Available Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds ('pathway sensitivity' and the maximal activation level upon strong stimulation. Minimal kinase cascades with gradual dose-response behavior show strong variability, because the pathway sensitivity and the maximal activation level cannot be simultaneously invariant. Negative feedback regulation resolves this trade-off and coordinately reduces fluctuations in the pathway sensitivity and maximal activation. Feedbacks acting at different levels in the cascade control different aspects of the dose-response curve, thereby synergistically reducing the variability. We also investigated more complex, ultrasensitive signaling cascades capable of switch-like decision making, and found that these can be inherently robust to protein concentration fluctuations. We describe how the cell-to-cell variability of ultrasensitive signaling systems can be actively regulated, e.g., by altering the expression of phosphatase(s or by feedback/feedforward loops. Our calculations reveal that slow transcriptional negative feedback loops allow for variability suppression while maintaining switch-like decision making. Taken together, we describe design principles of signaling cascades that promote robustness. Our results may explain why certain signaling cascades like the yeast pheromone pathway show switch-like decision making with little cell-to-cell variability.
Reyes, Luz Marina; Bellini, Mauricio
2010-01-01
We develop a stochastic approach to study scalar field fluctuations of the inflaton field in an early inflationary universe with a Black-Hole (BH), which is described by an effective 4D SdS metric. The extended cosmological metric is obtained after make a planar coordinate transformation on a 5D Ricci-flat Schwarzschild-de Sitter (SdS) static metric. We found that at the end of inflation the spectrum of the squared field fluctuations of the inflaton field depends on the mass $M$ of the BH, but, in the limit of very small BH's mass, this spectrum agrees with whole obtained in standard inflation for a de Sitter expansion.
Listening to the noise: random fluctuations reveal gene network parameters.
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2009-01-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations show cell-to-cell variability that can manifest significant phenotypic differences. Noise-induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We show that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. This establishes a potentially powerful approach for the identification of gene networks and offers a new window into the workings of these networks. PMID:19888213
Cell-to-cell movement of mitochondria in plants.
Gurdon, Csanad; Svab, Zora; Feng, Yaping; Kumar, Dibyendu; Maliga, Pal
2016-03-22
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer fromNicotiana sylvestrisintoNicotiana tabacumcells. The alloplasmicN. tabacumline we used carriesNicotiana undulatacytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer fromN. sylvestristoN. tabacumcould be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility toorf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation. PMID:26951647
Cell-to-cell communication within intact human skin.
Salomon, D.; Saurat, J. H.; Meda, P.
1988-01-01
We have characterized cell-to-cell communication (coupling) within intact human skin by microinjecting single keratinocytes with a gap junction-permeant tracer (Lucifer Yellow). 25-50 keratinocytes from different layers of the epidermis were seen to be coupled after most injections (n = 31). A few noncommunicating cells were also microinjected (n = 3) or observed within large territories of coupled keratinocytes. Microinjections of dermal fibroblasts demonstrated an extensive coupling (greate...
Tetherin restricts productive HIV-1 cell-to-cell transmission.
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Nicoletta Casartelli
Full Text Available The IFN-inducible antiviral protein tetherin (or BST-2/CD317/HM1.24 impairs release of mature HIV-1 particles from infected cells. HIV-1 Vpu antagonizes the effect of tetherin. The fate of virions trapped at the cell surface remains poorly understood. Here, we asked whether tetherin impairs HIV cell-to-cell transmission, a major means of viral spread. Tetherin-positive or -negative cells, infected with wild-type or DeltaVpu HIV, were used as donor cells and cocultivated with target lymphocytes. We show that tetherin inhibits productive cell-to-cell transmission of DeltaVpu to targets and impairs that of WT HIV. Tetherin accumulates with Gag at the contact zone between infected and target cells, but does not prevent the formation of virological synapses. In the presence of tetherin, viruses are then mostly transferred to targets as abnormally large patches. These viral aggregates do not efficiently promote infection after transfer, because they accumulate at the surface of target cells and are impaired in their fusion capacities. Tetherin, by imprinting virions in donor cells, is the first example of a surface restriction factor limiting viral cell-to-cell spread.
Regulation of cell-to-cell variability in divergent gene expression
Yan, Chao; Wu, Shuyang; Pocetti, Christopher; Bai, Lu
2016-03-01
Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically `leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs.
Matsakos, T; Stehlé, C; González, M; Ibgui, L; de Sá, L; Lanz, T; Orlando, S; Bonito, R; Argiroffi, C; Reale, F; Peres, G
2013-01-01
Context. Theoretical arguments and numerical simulations of radiative shocks produced by the impact of the accreting gas onto young stars predict quasi-periodic oscillations in the emitted radiation. However, observational data do not show evidence of such periodicity. Aims. We investigate whether physically plausible perturbations in the accretion column or in the chromosphere could disrupt the shock structure influencing the observability of the oscillatory behavior. Methods. We performed local 2D magneto-hydrodynamical simulations of an accretion shock impacting a chromosphere, taking optically thin radiation losses and thermal conduction into account. We investigated the effects of several perturbation types, such as clumps in the accretion stream or chromospheric fluctuations, and also explored a wide range of plasma-\\beta values. Results. In the case of a weak magnetic field, the post-shock region shows chaotic motion and mixing, smoothing out the perturbations and retaining a global periodic signature....
International Nuclear Information System (INIS)
We show that the general two-variable Langevin equations with inhomogeneous noise and friction can generate many different forms of power-law distributions. By solving the corresponding stationary Fokker–Planck equation, we can obtain a condition under which these power-law distributions are accurately created in a system away from equilibrium. This condition is an energy-dependent relation between the diffusion coefficient and the friction coefficient and thus it provides a fluctuation-dissipation relation for nonequilibrium systems with power-law distributions. Further, we study the specific forms of the Fokker–Planck equation that correctly lead to such power-law distributions, and then present a possible generalization of the Klein–Kramers equation and the Smoluchowski equation to a complex system, whose stationary-state solutions are exactly a Tsallis distribution
Quantifying Cell-to-Cell Variations in Lithium Ion Batteries
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Shriram Santhanagopalan
2012-01-01
Full Text Available Lithium ion batteries have conventionally been manufactured in small capacities but large volumes for consumer electronics applications. More recently, the industry has seen a surge in the individual cell capacities, as well as the number of cells used to build modules and packs. Reducing cell-to-cell and lot-to-lot variations has been identified as one of the major means to reduce the rejection rate when building the packs as well as to improve pack durability. The tight quality control measures have been passed on from the pack manufactures to the companies building the individual cells and in turn to the components. This paper identifies a quantitative procedure utilizing impedance spectroscopy, a commonly used tool, to determine the effects of material variability on the cell performance, to compare the relative importance of uncertainties in the component properties, and to suggest a rational procedure to set quality control specifications for the various components of a cell, that will reduce cell-to-cell variability, while preventing undue requirements on uniformity that often result in excessive cost of manufacturing but have a limited impact on the cells' performance.
Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission
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Christine Gross
2016-03-01
Full Text Available The tumorvirus human T-cell lymphotropic virus type 1 (HTLV-1, a member of the delta-retrovirus family, is transmitted via cell-containing body fluids such as blood products, semen, and breast milk. In vivo, HTLV-1 preferentially infects CD4+ T-cells, and to a lesser extent, CD8+ T-cells, dendritic cells, and monocytes. Efficient infection of CD4+ T-cells requires cell-cell contacts while cell-free virus transmission is inefficient. Two types of cell-cell contacts have been described to be critical for HTLV-1 transmission, tight junctions and cellular conduits. Further, two non-exclusive mechanisms of virus transmission at cell-cell contacts have been proposed: (1 polarized budding of HTLV-1 into synaptic clefts; and (2 cell surface transfer of viral biofilms at virological synapses. In contrast to CD4+ T-cells, dendritic cells can be infected cell-free and, to a greater extent, via viral biofilms in vitro. Cell-to-cell transmission of HTLV-1 requires a coordinated action of steps in the virus infectious cycle with events in the cell-cell adhesion process; therefore, virus propagation from cell-to-cell depends on specific interactions between cellular and viral proteins. Here, we review the molecular mechanisms of HTLV-1 transmission with a focus on the HTLV-1-encoded proteins Tax and p8, their impact on host cell factors mediating cell-cell contacts, cytoskeletal remodeling, and thus, virus propagation.
Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission.
Gross, Christine; Thoma-Kress, Andrea K
2016-01-01
The tumorvirus human T-cell lymphotropic virus type 1 (HTLV-1), a member of the delta-retrovirus family, is transmitted via cell-containing body fluids such as blood products, semen, and breast milk. In vivo, HTLV-1 preferentially infects CD4⁺ T-cells, and to a lesser extent, CD8⁺ T-cells, dendritic cells, and monocytes. Efficient infection of CD4⁺ T-cells requires cell-cell contacts while cell-free virus transmission is inefficient. Two types of cell-cell contacts have been described to be critical for HTLV-1 transmission, tight junctions and cellular conduits. Further, two non-exclusive mechanisms of virus transmission at cell-cell contacts have been proposed: (1) polarized budding of HTLV-1 into synaptic clefts; and (2) cell surface transfer of viral biofilms at virological synapses. In contrast to CD4⁺ T-cells, dendritic cells can be infected cell-free and, to a greater extent, via viral biofilms in vitro. Cell-to-cell transmission of HTLV-1 requires a coordinated action of steps in the virus infectious cycle with events in the cell-cell adhesion process; therefore, virus propagation from cell-to-cell depends on specific interactions between cellular and viral proteins. Here, we review the molecular mechanisms of HTLV-1 transmission with a focus on the HTLV-1-encoded proteins Tax and p8, their impact on host cell factors mediating cell-cell contacts, cytoskeletal remodeling, and thus, virus propagation. PMID:27005656
Stochastic Physicochemical Dynamics
Tsekov, Roumen
2001-01-01
The monograph considers thermodynamic relaxation in quantum systems, stochastic dynamics of gas molecules, fluctuation stability of thin liquid films, resonant diffusion in modulated solid structures and catalytic kinetics of chemical dissociation.
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.
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Tuoqi Liu
2016-05-01
Full Text Available According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
Directory of Open Access Journals (Sweden)
Gaëtan Gruel
Full Text Available Most studies that aim to understand the interactions between different types of photon radiation and cellular DNA assume homogeneous cell irradiation, with all cells receiving the same amount of energy. The level of DNA damage is therefore generally determined by averaging it over the entire population of exposed cells. However, evaluating the molecular consequences of a stochastic phenomenon such as energy deposition of ionizing radiation by measuring only an average effect may not be sufficient for understanding some aspects of the cellular response to this radiation. The variance among the cells associated with this average effect may also be important for the behaviour of irradiated tissue. In this study, we accurately estimated the distribution of the number of radiation-induced γH2AX foci (RIF per cell nucleus in a large population of endothelial cells exposed to 3 macroscopic doses of gamma rays from 60Co. The number of RIF varied significantly and reproducibly from cell to cell, with its relative standard deviation ranging from 36% to 18% depending on the macroscopic dose delivered. Interestingly, this relative cell-to-cell variability increased as the dose decreased, contrary to the mean RIF count per cell. This result shows that the dose effect, in terms of the number of DNA lesions indicated by RIF is not as simple as a purely proportional relation in which relative SD is constant with dose. To analyse the origins of this observed variability, we calculated the spread of the specific energy distribution for the different target volumes and subvolumes in which RIF can be generated. Variances, standard deviations and relative standard deviations all changed similarly from dose to dose for biological and calculated microdosimetric values. This similarity is an important argument that supports the hypothesis of the conservation of the association between the number of RIF per nucleus and the specific energy per DNA molecule. This
Eichhorn, Ralf; Aurell, Erik
2014-04-01
'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response
Johnson, Philip R.; Hu, B. L.
2000-01-01
We apply the open systems concept and the influence functional formalism introduced in Paper I to establish a stochastic theory of relativistic moving spinless particles in a quantum scalar field. The stochastic regime resting between the quantum and semi-classical captures the statistical mechanical attributes of the full theory. Applying the particle-centric world-line quantization formulation to the quantum field theory of scalar QED we derive a time-dependent (scalar) Abraham-Lorentz-Dira...
Ahmet, Kara
2015-01-01
This paper presents a simple model of the provision of higher educational services that considers and exemplifies nonlinear, stochastic, and potentially chaotic processes. I use the methods of system dynamics to simulate these processes in the context of a particular sociologically interesting case, namely that of the Turkish higher education…
Nieto-Vesperinas, Manuel
2014-01-01
The mechanical action on matter of the electromagnetic field emitted by a fluctuating source is governed by its statistics. In particular, thermal sources and vacuum fluctuations exert on bodies those well-known Casimir (C) and Van der Waals (VdW) forces. However, we have recently demonstrated that partially coherent random electromagnetic fields emitted by tailored optical sources, induce a photonic force on particles which, in particular, may be equivalent to those of Van der Waals and Casimir.
Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2010-03-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations exhibit cell-to-cell variability that can manifest significant prototypical differences. Noise induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified using flow cytometry, single molecule fluorescence in situ hybridization, time lapse fluorescence microscopy and other single cell and single molecule measurement techniques. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. We use theoretical investigations to establish experimental guidelines for the identification of gene regulatory networks, and we apply these guideline to experimentally identify predictive models for different regulatory mechanisms in bacteria and yeast.
Protease inhibitors effectively block cell-to-cell spread of HIV-1 between T cells
Titanji, Boghuma; Aasa-Chapman, Marlen; Pillay, Deenan; Jolly, Clare
2013-01-01
Background; The Human Immunodeficiency Virus type-1 (HIV-1) spreads by cell-free diffusion and by direct cell-to-cell transfer, the latter being a significantly more efficient mode of transmission. Recently it has been suggested that cell-to-cell spread may permit ongoing virus replication in the presence of antiretroviral therapy (ART) based on studies performed using Reverse Transcriptase Inhibitors (RTIs). Protease Inhibitors (PIs) constitute an important component of ART; however whether ...
Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan
2016-01-01
Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911
Stochastic TDHF and the Boltzman-Langevin equation
International Nuclear Information System (INIS)
Outgoing from a time-dependent theory of correlations, we present a stochastic differential equation for the propagation of ensembles of Slater determinants, called Stochastic Time-Dependent Hartree-Fock (Stochastic TDHF). These ensembles are allowed to develop large fluctuations in the Hartree-Fock mean fields. An alternative stochastic differential equation, the Boltzmann-Langevin equation, can be derived from Stochastic TDHF by averaging over subensembles with small fluctuations
Stochastic volatility and stochastic leverage
Veraart, Almut; Veraart, Luitgard A. M.
2009-01-01
This paper proposes the new concept of stochastic leverage in stochastic volatility models.Stochastic leverage refers to a stochastic process which replaces the classical constant correlationparameter between the asset return and the stochastic volatility process. We provide a systematictreatment of stochastic leverage and propose to model the stochastic leverage effect explicitly,e.g. by means of a linear transformation of a Jacobi process. Such models are both analyticallytractable and allo...
On the stochastic stability of MHD equilibria
International Nuclear Information System (INIS)
The stochastic stability in the large of stationary equilibria of ideal and dissipative magnetohydrodynamics under the influence of stationary random fluctuations is studied using the direct Liapunov method. Sufficient and necessary conditions for stability of the linearized Euler-Lagrangian systems are given. The destabilizing effect of stochastic fluctuations is demonstrated. (orig.)
Role of Exosome Shuttle RNA in Cell-to-Cell Communication.
Zhang, Wei; Peng, Peng; Shen, Keng
2016-08-01
There are several ways that transpire in cell-to-cell communication,with or without cell contact. Exosomes play an important role in cell-to-cell communication,which do not need cell contact,as that can result in a relatively long-distance influence. Exosome contains RNA components including mRNA and micro-RNA,which are protected by exosomes rigid membranes. This allows those components be passed long distance through the circulatory system. The mRNA components are far different from their donor cells,and the micro-RNA components may reflect the cell they originated. In this article we review the role of exosomes in cell-to-cell communication,with particular focus on their potentials in both diagnostic and therapeutic applications. PMID:27594165
Influence of viral genes on the cell-to-cell spread of RNA silencing
Zhou, Yu; Ryabov, Eugene; Zhang, Xuemei; Hong, Yiguo
2008-01-01
The turnip crinkle virus-based vector TCV–GFPΔCP had been devised previously to study cell-to-cell and long-distance spread of virus-induced RNA silencing. TCV–GFPΔCP, which had been constructed by replacing the coat protein (CP) gene with a green fluorescent protein (GFP) coding sequence, was able to induce RNA silencing in single epidermal cells, from which RNA silencing spread from cell-to-cell. Using this unique local silencing assay together with mutagenesis analysis, two TCV genes, p8 a...
Measuring and modelling cell-to-cell variation in uptake of gold nanoparticles
Jeynes, JCG; Jeynes, C.; Merchant, MJ; Kirkby, KJ
2013-01-01
The cell-to-cell variation of gold nanoparticle (GNP) uptake is important for therapeutic applications. We directly counted the GNPs in hundreds of individual cells, and showed that the large variation from cell-to-cell could be directly modelled by assuming log-normal distributions of both cell mass and GNP rate of uptake. This was true for GNPs non-specifically bound to fetal bovine serum or conjugated to a cell penetrating peptide. Within a population of cells, GNP content varied naturally...
A recurrent stochastic binary network
Institute of Scientific and Technical Information of China (English)
赵杰煜
2001-01-01
Stochastic neural networks are usually built by introducing random fluctuations into the network. A natural method is to use stochastic connections rather than stochastic activation functions. We propose a new model in which each neuron has very simple functionality but all the connections are stochastic. It is shown that the stationary distribution of the network uniquely exists and it is approximately a Boltzmann-Gibbs distribution. The relationship between the model and the Markov random field is discussed. New techniques to implement simulated annealing and Boltzmann learning are proposed. Simulation results on the graph bisection problem and image recognition show that the network is powerful enough to solve real world problems.
Gambling with Superconducting Fluctuations
Foltyn, Marek; Zgirski, Maciej
2015-08-01
Josephson junctions and superconducting nanowires, when biased close to superconducting critical current, can switch to a nonzero voltage state by thermal or quantum fluctuations. The process is understood as an escape of a Brownian particle from a metastable state. Since this effect is fully stochastic, we propose to use it for generating random numbers. We present protocol for obtaining random numbers and test the experimentally harvested data for their fidelity. Our work is prerequisite for using the Josephson junction as a tool for stochastic (probabilistic) determination of physical parameters such as magnetic flux, temperature, and current.
MEMS-based dynamic cell-to-cell culture platforms using electrochemical surface modifications
International Nuclear Information System (INIS)
MEMS-based biological platforms with the capability of both spatial placements and time releases of living cells for cell-to-cell culture experiments have been designed and demonstrated utilizing electrochemical surface modification effects. The spatial placement is accomplished by electrochemical surface modification of substrate surfaces to be either adhesive or non-adhesive for living cells. The time control is achieved by the electrical activation of the selective indium tin oxide co-culture electrode to allow the migration of living cells onto the electrode to start the cell-to-cell culture studies. Prototype devices have a three-electrode design with an electrode size of 50 × 50 µm2 and the separation gaps of 2 µm between them. An electrical voltage of −1.5 V has been used to activate the electrodes independently and sequentially to demonstrate the dynamic cell-to-cell culture experiments of NIH 3T3 fibroblast and Madin Darby canine kidney cells. As such, this MEMS platform could be a basic yet versatile tool to characterize transient cell-to-cell interactions
The Arabidopsis synaptotagmin SYTA regulates the cell-to-cell movement of diverse plant viruses
Directory of Open Access Journals (Sweden)
Asako eUchiyama
2014-11-01
Full Text Available Synaptotagmins are a large gene family in animals that have been extensively characterized due to their role as calcium sensors to regulate synaptic vesicle exocytosis and endocytosis in neurons, and dense core vesicle exocytosis for hormone secretion from neuroendocrine cells. Thought to be exclusive to animals, synaptotagmins have recently been characterized in Arabidopsis thaliana, in which they comprise a five gene family. Using infectivity and leaf-based functional assays, we have shown that Arabidopsis SYTA regulates endocytosis and marks an endosomal vesicle recycling pathway to regulate movement protein-mediated trafficking of the Begomovirus Cabbage leaf curl virus (CaLCuV and the Tobamovirus Tobacco mosaic virus (TMV through plasmodesmata (Lewis and Lazarowitz, 2010. To determine whether SYTA has a central role in regulating the cell-to-cell trafficking of a wider range of diverse plant viruses, we extended our studies here to examine the role of SYTA in the cell-to-cell movement of additional plant viruses that employ different modes of movement, namely the Potyvirus Turnip mosaic virus (TuMV, the Caulimovirus Cauliflower mosaic virus (CaMV and the Tobamovirus Turnip vein clearing virus (TVCV, which in contrast to TMV does efficiently infect Arabidopsis. We found that both TuMV and TVCV systemic infection, and the cell-to-cell trafficking of the their movement proteins, were delayed in the Arabidopsis Col-0 syta-1 knockdown mutant. In contrast, CaMV systemic infection was not inhibited in syta-1. Our studies show that SYTA is a key regulator of plant virus intercellular movement, being necessary for the ability of diverse cell-to-cell movement proteins encoded by Begomoviruses (CaLCuV MP, Tobamoviruses (TVCV and TMV 30K protein and Potyviruses (TuMV P3N-PIPO to alter PD and thereby mediate virus cell-to-cell spread.
Stochastic volatility and stochastic leverage
DEFF Research Database (Denmark)
Veraart, Almut; Veraart, Luitgard A. M.
models which allow for a stochastic leverage effect: the generalised Heston model and the generalised Barndorff-Nielsen & Shephard model. We investigate the impact of a stochastic leverage effect in the risk neutral world by focusing on implied volatilities generated by option prices derived from our new......This paper proposes the new concept of stochastic leverage in stochastic volatility models. Stochastic leverage refers to a stochastic process which replaces the classical constant correlation parameter between the asset return and the stochastic volatility process. We provide a systematic...... treatment of stochastic leverage and propose to model the stochastic leverage effect explicitly, e.g. by means of a linear transformation of a Jacobi process. Such models are both analytically tractable and allow for a direct economic interpretation. In particular, we propose two new stochastic volatility...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread
Czuczman, Mark A.; Fattouh, Ramzi; van Rijn, Jorik; Canadien, Veronica; Osborne, Suzanne; Aleixo M Muise; Kuchroo, Vijay K.; Higgins, Darren E.; Brumell, John H.
2014-01-01
Efferocytosis, the process by which dying/dead cells are removed by phagocytosis, plays an important role in development, tissue homeostasis and innate immunity 1 . Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes (Lm), can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can esca...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread
Czuczman, Mark A.; Fattouh, Ramzi; van Rijn, Jorik; Canadien, Veronica; Osborne, Suzanne; Aleixo M Muise; Kuchroo, Vijay K.; Higgins, Darren E.; Brumell, John H.
2014-01-01
Efferocytosis, the process by which dying/dead cells are removed by phagocytosis, plays an important role in development, tissue homeostasis and innate immunity1. Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes (Lm), can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can escape...
The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks.
Chevalier, Michael; Venturelli, Ophelia; El-Samad, Hana
2015-10-01
Stochastic fluctuations in signaling and gene expression limit the ability of cells to sense the state of their environment, transfer this information along cellular pathways, and respond to it with high precision. Mutual information is now often used to quantify the fidelity with which information is transmitted along a cellular pathway. Mutual information calculations from experimental data have mostly generated low values, suggesting that cells might have relatively low signal transmission fidelity. In this work, we demonstrate that mutual information calculations might be artificially lowered by cell-to-cell variability in both initial conditions and slowly fluctuating global factors across the population. We carry out our analysis computationally using a simple signaling pathway and demonstrate that in the presence of slow global fluctuations, every cell might have its own high information transmission capacity but that population averaging underestimates this value. We also construct a simple synthetic transcriptional network and demonstrate using experimental measurements coupled to computational modeling that its operation is dominated by slow global variability, and hence that its mutual information is underestimated by a population averaged calculation. PMID:26484538
Bible, Amber N.; Khalsa-Moyers, Gurusahai K.; Mukherjee, Tanmoy; Green, Calvin S.; Mishra, Priyanka; Purcell, Alicia; Aksenova, Anastasia; Hurst, Gregory B.
2015-01-01
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists. PMID:26407887
Enhancement of Chemotactic Cell Aggregation by Haptotactic Cell-To-Cell Interaction.
Directory of Open Access Journals (Sweden)
Tae-Goo Kwon
Full Text Available The crawling of biological cell is a complex phenomenon involving various biochemical and mechanical processes. Some of these processes are intrinsic to individual cells, while others pertain to cell-to-cell interactions and to their responses to extrinsically imposed cues. Here, we report an interesting aggregation dynamics of mathematical model cells, when they perform chemotaxis in response to an externally imposed global chemical gradient while they influence each other through a haptotaxis-mediated social interaction, which confers intriguing trail patterns. In the absence of the cell-to-cell interaction, the equilibrium population density profile fits well to that of a simple Keller-Segal population dynamic model, in which a chemotactic current density [Formula: see text] competes with a normal diffusive current density [Formula: see text], where p and ρ refer to the concentration of chemoattractant and population density, respectively. We find that the cell-to-cell interaction confers a far more compact aggregation resulting in a much higher peak equilibrium cell density. The mathematical model system is applicable to many biological systems such as swarming microglia and neutrophils or accumulating ants towards a localized food source.
Bible, Amber N; Khalsa-Moyers, Gurusahai K; Mukherjee, Tanmoy; Green, Calvin S; Mishra, Priyanka; Purcell, Alicia; Aksenova, Anastasia; Hurst, Gregory B; Alexandre, Gladys
2015-12-01
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists. PMID:26407887
Phenomenology of Space Time Fluctuations
Aloisio, R.; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); Grillo, A. F.
2004-01-01
Quantum gravitational effects may induce stochastic fluctuations in the structure of space-time, to produce a characteristic foamy structure. It has been known for some time now that these fluctuations may have observable consequences for the propagation of cosmic ray particles over cosmological distances. While invoked as a possible explanation for the detection of the puzzling cosmic rays with energies in excess of the threshold for photopion production (the so-called super-GZK particles), ...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread.
Czuczman, Mark A; Fattouh, Ramzi; van Rijn, Jorik M; Canadien, Veronica; Osborne, Suzanne; Muise, Aleixo M; Kuchroo, Vijay K; Higgins, Darren E; Brumell, John H
2014-05-01
Efferocytosis, the process by which dying or dead cells are removed by phagocytosis, has an important role in development, tissue homeostasis and innate immunity. Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes, can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can escape the phagosome in host cells by using the pore-forming toxin listeriolysin O (LLO) and two phospholipase C enzymes. Expression of the cell surface protein ActA allows L. monocytogenes to activate host actin regulatory factors and undergo actin-based motility in the cytosol, eventually leading to formation of actin-rich protrusions at the cell surface. Here we show that protrusion formation is associated with plasma membrane damage due to LLO's pore-forming activity. LLO also promotes the release of bacteria-containing protrusions from the host cell, generating membrane-derived vesicles with exofacial PS. The PS-binding receptor TIM-4 (encoded by the Timd4 gene) contributes to efficient cell-to-cell spread by L. monocytogenes in macrophages in vitro and growth of these bacteria is impaired in Timd4(-/-) mice. Thus, L. monocytogenes promotes its dissemination in a host by exploiting efferocytosis. Our results indicate that PS-targeted therapeutics may be useful in the fight against infections by L. monocytogenes and other bacteria that use similar strategies of cell-to-cell spread during infection. PMID:24739967
Initial activation of EpCAM cleavage via cell-to-cell contact
International Nuclear Information System (INIS)
Epithelial cell adhesion molecule EpCAM is a transmembrane glycoprotein, which is frequently over-expressed in simple epithelia, progenitors, embryonic and tissue stem cells, carcinoma and cancer-initiating cells. Besides functioning as a homophilic adhesion protein, EpCAM is an oncogenic receptor that requires regulated intramembrane proteolysis for activation of its signal transduction capacity. Upon cleavage, the extracellular domain EpEX is released as a soluble ligand while the intracellular domain EpICD translocates into the cytoplasm and eventually into the nucleus in combination with four-and-a-half LIM domains protein 2 (FHL2) and β-catenin, and drives cell proliferation. EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were investigated under varying density conditions using confocal laser scanning microscopy, immunoblotting, cell counting, and conditional cell systems. EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were dependent on adequate cell-to-cell contact. If cell-to-cell contact was prohibited EpCAM did not provide growth advantages. If cells were allowed to undergo contact to each other, EpCAM transmitted proliferation signals based on signal transduction-related cleavage processes. Accordingly, the pre-cleaved version EpICD was not dependent on cell-to-cell contact in order to induce c-myc and cell proliferation, but necessitated nuclear translocation. For the case of contact-inhibited cells, although cleavage of EpCAM occurred, nuclear translocation of EpICD was reduced, as were EpCAM effects. Activation of EpCAM's cleavage and oncogenic capacity is dependent on cellular interaction (juxtacrine) to provide for initial signals of regulated intramembrane proteolysis, which then support signalling via soluble EpEX (paracrine)
Global Dynamics of a Virus Dynamical Model with Cell-to-Cell Transmission and Cure Rate
Directory of Open Access Journals (Sweden)
Tongqian Zhang
2015-01-01
Full Text Available The cure effect of a virus model with both cell-to-cell transmission and cell-to-virus transmission is studied. By the method of next generation matrix, the basic reproduction number is obtained. The locally asymptotic stability of the virus-free equilibrium and the endemic equilibrium is considered by investigating the characteristic equation of the model. The globally asymptotic stability of the virus-free equilibrium is proved by constructing suitable Lyapunov function, and the sufficient condition for the globally asymptotic stability of the endemic equilibrium is obtained by constructing suitable Lyapunov function and using LaSalle invariance principal.
Zhong, Peng; Agosto, Luis M.; Ilinskaya, Anna; Dorjbal, Batsukh; Truong, Rosaline; Derse, David; Uchil, Pradeep D; Heidecker, Gisela; Mothes, Walther
2013-01-01
Virus transmission can occur either by a cell-free mode through the extracellular space or by cell-to-cell transmission involving direct cell-to-cell contact. The factors that determine whether a virus spreads by either pathway are poorly understood. Here, we assessed the relative contribution of cell-free and cell-to-cell transmission to the spreading of the human immunodeficiency virus (HIV). We demonstrate that HIV can spread by a cell-free pathway if all the steps of the viral replication...
Ohira, Toru
2006-01-01
We present a simple dynamical model to address the question of introducing a stochastic nature in a time variable. This model includes noise in the time variable but not in the "space" variable, which is opposite to the normal description of stochastic dynamics. The notable feature is that these models can induce a "resonance" with varying noise strength in the time variable. Thus, they provide a different mechanism for stochastic resonance, which has been discussed within the normal context ...
Directory of Open Access Journals (Sweden)
Jennifer S. Liu
2012-11-01
Full Text Available Variability in signaling pathway activation between neighboring epithelial cells can arise from local differences in the microenvironment, noisy gene expression, or acquired genetic changes. To investigate the consequences of this cell-to-cell variability in signaling pathway activation on coordinated multicellular processes such as morphogenesis, we use DNA-programmed assembly to construct three-dimensional MCF10A microtissues that are mosaic for low-level expression of activated H-Ras. We find two emergent behaviors in mosaic microtissues: cells with activated H-Ras are basally extruded or lead motile multicellular protrusions that direct the collective motility of their wild-type neighbors. Remarkably, these behaviors are not observed in homogeneous microtissues in which all cells express the activated Ras protein, indicating that heterogeneity in Ras activity, rather than the total amount of Ras activity, is critical for these processes. Our results directly demonstrate that cell-to-cell variability in pathway activation within local populations of epithelial cells can drive emergent behaviors during epithelial morphogenesis.
Relation between radio-adaptive response and cell to cell communication
International Nuclear Information System (INIS)
Ionizing radiation has been considered to cause severe damages to DNA and do harm to cells in proportion to the dose, however low it might be. In 1984, Wolff et al. showed that human peripheral lymphocytes adapted to the low-dose radiation from 3H-TdR added in culture medium and became resistant to the subsequent irradiation with high-doses of X-rays. This response, which is called radio-adaptive response, is also induced by X-rays and gamma-rays in human lymphocytes and Chinese hamster V79 cells. However, the mechanisms of and conditions for adaptive responses to radiation have not been clarified. With an objective of clarifying the conditions for adaptive responses of cells to radiation, we examined how the cell to cell communication is involved in the adaptive responses. We irradiated normal human embryo-derived (HE) cells and cancer cells (HeLa) in culture at high density with low-dose X-ray and examined their radio-adaptive responses by measuring the changes in sensitivity to subsequent high-dose X-ray irradiation using the Trypan Blue dye-exclusion test method. We also conducted experiments to examine the effects of Ca2+ ions and Phorbol 12-Myristate 13-Acetate (TPA) which are supposed to be involved in cell to cell communication. (author)
Jacob, Christian L; Lamorte, Louie; Sepulveda, Eliud; Lorenz, Ivo C; Gauthier, Annick; Franti, Michael
2013-09-01
Infection with human cytomegalovirus (CMV) during pregnancy is the most common cause of congenital disorders, and can lead to severe life-long disabilities with associated high cost of care. Since there is no vaccine or effective treatment, current efforts are focused on identifying potent neutralizing antibodies. A panel of CMV monoclonal antibodies identified from patent applications, was synthesized and expressed in order to reproduce data from the literature showing that anti-glycoprotein B antibodies neutralized virus entry into all cell types and that anti-pentameric complex antibodies are highly potent in preventing virus entry into epithelial cells. It had not been established whether antibodies could prevent subsequent rounds of infection that are mediated primarily by direct cell-to-cell transmission. A thorough validation of a plaque reduction assay to monitor cell-to-cell spread led to the conclusion that neutralizing antibodies do not significantly inhibit plaque formation or reduce plaque size when they are added post-infection. PMID:23849792
Staggered Schemes for Fluctuating Hydrodynamics
Balboa, F; Delgado-Buscalioni, R; Donev, A; Fai, T; Griffith, B; Peskin, C S
2011-01-01
We develop numerical schemes for solving the isothermal compressible and incompressible equations of fluctuating hydrodynamics on a grid with staggered momenta. We develop a second-order accurate spatial discretization of the diffusive, advective and stochastic fluxes that satisfies a discrete fluctuation-dissipation balance, and construct temporal discretizations that are at least second-order accurate in time deterministically and in a weak sense. Specifically, the methods reproduce the correct equilibrium covariances of the fluctuating fields to third (compressible) and second (incompressible) order in the time step, as we verify numerically. We apply our techniques to model recent experimental measurements of giant fluctuations in diffusively mixing fluids in a micro-gravity environment [A. Vailati et. al., Nature Communications 2:290, 2011]. Numerical results for the static spectrum of non-equilibrium concentration fluctuations are in excellent agreement between the compressible and incompressible simula...
Notes on Black Hole Fluctuations and Backreaction
Hu, B. L.; Raval, Alpan; Sinha, Sukanya
1999-01-01
In these notes we prepare the ground for a systematic investigation into the issues of black hole fluctuations and backreaction by discussing the formulation of the problem, commenting on possible advantages and shortcomings of existing works, and introducing our own approach via a stochastic semiclassical theory of gravity based on the Einstein-Langevin equation and the fluctuation-dissipation relation for a self-consistent description of metric fluctuations and dissipative dynamics of the b...
Notes on Black Hole Fluctuations and Backreaction
Hu, B L; Sinha, S; Raval, Alpan; Sinha, Sukanya
1999-01-01
In these notes we prepare the ground for a systematic investigation into the issues of black hole fluctuations and backreaction by discussing the formulation of the problem, commenting on possible advantages and shortcomings of existing works, and introducing our own approach via a stochastic semiclassical theory of gravity based on the Einstein-Langevin equation and the fluctuation-dissipation relation for a self-consistent description of metric fluctuations and dissipative dynamics of the black hole with backreaction of its Hawking radiance.
Small RNA Control of Cell-to-Cell Communication in Vibrio Harveyi and Vibrio Cholerae
Svenningsen, Sine Lo
Quorum sensing is a process of cell-to-cell communication, by which bacteria coordinate gene expression and behavior on a population-wide scale. Quorum sensing is accomplished through production, secretion, and subsequent detection of chemical signaling molecules termed autoinducers. The human pathogen Vibrio cholerae and the marine bioluminescent bacterium Vibrio harveyi incorporate information from multiple autoinducers, and also environmental signals and metabolic cues into their quorum-sensing pathways. At the core of these pathways lie several homologous small regulatory RNA molecules, the Quorum Regulatory RNAs. Small noncoding RNAs have emerged throughout the bacterial and eukaryotic kingdoms as key regulators of behavioral and developmental processes. Here, I review our present understanding of the role of the Qrr small RNAs in integrating quorum-sensing signals and in regulating the individual cells response to this information.
Directory of Open Access Journals (Sweden)
HidetadaHirakawa
2013-05-01
Full Text Available Bacteria use a cell-to-cell communication activity termed “Quorum sensing” to coordinate group behaviors in a cell-density dependent manner. Quorum sensing influences the expression profile of diverse genes, including antibiotic tolerance and virulence determinants, via specific chemical compounds called “Auto-inducers”. During quorum sensing, Gram-negative bacteria typically use an acylated homoserine lactone (AHL called auto-inducer 1 (AI-1. Since the first discovery of quorum sensing in a marine bacterium, it has been recognized that more than 100 species possess this mechanism of cell-to-cell communication. In addition to being of interest from a biological standpoint, quorum sensing is a potential target for antimicrobial chemotherapy. This unique concept of antimicrobial control relies on reducing the burden of virulence rather than killing the bacteria. It is believed that this approach will not only suppress the development of antibiotic resistance, but will also improve the treatment of refractory infections triggered by multi-drug resistant (MDR pathogens. In this paper, we review and track recent progress in studies on AHL inhibitors/modulators from a biological standpoint. It has been discovered that both natural and synthetic compounds can disrupt quorum sensing by a variety of means, such as jamming signal transduction, inhibition of signal production and break-down and trapping of signal compounds. We also focus on the regulatory elements that attenuate quorum sensing activities and discuss their unique properties. Understanding the biological roles of regulatory elements might be useful in developing inhibitor applications and understanding how quorum sensing is controlled.
Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells
International Nuclear Information System (INIS)
Research highlights: → TGP52 cells display enhanced functionality in pseudoislet form. → Somatostatin content was reduced, but secretion increased in high glucose conditions. → Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mM glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.
Damodaran, Shima P; Eberhard, Stephan; Boitard, Laurent; Rodriguez, Jairo Garnica; Wang, Yuxing; Bremond, Nicolas; Baudry, Jean; Bibette, Jérôme; Wollman, Francis-André
2015-01-01
To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes. PMID:25760649
Directory of Open Access Journals (Sweden)
Shima P Damodaran
Full Text Available To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers and a significant subpopulation of slowly dividing cells (slow-growers. These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes.
Turbulent response in a stochastic regime
International Nuclear Information System (INIS)
The theory for the non-linear, turbulent response in a system with intrinsic stochasticity is considered. It is argued that perturbative Eulerian theories, such as the Direct Interaction Approximation (DIA), are inherently unsuited to describe such a system. The exponentiation property that characterizes stochasticity appears in the Lagrangian picture and cannot even be defined in the Eulerian representation. An approximation for stochastic systems - the Normal Stochastic Approximation - is developed and states that the perturbed orbit functions (Lagrangian fluctuations) behave as normally distributed random variables. This is independent of the Eulerian statistics and, in fact, we treat the Eulerian fluctuations as fixed. A simple model problem (appropriate for the electron response in the drift wave) is subjected to a series of computer experiments. To within numerical noise the results are in agreement with the Normal Stochastic Approximation. The predictions of the DIA for this mode show substantial qualitative and quantitative departures from the observations
Dynamics of stochastic systems
Klyatskin, Valery I
2005-01-01
Fluctuating parameters appear in a variety of physical systems and phenomena. They typically come either as random forces/sources, or advecting velocities, or media (material) parameters, like refraction index, conductivity, diffusivity, etc. The well known example of Brownian particle suspended in fluid and subjected to random molecular bombardment laid the foundation for modern stochastic calculus and statistical physics. Other important examples include turbulent transport and diffusion of particle-tracers (pollutants), or continuous densities (''''oil slicks''''), wave propagation and scattering in randomly inhomogeneous media, for instance light or sound propagating in the turbulent atmosphere.Such models naturally render to statistical description, where the input parameters and solutions are expressed by random processes and fields.The fundamental problem of stochastic dynamics is to identify the essential characteristics of system (its state and evolution), and relate those to the input parameters of ...
Multivariate fluctuation relations for currents
International Nuclear Information System (INIS)
This paper is devoted to multivariate fluctuation relations for all the currents flowing across an open system in contact with several reservoirs at different temperatures and chemical potentials, or driven by time-independent external mechanical forces. After some transient behavior, the open system is supposed to reach a nonequilibrium steady state that is controlled by the thermodynamic and mechanical forces, called the affinities. The time-reversal symmetry of the underlying Hamiltonian dynamics implies symmetry relations among the statistical properties of the fluctuating currents, depending on the values of the affinities. These multivariate fluctuation relations are not only compatible with the second law of thermodynamics, but they also imply remarkable relations between the linear or nonlinear response coefficients and the cumulants of the fluctuating currents. These relations include the Onsager and Casimir reciprocity relations, as well as their generalizations beyond linear response. Methods to deduce multivariate fluctuation relations are presented for classical, stochastic and quantum systems. In this way, multivariate fluctuation relations are obtained for energy or particle transport in the effusion of an ideal gas, heat transport in Hamiltonian systems coupled by Langevin stochastic forces to heat reservoirs, driven Brownian motion of an electrically charged particle subjected to an external magnetic field, and quantum electron transport in multi-terminal mesoscopic circuits where the link to the scattering approach is established. (paper)
Parzen, Emanuel
2015-01-01
Well-written and accessible, this classic introduction to stochastic processes and related mathematics is appropriate for advanced undergraduate students of mathematics with a knowledge of calculus and continuous probability theory. The treatment offers examples of the wide variety of empirical phenomena for which stochastic processes provide mathematical models, and it develops the methods of probability model-building.Chapter 1 presents precise definitions of the notions of a random variable and a stochastic process and introduces the Wiener and Poisson processes. Subsequent chapters examine
Simulated microgravity allows to demonstrate cell-to-cell communication in bacteria
Mastroleo, Felice; van Houdt, Rob; Mergeay, Max; Hendrickx, Larissa; Wattiez, Ruddy; Leys, Natalie
Through the MELiSSA project, the European Space Agency aims to develop a closed life support system for oxygen, water and food production to support human life in space in forth-coming long term space exploration missions. This production is based on the recycling of the missions organic waste, including CO2 and minerals. The photosynthetic bacterium Rhodospir-illum rubrum S1H is used in MELiSSA to degrade organics with light energy and is the first MELiSSA organism that has been studied in space related environmental conditions (Mastroleo et al., 2009). It was tested in actual space flight to the International Space Station (ISS) as well as in ground simulations of ISS-like ionizing radiation and microgravity. In the present study, R. rubrum S1H was cultured in liquid medium in 2 devices simulating microgravity conditions, i.e. the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM). The re-sponse of the bacterium was evaluated at both the transcriptomic and proteomic levels using respectively a dedicated whole-genome microarray and high-throughput gel-free quantitative proteomics. Both at transcriptomic and proteomic level, the bacterium showed a significant response to cultivation in simulated microgravity. The response to low fluid shear modeled microgravity in RWV was different than to randomized microgravity in RPM. Nevertheless, both tests pointed out a change in and a likely interrelation between cell-to-cell communica-tion (i.e. quorum sensing) and cell pigmentation (i.e. photosynthesis) for R. rubrum S1H in microgravity conditions. A new type of cell-to-cell communication molecule in R. rubrum S1H was discovered and characterized. It is hypothised that the lack of convection currents and the fluid quiescence in (simulated) microgravity limits communications molecules to be spread throughout the medium. Cultivation in this new artificial environment of simulated micro-gravity has showed new properties of this well know bacterium
Schneider, Johannes J
2007-01-01
This book addresses stochastic optimization procedures in a broad manner. The first part offers an overview of relevant optimization philosophies; the second deals with benchmark problems in depth, by applying a selection of optimization procedures. Written primarily with scientists and students from the physical and engineering sciences in mind, this book addresses a larger community of all who wish to learn about stochastic optimization techniques and how to use them.
The Potato virus X TGBp3 protein associates with the ER network for virus cell-to-cell movement
Krishnamurthy, Konduru; Heppler, Marty; Mitra, Ruchira; Blancaflor, Elison; Payton, Mark; Nelson, Richard S.; Verchot-Lubicz, Jeanmarie
2003-01-01
Potato virus X (PVX) TGBp3 is required for virus cell-to-cell movement. Cell-to-cell movement of TGBp3 was studied using biolistic bombardment of plasmids expressing GFP:TGBp3. TGBp3 moves between cells in Nicotiana benthamiana, but requires TGBp1 to move in N. tabacum leaves. In tobacco leaves GFP:TGBp3 accumulated in a pattern resembling the endoplasmic reticulum (ER). To determine if the ER network is important for GFP:TGBp3 and for PVX cell-to-cell movement, a single mutation inhibiting membrane binding of TGBp3 was introduced into GFP:TGBp3 and into PVX. This mutation disrupted movement of GFP:TGBp3 and PVX. Brefeldin A, which disrupts the ER network, also inhibited GFP:TGBp3 movement in both Nicotiana species. Two deletion mutations, that do not affect membrane binding, hindered GFP:TGBp3 and PVX cell-to-cell movement. Plasmids expressing GFP:TGBp2 and GFP:TGBp3 were bombarded to several other PVX hosts and neither protein moved between adjacent cells. In most hosts, TGBp2 or TGBp3 cannot move cell-to-cell.
Can Cell to Cell Thermal Runaway Propagation be Prevented in a Li-ion Battery Module?
Jeevarajan, Judith; Lopez, Carlos; Orieukwu, Josephat
2014-01-01
Increasing cell spacing decreased adjacent cell damage center dotElectrically connected adjacent cells drained more than physically adjacent cells center dotRadiant barrier prevents propagation when fully installed between BP cells center dotBP cells vent rapidly and expel contents at 100% SOC -Slower vent with flame/smoke at 50% -Thermal runaway event typically occurs at 160 degC center dotLG cells vent but do not expel contents -Thermal runaway event typically occurs at 200 degC center dotSKC LFP modules did not propagate; fuses on negative terminal of cell may provide a benefit in reducing cell to cell damage propagation. New requirement in NASA-Battery Safety Requirements document: JSC 20793 Rev C 5.1.5.1 Requirements - Thermal Runaway Propagation a. For battery designs greater than a 80-Wh energy employing high specific energy cells (greater than 80 watt-hours/kg, for example, lithium-ion chemistries) with catastrophic failure modes, the battery shall be evaluated to ascertain the severity of a worst-case single-cell thermal runaway event and the propensity of the design to demonstrate cell-to-cell propagation in the intended application and environment. NASA has traditionally addressed the threat of thermal runaway incidents in its battery deployments through comprehensive prevention protocols. This prevention-centered approach has included extensive screening for manufacturing defects, as well as robust battery management controls that prevent abuse-induced runaway even in the face of multiple system failures. This focused strategy has made the likelihood of occurrence of such an event highly improbable. b. The evaluation shall include all necessary analysis and test to quantify the severity (consequence) of the event in the intended application and environment as well as to identify design modifications to the battery or the system that could appreciably reduce that severity. In addition to prevention protocols, programs developing battery designs with
Stochastic Simulation of Turing Patterns
Institute of Scientific and Technical Information of China (English)
FU Zheng-Ping; XU Xin-Hang; WANG Hong-Li; OUYANG Qi
2008-01-01
@@ We investigate the effects of intrinsic noise on Turing pattern formation near the onset of bifurcation from the homogeneous state to Turing pattern in the reaction-diffusion Brusselator. By performing stochastic simulations of the master equation and using Gillespie's algorithm, we check the spatiotemporal behaviour influenced by internal noises. We demonstrate that the patterns of occurrence frequency for the reaction and diffusion processes are also spatially ordered and temporally stable. Turing patterns are found to be robust against intrinsic fluctuations. Stochastic simulations also reveal that under the influence of intrinsic noises, the onset of Turing instability is advanced in comparison to that predicted deterministically.
Plasmodesmal-mediated cell-to-cell transport in wheat roots is modulated by anaerobic stress
Cleland, R. E.; Fujiwara, T.; Lucas, W. J.
1994-01-01
Cell-to-cell transport of small molecules and ions occurs in plants through plasmodesmata. Plant roots are frequently subjected to localized anaerobic stress, with a resultant decrease in ATP. In order to determine the effect of this stress on plasmodesmal transport, fluorescent dyes of increasing molecular weight (0.46 to 1OkDa) were injected into epidermal and cortical cells of 3-day-old wheat roots, and their movement into neighboring cells was determined by fluorescence microscopy. Anaerobiosis was generated by N2 gas or simulated by the presence of sodium azide, both of which reduced the ATP levels in the tissue by over 80%. In the absence of such stress, the upper limit for movement, or size exclusion limit (SEL), of cortical plasmodesmata was cells. Upon imposition of stress, the SEL rose to between 5 and 10 kDa. This response of plasmodesmata to a decrease in the level of ATP suggests that they are constricted by an ATP-dependent process so as to maintain a restricted SEL. When roots are subjected to anaerobic stress, an increase in SEL may permit enhanced delivery of sugars to the affected cells of the root where anaerobic respiration could regenerate the needed ATP.
Institute of Scientific and Technical Information of China (English)
Ingrid Rupp; Gabriele Pradel; Ludmilla Sologub; Kim C Williamson; Matthias Scheuermayer; Luc Reininger; Christian Doerig; Saliha Eksi; Davy U Kombilaa; Matthias Frank
2011-01-01
Physical contact is important for the interaction between animal cells, but it can represent a major challenge for protists like malaria parasites. Recently, novel filamentous cell-cell contacts have been identified in different types of eukaryotic cells and termed nanotubes due to their morphological appearance. Nanotubes represent small dynamic membranous extensions that consist of F-actin and are considered an ancient feature evolved by eukaryotic cells to establish contact for communication. We here describe similar tubular structures in the malaria pathogen Plasmodium falciparum, which emerge from the surfaces of the forming gametes upon gametocyte activation in the mosquito midgut. The filaments can exhibit a length of>100 μm and contain the F-actin isoform actin 2. They actively form within a few minutes after gametocyte activation and persist until the zygote transforms into the ookinete. The filaments originate from the parasite plasma membrane, are close ended and express adhesion proteins on their surfaces that are typically found in gametes, like Pfs230, Pfs48/45 or Pfs25, but not the zygote surface protein Pfs28. We show that these tubular structures represent long-distance cell-to-cell connections between sexual stage parasites and demonstrate that they meet the characteristics of nanotubes. We propose that malaria parasites utilize these adhesive "nanotubes" in order to facilitate intercellular contact between gametes during reproduction in the mosquito midgut.
Directory of Open Access Journals (Sweden)
G. Natale
2013-03-01
Full Text Available Formation, aggregation and transmission of abnormal proteins are common features in neurodegenerative disorders including Parkinson’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis, and Huntington’s disease. The mechanisms underlying protein alterations in neurodegenerative diseases remain controversial. Novel findings highlighted altered protein clearing systems as common biochemical pathways which generate protein misfolding, which in turn causes protein aggregation and protein spreading. In fact, proteinaceous aggregates are prone to cell-to-cell propagation. This is reminiscent of what happens in prion disorders, where the prion protein misfolds thus forming aggregates which spread to neighbouring cells. For this reason, the term prionoids is currently used to emphasize how several misfolded proteins are transmitted in neurodegenerative diseases following this prion-like pattern. Histochemical techniques including the use of specific antibodies covering both light and electron microscopy offer a powerful tool to describe these phenomena and investigate specific molecular steps. These include: prion like protein alterations; glycation of prion-like altered proteins to form advanced glycation end-products (AGEs; mechanisms of extracellular secretion; interaction of AGEs with specific receptors placed on neighbouring cells (RAGEs. The present manuscript comments on these phenomena aimed to provide a consistent scenario of the available histochemical approaches to dissect each specific step.
Khang, Chang Hyun; Berruyer, Romain; Giraldo, Martha C; Kankanala, Prasanna; Park, Sook-Young; Czymmek, Kirk; Kang, Seogchan; Valent, Barbara
2010-04-01
Knowledge remains limited about how fungal pathogens that colonize living plant cells translocate effector proteins inside host cells to regulate cellular processes and neutralize defense responses. To cause the globally important rice blast disease, specialized invasive hyphae (IH) invade successive living rice (Oryza sativa) cells while enclosed in host-derived extrainvasive hyphal membrane. Using live-cell imaging, we identified a highly localized structure, the biotrophic interfacial complex (BIC), which accumulates fluorescently labeled effectors secreted by IH. In each newly entered rice cell, effectors were first secreted into BICs at the tips of the initially filamentous hyphae in the cell. These tip BICs were left behind beside the first-differentiated bulbous IH cells as the fungus continued to colonize the host cell. Fluorescence recovery after photobleaching experiments showed that the effector protein PWL2 (for prevents pathogenicity toward weeping lovegrass [Eragrostis curvula]) continued to accumulate in BICs after IH were growing elsewhere. PWL2 and BAS1 (for biotrophy-associated secreted protein 1), BIC-localized secreted proteins, were translocated into the rice cytoplasm. By contrast, BAS4, which uniformly outlines the IH, was not translocated into the host cytoplasm. Fluorescent PWL2 and BAS1 proteins that reached the rice cytoplasm moved into uninvaded neighbors, presumably preparing host cells before invasion. We report robust assays for elucidating the molecular mechanisms that underpin effector secretion into BICs, translocation to the rice cytoplasm, and cell-to-cell movement in rice. PMID:20435900
Rudnicka, Dominika; Feldmann, Jérôme; Porrot, Françoise; Wietgrefe, Steve; Guadagnini, Stéphanie; Prévost, Marie-Christine; Estaquier, Jérôme; Haase, Ashley T.; Sol-Foulon, Nathalie; Schwartz, Olivier
2009-01-01
Human immunodeficiency virus type 1 (HIV-1) efficiently propagates through cell-to-cell contacts, which include virological synapses (VS), filopodia, and nanotubes. Here, we quantified and characterized further these diverse modes of contact in lymphocytes. We report that viral transmission mainly occurs across VS and through “polysynapses,” a rosette-like structure formed between one infected cell and multiple adjacent recipients. Polysynapses are characterized by simultaneous HIV clustering and transfer at multiple membrane regions. HIV Gag proteins often adopt a ring-like supramolecular organization at sites of intercellular contacts and colocalize with CD63 tetraspanin and raft components GM1, Thy-1, and CD59. In donor cells engaged in polysynapses, there is no preferential accumulation of Gag proteins at contact sites facing the microtubule organizing center. The LFA-1 adhesion molecule, known to facilitate viral replication, enhances formation of polysynapses. Altogether, our results reveal an underestimated mode of viral transfer through polysynapses. In HIV-infected individuals, these structures, by promoting concomitant infection of multiple targets in the vicinity of infected cells, may facilitate exponential viral growth and escape from immune responses. PMID:19369333
Reversible Diffusion by Thermal Fluctuations
Donev, A.; Fai, T. G.; Vanden-Eijnden, and E.
2013-01-01
A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to satisfy a closed-form stochastic advection-diffusion equation that is used to investigate the collective diffusion of hydrodynamically-correlated tracers through a combination of Eulerian and Lagrangian numerical methods. This analysis indicates that transport ...
Fluctuating-friction molecular motors
Marrucci, Lorenzo; Paparo, Domenico; Kreuzer, Markus
2001-01-01
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of this motion requires the presence of two additional independent bodies interacting with the particle via friction and via the energy potential, respectively, which can move relative to each other. Such three-body system generalizes the classical Brownian r...
International Nuclear Information System (INIS)
Evolution of waves subject to a randomly varying growth rate is considered and the statistical properties of the waves are calculated in terms of the mean, variance, and correlation time of the growth rate. This enables stochastic growth to be studied without needing full knowledge of the microphysics. However, where the microphysics is understood, this approach also allows it to be easily incorporated into studies of larger-scale phenomena involving stochastic growth. Stochastic differential equations and Fokker--Planck equations are obtained, which describe the wave evolution in the presence of a variety of linear and nonlinear processes and boundary conditions, and it is shown that these phenomena can be diagnosed observationally through their effects on the statistical distribution of the wave field strengths. The results are particularly useful for waves with small dispersion, where they explain the strong wave clumping often observed in nature and emphasize the role of marginal stability in setting the level about which fluctuations occur and in determining their magnitude. Application to type III solar radio bursts illustrates many of the main results and verifies and generalizes earlier conclusions reached using a less rigorous approach. In particular, a new condition for marginally stable propagation of type III solar electron beams is found. copyright 1995 American Institute of Physics
Chang, Mou-Hsiung
2015-01-01
The classical probability theory initiated by Kolmogorov and its quantum counterpart, pioneered by von Neumann, were created at about the same time in the 1930s, but development of the quantum theory has trailed far behind. Although highly appealing, the quantum theory has a steep learning curve, requiring tools from both probability and analysis and a facility for combining the two viewpoints. This book is a systematic, self-contained account of the core of quantum probability and quantum stochastic processes for graduate students and researchers. The only assumed background is knowledge of the basic theory of Hilbert spaces, bounded linear operators, and classical Markov processes. From there, the book introduces additional tools from analysis, and then builds the quantum probability framework needed to support applications to quantum control and quantum information and communication. These include quantum noise, quantum stochastic calculus, stochastic quantum differential equations, quantum Markov semigrou...
Gibson, Daniel; Chang, Frederick; Gnad, Florian; Gunawardena, Jeremy
2016-01-01
The molecular complexity within a cell may be seen as an evolutionary response to the external complexity of the cell’s environment. This suggests that the external environment may be harnessed to interrogate the cell’s internal molecular architecture. Cells, however, are not only nonlinear and non-stationary, but also exhibit heterogeneous responses within a clonal, isogenic population. In effect, each cell undertakes its own experiment. Here, we develop a method of cellular interrogation using programmable microfluidic devices which exploits the additional information present in cell-to-cell variation, without requiring model parameters to be fitted to data. We focussed on Ca2+ signalling in response to hormone stimulation, which exhibits oscillatory spiking in many cell types and chose eight models of Ca2+ signalling networks which exhibit similar behaviour in simulation. We developed a nonlinear frequency analysis for non-stationary responses, which could classify models into groups under parameter variation, but found that this question alone was unable to distinguish critical feedback loops. We further developed a nonlinear amplitude analysis and found that the combination of both questions ruled out six of the models as inconsistent with the experimentally-observed dynamics and heterogeneity. The two models that survived the double interrogation were mathematically different but schematically identical and yielded the same unexpected predictions that we confirmed experimentally. Further analysis showed that subtle mathematical details can markedly influence non-stationary responses under parameter variation, emphasising the difficulty of finding a “correct” model. By developing questions for the pathway being studied, and designing more versatile microfluidics, cellular interrogation holds promise as a systematic strategy that can complement direct intervention by genetics or pharmacology. PMID:27367445
Modelling the Impact of Cell-To-Cell Transmission in Hepatitis B Virus.
Goyal, Ashish; Murray, John M
2016-01-01
Cell-free virus is a well-recognized and efficient mechanism for the spread of hepatitis B virus (HBV) infection in the liver. Cell-to-cell transmission (CCT) can be a more efficient means of virus propagation. Despite experimental evidence implying CCT occurs in HBV, its relative impact is uncertain. We develop a 3-D agent-based model where each hepatocyte changes its viral state according to a dynamical process driven by cell-free virus infection, CCT and intracellular replication. We determine the relative importance of CCT in the development and resolution of acute HBV infection in the presence of cytolytic (CTL) and non-CTL mechanisms. T cell clearance number is defined as the minimum number of infected cells needed to be killed by each T cell at peak infection that results in infection clearance within 12 weeks with hepatocyte turnover (HT, number of equivalent livers) ≤3. We find that CCT has very little impact on the establishment of infection as the mean cccDNA copies/cell remains between 15 to 20 at the peak of the infection regardless of CCT strength. In contrast, CCT inhibit immune-mediated clearance of acute HBV infection as higher CCT strength requires higher T cell clearance number and increases the probability of T cell exhaustion. An effective non-CTL inhibition can counter these negative effects of higher strengths of CCT by supporting rapid, efficient viral clearance and with little liver destruction. This is evident as the T cell clearance number drops by approximately 50% when non-CTL inhibition is increased from 10% to 80%. Higher CCT strength also increases the probability of the incidence of fulminant hepatitis with this phenomenon being unlikely to arise for no CCT. In conclusion, we report the possibility of CCT impacting HBV clearance and its contribution to fulminant hepatitis. PMID:27560827
Fattouh, Ramzi; Kwon, Hyunwoo; Czuczman, Mark A; Copeland, John W; Pelletier, Laurence; Quinlan, Margot E; Muise, Aleixo M; Higgins, Darren E; Brumell, John H
2015-04-01
The Gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen whose virulence depends on its ability to spread from cell to cell within an infected host. Although the actin-related protein 2/3 (Arp2/3) complex is necessary and sufficient for Listeria actin tail assembly, previous studies suggest that other actin polymerization factors, such as formins, may participate in protrusion formation. Here, we show that Arp2/3 localized to only a minor portion of the protrusion. Moreover, treatment of L. monocytogenes-infected HeLa cells with a formin FH2-domain inhibitor significantly reduced protrusion length. In addition, the Diaphanous-related formins 1-3 (mDia1-3) localized to protrusions, and knockdown of mDia1, mDia2, and mDia3 substantially decreased cell-to-cell spread of L. monocytogenes. Rho GTPases are known to be involved in formin activation. Our studies also show that knockdown of several Rho family members significantly influenced bacterial cell-to-cell spread. Collectively, these findings identify a Rho GTPase-formin network that is critically involved in the cell-to-cell spread of L. monocytogenes. PMID:25281757
A stochastic approach to microphysics
International Nuclear Information System (INIS)
The presently widespread idea of ''vacuum population'', together with the quantum concept of vacuum fluctuations leads to assume a random level below that of matter. This stochastic approach starts by a reminder of the author's previous work, first on the relation of diffusion laws with the foundations of microphysics, and then on hadron spectrum. Following the latter, a random quark model is advanced; it gives to quark pairs properties similar to those of a harmonic oscillator or an elastic string, imagined as an explanation to their asymptotic freedom and their confinement. The stochastic study of such interactions as electron-nucleon, jets in e+e- collisions, or pp → π0 + X, gives form factors closely consistent with experiment. The conclusion is an epistemological comment (complementarity between stochastic and quantum domains, E.P.R. paradox, etc...)
Crossing Statistics of Anisotropic Stochastic Surface
Nezhadhaghighi, M Ghasemi; Yasseri, T; Allaei, S M Vaez
2015-01-01
We use crossing statistics and its generalization to determine the anisotropic direction imposed on a stochastic fields in $(2+1)$Dimension. This approach enables us to examine not only the rotational invariance of morphology but also we can determine the Gaussianity of underlying stochastic field in various dimensions. Theoretical prediction of up-crossing statistics (crossing with positive slope at a given threshold $\\alpha$ of height fluctuation), $\
On the stochastic dynamics of molecular conformation
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.
International Nuclear Information System (INIS)
Stochastic cooling is the damping of betatron oscillations and momentum spread of a particle beam by a feedback system. In its simplest form, a pickup electrode detects the transverse positions or momenta of particles in a storage ring, and the signal produced is amplified and applied downstream to a kicker. The time delay of the cable and electronics is designed to match the transit time of particles along the arc of the storage ring between the pickup and kicker so that an individual particle receives the amplified version of the signal it produced at the pick-up. If there were only a single particle in the ring, it is obvious that betatron oscillations and momentum offset could be damped. However, in addition to its own signal, a particle receives signals from other beam particles. In the limit of an infinite number of particles, no damping could be achieved; we have Liouville's theorem with constant density of the phase space fluid. For a finite, albeit large number of particles, there remains a residue of the single particle damping which is of practical use in accumulating low phase space density beams of particles such as antiprotons. It was the realization of this fact that led to the invention of stochastic cooling by S. van der Meer in 1968. Since its conception, stochastic cooling has been the subject of much theoretical and experimental work. The earliest experiments were performed at the ISR in 1974, with the subsequent ICE studies firmly establishing the stochastic cooling technique. This work directly led to the design and construction of the Antiproton Accumulator at CERN and the beginnings of p anti p colliding beam physics at the SPS. Experiments in stochastic cooling have been performed at Fermilab in collaboration with LBL, and a design is currently under development for a anti p accumulator for the Tevatron
Stochastic deformation of a thermodynamic symplectic structure
Kazinski, P. O.
2009-01-01
A stochastic deformation of a thermodynamic symplectic structure is studied. The stochastic deformation is analogous to the deformation of an algebra of observables such as deformation quantization, but for an imaginary deformation parameter (the Planck constant). Gauge symmetries of thermodynamics and corresponding stochastic mechanics, which describes fluctuations of a thermodynamic system, are revealed and gauge fields are introduced. A physical interpretation to the gauge transformations and gauge fields is given. An application of the formalism to a description of systems with distributed parameters in a local thermodynamic equilibrium is considered.
International Nuclear Information System (INIS)
Fluctuation phenomena are the ''tip of the iceberg'' revealing the existence, behind even the most quiescent appearing macroscopic states, of an underlying world of agitated, ever-changing microscopic processes. While the presence of these fluctuations can be ignored in some cases, e.g. if one is satisfied with purely thermostatic description of systems in equilibrium, they are central to the understanding of other phenomena, e.g. the nucleation of a new phase following the quenching of a system into the co-existence region. This volume contains a collection of review articles, written by experts in the field, on the subject of fluctuation phenomena. Some of the articles are of a very general nature discussing the modern mathematical formulation of the problems involved, while other articles deal with specific topics such as kinetics of phase transitions and conductivity in solids. The juxtaposition of the variety of physical situations in which fluctuation phenomena play an important role is novel and should give the reader an insight into this subject
Exploration of the spontaneous fluctuating activity of single enzyme molecules
Schwabe, Anne; Maarleveld, Timo; Bruggeman, Frank
2013-01-01
Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activity, such as transcription, replication, translation, and histone modifications. Here we introduce the main theoretical concepts of stochastic single-enzyme activity starting from the Michaelis–Men...
Exploration of the spontaneous fluctuating activity of single enzyme molecules
Schwabe, A.; Maarleveld, T.R.; Bruggeman, F.J.
2013-01-01
Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activ
From cusps to cores: a stochastic model
El-Zant, Amr; Combes, Francoise
2016-01-01
The cold dark matter model of structure formation faces apparent problems on galactic scales. Several threads point to excessive halo concentration, including central densities that rise too steeply with decreasing radius. Yet, random fluctuations in the gaseous component can 'heat' the centres of haloes, decreasing their densities. We present a theoretical model deriving this effect from first principles: stochastic variations in the gas density are converted into potential fluctuations that act on the dark matter; the associated force correlation function is calculated and the corresponding stochastic equation solved. Assuming a power law spectrum of fluctuations with maximal and minimal cutoff scales, we derive the velocity dispersion imparted to the halo particles and the relevant relaxation time. We further perform numerical simulations, with fluctuations realised as a Gaussian random field, which confirm the formation of a core within a timescale comparable to that derived analytically. Non-radial colle...
Crisan, Dan
2011-01-01
"Stochastic Analysis" aims to provide mathematical tools to describe and model high dimensional random systems. Such tools arise in the study of Stochastic Differential Equations and Stochastic Partial Differential Equations, Infinite Dimensional Stochastic Geometry, Random Media and Interacting Particle Systems, Super-processes, Stochastic Filtering, Mathematical Finance, etc. Stochastic Analysis has emerged as a core area of late 20th century Mathematics and is currently undergoing a rapid scientific development. The special volume "Stochastic Analysis 2010" provides a sa
Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise
David Frigola; Laura Casanellas; Sancho, José M.; Marta Ibañes
2012-01-01
Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are i...
A Nonlinear Dynamic Characterization of The Universal Scrape-off Layer Plasma Fluctuations
Mekkaoui, A
2012-01-01
A stochastic differential equation of plasma density dynamic is derived, consistent with the experimentally measured pdf and the theoretical quadratic nonlinearity. The plasma density evolves on the turbulence correlation time scale and is driven by a stochastic white noise proportional to the turbulence fluctuations amplitude, while the linear growth is quadratically damped by the fluctuation level $n_e(t)/\\bar{n}_e$.
Shephard, Neil
2005-01-01
Stochastic volatility (SV) is the main concept used in the fields of financial economics and mathematical finance to deal with the endemic time-varying volatility and codependence found in financial markets. Such dependence has been known for a long time, early comments include Mandelbrot (1963) and Officer (1973). It was also clear to the founding fathers of modern continuous time finance that homogeneity was an unrealistic if convenient simplification, e.g. Black and Scholes (1972, p. 416) ...
Dynamics of a Stochastic Functional System for Wastewater Treatment
Xuehui Ji; Sanling Yuan
2013-01-01
The dynamics of a delayed stochastic model simulating wastewater treatment process are studied. We assume that there are stochastic fluctuations in the concentrations of the nutrient and microbes around a steady state, and introduce two distributed delays to the model describing, respectively, the times involved in nutrient recycling and the bacterial reproduction response to nutrient uptake. By constructing Lyapunov functionals, sufficient conditions for the stochastic stability of its posit...
Energy Technology Data Exchange (ETDEWEB)
Tiwari, Vaibhav [Department of Ophthalmology, University of Illinois at Chicago, Chicago, IL 60612 (United States); Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 (United States); Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific and College of Optometry, Western University of Health Sciences, Pomona, CA 91766 (United States); Darmani, Nissar A.; Thrush, Gerald R. [Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific and College of Optometry, Western University of Health Sciences, Pomona, CA 91766 (United States); Shukla, Deepak, E-mail: dshukla@uic.edu [Department of Ophthalmology, University of Illinois at Chicago, Chicago, IL 60612 (United States); Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 (United States)
2009-12-18
Human herpesvirus-8 (HHV-8) is known to interact with cell surface heparan sulfate (HS) for entry into a target cell. Here we investigated the role of HS during HHV-8 glycoproteins-induced cell fusion. Interestingly, the observed fusion demonstrated an unusual dependence on HS as evident from following lines of evidence: (1) a significant reduction in cell-to-cell fusion occurred when target cells were treated with heparinase; (2) in a competition assay, when the effector cells expressing HHV-8 glycoproteins were challenged with soluble HS, cell-to-cell fusion was reduced; and, (3) co-expression of HHV-8 glycoproteins gH-gL on target cells resulted in inhibition of cell surface HS expression. Taken together, our results indicate that cell surface HS can play an additional role during HHV-8 pathogenesis.
International Nuclear Information System (INIS)
Human herpesvirus-8 (HHV-8) is known to interact with cell surface heparan sulfate (HS) for entry into a target cell. Here we investigated the role of HS during HHV-8 glycoproteins-induced cell fusion. Interestingly, the observed fusion demonstrated an unusual dependence on HS as evident from following lines of evidence: (1) a significant reduction in cell-to-cell fusion occurred when target cells were treated with heparinase; (2) in a competition assay, when the effector cells expressing HHV-8 glycoproteins were challenged with soluble HS, cell-to-cell fusion was reduced; and, (3) co-expression of HHV-8 glycoproteins gH-gL on target cells resulted in inhibition of cell surface HS expression. Taken together, our results indicate that cell surface HS can play an additional role during HHV-8 pathogenesis.
Stochastic Quantization and Casimir Forces
Rodriguez-Lopez, Pablo; Soto, Rodrigo
2011-01-01
In this paper we show how the stochastic quantization method developed by Parisi and Wu can be used to obtain Casimir forces. Both quantum and thermal fluctuations are taken into account by a Langevin equation for the field. The method allows the Casimir force to be obtained directly, derived from the stress tensor instead of the free energy. It only requires the spectral decomposition of the Laplacian operator in the given geometry. The formalism provides also an expression for the fluctuations of the force. As an application we compute the Casimir force on the plates of a finite piston of arbitrary cross section. Fluctuations of the force are also directly obtained, and it is shown that, in the piston case, the variance of the force is twice the force squared.
Balachandran, Suchandra; Xiang, Yu; Schobert, Christian; Thompson, Gary A.; Lucas, William J.
1997-01-01
In angiosperms, the functional enucleate sieve tube system of the phloem appears to be maintained by the surrounding companion cells. In this study, we tested the hypothesis that polypeptides present within the phloem sap traffic cell to cell from the companion cells, where they are synthesized, into the sieve tube via plasmodesmata. Coinjection of fluorescently labeled dextrans along with size-fractionated Cucurbita maxima phloem proteins, ranging in size from 10 to 200 kDa, as well as injec...
Cell-to-cell variability in cell death: can systems biology help us make sense of it all?
Xia, X; Owen, M. S.; Lee, R E C; Gaudet, S
2014-01-01
One of the most common observations in cell death assays is that not all cells die at the same time, or at the same treatment dose. Here, using the perspective of the systems biology of apoptosis and the context of cancer treatment, we discuss possible sources of this cell-to-cell variability as well as its implications for quantitative measurements and computational models of cell death. Many different factors, both within and outside of the apoptosis signaling networks, have been correlated...
A stochastic reorganizational bath model for electronic energy transfer
Fujita, Takatoshi; Aspuru-Guzik, Alan
2014-01-01
The fluctuations of optical gap induced by the environment play crucial roles in electronic energy transfer dynamics. One of the simplest approaches to incorporate such fluctuations in energy transfer dynamics is the well known Haken-Strobl-Reineker model, in which the energy-gap fluctuation is approximated as a white noise. Recently, several groups have employed molecular dynamics simulations and excited-state calculations in conjunction to take the thermal fluctuation of excitation energies into account. Here, we discuss a rigorous connection between the stochastic and the atomistic bath models. If the phonon bath is treated classically, time evolution of the exciton-phonon system can be described by Ehrenfest dynamics. To establish the relationship between the stochastic and atomistic bath models, we employ a projection operator technique to derive the generalized Langevin equations for the energy-gap fluctuations. The stochastic bath model can be obtained as an approximation of the atomistic Ehrenfest equ...
Stochastic Gravity: Theory and Applications
Directory of Open Access Journals (Sweden)
Hu Bei Lok
2004-01-01
Full Text Available Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel. The noise kernel is the vacuum expectation value of the (operator-valued stress-energy bi-tensor which describes the fluctuations of quantum matter fields in curved spacetimes. In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. The axiomatic approach is useful to see the structure of the theory from the framework of semiclassical gravity, showing the link from the mean value of the stress-energy tensor to their correlation functions. The functional approach uses the Feynman-Vernon influence functional and the Schwinger-Keldysh closed-time-path effective action methods which are convenient for computations. It also brings out the open systems concepts and the statistical and stochastic contents of the theory such as dissipation, fluctuations, noise, and decoherence. We then focus on the properties of the stress-energy bi-tensor. We obtain a general expression for the noise kernel of a quantum field defined at two distinct points in an arbitrary curved spacetime as products of covariant derivatives of the quantum field's Green function. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime. We offer an analytical solution of the Einstein-Langevin equation and compute the two-point correlation functions for the linearized Einstein tensor and for the metric perturbations. Second, we discuss structure formation from the stochastic gravity viewpoint, which can go beyond the standard treatment by incorporating the full quantum effect of the inflaton fluctuations. Third, we discuss the backreaction
Sasaki, Nobumitsu; Ogata, Takuya; Deguchi, Masakazu; Nagai, Shoko; Tamai, Atsushi; Meshi, Tetsuo; Kawakami, Shigeki; Watanabe, Yuichiro; Matsushita, Yasuhiko; Nyunoya, Hiroshi
2009-03-01
Tomato mosaic virus (ToMV) encodes a movement protein (MP) that is necessary for virus cell-to-cell movement. We have demonstrated previously that KELP, a putative transcriptional coactivator of Arabidopsis thaliana, and its orthologue from Brassica campestris can bind to ToMV MP in vitro. In this study, we examined the effects of the transient over-expression of KELP on ToMV infection and the intracellular localization of MP in Nicotiana benthamiana, an experimental host of the virus. In co-bombardment experiments, the over-expression of KELP inhibited virus cell-to-cell movement. The N-terminal half of KELP (KELPdC), which had been shown to bind to MP, was sufficient for inhibition. Furthermore, the over-expression of KELP and KELPdC, both of which were co-localized with ToMV MP, led to a reduction in the plasmodesmal association of MP. In the absence of MP expression, KELP was localized in the nucleus and the cytoplasm by the localization signal in its N-terminal half. It was also shown that ToMV amplified normally in protoplasts prepared from leaf tissue that expressed KELP transiently. These results indicate that over-expressed KELP interacts with MP in vivo and exerts an inhibitory effect on MP function for virus cell-to-cell movement, but not on virus amplification in individual cells. PMID:19236566
Stochastic Gravity: Theory and Applications
Directory of Open Access Journals (Sweden)
Hu Bei Lok
2008-05-01
Full Text Available Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein–Langevin equation, which has, in addition, sources due to the noise kernel. The noise kernel is the vacuum expectation value of the (operator-valued stress-energy bitensor, which describes the fluctuations of quantum-matter fields in curved spacetimes. A new improved criterion for the validity of semiclassical gravity may also be formulated from the viewpoint of this theory. In the first part of this review we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. The axiomatic approach is useful to see the structure of the theory from the framework of semiclassical gravity, showing the link from the mean value of the stress-energy tensor to the correlation functions. The functional approach uses the Feynman–Vernon influence functional and the Schwinger–Keldysh closed-time-path effective action methods. In the second part, we describe three applications of stochastic gravity. First, we consider metric perturbations in a Minkowski spacetime, compute the two-point correlation functions of these perturbations and prove that Minkowski spacetime is a stable solution of semiclassical gravity. Second, we discuss structure formation from the stochastic-gravity viewpoint, which can go beyond the standard treatment by incorporating the full quantum effect of the inflaton fluctuations. Third, using the Einstein–Langevin equation, we discuss the backreaction of Hawking radiation and the behavior of metric fluctuations for both the quasi-equilibrium condition of a black-hole in a box and the fully nonequilibrium condition of an evaporating black hole spacetime. Finally, we briefly discuss the theoretical structure of stochastic gravity in relation to quantum gravity and point out
Institute of Scientific and Technical Information of China (English)
赵越; 覃大清; 刘文杰; 徐用良; 许建新
2012-01-01
本文采用试验和统计分析的方法,根据在某中水头模型水轮机的相同工况下采集的300组压力脉动数据,采用比较试验数据随机不确定度的方法,研究了特征峰峰值、均方根、标准偏差和最大分频幅值等表征压力脉动程度的特征参数的随机不确定度情况,并以此提出了采用均方根值来表征压力脉动程度的建议.%In this paper, according t0 300 groups of test data of pressure fluctuation at same operation condition on a middle head Francis turbine model, the statistical behaviors ofcharacteristicpeak-to-peak value, root-mean-square, standard deviation and main frequency amplitude are explored on stochastic uncertainty method. Root-mean-square is suggested to denote the extent of pressure fluctuation.
Fluctuations for galaxy formation from inflation models
Energy Technology Data Exchange (ETDEWEB)
Salopek, D.S.
1989-01-01
The theory of fluctuations for galaxy formation from chaotic inflation models is extended to include the effects of (1) multiple scalar fields, (2) curvature coupling of scalar fields to gravity, (3) nonlinear evolution of long wavelength metric and scalar fields, and (4) stochastic generation of initial conditions. Multiple scalar field models may generate more large scale power than the standard Cold Dark Matter (CDM) model if the Universe undergoes two inflation epochs giving a CDM+ plateau spectrum. If the scalar fields pass over a mogul in the potential, then CDM+ mountain fluctuations spectral may be generated. The chaotic inflation scenario may be housed within a grand unified theory (GUT) framework through a coupling of scalar Higgs field to curvature. Radiative corrections to the Higgs potential are small and the reheat temperature is typically high yielding successful baryogenesis. Using Hamilton-Jacobi theory, a general formalism is presented for following the nonlinear evolution of the metric (scalar, vector, and tensor modes) and scalar fields for fluctuations with wavelength greater than the Hubble radius. It is shown how nonlinear effects of the metric and scalar fields may be included in Starobinski's formulation of stochastic inflation. Stochastic noise terms in the long wavelength evolution equations model quantum fluctuations that are assumed to become classical at horizon crossing and which then contribute to the background. T = ln(Ha) proves to be a useful time variable because it enables one to solve for scalar field quantum fluctuations within the horizon in an inhomogeneous background.
Stochastic Resonance in Protein Folding Dynamics.
Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A
2016-05-01
Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics. PMID:26992148
A fluctuating energy-momentum may produce an unstable world
R. AloisioINFN/LNGS; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); Grillo, A. F.
2015-01-01
Quantum gravitational effects may induce stochastic fluctuations in the structure of space-time, to produce a characteristic foamy structure. It has been known for some time now that these fluctuations may have observable consequencies for the propagation of cosmic ray particles over cosmological distances. We note here that the same fluctuations, if they exist, imply that some decay reactions normally forbidden by elementary conservation laws, become kinematically allowed, inducing the decay...
Space Time Fluctuations and Ultra High Energy Cosmic Ray Interactions
R. AloisioINFN/LNGS; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); P. L. Ghia(CNR and INFN Torino); Grillo, A. F.
2002-01-01
The intimate geometry of space-time is expected to suffer stochastic fluctuations as a result of quantum gravitational effects. These fluctuations may induce observable consequences on the propagation of high energy particles over large distances, so that the strength and the characteristics of these fluctuations may be constrained, mainly in the range of energies of interest for cosmic ray physics. While invoked as a possible explanation for the detection of the puzzling co...
International Nuclear Information System (INIS)
Cucumber mosaic virus (CMV, a cucumovirus) and Brome mosaic virus (BMV, a bromovirus) require the coat protein (CP) in addition to the 3a movement protein (MP) for cell-to-cell movement, while Cowpea chlorotic mottle virus (CCMV, a bromovirus) does not. Using bombardment-mediated transcomplementation assays, we investigated whether the movement functions encoded by these viruses potentiate cell-to-cell movement of movement-defective Tomato mosaic virus (ToMV, a tobamovirus) and Potato virus X (PVX, a potexvirus) mutants in Nicotiana benthamiana. Coexpression of CMV 3a and CP, but neither protein alone, complemented the defective movement of ToMV and PVX. A C-terminal deletion in CMV 3a (3aΔC33) abolished the requirement of CP in transporting the ToMV genome. The action of 3aΔC33 was inhibited by coexpression of wild-type 3a. These findings were confirmed in tobacco with ToMV-CMV chimeric viruses. Either BMV 3a or CCMV 3a alone efficiently complemented the movement-defective phenotype of the ToMV mutant. Therefore, every 3a protein examined intrinsically possesses the activity required to act as MP. In transcomplementation of the PVX mutant, the activities of BMV 3a, CCMV 3a, and CMV 3aΔC33 were very low. The activities of the bromovirus 3a proteins were enhanced by coexpression of the cognate CP but the activity of CMV 3aΔC33 was not. Based on these results, possible roles of cucumo- and bromovirus CPs in cell-to-cell movement are discussed
Tamai, Atsushi; Kubota, Kenji; Nagano, Hideaki; Yoshii, Motoyasu; Ishikawa, Masayuki; Mise, Kazuyuki; Meshi, Tetsuo
2003-10-10
Cucumber mosaic virus (CMV, a cucumovirus) and Brome mosaic virus (BMV, a bromovirus) require the coat protein (CP) in addition to the 3a movement protein (MP) for cell-to-cell movement, while Cowpea chlorotic mottle virus (CCMV, a bromovirus) does not. Using bombardment-mediated transcomplementation assays, we investigated whether the movement functions encoded by these viruses potentiate cell-to-cell movement of movement-defective Tomato mosaic virus (ToMV, a tobamovirus) and Potato virus X (PVX, a potexvirus) mutants in Nicotiana benthamiana. Coexpression of CMV 3a and CP, but neither protein alone, complemented the defective movement of ToMV and PVX. A C-terminal deletion in CMV 3a (3a Delta C33) abolished the requirement of CP in transporting the ToMV genome. The action of 3a Delta C33 was inhibited by coexpression of wild-type 3a. These findings were confirmed in tobacco with ToMV-CMV chimeric viruses. Either BMV 3a or CCMV 3a alone efficiently complemented the movement-defective phenotype of the ToMV mutant. Therefore, every 3a protein examined intrinsically possesses the activity required to act as MP. In transcomplementation of the PVX mutant, the activities of BMV 3a, CCMV 3a, and CMV 3a Delta C33 were very low. The activities of the bromovirus 3a proteins were enhanced by coexpression of the cognate CP but the activity of CMV 3a Delta C33 was not. Based on these results, possible roles of cucumo- and bromovirus CPs in cell-to-cell movement are discussed. PMID:14592759
Communication: Embedded fragment stochastic density functional theory
International Nuclear Information System (INIS)
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals
Assessing the quality of stochastic oscillations
Indian Academy of Sciences (India)
Guillermo Abramson; Sebastián Risau-Gusman
2008-06-01
We analyze the relationship between the macroscopic and microscopic descriptions of two-state systems, in particular the regime in which the microscopic one shows sustained `stochastic oscillations' while the macroscopic tends to a fixed point. We propose a quantification of the oscillatory appearance of the fluctuating populations, and show that good stochastic oscillations are present if a parameter of the macroscopic model is small, and that no microscopic model will show oscillations if that parameter is large. The transition between these two regimes is smooth. In other words, given a macroscopic deterministic model, one can know whether any microscopic stochastic model that has it as a limit, will display good sustained stochastic oscillations.
Stochastic Effects; Application in Nuclear Physics
International Nuclear Information System (INIS)
Stochastic effects in nuclear physics refer to the study of the dynamics of nuclear systems evolving under stochastic equations of motion. In this dissertation we restrict our attention to classical scattering models. We begin with introduction of the model of nuclear dynamics and deterministic equations of evolution. We apply a Langevin approach - an additional property of the model, which reflect the statistical nature of low energy nuclear behaviour. We than concentrate our attention on the problem of calculating tails of distribution functions, which actually is the problem of calculating probabilities of rare outcomes. Two general strategies are proposed. Result and discussion follow. Finally in the appendix we consider stochastic effects in nonequilibrium systems. A few exactly solvable models are presented. For one model we show explicitly that stochastic behaviour in a microscopic description can lead to ordered collective effects on the macroscopic scale. Two others are solved to confirm the predictions of the fluctuation theorem. (author)
Embedded fragment stochastic density functional theory
Neuhauser, Daniel; Rabani, Eran
2014-01-01
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals.
Fattouh, Ramzi; Kwon, Hyunwoo; Czuczman, Mark A.; Copeland, John W.; Pelletier, Laurence; Quinlan, Margot E.; Aleixo M Muise; Higgins, Darren E.; Brumell, John H.
2014-01-01
The Gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen whose virulence depends on its ability to spread from cell to cell within an infected host. Although the actin-related protein 2/3 (Arp2/3) complex is necessary and sufficient for Listeria actin tail assembly, previous studies suggest that other actin polymerization factors, such as formins, may participate in protrusion formation. Here, we show that Arp2/3 localized to only a minor portion of the protr...
Mitarai, Namiko; Semsey, Szabolcs; Sneppen, Kim
2015-08-01
Transcriptional repression may cause transcriptional noise by a competition between repressor and RNA polymerase binding. Although promoter activity is often governed by a single limiting step, we argue here that the size of the noise strongly depends on whether this step is the initial equilibrium binding or one of the subsequent unidirectional steps. Overall, we show that nonequilibrium steps of transcription initiation systematically increase the cell-to-cell heterogeneity in bacterial populations. In particular, this allows also weak promoters to give substantial transcriptional noise. PMID:26382435
Xu, Jinhu; Zhou, Yicang
2016-04-01
A within-host viral infection model with both virus-to-cell and cell-to-cell transmissions and time delay in immune response is investigated. Mathematical analysis shows that delay may destabilize the infected steady state and lead to Hopf bifurcation. Moreover, the direction of the Hopf bifurcation and the stability of the periodic solutions are investigated by normal form and center manifold theory. Numerical simulations are done to explore the rich dynamics, including stability switches, Hopf bifurcations, and chaotic oscillations. PMID:27105992
Stochastic inflation and nonlinear gravity
Salopek, D. S.; Bond, J. R.
1991-02-01
We show how nonlinear effects of the metric and scalar fields may be included in stochastic inflation. Our formalism can be applied to non-Gaussian fluctuation models for galaxy formation. Fluctuations with wavelengths larger than the horizon length are governed by a network of Langevin equations for the physical fields. Stochastic noise terms arise from quantum fluctuations that are assumed to become classical at horizon crossing and that then contribute to the background. Using Hamilton-Jacobi methods, we solve the Arnowitt-Deser-Misner constraint equations which allows us to separate the growing modes from the decaying ones in the drift phase following each stochastic impulse. We argue that the most reasonable choice of time hypersurfaces for the Langevin system during inflation is T=ln(Ha), where H and a are the local values of the Hubble parameter and the scale factor, since T is the natural time for evolving the short-wavelength scalar field fluctuations in an inhomogeneous background. We derive a Fokker-Planck equation which describes how the probability distribution of scalar field values at a given spatial point evolves in T. Analytic Green's-function solutions obtained for a single scalar field self-interacting through an exponential potential are used to demonstrate (1) if the initial condition of the Hubble parameter is chosen to be consistent with microwave-background limits, H(φ0)/mρUniverse, the distribution is non-Gaussian, with a tail extending to large energy densities; although there are no observable manifestations, it does show eternal inflation. Lattice simulations of our Langevin network for the exponential potential demonstrate how spatial correlations are incorporated. An initially homogeneous and isotropic lattice develops fluctuations as more and more quantum fluctuation modes leave the horizon, yielding Gaussian contour maps for a region corresponding to our observable patch and non-Gaussian contour maps for the ultra
Wei, Fengying; Chen, Fangxiang
2016-07-01
This article discusses a stochastic SIQS epidemic model with saturated incidence. We assume that random perturbations always fluctuate at the endemic equilibrium. The existence of a global positive solution is obtained by constructing a suitable Lyapunov function. Under some suitable conditions, we derive the stochastic boundedness and stochastic permanence of the solutions of a stochastic SIQS model. Some numerical simulations are carried out to check our results.
Energy Technology Data Exchange (ETDEWEB)
Blaskiewicz, M.
2011-01-01
Stochastic Cooling was invented by Simon van der Meer and was demonstrated at the CERN ISR and ICE (Initial Cooling Experiment). Operational systems were developed at Fermilab and CERN. A complete theory of cooling of unbunched beams was developed, and was applied at CERN and Fermilab. Several new and existing rings employ coasting beam cooling. Bunched beam cooling was demonstrated in ICE and has been observed in several rings designed for coasting beam cooling. High energy bunched beams have proven more difficult. Signal suppression was achieved in the Tevatron, though operational cooling was not pursued at Fermilab. Longitudinal cooling was achieved in the RHIC collider. More recently a vertical cooling system in RHIC cooled both transverse dimensions via betatron coupling.
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
In this paper, the stochastic flow of mappings generated by a Feller convolution semigroup on a compact metric space is studied. This kind of flow is the generalization of superprocesses of stochastic flows and stochastic diffeomorphism induced by the strong solutions of stochastic differential equations.
Stochastic Averaging and Stochastic Extremum Seeking
Liu, Shu-Jun
2012-01-01
Stochastic Averaging and Stochastic Extremum Seeking develops methods of mathematical analysis inspired by the interest in reverse engineering and analysis of bacterial convergence by chemotaxis and to apply similar stochastic optimization techniques in other environments. The first half of the text presents significant advances in stochastic averaging theory, necessitated by the fact that existing theorems are restricted to systems with linear growth, globally exponentially stable average models, vanishing stochastic perturbations, and prevent analysis over infinite time horizon. The second half of the text introduces stochastic extremum seeking algorithms for model-free optimization of systems in real time using stochastic perturbations for estimation of their gradients. Both gradient- and Newton-based algorithms are presented, offering the user the choice between the simplicity of implementation (gradient) and the ability to achieve a known, arbitrary convergence rate (Newton). The design of algorithms...
Fluctuation preserving coarse graining for biochemical systems
Altaner, Bernhard
2011-01-01
Finite stochastic Markov models play a major role for modelling biochemical pathways. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a certain extend arbitrary since it depends on the resolution of accomodating measurements. Here, we present a way to simplify such stochastic descriptions, which preserves both the meso-micro and the meso-macro connection. The former is achieved by demanding locality, the latter by considering cycles on the network of states. Using single- and multicycle examples we demonstrate how our new method preserves fluctuations of observables much better than na\\"ive approaches.
Stochastic modeling of the auroral electrojet index
Anh, V. V.; Yong, J. M.; Yu, Z. G.
2008-10-01
Substorms are often identified by bursts of activities in the magnetosphere-ionosphere system characterized by the auroral electrojet (AE) index. The highly complex nature of substorm-related bursts suggests that a stochastic approach would be needed. Stochastic models including fractional Brownian motion, linear fractional stable motion, Fokker-Planck equation and Itô-type stochastic differential equation have been suggested to model the AE index. This paper provides a stochastic model for the AE in the form of fractional stochastic differential equation. The long memory of the AE time series is represented by a fractional derivative, while its bursty behavior is modeled by a Lévy noise with inverse Gaussian marginal distribution. The equation has the form of the classical Stokes-Boussinesq-Basset equation of motion for a spherical particle in a fluid with retarded viscosity. Parameter estimation and approximation schemes are detailed for the simulation of the equation. The fractional order of the equation conforms with the previous finding that the fluctuations of the magnetosphere-ionosphere system as seen in the AE reflect the fluctuations in the solar wind: they both possess the same extent of long-range dependence. The introduction of a fractional derivative term into the equation to capture the extent of long-range dependence together with an inverse Gaussian noise input describe the right amount of intermittency inherent in the AE data.
Stochastic growth of localized plasma waves
International Nuclear Information System (INIS)
Localized bursty plasma waves are detected by spacecraft in many space plasmas. The large spatiotemporal scales involved imply that beam and other instabilities relax to marginal stability and that mean wave energies are low. Stochastic wave growth occurs when ambient fluctuations perturb the system, causing fluctuations about marginal stability. This yields regions where growth is enhanced and others where damping is increased; bursts are associated with enhanced growth and can occur even when the mean growth rate is negative. In stochastic growth, energy loss from the source is suppressed relative to secular growth, preserving it far longer than otherwise possible. Linear stochastic growth can operate at wave levels below thresholds of nonlinear wave-clumping mechanisms such as strong-turbulence modulational instability and is not subject to their coherence and wavelength limits. These mechanisms can be distinguished by statistics of the fields, whose strengths are lognormally distributed if stochastically growing and power-law distributed in strong turbulence. Recent applications of stochastic growth theory (SGT) are described, involving bursty plasma waves and unstable particle distributions in type III solar radio sources, the Earth's foreshock, magnetosheath, and polar cap regions. It is shown that when combined with wave-wave processes, SGT also accounts for associated radio emissions
Stochastic effects in a seasonally forced epidemic model
Rozhnova, Ganna
2010-01-01
The interplay of seasonality, the system's nonlinearities and intrinsic stochasticity is studied for a seasonally forced susceptible-exposed-infective-recovered stochastic model. The model is explored in the parameter region that corresponds to childhood infectious diseases such as measles. The power spectrum of the stochastic fluctuations around the attractors of the deterministic system that describes the model in the thermodynamic limit is computed analytically and validated by stochastic simulations for large system sizes. Size effects are studied through additional simulations. Other effects such as switching between coexisting attractors induced by stochasticity often mentioned in the literature as playing an important role in the dynamics of childhood infectious diseases are also investigated. The main conclusion is that stochastic amplification, rather than these effects, is the key ingredient to understand the observed incidence patterns.
Pokharel, Deep; Wijesinghe, Philip; Oenarto, Vici; Lu, Jamie F; Sampson, David D; Kennedy, Brendan F; Wallace, Vincent P; Bebawy, Mary
2016-08-01
Deciphering the role of cell-to-cell communication in acquisition of cancer traits such as metastasis is one of the key challenges of integrative biology and clinical oncology. In this context, extracellular vesicles (EVs) are important vectors in cell-to-cell communication and serve as conduits in the transfer of cellular constituents required for cell function and for the establishment of cellular phenotypes. In the case of malignancy, they have been shown to support the acquisition of common traits defined as constituting the hallmarks of cancer. Cellular biophysics has contributed to our understanding of some of these central traits with changes in tissue biomechanics reflective of cell state. Indeed, much is known about stiffness of the tissue scaffold in the context of cell invasion and migration. This article advances this knowledge frontier by showing for the first time that EVs are mediators of tissue biomechanical properties and, importantly, demonstrates a link between the acquisition of cancer multidrug resistance and increased tissue stiffness of the malignant mass. The methodology used in the study employed optical coherence elastography and atomic force microscopy on breast cancer cell monolayers and tumor spheroids. Specifically, we show here that the acquired changes in tissue stiffness can be attributed to the intracellular transfer of a protein complex comprising ezrin, radixin, moesin, CD44, and P-glycoprotein. This has important implications in facilitating mechano-transduced signaling cascades that regulate the acquisition of cancer traits, such as invasion and metastasis. Finally, this study also introduces novel targets and strategies for diagnostic and therapeutic innovation in oncology, with a view to prevention of metastatic spread and personalized medicine in cancer treatment. PMID:27501296
Concentration fluctuations in gas releases by industrial accidents
DEFF Research Database (Denmark)
Nielsen, M.; Chatwin, P.C.; Ejsing Jørgensen, Hans;
2002-01-01
The COFIN project studied existing remote-sensing Lidar data on concentration fluctuations in atmospheric dispersion from continuous sources at ground level. Fluctuations are described by stochastic models developed by a combination of statisticalanalyses and surface-layer scaling. The statistical...... and the probability distribution for the plume centreline. The distance-neighbour function generalizedfor higher-order statistics has a universal exponential shape. Simulation tools for concentration fluctuations have been developed for either multiple correlated time series or multi-dimensional fields. These tools...... risk assessment is illustrated by implementation of a typical heavy-gas dispersion model, enhanced for prediction and simulation of concentration fluctuations....
Constraints on Fluctuations in Sparsely Characterized Biological Systems
Hilfinger, Andreas; Norman, Thomas M.; Vinnicombe, Glenn; Paulsson, Johan
2016-02-01
Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.
Stochastic flux freezing and magnetic dynamo
International Nuclear Information System (INIS)
Magnetic flux conservation in turbulent plasmas at high magnetic Reynolds numbers is argued neither to hold in the conventional sense nor to be entirely broken, but instead to be valid in a statistical sense associated to the ''spontaneous stochasticity'' of Lagrangian particle trajectories. The latter phenomenon is due to the explosive separation of particles undergoing turbulent Richardson diffusion, which leads to a breakdown of Laplacian determinism for classical dynamics. Empirical evidence is presented for spontaneous stochasticity, including numerical results. A Lagrangian path-integral approach is then exploited to establish stochastic flux freezing for resistive hydromagnetic equations and to argue, based on the properties of Richardson diffusion, that flux conservation must remain stochastic at infinite magnetic Reynolds number. An important application of these results is the kinematic, fluctuation dynamo in nonhelical, incompressible turbulence at magnetic Prandtl number (Prm) equal to unity. Numerical results on the Lagrangian dynamo mechanisms by a stochastic particle method demonstrate a strong similarity between the Prm=1 and 0 dynamos. Stochasticity of field-line motion is an essential ingredient of both. Finally, some consequences for nonlinear magnetohydrodynamic turbulence, dynamo, and reconnection are briefly considered.
Mechanical Autonomous Stochastic Heat Engine
Serra-Garcia, Marc; Foehr, André; Molerón, Miguel; Lydon, Joseph; Chong, Christopher; Daraio, Chiara
2016-07-01
Stochastic heat engines are devices that generate work from random thermal motion using a small number of highly fluctuating degrees of freedom. Proposals for such devices have existed for more than a century and include the Maxwell demon and the Feynman ratchet. Only recently have they been demonstrated experimentally, using, e.g., thermal cycles implemented in optical traps. However, recent experimental demonstrations of classical stochastic heat engines are nonautonomous, since they require an external control system that prescribes a heating and cooling cycle and consume more energy than they produce. We present a heat engine consisting of three coupled mechanical resonators (two ribbons and a cantilever) subject to a stochastic drive. The engine uses geometric nonlinearities in the resonating ribbons to autonomously convert a random excitation into a low-entropy, nonpassive oscillation of the cantilever. The engine presents the anomalous heat transport property of negative thermal conductivity, consisting in the ability to passively transfer energy from a cold reservoir to a hot reservoir.
Turbulence, Spontaneous Stochasticity and Climate
Eyink, Gregory
Turbulence is well-recognized as important in the physics of climate. Turbulent mixing plays a crucial role in the global ocean circulation. Turbulence also provides a natural source of variability, which bedevils our ability to predict climate. I shall review here a recently discovered turbulence phenomenon, called ``spontaneous stochasticity'', which makes classical dynamical systems as intrinsically random as quantum mechanics. Turbulent dissipation and mixing of scalars (passive or active) is now understood to require Lagrangian spontaneous stochasticity, which can be expressed by an exact ``fluctuation-dissipation relation'' for scalar turbulence (joint work with Theo Drivas). Path-integral methods such as developed for quantum mechanics become necessary to the description. There can also be Eulerian spontaneous stochasticity of the flow fields themselves, which is intimately related to the work of Kraichnan and Leith on unpredictability of turbulent flows. This leads to problems similar to those encountered in quantum field theory. To quantify uncertainty in forecasts (or hindcasts), we can borrow from quantum field-theory the concept of ``effective actions'', which characterize climate averages by a variational principle and variances by functional derivatives. I discuss some work with Tom Haine (JHU) and Santha Akella (NASA-Goddard) to make this a practical predictive tool. More ambitious application of the effective action is possible using Rayleigh-Ritz schemes.
Thermoemission of Ce+ ions and its fluctuations
Gladyszewski, Longin
1994-12-01
The surface ionization of cerium on tungsten and its fluctuatins (noises) have been studied using a single filament ion source in a 90° magnetic mass spectrometer. The statistical behaviour of the spectral density and autocorrelation functions for Ce+ ion thermoemission noise were investigated by means of a special stochastic analyser. These noises are generated as a result of adsorbate density fluctuations. The method used made it possible to determine the atom desorption and migration energy for cerium from tungsten.
Kallianpur, Gopinath; Hida, Takeyuki
1987-01-01
The use of probabilistic methods in the biological sciences has been so well established by now that mathematical biology is regarded by many as a distinct dis cipline with its own repertoire of techniques. The purpose of the Workshop on sto chastic methods in biology held at Nagoya University during the week of July 8-12, 1985, was to enable biologists and probabilists from Japan and the U. S. to discuss the latest developments in their respective fields and to exchange ideas on the ap plicability of the more recent developments in stochastic process theory to problems in biology. Eighteen papers were presented at the Workshop and have been grouped under the following headings: I. Population genetics (five papers) II. Measure valued diffusion processes related to population genetics (three papers) III. Neurophysiology (two papers) IV. Fluctuation in living cells (two papers) V. Mathematical methods related to other problems in biology, epidemiology, population dynamics, etc. (six papers) An important f...
Moawia Alghalith
2012-01-01
We present new stochastic differential equations, that are more general and simpler than the existing Ito-based stochastic differential equations. As an example, we apply our approach to the investment (portfolio) model.
Stochastic approximation: invited paper
Lai, Tze Leung
2003-01-01
Stochastic approximation, introduced by Robbins and Monro in 1951, has become an important and vibrant subject in optimization, control and signal processing. This paper reviews Robbins' contributions to stochastic approximation and gives an overview of several related developments.
Stochasticity or the fatal `imperfection' of cloning
Indian Academy of Sciences (India)
Reiner A Veitia
2005-02-01
The concept of clone is analysed with the aim of exploring the limits to which a phenotype can be said to be determined geneticaly. First of all, mutations that result from the replication, topological manipulation or lesion of DNA introduce a source of heritable variation in an otherwise identical genetic background. But more important, stochastic effects in many biological processes may superimpose a phenotypic variation which is not encoded in the genome. The source of stochasticity ranges from the random selection of alleles or whole chromosomes to be expressed in small cell populations, to fluctuations in processes such as gene expression, due to limiting amounts of the players involved. The picture emerging is that the term clone is a statistical over-simplification representing a series of individuals having essentially the same genome but capable of exhibiting wide phenotypic variation. Finally, to what extent fluctuations in biological processes, usually thought of as noise, are in fact signal is also discussed.
Stochastic tools in turbulence
Lumey, John L
2012-01-01
Stochastic Tools in Turbulence discusses the available mathematical tools to describe stochastic vector fields to solve problems related to these fields. The book deals with the needs of turbulence in relation to stochastic vector fields, particularly, on three-dimensional aspects, linear problems, and stochastic model building. The text describes probability distributions and densities, including Lebesgue integration, conditional probabilities, conditional expectations, statistical independence, lack of correlation. The book also explains the significance of the moments, the properties of the
Stochastic component mode synthesis
Bah, Mamadou T.; Nair, Prasanth B.; Bhaskar, Atul; Keane, Andy J.
2003-01-01
In this paper, a stochastic component mode synthesis method is developed for the dynamic analysis of large-scale structures with parameter uncertainties. The main idea is to represent each component displacement using a subspace spanned by a set of stochastic basis vectors in the same fashion as in stochastic reduced basis methods [1, 2]. These vectors represent however stochastic modes in contrast to the deterministic modes used in conventional substructuring methods [3]. The Craig-Bampton r...
Modeling stochasticity in biochemical reaction networks
Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.
2016-03-01
Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.
Validity conditions for moment closure approximations in stochastic chemical kinetics
Schnoerr, David; Sanguinetti, Guido; Grima, Ramon
2014-01-01
Approximations based on moment-closure (MA) are commonly used to obtain estimates of the mean molecule numbers and of the variance of fluctuations in the number of molecules of chemical systems. The advantage of this approach is that it can be far less computationally expensive than exact stochastic simulations of the chemical master equation. Here, we numerically study the conditions under which the MA equations yield results reflecting the true stochastic dynamics of the system. We show tha...
Dynamic correlations in stochastic rotation dynamics
Tuzel, Erkan; Ihle, Thomas; Kroll, Daniel M.
2006-01-01
The dynamic structure factor, vorticity and entropy density dynamic correlation functions are measured for Stochastic Rotation Dynamics (SRD), a particle based algorithm for fluctuating fluids. This allows us to obtain unbiased values for the longitudinal transport coefficients such as thermal diffusivity and bulk viscosity. The results are in good agreement with earlier numerical and theoretical results, and it is shown for the first time that the bulk viscosity is indeed zero for this algor...
Quasiparticle spectra via Kolmogorov stochasticity parameter
International Nuclear Information System (INIS)
In this study on three-quasiparticle states, we present results of statistical analysis of the one-quasiparticle (1qp) and three-quasiparticle (3qp) excitations by calculating a stochasticity parameter introduced by Kolmogorov. The objective for this statistical study is to test whether there is any change in the fluctuation properties (i.e. any transition from chaotic to integrable domain or vice versa) while going from the 1qp excitations to the 3qp excitations
The stochastic dynamics of biochemical systems
Challenger, Joseph Daniel
2013-01-01
The topic of this thesis is the stochastic dynamics of biochemical reaction systems. The importance of the intrinsic fluctuations in these systems has become more widely appreciated in recent years, and should be accounted for when modelling such systems mathematically. These models are described as continuous time Markov processes and their dynamics defined by a master equation. Analytical progress is made possible by the use of the van Kampen system-size expansion, which splits the dynamics...
Stochastic strategies in the Minority Game
Hart, M.; Jefferies, P.; Johnson, N. F.; Hui, P. M.
2000-01-01
We show analytically how the fluctuations (i.e. standard deviation) in the Minority Game (MG) can decrease below the random coin-toss limit if the agents use more general, stochastic strategies. This suppression of the standard deviation results from a cancellation between the actions of a crowd, in which agents act collectively and make the same decision, and an anticrowd in which agents act collectively by making the opposite decision to the crowd.
Mellin Transform Method for European Option Pricing with Hull-White Stochastic Interest Rate
Directory of Open Access Journals (Sweden)
Ji-Hun Yoon
2014-01-01
Full Text Available Even though interest rates fluctuate randomly in the marketplace, many option-pricing models do not fully consider their stochastic nature owing to their generally limited impact on option prices. However, stochastic dynamics in stochastic interest rates may have a significant impact on option prices as we take account of issues of maturity, hedging, or stochastic volatility. In this paper, we derive a closed form solution for European options in Black-Scholes model with stochastic interest rate using Mellin transform techniques.
Stochastic transport processes in discrete biological systems
Frehland, Eckart
1982-01-01
These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio logical 'transport systems can be complex. For example, the tr...
Modified diffusion with memory for cyclone track fluctuations
Energy Technology Data Exchange (ETDEWEB)
Bernido, Christopher C., E-mail: cbernido@mozcom.com [Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol 6308 (Philippines); Carpio-Bernido, M. Victoria [Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol 6308 (Philippines); Escobido, Matthew G.O. [W. Sycip Graduate School of Business, Asian Institute of Management, 123 Paseo de Roxas Ave., Makati City 1260 (Philippines)
2014-06-13
Fluctuations in a time series for tropical cyclone tracks are investigated based on an exponentially modified Brownian motion. The mean square displacement (MSD) is evaluated and compared to a recent work on cyclone tracks based on fractional Brownian motion (fBm). Unlike the work based on fBm, the present approach is found to capture the behavior of MSD versus time graphs for cyclones even for large values of time. - Highlights: • Cyclone track fluctuations are modeled as stochastic processes with memory. • Stochastic memory functions beyond fractional Brownian motion are introduced. • The model captures the behavior of cyclone track fluctuations for longer periods of time. • The approach can model time series for other fluctuating phenomena.
Modified diffusion with memory for cyclone track fluctuations
International Nuclear Information System (INIS)
Fluctuations in a time series for tropical cyclone tracks are investigated based on an exponentially modified Brownian motion. The mean square displacement (MSD) is evaluated and compared to a recent work on cyclone tracks based on fractional Brownian motion (fBm). Unlike the work based on fBm, the present approach is found to capture the behavior of MSD versus time graphs for cyclones even for large values of time. - Highlights: • Cyclone track fluctuations are modeled as stochastic processes with memory. • Stochastic memory functions beyond fractional Brownian motion are introduced. • The model captures the behavior of cyclone track fluctuations for longer periods of time. • The approach can model time series for other fluctuating phenomena
Going with the flow: enhancing stochastic switching rates in multi-gyre systems
Heckman, Christoffer R; Schwartz, Ira B
2014-01-01
A control strategy is employed that modifies the stochastic escape times from one basin of attraction to another in a model of a double-gyre flow. The system studied captures the behavior of a large class of fluid flows that circulate and have multiple almost invariant sets. In the presence of noise, a particle in one gyre may randomly switch to an adjacent gyre due to a rare large fluctuation. We show that large fluctuation theory may be applied for controlling autonomous agents in a stochastic environment, in fact leveraging the stochastic- ity to the advantage of switching between regions of interest and concluding that patterns may be broken or held over time as the result of noise. We demonstrate that a controller can effectively manipulate the probability of a large fluctuation, thereby modifying escape times exponentially; this demonstrates the potential of optimal control strategies that work in combination with the endemic stochastic environment. To demonstrate this, stochastic simulations and numeri...
Fluctuation geometry: A counterpart approach of inference geometry
Velazquez, L.
2011-01-01
Starting from an axiomatic perspective, \\emph{fluctuation geometry} is developed as a counterpart approach of inference geometry. This approach is inspired on the existence of a notable analogy between the general theorems of \\emph{inference theory} and the the \\emph{general fluctuation theorems} associated with a parametric family of distribution functions $dp(I|\\theta)=\\rho(I|\\theta)dI$, which describes the behavior of a set of \\emph{continuous stochastic variables} driven by a set of contr...
Semiclassical Aspects of Quantum Mechanics by Classical Fluctuations
De Martino, S; Illuminati, F; Martino, Salvatore De; Siena, Silvio De
1998-01-01
Building on a model recently proposed by F. Calogero, we postulate the existence of a coherent, long--range universal tremor affecting any stable and confined classical dynamical system. Deriving the characteristic fluctuative unit of action for each classical interaction, we obtain in all cases its numerical coincidence with the Planck action constant. We therefore suggest that quantum corrections to classical dynamics can be simulated by suitable classical stochastic fluctuations.
Directory of Open Access Journals (Sweden)
Gabriella Schiera
2015-01-01
Full Text Available Extracellular vesicles are involved in a great variety of physiological events occurring in the nervous system, such as cross talk among neurons and glial cells in synapse development and function, integrated neuronal plasticity, neuronal-glial metabolic exchanges, and synthesis and dynamic renewal of myelin. Many of these EV-mediated processes depend on the exchange of proteins, mRNAs, and noncoding RNAs, including miRNAs, which occurs among glial and neuronal cells. In addition, production and exchange of EVs can be modified under pathological conditions, such as brain cancer and neurodegeneration. Like other cancer cells, brain tumours can use EVs to secrete factors, which allow escaping from immune surveillance, and to transfer molecules into the surrounding cells, thus transforming their phenotype. Moreover, EVs can function as a way to discard material dangerous to cancer cells, such as differentiation-inducing proteins, and even drugs. Intriguingly, EVs seem to be also involved in spreading through the brain of aggregated proteins, such as prions and aggregated tau protein. Finally, EVs can carry useful biomarkers for the early diagnosis of diseases. Herein we summarize possible roles of EVs in brain physiological functions and discuss their involvement in the horizontal spreading, from cell to cell, of both cancer and neurodegenerative pathologies.
Tubule-guided cell-to-cell movement of a plant virus requires class XI myosin motors.
Directory of Open Access Journals (Sweden)
Khalid Amari
2011-10-01
Full Text Available Cell-to-cell movement of plant viruses occurs via plasmodesmata (PD, organelles that evolved to facilitate intercellular communications. Viral movement proteins (MP modify PD to allow passage of the virus particles or nucleoproteins. This passage occurs via several distinct mechanisms one of which is MP-dependent formation of the tubules that traverse PD and provide a conduit for virion translocation. The MP of tubule-forming viruses including Grapevine fanleaf virus (GFLV recruit the plant PD receptors called Plasmodesmata Located Proteins (PDLP to mediate tubule assembly and virus movement. Here we show that PDLP1 is transported to PD through a specific route within the secretory pathway in a myosin-dependent manner. This transport relies primarily on the class XI myosins XI-K and XI-2. Inactivation of these myosins using dominant negative inhibition results in mislocalization of PDLP and MP and suppression of GFLV movement. We also found that the proper targeting of specific markers of the Golgi apparatus, the plasma membrane, PD, lipid raft subdomains within the plasma membrane, and the tonoplast was not affected by myosin XI-K inhibition. However, the normal tonoplast dynamics required myosin XI-K activity. These results reveal a new pathway of the myosin-dependent protein trafficking to PD that is hijacked by GFLV to promote tubule-guided transport of this virus between plant cells.
Spinner, Neil S.; Field, Christopher R.; Hammond, Mark H.; Williams, Bradley A.; Myers, Kristina M.; Lubrano, Adam L.; Rose-Pehrsson, Susan L.; Tuttle, Steven G.
2015-04-01
A 5-cubic meter decompression chamber was re-purposed as a fire test chamber to conduct failure and abuse experiments on lithium-ion batteries. Various modifications were performed to enable remote control and monitoring of chamber functions, along with collection of data from instrumentation during tests including high speed and infrared cameras, a Fourier transform infrared spectrometer, real-time gas analyzers, and compact reconfigurable input and output devices. Single- and multi-cell packages of LiCoO2 chemistry 18650 lithium-ion batteries were constructed and data was obtained and analyzed for abuse and failure tests. Surrogate 18650 cells were designed and fabricated for multi-cell packages that mimicked the thermal behavior of real cells without using any active components, enabling internal temperature monitoring of cells adjacent to the active cell undergoing failure. Heat propagation and video recordings before, during, and after energetic failure events revealed a high degree of heterogeneity; some batteries exhibited short burst of sparks while others experienced a longer, sustained flame during failure. Carbon monoxide, carbon dioxide, methane, dimethyl carbonate, and ethylene carbonate were detected via gas analysis, and the presence of these species was consistent throughout all failure events. These results highlight the inherent danger in large format lithium-ion battery packs with regards to cell-to-cell failure, and illustrate the need for effective safety features.
In Vivo HIV-1 Cell-to-Cell Transmission Promotes Multicopy Micro-compartmentalized Infection
Directory of Open Access Journals (Sweden)
Kenneth M. Law
2016-06-01
Full Text Available HIV-1 infection is enhanced by adhesive structures that form between infected and uninfected T cells called virological synapses (VSs. This mode of transmission results in the frequent co-transmission of multiple copies of HIV-1 across the VS, which can reduce sensitivity to antiretroviral drugs. Studying HIV-1 infection of humanized mice, we measured the frequency of co-transmission and the spatiotemporal organization of infected cells as indicators of cell-to-cell transmission in vivo. When inoculating mice with cells co-infected with two viral genotypes, we observed high levels of co-transmission to target cells. Additionally, micro-anatomical clustering of viral genotypes within lymphoid tissue indicates that viral spread is driven by local processes and not a diffuse viral cloud. Intravital splenic imaging reveals that anchored HIV-infected cells induce arrest of interacting, uninfected CD4+ T cells to form Env-dependent cell-cell conjugates. These findings suggest that HIV-1 spread between immune cells can be anatomically localized into infectious clusters.
International Nuclear Information System (INIS)
Cell-to-cell communication is an important factor for understanding the mechanisms of radiation-induced responses such as bystander effects. In this study, a new mathematical model of intercellular signalling between individual cells in a cellular population is proposed. The authors considered two types of transmission of signals: via culture medium and via gap junction. They focus on the effects that radiation and intercellular signalling have on cell-cycle modification. The cell cycle is represented as a virtual clock that includes several checkpoint pathways within a cyclic process. They also develop a grid model and set up diffusion equations to model the propagation of signals to and from spatially located cells. The authors have also considered the role that DNA damage plays in the cycle of cells which can progress through the cell cycle or stop at the G1, S, G2 or M-phase checkpoints. Results of testing show that the proposed model can simulate intercellular signalling and cell-cycle progression in individual cells during and after irradiation. (authors)
Ding, Chuanlin; Cai, Yihua; Marroquin, Jose; Ildstad, Suzanne T; Yan, Jun
2009-12-01
Plasmacytoid dendritic cells (pDCs) are specialized type I IFN producers, which play an important role in pathogenesis of autoimmune disorders. Dysregulated autoreactive B cell activation is a hallmark in most autoimmune diseases. This study was undertaken to investigate interactions between pDCs and autoreactive B cells. After coculture of autoreactive B cells that recognize self-Ag small nuclear ribonucleoprotein particles with activated pDCs, we found that pDCs significantly enhance autoreactive B cell proliferation, autoantibody production, and survival in response to TLR and BCR stimulation. Neutralization of IFN-alpha/beta and IL-6 abrogated partially pDC-mediated enhancement of autoreactive B cell activation. Transwell studies demonstrated that pDCs could provide activation signals to autoreactive B cells via a cell-to-cell contact manner. The involvement of the ICAM-1-LFA-1 pathway was revealed as contributing to this effect. This in vitro enhancement effect was further demonstrated by an in vivo B cell adoptive transfer experiment, which showed that autoreactive B cell proliferation and activation were significantly decreased in MyD88-deficient mice compared with wild-type mice. These data suggest the dynamic interplay between pDCs and B cells is required for full activation of autoreactive B cells upon TLR or BCR stimulation. PMID:19890051
Competitive learning behavior in a stochastic neural network
Cho, Myoung Won
2015-11-01
Stochastic behavior is a natural and inevitable property of biological neurons. The effect of stochastic behavior or thermal fluctuation in neural firings on the learning process in a neural system is investigated. A learning model, which is derived from the stochastic differential equation of the firing-rate model, is presented as an estimate of the gradient flow of free energy. The model reveals that the learning process becomes competitive owing to the effect of entropy even through the synapse modifications only follow the simple Hebbian rule.
Stochastic samples versus vacuum expectation values in cosmology
Energy Technology Data Exchange (ETDEWEB)
Tsamis, N.C.; Tzetzias, Aggelos [Department of Physics, University of Crete, GR-710 03 Heraklion (Greece); Woodard, R.P., E-mail: tsamis@physics.uoc.gr, E-mail: tzetzias@physics.uoc.gr, E-mail: woodard@phys.ufl.edu [Department of Physics, University of Florida, Gainesville, FL 32611 (United States)
2010-09-01
Particle theorists typically use expectation values to study the quantum back-reaction on inflation, whereas many cosmologists stress the stochastic nature of the process. While expectation values certainly give misleading results for some things, such as the stress tensor, we argue that operators exist for which there is no essential problem. We quantify this by examining the stochastic properties of a noninteracting, massless, minimally coupled scalar on a locally de Sitter background. The square of the stochastic realization of this field seems to provide an example of great relevance for which expectation values are not misleading. We also examine the frequently expressed concern that significant back-reaction from expectation values necessarily implies large stochastic fluctuations between nearby spatial points. Rather than viewing the stochastic formalism in opposition to expectation values, we argue that it provides a marvelously simple way of capturing the leading infrared logarithm corrections to the latter, as advocated by Starobinsky.
Stochastic Samples versus Vacuum Expectation Values in Cosmology
Tsamis, N C; Woodard, R P
2010-01-01
Particle theorists typically use expectation values to study the quantum back-reaction on inflation, whereas many cosmologists stress the stochastic nature of the process. While expectation values certainly give misleading results for some things, such as the stress tensor, we argue that operators exist for which there is no essential problem. We quantify this by examining the stochastic properties of a noninteracting, massless, minimally coupled scalar on a locally de Sitter background. The square of the stochastic realization of this field seems to provide an example of great relevance for which expectation values are not misleading. We also examine the frequently expressed concern that significant back-reaction from expectation values necessarily implies large stochastic fluctuations between nearby spatial points. Rather than viewing the stochastic formalism in opposition to expectation values, we argue that it provides a marvelously simple way of capturing the leading infrared logarithm corrections to the...
A NOTE ON THE STOCHASTIC ROOTS OF STOCHASTIC MATRICES
Institute of Scientific and Technical Information of China (English)
Qi-Ming HE; Eldon GUNN
2003-01-01
In this paper, we study the stochastic root matrices of stochastic matrices. All stochastic roots of 2×2 stochastic matrices are found explicitly. A method based on characteristic polynomial of matrix is developed to find all real root matrices that are functions of the original 3×3 matrix, including all possible (function) stochastic root matrices. In addition, we comment on some numerical methods for computing stochastic root matrices of stochastic matrices.
Stochastic Lie group integrators
Malham, Simon J A
2007-01-01
We present Lie group integrators for nonlinear stochastic differential equations with non-commutative vector fields whose solution evolves on a smooth finite dimensional manifold. Given a Lie group action that generates transport along the manifold, we pull back the stochastic flow on the manifold to the Lie group via the action, and subsequently pull back the flow to the corresponding Lie algebra via the exponential map. We construct an approximation to the stochastic flow in the Lie algebra via closed operations and then push back to the Lie group and then to the manifold, thus ensuring our approximation lies in the manifold. We call such schemes stochastic Munthe-Kaas methods after their deterministic counterparts. We also present stochastic Lie group integration schemes based on Castell--Gaines methods. These involve using an underlying ordinary differential integrator to approximate the flow generated by a truncated stochastic exponential Lie series. They become stochastic Lie group integrator schemes if...
Fluctuation-Enhanced Sensing of Bacterium Odors
Chang, Hung-Chih; King, Maria D; Kwan, Chiman
2009-01-01
The goal of this paper is to explore the possibility to detect and identify bacteria by sensing their odor via fluctuation-enhanced sensing with commercial Taguchi sensors. The fluctuations of the electrical resistance during exposure to different bacterial odors, Escherichia coli and anthrax-surrogate Bacillus subtilis, have been measured and analyzed. In the present study, the simplest method, the measurement and analysis of power density spectra was used. The sensors were run in the normal heated and the sampling-and-hold working modes, respectively. The results indicate that Taguchi sensors used in these fluctuation-enhanced modes are effective tools of bacterium detection and identification even when they are utilizing only the power density spectrum of the stochastic sensor signal.
Energy Technology Data Exchange (ETDEWEB)
X. Frank Xu
2010-03-30
Multiscale modeling of stochastic systems, or uncertainty quantization of multiscale modeling is becoming an emerging research frontier, with rapidly growing engineering applications in nanotechnology, biotechnology, advanced materials, and geo-systems, etc. While tremendous efforts have been devoted to either stochastic methods or multiscale methods, little combined work had been done on integration of multiscale and stochastic methods, and there was no method formally available to tackle multiscale problems involving uncertainties. By developing an innovative Multiscale Stochastic Finite Element Method (MSFEM), this research has made a ground-breaking contribution to the emerging field of Multiscale Stochastic Modeling (MSM) (Fig 1). The theory of MSFEM basically decomposes a boundary value problem of random microstructure into a slow scale deterministic problem and a fast scale stochastic one. The slow scale problem corresponds to common engineering modeling practices where fine-scale microstructure is approximated by certain effective constitutive constants, which can be solved by using standard numerical solvers. The fast scale problem evaluates fluctuations of local quantities due to random microstructure, which is important for scale-coupling systems and particularly those involving failure mechanisms. The Green-function-based fast-scale solver developed in this research overcomes the curse-of-dimensionality commonly met in conventional approaches, by proposing a random field-based orthogonal expansion approach. The MSFEM formulated in this project paves the way to deliver the first computational tool/software on uncertainty quantification of multiscale systems. The applications of MSFEM on engineering problems will directly enhance our modeling capability on materials science (composite materials, nanostructures), geophysics (porous media, earthquake), biological systems (biological tissues, bones, protein folding). Continuous development of MSFEM will
Density dependence and stochastic variation in a newly established population of a small songbird
Sæther, Bernt-Erik; Engen, Steinar; Lande, Russell; Both, Christiaan; Visser, Marcel E.
2002-01-01
Models describing fluctuations in population size should include both density dependence and stochastic effects. We examine the relative contribution of variation in parameters of the expected dynamics as well as demographic and environmental stochasticity to fluctuations in a population of a small passerine bird, the pied flycatcher, that was newly established in a Dutch study area. Using the theta-logistic model of density regulation, we demonstrate that the estimated quasi-stationary distr...
Ramsey Stochastic Model via Multistage Stochastic Programming
Czech Academy of Sciences Publication Activity Database
Kaňková, Vlasta
Vol. Part II. České Budějovice: University of South Bohemia in České Budějovice, Faculty of Economy , 2010 - (Houda, M.; Friebelová, J.), s. 328-333 ISBN 978-80-7394-218-2. [28th International Conference on Mathematical Methods in Economics 2010. České Budějovice (CZ), 08.09.2010-10.09.2010] R&D Projects: GA ČR GAP402/10/0956; GA ČR(CZ) GA402/08/0107; GA ČR GAP402/10/1610 Institutional research plan: CEZ:AV0Z10750506 Keywords : Ramsey stochastic model * Multistage stochastic programming * Confidence intervals * Autoregressive sequences * Stability * Empirical estimates Subject RIV: AH - Economics http://library.utia.cas.cz/separaty/2010/E/kankova-ramsey stochastic model via multistage stochastic programming.pdf
Anisotropies in the Gravitational-Wave Stochastic Background
Olmez, S; Siemens, X
2011-01-01
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a function of angle and frequency.
Anisotropies in the Gravitational-Wave Stochastic Background
Olmez, S.; Mandic, V.; Siemens, X.
2011-01-01
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a ...
Anisotropies in the gravitational-wave stochastic background
International Nuclear Information System (INIS)
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a function of angle and frequency
Extension of Nelson's Stochastic Quantization to Finite Temperature Using Thermo Field Dynamics
Kobayashi, Keita; Yamanaka, Yoshiya
2010-01-01
We present an extension of Nelson's stochastic quantum mechanics to finite temperature. Utilizing the formulation of Thermo Field Dynamics (TFD), we can show that Ito's stochastic equations for tilde and non-tilde particle positions reproduce the TFD-type Schr\\"odinger equation which is equivalent to the Liouville-von Neumann equation. In our formalism, the drift terms in the Ito's stochastic equation have the temperature dependence and the thermal fluctuation is induced through the correlati...
Lee, Soo Young; Gertler, Frank B; Goldberg, Marcia B
2015-11-01
Shigella spp. are intracellular bacterial pathogens that cause diarrhoeal disease in humans. Shigella utilize the host actin cytoskeleton to enter cells, move through the cytoplasm of cells and pass into adjacent cells. Ena/VASP family proteins are highly conserved proteins that participate in actin-dependent dynamic cellular processes. We tested whether Ena/VASP family members VASP (vasodilator-stimulated phosphoprotein), Mena (mammalian-enabled) or EVL (Ena-VASP-like) contribute to Shigella flexneri spread through cell monolayers. VASP and EVL restricted cell-to-cell spread without significantly altering actin-based motility, whereas Mena had no effect on these processes. Phosphorylation of VASP on Ser153, Ser235 and Thr274 regulated its subcellular distribution and function. VASP derivatives that lack the Ena/VASP homology 1 (EVH1) domain or contain a phosphoablative mutation of Ser153 were defective in restricting S. flexneri spread, indicating that the EVH1 domain and phosphorylation on Ser153 are required for this process. The EVH1 domain and Ser153 of VASP were required for VASP localization to focal adhesions, and localization of VASP to focal adhesions and/or the leading edge was required for restriction of spread. The contribution of the EVH1 domain was from both the donor and the recipient cell, whereas the contribution of Ser153 phosphorylation was only from the donor cell. Thus, unlike host proteins characterized in Shigella pathogenesis that promote bacterial spread, VASP and EVL function to limit it. The ability of VASP and EVL to limit spread highlights the critical role of focal adhesion complexes and/or the leading edge in bacterial passage between cells. PMID:26358985
Energy Technology Data Exchange (ETDEWEB)
Takegahara, Yuki; Yamanouchi, Keitaro, E-mail: akeita@mail.ecc.u-tokyo.ac.jp; Nakamura, Katsuyuki; Nakano, Shin-ichi; Nishihara, Masugi
2014-05-15
Intramuscular adipose tissue (IMAT) formation is observed in some pathological conditions such as Duchenne muscular dystrophy (DMD) and sarcopenia. Several studies have suggested that IMAT formation is not only negatively correlated with skeletal muscle mass but also causes decreased muscle contraction in sarcopenia. In the present study, we examined w hether adipocytes affect myogenesis. For this purpose, skeletal muscle progenitor cells were transfected with siRNA of PPARγ (siPPARγ) in an attempt to inhibit adipogenesis. Myosin heavy chain (MHC)-positive myotube formation was promoted in cells transfected with siPPARγ compared to that of cells transfected with control siRNA. To determine whether direct cell-to-cell contact between adipocytes and myoblasts is a prerequisite for adipocytes to affect myogenesis, skeletal muscle progenitor cells were cocultured with pre- or mature adipocytes in a Transwell coculture system. MHC-positive myotube formation was inhibited when skeletal muscle progenitor cells were cocultured with mature adipocytes, but was promoted when they were cocultured with preadipocytes. Similar effects were observed when pre- or mature adipocyte-conditioned medium was used. These results indicate that preadipocytes play an important role in maintaining skeletal muscle mass by promoting myogenesis; once differentiated, the resulting mature adipocytes negatively affect myogenesis, leading to the muscle deterioration observed in skeletal muscle pathologies. - Highlights: • We examined the effects of pre- and mature adipocytes on myogenesis in vitro. • Preadipocytes and mature adipocytes affect myoblast fusion. • Preadipocytes play an important role in maintaining skeletal muscle mass. • Mature adipocytes lead to muscle deterioration observed in skeletal muscle pathologies.
Growth and decay of large fluctuations far from equilibrium
Indian Academy of Sciences (India)
Shrabani Sen; Syed Shahed Riaz; Deb Shankar Ray
2009-09-01
We have explored the weak noise limit of stochastic processes in nonlinear dissipative systems which admit of stable dynamical attractors in absence of noise. An interesting `detailed balance’ like condition in the steady state which is manifested in the time reversal symmetry between growth and decay of fluctuation far from equilibrium, similar to what is observed in thermally equilibrated systems, is demonstrated.
Entanglement and quantum fluctuations
Klyachko, Alexander A.; Shumovsky, Alexander S.
2003-01-01
We discuss maximum entangled states of quantum systems in terms of quantum fluctuations of all essential measurements responsible for manifestation of entanglement. Namely, we consider maximum entanglement as a property of states, for which quantum fluctuations come to their extreme.
International Nuclear Information System (INIS)
The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed
The Potexvirus Alternanthera mosaic virus has multifunctional triple gene block (TGB) proteins, among which our studies have focused on the properties of the TGB1 protein. The TGB1 of AltMV has functions including RNA binding, RNA silencing suppression, and cell-to-cell movement, and is known to for...
Verhoosel, C.V.; Gutiérrez, M. A.; Hulshoff, S.J.
2006-01-01
The field of fluid-structure interaction is combined with the field of stochastics to perform a stochastic flutter analysis. Various methods to directly incorporate the effects of uncertainties in the flutter analysis are investigated. The panel problem with a supersonic fluid flowing over it is considered as a testcase. The stochastic moments (mean, standard deviation, etc.) of the flutter point are computed by an uncertainty analysis. Sensitivity-based methods are used to determine the stoc...
Directory of Open Access Journals (Sweden)
Nicolas Richerioux
Full Text Available Marek's Disease Virus (MDV is an avian alpha-herpesvirus that only spreads from cell-to-cell in cell culture. While its cell-to-cell spread has been shown to be dependent on actin filament dynamics, the mechanisms regulating this spread remain largely unknown. Using a recombinant BAC20 virus expressing an EGFPVP22 tegument protein, we found that the actin cytoskeleton arrangements and cell-cell contacts differ in the center and periphery of MDV infection plaques, with cells in the latter areas showing stress fibers and rare cellular projections. Using specific inhibitors and activators, we determined that Rho-ROCK pathway, known to regulate stress fiber formation, and Rac-PAK, known to promote lamellipodia formation and destabilize stress fibers, had strong contrasting effects on MDV cell-to-cell spread in primary chicken embryo skin cells (CESCs. Inhibition of Rho and its ROCKs effectors led to reduced plaque sizes whereas inhibition of Rac or its group I-PAKs effectors had the adverse effect. Importantly, we observed that the shape of MDV plaques is related to the semi-ordered arrangement of the elongated cells, at the monolayer level in the vicinity of the plaques. Inhibition of Rho-ROCK signaling also resulted in a perturbation of the cell arrangement and a rounding of plaques. These opposing effects of Rho and Rac pathways in MDV cell-to-cell spread were validated for two parental MDV recombinant viruses with different ex vivo spread efficiencies. Finally, we demonstrated that Rho/Rac pathways have opposing effects on the accumulation of N-cadherin at cell-cell contact regions between CESCs, and defined these contacts as adherens junctions. Considering the importance of adherens junctions in HSV-1 cell-to-cell spread in some cell types, this result makes of adherens junctions maintenance one potential and attractive hypothesis to explain the Rho/Rac effects on MDV cell-to-cell spread. Our study provides the first evidence that MDV cell-to-cell
Decoherence of gauge-invariant metric fluctuations during inflation
Bellini, Mauricio
2001-01-01
I study the gauge-invariant fluctuations of the metric during inflation. In the infrared sector the metric fluctuations can be represented by a coarse-grained field. We can write a Schroedinger equation for the coarse-grained metric fluctuations which is related to an effective Hamiltonian for a time dependent parameter of mass harmonic oscillator with a stochastic external force. I study the wave function for a power-law expanding universe. I find that the phase space of the quantum state fo...
Single-molecule stochastic resonance
Hayashi, K; Manosas, M; Huguet, J M; Ritort, F; 10.1103/PhysRevX.2.031012
2012-01-01
Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively folding/unfolding transitions under the action of an applied oscillating mechanical force with optical tweezers. By varying the frequency of the force oscillation, we investigated the folding/unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measured several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins is a good quantifier of the SR. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance match...
STOCHASTIC STABILITY OF NONLINEAR FLUCTUATIONS IN VISCOELASTIC BODIES
Directory of Open Access Journals (Sweden)
A. Chigarev
2014-10-01
Full Text Available The paper considers a wave dynamics of a viscoelastic body (Kelvin – Voight model which is described by a system of nonlinear differential equations in partial derivatives. Transition from a system of partial derivatives to an ordinary differential equations system for the coordinate functions is executed with the purpose to study the system behavior over time using the Bubnov – Galerkin method.A solution for one-dimensional case is obtained, which for negligible viscosity is reduced to the Duffing equation describing behavior of a nonlinear elastic rod in time at external actions. The paper shows that if an external influence is a deterministic periodic pulse process then oscillations starting from some time under certain conditions are transited into regime of deterministic chaos. In this case the stability can be investigated by criteria of probabilistic character. The paper considers stability of a nonlinear dynamical system in chaotic regime based on the mean-square criteria.
Searching for optimal variables in real multivariate stochastic data
International Nuclear Information System (INIS)
By implementing a recent technique for the determination of stochastic eigendirections of two coupled stochastic variables, we investigate the evolution of fluctuations of NO2 concentrations at two monitoring stations in the city of Lisbon, Portugal. We analyze the stochastic part of the measurements recorded at the monitoring stations by means of a method where the two concentrations are considered as stochastic variables evolving according to a system of coupled stochastic differential equations. Analysis of their structure allows for transforming the set of measured variables to a set of derived variables, one of them with reduced stochasticity. For the specific case of NO2 concentration measures, the set of derived variables are well approximated by a global rotation of the original set of measured variables. We conclude that the stochastic sources at each station are independent from each other and typically have amplitudes of the order of the deterministic contributions. Such findings show significant limitations when predicting such quantities. Still, we briefly discuss how predictive power can be increased in general in the light of our methods. -- Highlights: ► Modeling NO2 concentration in Lisbon as coupled Langevin equations. ► Detrending required to remove periodic components. ► Eigenvalues of diffusion matrix suggest transform to decoupled stochastic coordinates.
Fermionic influence on inflationary fluctuations
Boyanovsky, Daniel
2016-04-01
Motivated by apparent persistent large scale anomalies in the cosmic microwave background we study the influence of fermionic degrees of freedom on the dynamics of inflaton fluctuations as a possible source of violations of (nearly) scale invariance on cosmological scales. We obtain the nonequilibrium effective action of an inflaton-like scalar field with Yukawa interactions (YD ,M) to light fermionic degrees of freedom both for Dirac and Majorana fields in de Sitter space-time. The effective action leads to Langevin equations of motion for the fluctuations of the inflaton-like field, with self-energy corrections and a stochastic Gaussian noise. We solve the Langevin equation in the super-Hubble limit implementing a dynamical renormalization group resummation. For a nearly massless inflaton its power spectrum of super-Hubble fluctuations is enhanced, P (k ;η )=(H/2 π )2eγt[-k η ] with γt[-k η ]=1/6 π2 [∑i =1 NDYi,D 2+2 ∑j =1 NMYj,M 2]{ln2[-k η ]-2 ln [-k η ]ln [-k η0]} for ND Dirac and NM Majorana fermions, and η0 is the renormalization scale at which the inflaton mass vanishes. The full power spectrum is shown to be renormalization group invariant. These corrections to the super-Hubble power spectrum entail a violation of scale invariance as a consequence of the coupling to the fermionic fields. The effective action is argued to be exact in the limit of a large number of fermionic fields. A cancellation between the enhancement from fermionic degrees of freedom and suppression from light scalar degrees of freedom conformally coupled to gravity suggests the possibility of a finely tuned supersymmetry among these fields.
Time Evolution of the Dynamical Variables of a Stochastic System.
de la Pena, L.
1980-01-01
By using the method of moments, it is shown that several important and apparently unrelated theorems describing average properties of stochastic systems are in fact particular cases of a general law; this method is applied to generalize the virial theorem and the fluctuation-dissipation theorem to the time-dependent case. (Author/SK)
A contribution to the systematics of stochastic volatility models
Czech Academy of Sciences Publication Activity Database
Slanina, František
2010-01-01
Roč. 389, č. 16 (2010), s. 3230-3239. ISSN 0378-4371 R&D Projects: GA MŠk OC09078 Institutional research plan: CEZ:AV0Z10100520 Keywords : fluctuations * econophysics * stochastic differential equations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.521, year: 2010
Fluctuating hydrodynamics of multi-species reactive mixtures.
Bhattacharjee, Amit Kumar; Balakrishnan, Kaushik; Garcia, Alejandro L; Bell, John B; Donev, Aleksandar
2015-06-14
We formulate and study computationally the fluctuating compressible Navier-Stokes equations for reactive multi-species fluid mixtures. We contrast two different expressions for the covariance of the stochastic chemical production rate in the Langevin formulation of stochastic chemistry, and compare both of them to predictions of the chemical master equation for homogeneous well-mixed systems close to and far from thermodynamic equilibrium. We develop a numerical scheme for inhomogeneous reactive flows, based on our previous methods for non-reactive mixtures [Balakrishnan , Phys. Rev. E 89, 013017 (2014)]. We study the suppression of non-equilibrium long-ranged correlations of concentration fluctuations by chemical reactions, as well as the enhancement of pattern formation by spontaneous fluctuations. Good agreement with available theory demonstrates that the formulation is robust and a useful tool in the study of fluctuations in reactive multi-species fluids. At the same time, several problems with Langevin formulations of stochastic chemistry are identified, suggesting that future work should examine combining Langevin and master equation descriptions of hydrodynamic and chemical fluctuations. PMID:26071701
Fluctuating hydrodynamics of multi-species reactive mixtures
Energy Technology Data Exchange (ETDEWEB)
Bhattacharjee, Amit Kumar; Donev, Aleksandar [Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012 (United States); Balakrishnan, Kaushik [Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109 (United States); Garcia, Alejandro L. [Department of Physics and Astronomy, San Jose State University, 1 Washington Square, San Jose, California 95192 (United States); Bell, John B. [Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States)
2015-06-14
We formulate and study computationally the fluctuating compressible Navier-Stokes equations for reactive multi-species fluid mixtures. We contrast two different expressions for the covariance of the stochastic chemical production rate in the Langevin formulation of stochastic chemistry, and compare both of them to predictions of the chemical master equation for homogeneous well-mixed systems close to and far from thermodynamic equilibrium. We develop a numerical scheme for inhomogeneous reactive flows, based on our previous methods for non-reactive mixtures [Balakrishnan , Phys. Rev. E 89, 013017 (2014)]. We study the suppression of non-equilibrium long-ranged correlations of concentration fluctuations by chemical reactions, as well as the enhancement of pattern formation by spontaneous fluctuations. Good agreement with available theory demonstrates that the formulation is robust and a useful tool in the study of fluctuations in reactive multi-species fluids. At the same time, several problems with Langevin formulations of stochastic chemistry are identified, suggesting that future work should examine combining Langevin and master equation descriptions of hydrodynamic and chemical fluctuations.
A Lagrangian fluctuation-dissipation relation for scalar turbulence
Drivas, Theodore D
2016-01-01
An exact relation is derived between the dissipation of scalar fluctuations and the variance of the scalar inputs (due to initial scalar values, scalar sources, and boundary fluxes) as those are sampled by stochastic Lagrangian trajectories. Previous work on the Kraichnan (1968) model of turbulent scalar advection has shown that anomalous scalar dissipation, non-vanishing in the limit of vanishing viscosity and diffusivity, is in that model due to Lagrangian spontaneous stochasticity, or non-determinism of the Lagrangian particle trajectories in the limit. We here extend this result to scalars advected by any incompressible velocity field. For fluid flows in domains without walls (e.g. periodic boxes) and for insulating/impermeable walls with zero scalar fluxes, we prove that anomalous scalar dissipation and spontaneous stochasticity are completely equivalent. For flows with imposed scalar values or non-vanishing scalar fluxes at the walls, spontaneous stochasticity still implies anomalous scalar dissipation ...
Fluctuations for Galaxy Formation from Inflation Models.
Salopek, David Stephen
The theory of fluctuations for galaxy formation from chaotic inflation models is extended to include the effects of (1) multiple scalar fields, (2) curvature coupling of scalar fields to gravity, (3) nonlinear evolution of long wavelength metric and scalar fields, and (4) stochastic generation of initial conditions. Multiple scalar field models may generate more large scale power than the standard Cold Dark Matter (CDM) model if the Universe undergoes two inflation epochs giving a CDM+ plateau spectrum. If the scalar fields pass over a mogul in the potential, then CDM+ mountain fluctuation spectra may be generated. The chaotic inflation scenario may be housed within a grand unified theory (GUT) framework through a coupling of scalar Higgs field to curvature, -xi Rphi ^2/2. If the curvature coupling is chosen large and negative, xi~ -2 times 10^4, then a more natural value of scalar field self-coupling lambda ~ 0.05 gives the observed level of fluctuations. Radiative corrections to the Higgs potential are small and the reheat temperature is typically high yielding successful baryogenesis. Using Hamilton-Jacobi theory, a general formalism is presented for following the nonlinear evolution of the metric (scalar, vector, and tensor modes) and scalar fields for fluctuations with wavelengths greater than the Hubble radius. Employing an expansion accurate to first order in spatial gradients, the classical momentum constraint of the Arnowitt-Deser -Misner (ADM) formalism may be integrated exactly without recourse to linear perturbation theory. It is shown how nonlinear effects of the metric and scalar fields may be included in Starobinski's formulation of stochastic inflation. Stochastic noise terms in the long wavelength evolution equations model quantum fluctuations that are assumed to become classical at horizon crossing and which then contribute to the background. T = ln(Ha) proves to be a useful time variable because it enables one to solve for scalar field quantum
A Stochastic Employment Problem
Wu, Teng
2013-01-01
The Stochastic Employment Problem(SEP) is a variation of the Stochastic Assignment Problem which analyzes the scenario that one assigns balls into boxes. Balls arrive sequentially with each one having a binary vector X = (X[subscript 1], X[subscript 2],...,X[subscript n]) attached, with the interpretation being that if X[subscript i] = 1 the ball…
Stochastic Convection Parameterizations
Teixeira, Joao; Reynolds, Carolyn; Suselj, Kay; Matheou, Georgios
2012-01-01
computational fluid dynamics, radiation, clouds, turbulence, convection, gravity waves, surface interaction, radiation interaction, cloud and aerosol microphysics, complexity (vegetation, biogeochemistry, radiation versus turbulence/convection stochastic approach, non-linearities, Monte Carlo, high resolutions, large-Eddy Simulations, cloud structure, plumes, saturation in tropics, forecasting, parameterizations, stochastic, radiation-clod interaction, hurricane forecasts
Ole Peters; Alexander Adamou
2011-01-01
It is argued that the simple trading strategy of leveraging or deleveraging an investment in the market portfolio cannot outperform the market. Such stochastic market efficiency places strong constraints on the possible stochastic properties of the market. Historical data confirm the hypothesis.
Stochastic and non-stochastic radiation effects
International Nuclear Information System (INIS)
Both the carcinogenic and the mutagenic effects of ionizing radiation are thought to be induced by 'stochastic' mechanisms of action. It is generally accepted that the number of carcinogenic injury is proportional to the radiation dose applied, and that there is no direct relationship between radiation dose and severity of induced injury, so that no threshold dose can be defined. However, the severity of mutagenic effects, resulting for example from cell death or leading to functional disorders or malformations, has been observed to be a function of the radiation dose, so that in principle threshold doses can be defined. These latter effects are called non-stochastic radiation effects. (orig./DG)
Greenwood, Priscilla E
2016-01-01
This book describes a large number of open problems in the theory of stochastic neural systems, with the aim of enticing probabilists to work on them. This includes problems arising from stochastic models of individual neurons as well as those arising from stochastic models of the activities of small and large networks of interconnected neurons. The necessary neuroscience background to these problems is outlined within the text, so readers can grasp the context in which they arise. This book will be useful for graduate students and instructors providing material and references for applying probability to stochastic neuron modeling. Methods and results are presented, but the emphasis is on questions where additional stochastic analysis may contribute neuroscience insight. An extensive bibliography is included. Dr. Priscilla E. Greenwood is a Professor Emerita in the Department of Mathematics at the University of British Columbia. Dr. Lawrence M. Ward is a Professor in the Department of Psychology and the Brain...
Stochastic quantization and gravity
International Nuclear Information System (INIS)
We give a preliminary account of the application of stochastic quantization to the gravitational field. We start in Section I from Nelson's formulation of quantum mechanics as Newtonian stochastic mechanics and only then introduce the Parisi-Wu stochastic quantization scheme on which all the later discussion will be based. In Section II we present a generalization of the scheme that is applicable to fields in physical (i.e. Lorentzian) space-time and treat the free linearized gravitational field in this manner. The most remarkable result of this is the noncausal propagation of conformal gravitons. Moreover the concept of stochastic gauge-fixing is introduced and a complete discussion of all the covariant gauges is given. A special symmetry relating two classes of covariant gauges is exhibited. Finally Section III contains some preliminary remarks on full nonlinear gravity. In particular we argue that in contrast to gauge fields the stochastic gravitational field cannot be transformed to a Gaussian process. (Author)
Stochastic volatility selected readings
Shephard, Neil
2005-01-01
Neil Shephard has brought together a set of classic and central papers that have contributed to our understanding of financial volatility. They cover stocks, bonds and currencies and range from 1973 up to 2001. Shephard, a leading researcher in the field, provides a substantial introduction in which he discusses all major issues involved. General Introduction N. Shephard. Part I: Model Building. 1. A Subordinated Stochastic Process Model with Finite Variance for Speculative Prices, (P. K. Clark). 2. Financial Returns Modelled by the Product of Two Stochastic Processes: A Study of Daily Sugar Prices, 1961-7, S. J. Taylor. 3. The Behavior of Random Variables with Nonstationary Variance and the Distribution of Security Prices, B. Rosenberg. 4. The Pricing of Options on Assets with Stochastic Volatilities, J. Hull and A. White. 5. The Dynamics of Exchange Rate Volatility: A Multivariate Latent Factor ARCH Model, F. X. Diebold and M. Nerlove. 6. Multivariate Stochastic Variance Models. 7. Stochastic Autoregressive...
Single-molecule Michaelis-Menten kinetics: Effect of substrate fluctuations
International Nuclear Information System (INIS)
In this work we have simulated a stochastic model of single-molecule enzymatic kinetics and applied several statistics to find whether substrate fluctuations can cause significant deviations from the standard single-molecule Michaelis-Menten kinetics. We have found that substrate fluctuations can be detected under favorable conditions (i.e. for fast irreversible binding) when long turnover time trajectories are analyzed. However, for reversible and/or slow intrinsic binding substrate fluctuations may be difficult to observe experimentally
Stochastic energy balancing in substation energy management
Directory of Open Access Journals (Sweden)
Hassan Shirzeh
2015-12-01
Full Text Available In the current research, a smart grid is considered as a network of distributed interacting nodes represented by renewable energy sources, storage and loads. The source nodes become active or inactive in a stochastic manner due to the intermittent nature of natural resources such as wind and solar irradiance. Prediction and stochastic modelling of electrical energy flow is a critical task in such a network in order to achieve load levelling and/or peak shaving in order to minimise the fluctuation between off-peak and peak energy demand. An effective approach is proposed to model and administer the behaviour of source nodes in this grid through a scheduling strategy control algorithm using the historical data collected from the system. The stochastic model predicts future power consumption/injection to determine the power required for storage components. The stochastic models developed based on the Box-Jenkins method predict the most efficient state of the electrical energy flow between a distribution network and nodes and minimises the peak demand and off-peak consumption of acquiring electrical energy from the main grid. The performance of the models is validated against the autoregressive moving average (ARIMA and the Markov chain models used in previous work. The results demonstrate that the proposed method outperforms both the ARIMA and the Markov chain model in terms of forecast accuracy. Results are presented, the strengths and limitations of the approach are discussed, and possible future work is described.
Stochastic models of intracellular calcium signals
International Nuclear Information System (INIS)
Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed
Environmental variation, stochastic extinction, and competitive coexistence.
Adler, Peter B; Drake, John M
2008-11-01
Understanding how environmental fluctuations affect population persistence is essential for predicting the ecological impacts of expected future increases in climate variability. However, two bodies of theory make opposite predictions about the effect of environmental variation on persistence. Single-species theory, common in conservation biology and population viability analyses, suggests that environmental variation increases the risk of stochastic extinction. By contrast, coexistence theory has shown that environmental variation can buffer inferior competitors against competitive exclusion through a storage effect. We reconcile these two perspectives by showing that in the presence of demographic stochasticity, environmental variation can increase the chance of extinction while simultaneously stabilizing coexistence. Our stochastic simulations of a two-species storage effect model reveal a unimodal relationship between environmental variation and coexistence time, implying maximum coexistence at intermediate levels of environmental variation. The unimodal pattern reflects the fact that the stabilizing influence of the storage effect accumulates rapidly at low levels of environmental variation, whereas the risk of extinction due to the combined effects of environmental variation and demographic stochasticity increases most rapidly at higher levels of variation. Future increases in environmental variation could either increase or decrease an inferior competitor's expected persistence time, depending on the distance between the present level of environmental variation and the optimal level anticipated by this theory. PMID:18817458
Stochastic models of intracellular calcium signals
Energy Technology Data Exchange (ETDEWEB)
Rüdiger, Sten, E-mail: sten.ruediger@physik.hu-berlin.de
2014-01-10
Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed.
From cusps to cores: a stochastic model
El-Zant, Amr A.; Freundlich, Jonathan; Combes, Françoise
2016-09-01
The cold dark matter model of structure formation faces apparent problems on galactic scales. Several threads point to excessive halo concentration, including central densities that rise too steeply with decreasing radius. Yet, random fluctuations in the gaseous component can `heat' the centres of haloes, decreasing their densities. We present a theoretical model deriving this effect from first principles: stochastic variations in the gas density are converted into potential fluctuations that act on the dark matter; the associated force correlation function is calculated and the corresponding stochastic equation solved. Assuming a power-law spectrum of fluctuations with maximal and minimal cutoff scales, we derive the velocity dispersion imparted to the halo particles and the relevant relaxation time. We further perform numerical simulations, with fluctuations realized as a Gaussian random field, which confirm the formation of a core within a time-scale comparable to that derived analytically. Non-radial collective modes enhance the energy transport process that erases the cusp, though the parametrizations of the analytical model persist. In our model, the dominant contribution to the dynamical coupling driving the cusp-core transformation comes from the largest scale fluctuations. Yet, the efficiency of the transformation is independent of the value of the largest scale and depends weakly (linearly) on the power-law exponent; it effectively depends on two parameters: the gas mass fraction and the normalization of the power spectrum. This suggests that cusp-core transformations observed in hydrodynamic simulations of galaxy formation may be understood and parametrized in simple terms, the physical and numerical complexities of the various implementations notwithstanding.
Single-particle stochastic heat engine.
Rana, Shubhashis; Pal, P S; Saha, Arnab; Jayannavar, A M
2014-10-01
We have performed an extensive analysis of a single-particle stochastic heat engine constructed by manipulating a Brownian particle in a time-dependent harmonic potential. The cycle consists of two isothermal steps at different temperatures and two adiabatic steps similar to that of a Carnot engine. The engine shows qualitative differences in inertial and overdamped regimes. All the thermodynamic quantities, including efficiency, exhibit strong fluctuations in a time periodic steady state. The fluctuations of stochastic efficiency dominate over the mean values even in the quasistatic regime. Interestingly, our system acts as an engine provided the temperature difference between the two reservoirs is greater than a finite critical value which in turn depends on the cycle time and other system parameters. This is supported by our analytical results carried out in the quasistatic regime. Our system works more reliably as an engine for large cycle times. By studying various model systems, we observe that the operational characteristics are model dependent. Our results clearly rule out any universal relation between efficiency at maximum power and temperature of the baths. We have also verified fluctuation relations for heat engines in time periodic steady state. PMID:25375477
Aerodynamic Noise Prediction Using stochastic Turbulence Modeling
Directory of Open Access Journals (Sweden)
Arash Ahmadzadegan
2008-01-01
Full Text Available Amongst many approaches to determine the sound propagated from turbulent flows, hybrid methods, in which the turbulent noise source field is computed or modeled separately from the far field calculation, are frequently used. For basic estimation of sound propagation, less computationally intensive methods can be developed using stochastic models of the turbulent fluctuations (turbulent noise source field. A simple and easy to use stochastic model for generating turbulent velocity fluctuations called continuous filter white noise (CFWN model was used. This method based on the use of classical Langevian-equation to model the details of fluctuating field superimposed on averaged computed quantities. The resulting sound field due to the generated unsteady flow field was evaluated using Lighthill's acoustic analogy. Volume integral method used for evaluating the acoustic analogy. This formulation presents an advantage, as it confers the possibility to determine separately the contribution of the different integral terms and also integration regions to the radiated acoustic pressure. Our results validated by comparing the directivity and the overall sound pressure level (OSPL magnitudes with the available experimental results. Numerical results showed reasonable agreement with the experiments, both in maximum directivity and magnitude of the OSPL. This method presents a very suitable tool for the noise calculation of different engineering problems in early stages of the design process where rough estimates using cheaper methods are needed for different geometries.
Macroscopic fluctuations theory of aerogel dynamics
Lefevere, Raphael; Zambotti, Lorenzo
2010-01-01
We consider extensive deterministic dynamics made of $N$ particles modeling aerogels under a macroscopic fluctuation theory description. By using a stochastic model describing those dynamics after a diffusive rescaling, we show that the functional giving the exponential decay in $N$ of the probability of observing a given energy and current profile is not strictly convex as a function of the current. This behaviour is caused by the fact that the energy current is carried by particles which may have arbitrary low speed with sufficiently large probability.
Amplitude death of coupled hair bundles with stochastic channel noise
Kim, Kyung-Joong
2014-01-01
Hair cells conduct auditory transduction in vertebrates. In lower vertebrates such as frogs and turtles, due to the active mechanism in hair cells, hair bundles(stereocilia) can be spontaneously oscillating or quiescent. Recently, the amplitude death phenomenon has been proposed [K.-H. Ahn, J. R. Soc. Interface, {\\bf 10}, 20130525 (2013)] as a mechanism for auditory transduction in frog hair-cell bundles, where sudden cessation of the oscillations arises due to the coupling between non-identical hair bundles. The gating of the ion channel is intrinsically stochastic due to the stochastic nature of the configuration change of the channel. The strength of the noise due to the channel gating can be comparable to the thermal Brownian noise of hair bundles. Thus, we perform stochastic simulations of the elastically coupled hair bundles. In spite of stray noisy fluctuations due to its stochastic dynamics, our simulation shows the transition from collective oscillation to amplitude death as inter-bundle coupling str...
Stochastic string motion above and below the world sheet horizon
International Nuclear Information System (INIS)
We study the stochastic motion of a relativistic trailing string in black hole AdS5. The classical string solution develops a world-sheet horizon and we determine the associated Hawking radiation spectrum. The emitted radiation causes fluctuations on the string both above and below the world-sheet horizon. In contrast to standard black hole physics, the fluctuations below the horizon are causally connected with the boundary of AdS. We derive a bulk stochastic equation of motion for the dual string and use the AdS/CFT correspondence to determine the evolution of a fast heavy quark in the strongly coupled N = 4 plasma. We find that the kinetic mass of the quark decreases by ΔM = -(γλ)1/2T/2 while the correlation time of world sheet fluctuations increases by γ1/2.
Control of stochastic resonance in bistable systems by using periodic signals
Institute of Scientific and Technical Information of China (English)
Lin Min; Fang Li-Min; Zheng Yong-Jun
2009-01-01
According to the characteristic structure of double wells in bistable systems, this paper analyses stochastic fluctu-ations in the single potential well and probability transitions between the two potential wells and proposes a method of controlling stochastic resonance by using a periodic signal. Results of theoretical analysis and numerical simulation show that the phenomenon of stochastic resonance happens when the time scales of the periodic signal and the noise-induced probability transitions between the two potential wells achieve stochastic synchronization. By adding a bistable system with a controllable periodic signal, fluctuations in the single potential well can be effectively controlled, thus affecting the probability transitions between the two potential wells. In this way, an effective control can be achieved which allows one to either enhance or realize stochastic resonance.
Control of stochastic resonance in bistable systems by using periodic signals
International Nuclear Information System (INIS)
According to the characteristic structure of double wells in bistable systems, this paper analyses stochastic fluctuations in the single potential well and probability transitions between the two potential wells and proposes a method of controlling stochastic resonance by using a periodic signal. Results of theoretical analysis and numerical simulation show that the phenomenon of stochastic resonance happens when the time scales of the periodic signal and the noise-induced probability transitions between the two potential wells achieve stochastic synchronization. By adding a bistable system with a controllable periodic signal, fluctuations in the single potential well can be effectively controlled, thus affecting the probability transitions between the two potential wells. In this way, an effective control can be achieved which allows one to either enhance or realize stochastic resonance
Institute of Scientific and Technical Information of China (English)
SUN; Zhaogang; ZHANG; Manfu
2005-01-01
The secreted alphaherpesvirus glycoprotein G (gG) works differently from other proteins. Analysis of the role of ILTV gG in virus attachment, penetration, direct cell-to-cell spread (CTCS) and the growth curve showed that gG or its antibody had no effect on ILTV attachment and penetration and that the gG antibody reduced the virus plaque size and the one-step growth curve on chicken embryo liver (CEL) cells, but gG did not affect the virus plaque size or the one-step growth curve on CEL cells. Laser scanning confocal microscopy (LSCM) detection showed that ILTV gG is located in the perinuclear region and the membrane of the CEL cells. These results suggested that ILTV gG might contribute to direct cell-to-cell transmission.
Wyss-Fluehmann, Gaby; Zurbriggen, Andreas; Vandevelde, Marc; Plattet, Philippe
2010-01-01
The mechanism of viral persistence, the driving force behind the chronic progression of inflammatory demyelination in canine distemper virus (CDV) infection, is associated with non-cytolytic viral cell-to-cell spread. Here, we studied the molecular mechanisms of viral spread of a recombinant fluorescent protein-expressing virulent CDV in primary canine astrocyte cultures. Time-lapse video microscopy documented that CDV spread was very efficient using cell processes contacting remote target ce...
Energy Technology Data Exchange (ETDEWEB)
None
1980-01-01
This report covers the studies on basic mechanisms of cellular interactions, utilizing platelets as a model system and, when possible, concentrating on the influence that environmental factors (nutritional, metabolic, cellular, immunologic and others) have on them. The four major sections include: platelet interaction with tumor cells; a model for the study of cell-to-cell interaction; interaction of platelets with vessel walls; and platelet interactions with immune proteins.
Cytoskeleton dynamics: Fluctuations within the network
International Nuclear Information System (INIS)
Out-of-equilibrium systems, such as the dynamics of a living cytoskeleton (CSK), are inherently noisy with fluctuations arising from the stochastic nature of the underlying biochemical and molecular events. Recently, such fluctuations within the cell were characterized by observing spontaneous nano-scale motions of an RGD-coated microbead bound to the cell surface [Bursac et al., Nat. Mater. 4 (2005) 557-561]. While these reported anomalous bead motions represent a molecular level reorganization (remodeling) of microstructures in contact with the bead, a precise nature of these cytoskeletal constituents and forces that drive their remodeling dynamics are largely unclear. Here, we focused upon spontaneous motions of an RGD-coated bead and, in particular, assessed to what extent these motions are attributable to (i) bulk cell movement (cell crawling), (ii) dynamics of focal adhesions, (iii) dynamics of lipid membrane, and/or (iv) dynamics of the underlying actin CSK driven by myosin motors
Fractality feature in oil price fluctuations
Momeni, M; Talebi, K
2008-01-01
The scaling properties of oil price fluctuations are described as a non-stationary stochastic process realized by a time series of finite length. An original model is used to extract the scaling exponent of the fluctuation functions within a non-stationary process formulation. It is shown that, when returns are measured over intervals less than 10 days, the Probability Density Functions (PDFs) exhibit self-similarity and monoscaling, in contrast to the multifractal behavior of the PDFs at macro-scales (typically larger than one month). We find that the time evolution of the distributions are well fitted by a Levy distribution law at micro-scales. The relevance of a Levy distribution is made plausible by a simple model of nonlinear transfer
Stochastic behavior of nanoscale dielectric wall buckling
Friedman, Lawrence H.; Levin, Igor; Cook, Robert F.
2016-03-01
The random buckling patterns of nanoscale dielectric walls are analyzed using a nonlinear multi-scale stochastic method that combines experimental measurements with simulations. The dielectric walls, approximately 200 nm tall and 20 nm wide, consist of compliant, low dielectric constant (low-k) fins capped with stiff, compressively stressed TiN lines that provide the driving force for buckling. The deflections of the buckled lines exhibit sinusoidal pseudoperiodicity with amplitude fluctuation and phase decorrelation arising from stochastic variations in wall geometry, properties, and stress state at length scales shorter than the characteristic deflection wavelength of about 1000 nm. The buckling patterns are analyzed and modeled at two length scales: a longer scale (up to 5000 nm) that treats randomness as a longer-scale measurable quantity, and a shorter-scale (down to 20 nm) that treats buckling as a deterministic phenomenon. Statistical simulation is used to join the two length scales. Through this approach, the buckling model is validated and material properties and stress states are inferred. In particular, the stress state of TiN lines in three different systems is determined, along with the elastic moduli of low-k fins and the amplitudes of the small-scale random fluctuations in wall properties—all in the as-processed state. The important case of stochastic effects giving rise to buckling in a deterministically sub-critical buckling state is demonstrated. The nonlinear multiscale stochastic analysis provides guidance for design of low-k structures with acceptable buckling behavior and serves as a template for how randomness that is common to nanoscale phenomena might be measured and analyzed in other contexts.
Directory of Open Access Journals (Sweden)
Alessia Fabbri
2015-11-01
Full Text Available Eukaryotic cells secrete extracellular vesicles (EVs, either constitutively or in a regulated manner, which represent an important mode of intercellular communication. EVs serve as vehicles for transfer between cells of membrane and cytosolic proteins, lipids and RNA. Furthermore, certain bacterial protein toxins, or possibly their derived messages, can be transferred cell to cell via EVs. We have herein demonstrated that eukaryotic EVs represent an additional route of cell-to-cell propagation for the Escherichia coli protein toxin cytotoxic necrotizing factor 1 (CNF1. Our results prove that EVs from CNF1 pre-infected epithelial cells can induce cytoskeleton changes, Rac1 and NF-κB activation comparable to that triggered by CNF1. The observation that the toxin is detectable inside EVs derived from CNF1-intoxicated cells strongly supports the hypothesis that extracellular vesicles can offer to the toxin a novel route to travel from cell to cell. Since anthrax and tetanus toxins have also been reported to engage in the same process, we can hypothesize that EVs represent a common mechanism exploited by bacterial toxins to enhance their pathogenicity.
Stochastic Processes in Electrochemistry.
Singh, Pradyumna S; Lemay, Serge G
2016-05-17
Stochastic behavior becomes an increasingly dominant characteristic of electrochemical systems as we probe them on the smallest scales. Advances in the tools and techniques of nanoelectrochemistry dictate that stochastic phenomena will become more widely manifest in the future. In this Perspective, we outline the conceptual tools that are required to analyze and understand this behavior. We draw on examples from several specific electrochemical systems where important information is encoded in, and can be derived from, apparently random signals. This Perspective attempts to serve as an accessible introduction to understanding stochastic phenomena in electrochemical systems and outlines why they cannot be understood with conventional macroscopic descriptions. PMID:27120701
Stochastic Schroedinger equations
International Nuclear Information System (INIS)
A derivation of Belavkin's stochastic Schroedinger equations is given using quantum filtering theory. We study an open system in contact with its environment, the electromagnetic field. Continuous observation of the field yields information on the system: it is possible to keep track in real time of the best estimate of the system's quantum state given the observations made. This estimate satisfies a stochastic Schroedinger equation, which can be derived from the quantum stochastic differential equation for the interaction picture evolution of system and field together. Throughout the paper we focus on the basic example of resonance fluorescence
Sequential stochastic optimization
Cairoli, Renzo
1996-01-01
Sequential Stochastic Optimization provides mathematicians and applied researchers with a well-developed framework in which stochastic optimization problems can be formulated and solved. Offering much material that is either new or has never before appeared in book form, it lucidly presents a unified theory of optimal stopping and optimal sequential control of stochastic processes. This book has been carefully organized so that little prior knowledge of the subject is assumed; its only prerequisites are a standard graduate course in probability theory and some familiarity with discrete-paramet
Entropic Stochastic Resonance Driven by Colored Noise
International Nuclear Information System (INIS)
The phenomenon of entropic stochastic resonance (ESR) in a two-dimensional confined system driven by a transverse periodic force is investigated when the colored fluctuation is included in the system. Applying the method of unified colored noise approximation, the approximate Fokker–Planck equation can be derived in the absence of the periodic force. Through the escaping rate of the Brownian particle from one well to the other, the power spectral amplification can be obtained. It is found that increasing the values of the noise correlation time and the signal frequency can suppress the ESR of the system
Stochastic rotation dynamics for nematic liquid crystals
Energy Technology Data Exchange (ETDEWEB)
Lee, Kuang-Wu, E-mail: jeff.lee@ds.mpg.de; Mazza, Marco G., E-mail: marco.mazza@ds.mpg.de [Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen (Germany)
2015-04-28
We introduce a new mesoscopic model for nematic liquid crystals (LCs). We extend the particle-based stochastic rotation dynamics method, which reproduces the Navier-Stokes equation, to anisotropic fluids by including a simplified Ericksen-Leslie formulation of nematodynamics. We verify the applicability of this hybrid model by studying the equilibrium isotropic-nematic phase transition and nonequilibrium problems, such as the dynamics of topological defects and the rheology of sheared LCs. Our simulation results show that this hybrid model captures many essential aspects of LC physics at the mesoscopic scale, while preserving microscopic thermal fluctuations.
Stochastic dynamic model of SARS spreading
Institute of Scientific and Technical Information of China (English)
SHI Yaolin
2003-01-01
Based upon the simulation of the stochastic process of infection, onset and spreading of each SARS patient, a system dynamic model of SRAS spreading is constructed. Data from Vietnam is taken as an example for Monte Carlo test. The preliminary results indicate that the time-dependent infection rate is the most important control factor for SARS spreading. The model can be applied to prediction of the course with fluctuations of the epidemics, if the previous history of the epidemics and the future infection rate under control measures are known.
Stochastic calculus with infinitesimals
Herzberg, Frederik
2013-01-01
Stochastic analysis is not only a thriving area of pure mathematics with intriguing connections to partial differential equations and differential geometry. It also has numerous applications in the natural and social sciences (for instance in financial mathematics or theoretical quantum mechanics) and therefore appears in physics and economics curricula as well. However, existing approaches to stochastic analysis either presuppose various concepts from measure theory and functional analysis or lack full mathematical rigour. This short book proposes to solve the dilemma: By adopting E. Nelson's "radically elementary" theory of continuous-time stochastic processes, it is based on a demonstrably consistent use of infinitesimals and thus permits a radically simplified, yet perfectly rigorous approach to stochastic calculus and its fascinating applications, some of which (notably the Black-Scholes theory of option pricing and the Feynman path integral) are also discussed in the book.
Stochastic processes inference theory
Rao, Malempati M
2014-01-01
This is the revised and enlarged 2nd edition of the authors’ original text, which was intended to be a modest complement to Grenander's fundamental memoir on stochastic processes and related inference theory. The present volume gives a substantial account of regression analysis, both for stochastic processes and measures, and includes recent material on Ridge regression with some unexpected applications, for example in econometrics. The first three chapters can be used for a quarter or semester graduate course on inference on stochastic processes. The remaining chapters provide more advanced material on stochastic analysis suitable for graduate seminars and discussions, leading to dissertation or research work. In general, the book will be of interest to researchers in probability theory, mathematical statistics and electrical and information theory.
Stochastic modeling and performance monitoring of wind farm power production
Milan, Patrick; Peinke, Joachim
2015-01-01
We present a new stochastic approach to describe and remodel the conversion process of a wind farm at a sampling frequency of 1Hz. When conditioning on various wind direction sectors, the dynamics of the conversion process appear as a fluctuating trajectory around an average IEC-like power curve, see section II. Our approach is to consider the wind farm as a dynamical system that can be described as a stochastic drift/diffusion model, where a drift coefficient describes the attraction towards the power curve and a diffusion coefficient quantifies additional turbulent fluctuations. These stochastic coefficients are inserted into a Langevin equation that, once properly adapted to our particular system, models a synthetic signal of power output for any given wind speed/direction signals, see section III. When combined with a pre-model for turbulent wind fluctuations, the stochastic approach models the power output of the wind farm at a sampling frequency of 1Hz using only ten-minute average values of wind speed ...
International Nuclear Information System (INIS)
A brief history of the study of fluctuations in high energy nuclear collisions at the CERN SPS by NA49 is presented. The ideas and the corresponding experimental data on fluctuations are discussed from the point of view of their sensitivity to the onset of deconfinement
Energy Technology Data Exchange (ETDEWEB)
Aggarwal, M.M.; Ahammed, Z.; Angelis, A.L.S.; Antonenko, V.; Arefiev, V.; Astakhov, V.; Avdeitchikov, V.; Awes, T.C.; Baba, P.V.K.S.; Badyal, S.K.; Bathe, S.; Batiounia, B.; Bernier, T.; Bhalla, K.B.; Bhatia, V.S.; Blume, C.; Bucher, D.; Buesching, H.; Carlen, L.; Chattopadhyay, S.; Das, A.C.; Decowski, M.P.; Donni, P.; Dubey, A.K.; Dutta Majumdar, M.R.; Enosawa, K.; Fokin, S.; Frolov, V.; Ganti, M.S.; Garpman, S.; Gavrishcuk, O.; Geurts, F.J.M.; Glasow, R.; Guskov, B.; Gustafsson, H.A.; Gutbrod, H.H.; Hrivnacova, I.; Ippolitov, M.; Kalechofsky, H.; Kamermans, R.; Karadjev, K.; Karpio, K.; Kolb, B.W.; Kosarev, I.; Koutcheryaev, I.; Kugler, A.; Kulinich, P.; Kurata, M.; Lebedev, A.; Loehner, H.; Mahapatra, D.P.; Manko, V.; Martin, M.; Miake, Y.; Mishra, G.C.; Mohanty, B.; Morrison, D.; Mukhopadhayay, D.S.; Naef, H.; Nandi, B.K.; Nayak, S.K.; Nayak, T.K.; Nianine, A.; Nikitine, V.; Nikolaev, S.; Nishimura, S.; Nomokov, P.; Petracek, V.; Plasil, F.; Purschke, M.L.; Rak, J.; Raniwala, R.; Raniwala, S.; Rao, N.K.; Retiere, F.; Reygers, K.; Roland, G.; Rosselet, L.; Roufanov, I.; Rubio, J.M.; Sambyal, S.S.; Santo, R.; Sato, S.; Schlagheck, H.; Schmidt, H.-R.; Schutz, Y.; Shabratova, G.; Sibiriak, I.; Siemiarczuk, T.; Sinha, B.C.; Slavine, N.; Soederstroem, K.; Sood, G.; Soerensen, S.P.; Stankus, P.; Steinberg, P.; Stenlund, E.; Sumbera, M.; Svensson, T.; Trivedi, M.D.; Tsvetkov, A.; Tykarski, L.; Urbahn, J.; Eijinhoven, N. van; Niewenhuizen, G.J. van; Vinogradov, A.; Viyogi, Y.P.; Vodopianov, A.; Voeroes, S.; Wyslouch, B.; Young, G.R
2003-03-10
Event-by-event fluctuations in the multiplicities of charged particles and photons at SPS energies are discussed. Fluctuations are studied by controlling the centrality of the reaction and rapidity acceptance of the detectors. Results are also presented on the event-by-event study of correlations between the multiplicity of charged particles and photons to search for DCC-like signals.
International Nuclear Information System (INIS)
Event-by-event fluctuations in the multiplicities of charged particles and photons at SPS energies are discussed. Fluctuations are studied by controlling the centrality of the reaction and rapidity acceptance of the detectors. Results are also presented on the event-by-event study of correlations between the multiplicity of charged particles and photons to search for DCC-like signals
Dynamics of Double Stochastic Operators
Saburov, Mansoor
2016-03-01
A double stochastic operator is a generalization of a double stochastic matrix. In this paper, we study the dynamics of double stochastic operators. We give a criterion for a regularity of a double stochastic operator in terms of absences of its periodic points. We provide some examples to insure that, in general, a trajectory of a double stochastic operator may converge to any interior point of the simplex.
Stochastic differential equations and applications
Friedman, Avner
2006-01-01
This text develops the theory of systems of stochastic differential equations, and it presents applications in probability, partial differential equations, and stochastic control problems. Originally published in two volumes, it combines a book of basic theory and selected topics with a book of applications.The first part explores Markov processes and Brownian motion; the stochastic integral and stochastic differential equations; elliptic and parabolic partial differential equations and their relations to stochastic differential equations; the Cameron-Martin-Girsanov theorem; and asymptotic es
International Nuclear Information System (INIS)
After a brief review of the BRST formalism and of the Parisi-Wu stochastic quantization method we introduce the BRST stochastic quantization scheme. It allows the second quantization of constrained Hamiltonian systems in a manifestly gauge symmetry preserving way. The examples of the relativistic particle, the spinning particle and the bosonic string are worked out in detail. The paper is closed by a discussion on the interacting field theory associated to the relativistic point particle system. 58 refs. (Author)
What is Stochastic Independence?
Franz, Uwe
2002-01-01
The notion of a tensor product with projections or with inclusions is defined. It is shown that the definition of stochastic independence relies on such a structure and that independence can be defined in an arbitrary category with a tensor product with inclusions or projections. In this context, the classifications of quantum stochastic independence by Muraki, Ben Ghorbal, and Sch\\"urmann become classifications of the tensor products with inclusions for the categories of algebraic probabilit...
Stochastic Processes in Finance
Madan, Dilip B.
2010-01-01
Stochastic processes arising in the description of the risk-neutral evolution of equity prices are reviewed. Starting with Brownian motion, I review extensions to Lévy and Sato processes. These processes have independent increments; the former are homogeneous in time, whereas the latter are inhomogeneous. One-dimensional Markov processes such as local volatility and local Lévy are discussed next. Finally, I take up two forms of stochastic volatility that are due to either space scaling or tim...
Extension of Nelson's stochastic quantization to finite temperature using thermo field dynamics
Energy Technology Data Exchange (ETDEWEB)
Kobayashi, K., E-mail: keita-x@fuji.waseda.jp [Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555 (Japan); Yamanaka, Y., E-mail: yamanaka@waseda.jp [Department of Electronic and Photonic Systems, Waseda University, Tokyo 169-8555 (Japan)
2011-08-29
We present an extension of Nelson's stochastic quantum mechanics to finite temperature. Utilizing the formulation of Thermo Field Dynamics (TFD), we can show that Ito's stochastic equations for tilde and non-tilde particle positions reproduce the TFD-type Schroedinger equation which is equivalent to the Liouville-von Neumann equation. In our formalism, the drift terms in the Ito's stochastic equation have the temperature dependence and the thermal fluctuation is induced through the correlation of the non-tilde and tilde particles. We show that our formalism satisfies the position-momentum uncertainty relation at finite temperature. -- Highlights: → Utilizing TFD, we extend Nelson's stochastic method to finite temperature. → We introduce stochastic equations for tilde and non-tilde particles. → Our stochastic equations can reproduce the TFD-type Schroedinger equation. → Our formalism satisfies the uncertainly relation at finite temperature.
Astrometric effects of a stochastic gravitational wave background
International Nuclear Information System (INIS)
A stochastic gravitational wave background causes the apparent positions of distant sources to fluctuate, with angular deflections of order the characteristic strain amplitude of the gravitational waves. These fluctuations may be detectable with high precision astrometry, as first suggested by Braginsky et al. in 1990. Several researchers have made order of magnitude estimates of the upper limits obtainable on the gravitational wave spectrum Ωgw(f), at frequencies of order f∼1 yr-1, both for the future space-based optical interferometry missions GAIA and SIM, and for very long baseline interferometry in radio wavelengths with the SKA. For GAIA, tracking N∼106 quasars over a time of T∼1 yr with an angular accuracy of Δθ∼10μ as would yield a sensitivity level of Ωgw∼(Δθ)2/(NT2H02)∼10-6, which would be comparable with pulsar timing. In this paper we take a first step toward firming up these estimates by computing in detail the statistical properties of the angular deflections caused by a stochastic background. We compute analytically the two-point correlation function of the deflections on the sphere, and the spectrum as a function of frequency and angular scale. The fluctuations are concentrated at low frequencies (for a scale invariant stochastic background), and at large angular scales, starting with the quadrupole. The magnetic-type and electric-type pieces of the fluctuations have equal amounts of power.
Detection of Non-Equilibrium Fluctuations in Active Gels
Bacanu, Alexandru; Broedersz, Chase; Gladrow, Jannes; Mackintosh, Fred; Schmidt, Christoph; Fakhri, Nikta
Active force generation at the molecular scale in cells can result in stochastic non-equilibrium dynamics on mesoscpopic scales. Molecular motors such as myosin can drive steady-state stress fluctuations in cytoskeletal networks. Here, we present a non-invasive technique to probe non-equilibrium fluctuations in an active gel using single-walled carbon nanotubes (SWNTs). SWNTs are semiflexible polymers with intrinsic fluorescence in the near infrared. Both thermal and active motor-induced forces in the network induce transverse fluctuations of SWNTs. We demonstrate that active driven shape fluctuations of the SWNTs exhibit dynamics that reflect the non-equilibrium activity, in particular the emergence of correlations between the bending modes. We discuss the observation of breaking of detailed balance in this configurational space of the SWNT probes. Supported by National Defense Science and Engineering Graduate Student Fellowship (NDSEG).
Motion of Euglena Gracilis: Active Fluctuations and Velocity Distribution
Romanczuk, Pawel; Scholz, Dimitri; Lobaskin, Vladimir; Schimansky-Geier, Lutz
2015-01-01
We study the velocity distribution of unicellular swimming algae Euglena gracilis using optical microscopy and theory. To characterize a peculiar feature of the experimentally observed distribution at small velocities we use the concept of active fluctuations, which was recently proposed for the description of stochastically self-propelled particles [Romanczuk, P. and Schimansky-Geier, L., Phys. Rev. Lett. 106, 230601 (2011)]. In this concept, the fluctuating forces arise due to internal random performance of the propulsive motor. The fluctuating forces are directed in parallel to the heading direction, in which the propulsion acts. In the theory, we introduce the active motion via the depot model [Schweitzer et al., Phys. Rev. Lett. 80, 23, 5044 (1998)]. We demonstrate that the theoretical predictions based on the depot model with active fluctuations are consistent with the experimentally observed velocity distributions. In addition to the model with additive active noise, we obtain theoretical results for a...
Stochastic versus chaotic dynamics for genetic model - revisited
International Nuclear Information System (INIS)
The stroboscopic maps technique is applied to a model of the dynamics of a single haploid population with a natural selection in a fluctuating environment (genetic model). The stochastic perturbation is replaced by a deterministic chaotic system which - in a certain limit - has properties of a white noise generator. First, the white noise limit is discussed and tested using various statistical methods. The transition from the deterministic chaotic behaviour to the stochastic one, depending on the time scales separation is discussed. We also discuss the results of using different underlying chaotic dynamics on the macro scale properties, especially Lyapunov exponents and dimensions. (author). 30 refs, 18 figs
Hadronic Correlations and Fluctuations
Energy Technology Data Exchange (ETDEWEB)
Koch, Volker
2008-10-09
We will provide a review of some of the physics which can be addressed by studying fluctuations and correlations in heavy ion collisions. We will discuss Lattice QCD results on fluctuations and correlations and will put them into context with observables which have been measured in heavy-ion collisions. Special attention will be given to the QCD critical point and the first order co-existence region, and we will discuss how the measurement of fluctuations and correlations can help in an experimental search for non-trivial structures in the QCD phase diagram.
International Nuclear Information System (INIS)
The SARS-coronavirus (SARS-CoV) is the etiological agent of severe acute respiratory syndrome (SARS). The SARS-CoV spike (S) glycoprotein mediates membrane fusion events during virus entry and virus-induced cell-to-cell fusion. To delineate functional domains of the SARS-CoV S glycoprotein, single point mutations, cluster-to-lysine and cluster-to-alanine mutations, as well as carboxyl-terminal truncations were investigated in transient expression experiments. Mutagenesis of either the coiled-coil domain of the S glycoprotein amino terminal heptad repeat, the predicted fusion peptide, or an adjacent but distinct region, severely compromised S-mediated cell-to-cell fusion, while intracellular transport and cell-surface expression were not adversely affected. Surprisingly, a carboxyl-terminal truncation of 17 amino acids substantially increased S glycoprotein-mediated cell-to-cell fusion suggesting that the terminal 17 amino acids regulated the S fusogenic properties. In contrast, truncation of 26 or 39 amino acids eliminating either one or both of the two endodomain cysteine-rich motifs, respectively, inhibited cell fusion in comparison to the wild-type S. The 17 and 26 amino-acid deletions did not adversely affect S cell-surface expression, while the 39 amino-acid truncation inhibited S cell-surface expression suggesting that the membrane proximal cysteine-rich motif plays an essential role in S cell-surface expression. Mutagenesis of the acidic amino-acid cluster in the carboxyl terminus of the S glycoprotein as well as modification of a predicted phosphorylation site within the acidic cluster revealed that this amino-acid motif may play a functional role in the retention of S at cell surfaces. This genetic analysis reveals that the SARS-CoV S glycoprotein contains extracellular domains that regulate cell fusion as well as distinct endodomains that function in intracellular transport, cell-surface expression, and cell fusion
Directory of Open Access Journals (Sweden)
Shengniao Niu
Full Text Available Hibiscus chlorotic ringspot virus (HCRSV is a member of the genus Carmovirus in the family Tombusviridae. In order to study its coat protein (CP functions on virus replication and movement in kenaf (Hibiscus cannabinus L., two HCRSV mutants, designated as p2590 (A to G in which the first start codon ATG was replaced with GTG and p2776 (C to G in which proline 63 was replaced with alanine, were constructed. In vitro transcripts of p2590 (A to G were able to replicate to a similar level as wild type without CP expression in kenaf protoplasts. However, its cell-to-cell movement was not detected in the inoculated kenaf cotyledons. Structurally the proline 63 in subunit C acts as a kink for β-annulus formation during virion assembly. Progeny of transcripts derived from p2776 (C to G was able to move from cell-to-cell in inoculated cotyledons but its long-distance movement was not detected. Virions were not observed in partially purified mutant virus samples isolated from 2776 (C to G inoculated cotyledons. Removal of the N-terminal 77 amino acids of HCRSV CP by trypsin digestion of purified wild type HCRSV virions resulted in only T = 1 empty virus-like particles. Taken together, HCRSV CP is dispensable for viral RNA replication but essential for cell-to-cell movement, and virion is required for the virus systemic movement. The proline 63 is crucial for HCRSV virion assembly in kenaf plants and the N-terminal 77 amino acids including the β-annulus domain is required in T = 3 assembly in vitro.
Permanyer, Marc; Pauls, Eduardo; Badia, Roger; Esté, José A; Ballana, Ester
2013-01-01
Memory CD4+ T cells are preferentially infected by HIV-1 compared to naïve cells. HIV-1 fusion and entry is a dynamic process in which the cytoskeleton plays an important role by allowing virion internalization and uncoating. Here, we evaluate the role of the cortical actin in cell-to-cell transfer of virus antigens and infection of target CD4+ T cells. Using different actin remodeling compounds we demonstrate that efficiency of HIV-internalization was proportional to the actin polymerization...
Demmin, Gretchen L.; Clase, Amanda C.; Randall, Jessica A.; Enquist, L W; Banfield, Bruce W.
2001-01-01
The alphaherpesvirus Us4 gene encodes glycoprotein G (gG), which is conserved in most viruses of the alphaherpesvirus subfamily. In the swine pathogen pseudorabies virus (PRV), mutant viruses with internal deletions and insertions in the gG gene have shown no discernible phenotypes. We report that insertions in the gG locus of the attenuated PRV strain Bartha show reduced virulence in vivo and are defective in their ability to spread from cell to cell in a cell-type-specific manner. Similar i...
Directory of Open Access Journals (Sweden)
Patrycja Nzounza
Full Text Available BACKGROUND: Cell-to-cell virus transmission of Human immunodeficiency virus type-1 (HIV-1 is predominantly mediated by cellular structures such as the virological synapse (VS. The VS formed between an HIV-1-infected T cell and a target T cell shares features with the immunological synapse (IS. We have previously identified the human homologue of the Drosophila Discs Large (Dlg1 protein as a new cellular partner for the HIV-1 Gag protein and a negative regulator of HIV-1 infectivity. Dlg1, a scaffolding protein plays a key role in clustering protein complexes in the plasma membrane at cellular contacts. It is implicated in IS formation and T cell signaling, but its role in HIV-1 cell-to-cell transmission was not studied before. METHODOLOGY/PRINCIPAL FINDINGS: Kinetics of HIV-1 infection in Dlg1-depleted Jurkat T cells show that Dlg1 modulates the replication of HIV-1. Single-cycle infectivity tests show that this modulation does not take place during early steps of the HIV-1 life cycle. Immunofluorescence studies of Dlg1-depleted Jurkat T cells show that while Dlg1 depletion affects IS formation, it does not affect HIV-1-induced VS formation. Co-culture assays and quantitative cell-to-cell HIV-1 transfer analyses show that Dlg1 depletion does not modify transfer of HIV-1 material from infected to target T cells, or HIV-1 transmission leading to productive infection via cell contact. Dlg1 depletion results in increased virus yield and infectivity of the viral particles produced. Particles with increased infectivity present an increase in their cholesterol content and during the first hours of T cell infection these particles induce higher accumulation of total HIV-1 DNA. CONCLUSION: Despite its role in the IS formation, Dlg1 does not affect the VS and cell-to-cell spread of HIV-1, but plays a role in HIV-1 cell-free virus transmission. We propose that the effect of Dlg1 on HIV-1 infectivity is at the stage of virus entry.
Shi, Yan; Ryabov, Eugene V.; van Wezel, Rene; Li, Chunyang; Jin, Mingfei; Wang, Wenjing; Fan, Zaifeng; Hong, Yiguo
2009-01-01
The biological relationship between suppression of RNA silencing and virus movement poses an intriguing question in virus-plant interactions. Here, we have used a local RNA silencing assay, based on a movement-deficient Turnip crinkle virus TCV/GFPΔCP, to investigate the influence of silencing suppression by three different viral suppressors: the TCV 38K coat protein (CP), the 126K protein of Tobacco mosaic virus (TMV), and P19 of Tomato bushy stunt virus (TBSV) on cell-to-cell movement and l...
Tanaka, Yuki; Suenaga, Tadahiro; Matsumoto, Misako; Seya, Tsukasa; Arase, Hisashi
2013-01-01
The human herpesvirus 6 (HHV-6) envelope glycoprotein gH/gL/gQ1/gQ2 complex associates with host cell CD46 as its cellular receptor. Although gB has been suggested to be involved in HHV-6 infection, its function in membrane fusion has remained unclear. Here, we have developed an HHV-6A (strain GS)and HHV-6B (strain Z29) virus-free cell-to-cell fusion assay and demonstrate that gB and the gH/gL/gQ1/gQ2 complex are the minimum components required for membrane fusion by HHV-6.
Front Propagation in Stochastic Neural Fields
Bressloff, Paul C.
2012-01-01
We analyze the effects of extrinsic multiplicative noise on front propagation in a scalar neural field with excitatory connections. Using a separation of time scales, we represent the fluctuating front in terms of a diffusive-like displacement (wandering) of the front from its uniformly translating position at long time scales, and fluctuations in the front profile around its instantaneous position at short time scales. One major result of our analysis is a comparison between freely propagating fronts and fronts locked to an externally moving stimulus. We show that the latter are much more robust to noise, since the stochastic wandering of the mean front profile is described by an Ornstein-Uhlenbeck process rather than a Wiener process, so that the variance in front position saturates in the long time limit rather than increasing linearly with time. Finally, we consider a stochastic neural field that supports a pulled front in the deterministic limit, and show that the wandering of such a front is now subdiffusive. © 2012 Society for Industrial and Applied Mathematics.
International Nuclear Information System (INIS)
Classical transport of neutral particles in a binary, scattering, stochastic media is discussed. It is assumed that the cross-sections of the constituent materials and their volume fractions are known. The inner structure of the media is stochastic, but there exist a statistical knowledge about the lump sizes, shapes and arrangement. The transmission through the composite media depends on the specific heterogeneous realization of the media. The current research focuses on the averaged transmission through an ensemble of realizations, frm which an effective cross-section for the media can be derived. The problem of one dimensional transport in stochastic media has been studied extensively [1]. In the one dimensional description of the problem, particles are transported along a line populated with alternating material segments of random lengths. The current work discusses transport in two-dimensional stochastic media. The phenomenon that is unique to the multi-dimensional description of the problem is obstacle bypassing. Obstacle bypassing tends to reduce the opacity of the media, thereby reducing its effective cross-section. The importance of this phenomenon depends on the manner in which the obstacles are arranged in the media. Results of transport simulations in multi-dimensional stochastic media are presented. Effective cross-sections derived from the simulations are compared against those obtained for the one-dimensional problem, and against those obtained from effective multi-dimensional models, which are partially based on a Markovian assumption
Quantum Spontaneous Stochasticity
Eyink, Gregory L
2015-01-01
The quantum wave-function of a massive particle with small initial uncertainties (consistent with the uncertainty relation) is believed to spread very slowly, so that the dynamics is deterministic. This assumes that the classical motions for given initial data are unique. In fluid turbulence non-uniqueness due to "roughness" of the advecting velocity field is known to lead to stochastic motion of classical particles. Vanishingly small random perturbations are magnified by Richardson diffusion in a "nearly rough" velocity field so that motion remains stochastic as the noise disappears, or classical spontaneous stochasticity, . Analogies between stochastic particle motion in turbulence and quantum evolution suggest that there should be quantum spontaneous stochasticity (QSS). We show this for 1D models of a particle in a repulsive potential that is "nearly rough" with $V(x) \\sim C|x|^{1+\\alpha}$ at distances $|x|\\gg \\ell$ , for some UV cut-off $\\ell$, and for initial Gaussian wave-packet centered at 0. We consi...
Optimal escapement in stage-structured fisheries with environmental stochasticity.
Holden, Matthew H; Conrad, Jon M
2015-11-01
Stage-structured population models are commonly used to understand fish population dynamics and additionally for stock assessment. Unfortunately, there is little theory on the optimal harvest of stage-structured populations, especially in the presence of stochastic fluctuations. In this paper, we find closed form optimal equilibrium escapement policies for a three-dimensional, discrete-time, stage-structured population model with linear growth, post-harvest nonlinear recruitment, and stage-specific pricing and extend the analytic results to structured populations with environmental stochasticity. When only fishing reproductive adults, stochasticity does not affect optimal escapement policies. However, when harvesting immature fish, the addition of stochasticity can increase or decrease optimal escapement depending on the second and third derivative of the recruitment function. For logistic recruitment, stochasticity reduces optimal immature escapement by a multiplicative factor of one over one plus the variance of the environmental noise. Using hard clam, Mercenaria mercenaria, as an example and assuming Beverton-Holt recruitment, we show that optimal fishing of hard clam targets the immature stage class exclusively and that environmental stochasticity increases optimal escapement for low discount rates and decreases optimal escapement for high discount rates. PMID:26362229
Stochastic gravity: a primer with applications
International Nuclear Information System (INIS)
Stochastic semiclassical gravity of the 1990s is a theory naturally evolved from semiclassical gravity of the 1970s and 1980s. It improves on the semiclassical Einstein equation with source given by the expectation value of the stress-energy tensor of quantum matter fields in curved spacetime by incorporating an additional source due to their fluctuations. In stochastic semiclassical gravity the main object of interest is the noise kernel, the vacuum expectation value of the (operator-valued) stress-energy bi-tensor, and the centrepiece is the (semiclassical) Einstein-Langevin equation. We describe this new theory via two approaches: the axiomatic and the functional. The axiomatic approach is useful to see the structure of the theory from the framework of semiclassical gravity, showing the link from the mean value of the energy-momentum tensor to their correlation functions. The functional approach uses the Feynman-Vernon influence functional and the Schwinger-Keldysh closed-time-path effective action methods which are convenient for computations. It also brings out the open system concepts and the statistical and stochastic contents of the theory such as dissipation, fluctuations, noise and decoherence. We then describe the applications of stochastic gravity to the backreaction problems in cosmology and black-hole physics. In the first problem, we study the backreaction of conformally coupled quantum fields in a weakly inhomogeneous cosmology. In the second problem, we study the backreaction of a thermal field in the gravitational background of a quasi-static black hole (enclosed in a box) and its fluctuations. These examples serve to illustrate closely the ideas and techniques presented in the first part. This topical review is intended as a first introduction providing readers with some basic ideas and working knowledge. Thus, we place more emphasis here on pedagogy than completeness. (Further discussions of ideas, issues and ongoing research topics can be found
Stochastic gravity: a primer with applications
Energy Technology Data Exchange (ETDEWEB)
Hu, B L [Department of Physics, University of Maryland, College Park, MD 20742-4111 (United States); Verdaguer, E [Departament de Fisica Fonamental and CER en Astrofisica Fisica de Particules i Cosmologia, Universitat de Barcelona, Av. Diagonal 647, 08028 Barcelona (Spain)
2003-03-21
Stochastic semiclassical gravity of the 1990s is a theory naturally evolved from semiclassical gravity of the 1970s and 1980s. It improves on the semiclassical Einstein equation with source given by the expectation value of the stress-energy tensor of quantum matter fields in curved spacetime by incorporating an additional source due to their fluctuations. In stochastic semiclassical gravity the main object of interest is the noise kernel, the vacuum expectation value of the (operator-valued) stress-energy bi-tensor, and the centrepiece is the (semiclassical) Einstein-Langevin equation. We describe this new theory via two approaches: the axiomatic and the functional. The axiomatic approach is useful to see the structure of the theory from the framework of semiclassical gravity, showing the link from the mean value of the energy-momentum tensor to their correlation functions. The functional approach uses the Feynman-Vernon influence functional and the Schwinger-Keldysh closed-time-path effective action methods which are convenient for computations. It also brings out the open system concepts and the statistical and stochastic contents of the theory such as dissipation, fluctuations, noise and decoherence. We then describe the applications of stochastic gravity to the backreaction problems in cosmology and black-hole physics. In the first problem, we study the backreaction of conformally coupled quantum fields in a weakly inhomogeneous cosmology. In the second problem, we study the backreaction of a thermal field in the gravitational background of a quasi-static black hole (enclosed in a box) and its fluctuations. These examples serve to illustrate closely the ideas and techniques presented in the first part. This topical review is intended as a first introduction providing readers with some basic ideas and working knowledge. Thus, we place more emphasis here on pedagogy than completeness. (Further discussions of ideas, issues and ongoing research topics can be found
Models of the stochastic activity of neurones
Holden, Arun Vivian
1976-01-01
These notes have grown from a series of seminars given at Leeds between 1972 and 1975. They represent an attempt to gather together the different kinds of model which have been proposed to account for the stochastic activity of neurones, and to provide an introduction to this area of mathematical biology. A striking feature of the electrical activity of the nervous system is that it appears stochastic: this is apparent at all levels of recording, ranging from intracellular recordings to the electroencephalogram. The chapters start with fluctuations in membrane potential, proceed through single unit and synaptic activity and end with the behaviour of large aggregates of neurones: L have chgaen this seque~~e\\/~~';uggest that the interesting behaviourr~f :the nervous system - its individuality, variability and dynamic forms - may in part result from the stochastic behaviour of its components. I would like to thank Dr. Julio Rubio for reading and commenting on the drafts, Mrs. Doris Beighton for producing the fin...
Scaling metabolic rate fluctuations
Labra, Fabio A.; Marquet, Pablo A.; Bozinovic, Francisco
2007-01-01
Complex ecological and economic systems show fluctuations in macroscopic quantities such as exchange rates, size of companies or populations that follow non-Gaussian tent-shaped probability distributions of growth rates with power-law decay, which suggests that fluctuations in complex systems may be governed by universal mechanisms, independent of particular details and idiosyncrasies. We propose here that metabolic rate within individual organisms may be considered as an example of an emerge...
Fluctuations from dissipation in a hot non-Abelian plasma
Litim, Daniel F.; Manuel, Cristina
1999-01-01
We consider a transport equation of the Boltzmann-Langevin type for non-Abelian plasmas close to equilibrium to derive the spectral functions of the underlying microscopic fluctuations from the entropy. The correlator of the stochastic source is obtained from the dissipative processes in the plasma. This approach, based on classical transport theory, exploits the well-known link between a linearized collision integral, the entropy and the spectral functions. Applied to the ultra-soft modes of...
Fluctuations of Multi-Dimensional Kingman-L\\'Evy Processes
Nguyen, Thu
2009-01-01
In the recent paper \\cite{Ng5} we have introduced a method of studying the multi-dimensional Kingman convolutions and their associated stochastic processes by embedding them into some multi-dimensional ordinary convolutions which allows to study multi-dimensional Bessel processes in terms of the cooresponding Brownian motions. Our further aim in this paper is to introduce k-dimensional Kingman-L\\'evy (KL) processes and prove some of their fluctuation properties which are analoguous to that of...
Stochastic models of intracellular transport
Bressloff, Paul C.
2013-01-09
The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.
Stochastic metastability by spontaneous localisation
International Nuclear Information System (INIS)
Nonequilibrium, quasi-stationary states of a one-dimensional “hard” ϕ4 deterministic lattice, initially thermalised to a particular temperature, are investigated when brought into contact with a stochastic thermal bath at lower temperature. For lattice initial temperatures sufficiently higher than those of the bath, energy localisation through the formation of nonlinear excitations of the breather type during the cooling process occurs. These breathers keep the nonlinear lattice away from thermal equilibrium for relatively long times. In the course of time some breathers are destroyed by fluctuations, allowing thus the lattice to reach another nonequilibrium state of lower energy. The number of breathers thus reduces in time; the last remaining breather, however, exhibits amazingly long life-time demonstrated by extensive numerical simulations using a quasi-symplectic integration algorithm. For the single-breather states we have calculated the lattice velocity distribution unveiling non-Gaussian features describable in a closed functional form. Moreover, the influence of the coupling constant on the life-time of a single breather has been explored. The latter exhibits power-law behaviour as the coupling constant approaches the anticontinuous limit
Stochastic dynamics and irreversibility
Tomé, Tânia
2015-01-01
This textbook presents an exposition of stochastic dynamics and irreversibility. It comprises the principles of probability theory and the stochastic dynamics in continuous spaces, described by Langevin and Fokker-Planck equations, and in discrete spaces, described by Markov chains and master equations. Special concern is given to the study of irreversibility, both in systems that evolve to equilibrium and in nonequilibrium stationary states. Attention is also given to the study of models displaying phase transitions and critical phenomema both in thermodynamic equilibrium and out of equilibrium. These models include the linear Glauber model, the Glauber-Ising model, lattice models with absorbing states such as the contact process and those used in population dynamic and spreading of epidemic, probabilistic cellular automata, reaction-diffusion processes, random sequential adsorption and dynamic percolation. A stochastic approach to chemical reaction is also presented.The textbook is intended for students of ...
Stochastic modelling of turbulence
DEFF Research Database (Denmark)
Sørensen, Emil Hedevang Lohse
stochastic turbulence model based on ambit processes is proposed. It is shown how a prescribed isotropic covariance structure can be reproduced. Non-Gaussian turbulence models are obtained through non-Gaussian Lévy bases or through volatility modulation of Lévy bases. As opposed to spectral models operating......This thesis addresses stochastic modelling of turbulence with applications to wind energy in mind. The primary tool is ambit processes, a recently developed class of computationally tractable stochastic processes based on integration with respect to Lévy bases. The subject of ambit processes is...... still undergoing rapid development. Turbulence and wind energy are vast and complicated subjects. Turbulence has structures across a wide range of length and time scales, structures which cannot be captured by a Gaussian process that relies on only second order properties. Concerning wind energy, a wind...
Stochastic Geometric Wave Equations
Czech Academy of Sciences Publication Activity Database
Brzezniak, Z.; Ondreját, Martin
Cham: Springer, 2015, s. 157-188. (Progress in Probability. 68). ISBN 978-3-0348-0908-5. ISSN 1050-6977. [Stochastic analysis and applications at the Centre Interfacultaire Bernoulli, Ecole Polytechnique Fédérale de Lausanne. Lausanne (CH), 09.01.2012-29.6.2012] R&D Projects: GA ČR GAP201/10/0752 Institutional research plan: CEZ:AV0Z10750506 Institutional support: RVO:67985556 Keywords : Stochastic wave equation * Riemannian manifold * homogeneous space Subject RIV: BA - General Mathematics http://library.utia.cas.cz/separaty/2015/SI/ondrejat-0447803.pdf
Stochastic dynamics and control
Sun, Jian-Qiao; Zaslavsky, George
2006-01-01
This book is a result of many years of author's research and teaching on random vibration and control. It was used as lecture notes for a graduate course. It provides a systematic review of theory of probability, stochastic processes, and stochastic calculus. The feedback control is also reviewed in the book. Random vibration analyses of SDOF, MDOF and continuous structural systems are presented in a pedagogical order. The application of the random vibration theory to reliability and fatigue analysis is also discussed. Recent research results on fatigue analysis of non-Gaussian stress proc
Stochastic Electrochemical Kinetics
Beruski, O
2016-01-01
A model enabling the extension of the Stochastic Simulation Algorithm to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a chemical master equation are provided and discussed. The electrochemical driving forces are included in the mathematical framework, and equations are provided for the associated electric responses. The implementation for potentiostatic and galvanostatic systems is presented, with results pointing out the stochastic nature of the algorithm. The electric responses presented are in line with the expected results from the theory, providing a new tool for the modeling of electrochemical kinetics.
Decentralized stochastic control
Speyer, J. L.
1980-01-01
Decentralized stochastic control is characterized by being decentralized in that the information to one controller is not the same as information to another controller. The system including the information has a stochastic or uncertain component. This complicates the development of decision rules which one determines under the assumption that the system is deterministic. The system is dynamic which means the present decisions affect future system responses and the information in the system. This circumstance presents a complex problem where tools like dynamic programming are no longer applicable. These difficulties are discussed from an intuitive viewpoint. Particular assumptions are introduced which allow a limited theory which produces mechanizable affine decision rules.
Kemsawasd, Varongsiri; Branco, Patrícia; Almeida, Maria Gabriela; Caldeira, Jorge; Albergaria, Helena; Arneborg, Nils
2015-07-01
The roles of cell-to-cell contact and antimicrobial peptides in the early death of Lachanchea thermotolerans CBS2803 during anaerobic, mixed-culture fermentations with Saccharomyces cerevisiae S101 were investigated using a commercially available, double-compartment fermentation system separated by cellulose membranes with different pore sizes, i.e. 1000 kDa for mixed- and single-culture fermentations, and 1000 and 3.5-5 kDa for compartmentalized-culture fermentations. SDS-PAGE and gel filtration chromatography were used to determine an antimicrobial peptidic fraction in the fermentations. Our results showed comparable amounts of the antimicrobial peptidic fraction in the inner compartments of the mixed-culture and 1000 kDa compartmentalized-culture fermentations containing L. thermotolerans after 4 days of fermentation, but a lower death rate of L. thermotolerans in the 1000 kDa compartmentalized-culture fermentation than in the mixed-culture fermentation. Furthermore, L. thermotolerans died off even more slowly in the 3.5-5 kDa than in the 1000 kDa compartmentalized-culture fermentation, which coincided with the presence of less of the antimicrobial peptidic fraction in the inner compartment of that fermentation than of the 1000 kDa compartmentalized-culture fermentation. Taken together, these results indicate that the death of L. thermotolerans in mixed cultures with S. cerevisiae is caused by a combination of cell-to-cell contact and antimicrobial peptides. PMID:26109361
International Nuclear Information System (INIS)
The entry of canine distemper virus (CDV) is a multistep process that involves the attachment of CDV hemagglutinin (H) to its cellular receptor, followed by fusion between virus and cell membranes. Our laboratory recently identified PVRL4 (nectin-4) to be the epithelial receptor for measles and canine distemper viruses. In this study, we demonstrate that the V domain of PVRL4 is critical for CDV entry and virus cell-to-cell spread. Furthermore, four key amino acid residues within the V domain of dog PVRL4 and two within the CDV hemagglutinin were shown to be essential for receptor-mediated virus entry. - Highlights: • PVRL4 (nectin-4) is the epithelial cell receptor for measles and canine distemper viruses. • V domain of PVRL4 is critical for CDV entry, cell-to-cell spread, and syncytia formation. • Chimeric PVRL1 backbone substituted with the V domain of PVRL4 can function as a receptor. • Amino acids (F132/P133/A134/G135) within the V domain are essential for PVRL4 receptor activity. • Amino acids (P493/Y539) within CDV H protein are essential for PVRL4 receptor interaction
Mitra, Ruchira; Krishnamurthy, Konduru; Blancaflor, Elison; Payton, Mark; Nelson, Richard S.; Verchot-Lubicz, Jeanmarie
2003-01-01
Potato virus X (PVX) TGBp1, TGBp2, TGBp3, and coat protein are required for virus cell-to-cell movement. Plasmids expressing GFP fused to TGBp2 were bombarded to leaf epidermal cells and GFP:TGBp2 moved cell to cell in Nicotiana benthamiana leaves but not in Nicotiana tabacum leaves. GFP:TGBp2 movement was observed in TGBp1-transgenic N. tabacum, indicating that TGBp2 requires TGBp1 to promote its movement in N. tabacum. In this study, GFP:TGBp2 was detected in a polygonal pattern that resembles the endoplasmic reticulum (ER) network. Amino acid sequence analysis revealed TGBp2 has two putative transmembrane domains. Two mutations separately introduced into the coding sequences encompassing the putative transmembrane domains within the GFP:TGBp2 plasmids and PVX genome, disrupted membrane binding of GFP:TGBp2, inhibited GFP:TGBp2 movement in N. benthamiana and TGBp1-expressing N. tabacum, and inhibited PVX movement. A third mutation, lying outside the transmembrane domains, had no effect on GFP:TGBp2 ER association or movement in N. benthamiana but inhibited GFP:TGBp2 movement in TGBp1-expressing N. tabacum and PVX movement in either Nicotiana species. Thus, ER association of TGBp2 may be required but not be sufficient for virus movement. TGBp2 likely provides an activity for PVX movement beyond ER association.
Energy Technology Data Exchange (ETDEWEB)
Delpeut, Sebastien; Noyce, Ryan S. [The Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5 (Canada); IWK Health Centre, Canadian Center for Vaccinology, Goldbloom Pavilion, Halifax, Nova Scotia, Canada B3H 1X5 (Canada); Richardson, Christopher D., E-mail: chris.richardson@dal.ca [The Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5 (Canada); IWK Health Centre, Canadian Center for Vaccinology, Goldbloom Pavilion, Halifax, Nova Scotia, Canada B3H 1X5 (Canada); The Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia (Canada)
2014-04-15
The entry of canine distemper virus (CDV) is a multistep process that involves the attachment of CDV hemagglutinin (H) to its cellular receptor, followed by fusion between virus and cell membranes. Our laboratory recently identified PVRL4 (nectin-4) to be the epithelial receptor for measles and canine distemper viruses. In this study, we demonstrate that the V domain of PVRL4 is critical for CDV entry and virus cell-to-cell spread. Furthermore, four key amino acid residues within the V domain of dog PVRL4 and two within the CDV hemagglutinin were shown to be essential for receptor-mediated virus entry. - Highlights: • PVRL4 (nectin-4) is the epithelial cell receptor for measles and canine distemper viruses. • V domain of PVRL4 is critical for CDV entry, cell-to-cell spread, and syncytia formation. • Chimeric PVRL1 backbone substituted with the V domain of PVRL4 can function as a receptor. • Amino acids (F132/P133/A134/G135) within the V domain are essential for PVRL4 receptor activity. • Amino acids (P493/Y539) within CDV H protein are essential for PVRL4 receptor interaction.
Stochastic models, estimation, and control
Maybeck, Peter S
1982-01-01
This volume builds upon the foundations set in Volumes 1 and 2. Chapter 13 introduces the basic concepts of stochastic control and dynamic programming as the fundamental means of synthesizing optimal stochastic control laws.
STOCHASTIC COOLING FOR BUNCHED BEAMS.
Energy Technology Data Exchange (ETDEWEB)
BLASKIEWICZ, M.
2005-05-16
Problems associated with bunched beam stochastic cooling are reviewed. A longitudinal stochastic cooling system for RHIC is under construction and has been partially commissioned. The state of the system and future plans are discussed.
Rectifying thermal fluctuations: Minimal pumping and Maxwell's demon
Mandal, Dibyendu
Molecular complexes with movable components form the basis of nanoscale machines. Their inherent stochastic nature makes it a challenge to generate any controllable movement. Rather than fighting these fluctuations, one can utilize them by the periodic modulation of system parameters, or stochastic pumping. For the no-pumping theorem (NPT), which establishes minimal conditions for directed pumping, we present a simplified proof using an elementary graph theoretical construction. Motivated by recent experiments, we propose a new class of "hybrid" models combining elements of both the purely discrete and purely continuous descriptions prevalent in the field. We formulate the NPT in this hybrid framework to give a detailed justification of the original experiment observation. We also present an extension of the NPT to open stochastic systems. Next we consider the paradox of "Maxwell's demon," an imaginary intelligent being that rectifies thermal fluctuations in a manner that seems to violate the second law of thermodynamics. We present two exactly solvable, autonomous models that can reproduce the actions of the demon. Of necessity, both of these models write information on a memory device as part of their operation. By exposing their explicit, transparent mechanisms, our models offer simple paradigms to investigate the autonomous rectification of thermal fluctuations and the thermodynamics of information processing.
Fluctuations in the Kinetics of Linear Protein Self-Assembly
Michaels, Thomas C. T.; Dear, Alexander J.; Kirkegaard, Julius B.; Saar, Kadi L.; Weitz, David A.; Knowles, Tuomas P. J.
2016-06-01
Biological systems are characterized by compartmentalization from the subcellular to the tissue level, and thus reactions in small volumes are ubiquitous in living systems. Under such conditions, statistical number fluctuations, which are commonly negligible in bulk reactions, can become dominant and lead to stochastic behavior. We present here a stochastic model of protein filament formation in small volumes. We show that two principal regimes emerge for the system behavior, a small fluctuation regime close to bulk behavior and a large fluctuation regime characterized by single rare events. Our analysis shows that in both regimes the reaction lag-time scales inversely with the system volume, unlike in bulk. Finally, we use our stochastic model to connect data from small-volume microdroplet experiments of amyloid formation to bulk aggregation rates, and show that digital analysis of an ensemble of protein aggregation reactions taking place under microconfinement provides an accurate measure of the rate of primary nucleation of protein aggregates, a process that has been challenging to quantify from conventional bulk experiments.
Stochastic entrainment of a stochastic oscillator.
Wang, Guanyu; Peskin, Charles S
2015-11-01
In this work, we consider a stochastic oscillator described by a discrete-state continuous-time Markov chain, in which the states are arranged in a circle, and there is a constant probability per unit time of jumping from one state to the next in a specified direction around the circle. At each of a sequence of equally spaced times, the oscillator has a specified probability of being reset to a particular state. The focus of this work is the entrainment of the oscillator by this periodic but stochastic stimulus. We consider a distinguished limit, in which (i) the number of states of the oscillator approaches infinity, as does the probability per unit time of jumping from one state to the next, so that the natural mean period of the oscillator remains constant, (ii) the resetting probability approaches zero, and (iii) the period of the resetting signal approaches a multiple, by a ratio of small integers, of the natural mean period of the oscillator. In this distinguished limit, we use analytic and numerical methods to study the extent to which entrainment occurs. PMID:26651734
Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.
Directory of Open Access Journals (Sweden)
Andrea Maesani
2015-11-01
Full Text Available The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.
Fermionic influence (action) on inflationary fluctuations
Boyanovsky, Daniel
2016-01-01
Motivated by apparent persistent large scale anomalies in the CMB we study the influence of fermionic degrees of freedom on the dynamics of inflaton fluctuations as a possible source of violations of (nearly) scale invariance on cosmological scales. We obtain the non-equilibrium effective action of an inflaton-like scalar field with Yukawa interactions ($Y_{D,M}$) to light \\emph{fermionic} degrees of freedom both for Dirac and Majorana fields in de Sitter space-time. The effective action leads to Langevin equations of motion for the fluctuations of the inflaton-like field, with self-energy corrections and a stochastic gaussian noise. We solve the Langevin equation in the super-Hubble limit implementing a dynamical renormalization group resummation. For a nearly massless inflaton its power spectrum of super Hubble fluctuations is \\emph{enhanced}, $\\mathcal{P}(k;\\eta) = (\\frac{H}{2\\pi})^2\\,e^{\\gamma_t[-k\\eta] }$ with $\\gamma_t[-k\\eta] = \\frac{1}{6\\pi^2} \\Big[\\sum_{i=1}^{N_D}{Y^2_{i,D}}+2\\sum_{j=1}^{N_M}{Y^2_{j,...
Effects of demographic stochasticity on biological community assembly on evolutionary time scales
Murase, Yohsuke
2010-04-13
We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.
Stochastic resonance in a generalized Von Foerster population growth model
International Nuclear Information System (INIS)
The stochastic dynamics of a population growth model, similar to the Von Foerster model for human population, is studied. The influence of fluctuating environment on the carrying capacity is modeled as a multiplicative dichotomous noise. It is established that an interplay between nonlinearity and environmental fluctuations can cause single unidirectional discontinuous transitions of the mean population size versus the noise amplitude, i.e., an increase of noise amplitude can induce a jump from a state with a moderate number of individuals to that with a very large number, while by decreasing the noise amplitude an opposite transition cannot be effected. An analytical expression of the mean escape time for such transitions is found. Particularly, it is shown that the mean transition time exhibits a strong minimum at intermediate values of noise correlation time, i.e., the phenomenon of stochastic resonance occurs. Applications of the results in ecology are also discussed
Algorithm refinement for stochastic partial differential equations I. linear diffusion
Alexander, F J; Tartakovsky, D M
2002-01-01
A hybrid particle/continuum algorithm is formulated for Fickian diffusion in the fluctuating hydrodynamic limit. The particles are taken as independent random walkers; the fluctuating diffusion equation is solved by finite differences with deterministic and white-noise fluxes. At the interface between the particle and continuum computations the coupling is by flux matching, giving exact mass conservation. This methodology is an extension of Adaptive Mesh and Algorithm Refinement to stochastic partial differential equations. Results from a variety of numerical experiments are presented for both steady and time-dependent scenarios. In all cases the mean and variance of density are captured correctly by the stochastic hybrid algorithm. For a nonstochastic version (i.e., using only deterministic continuum fluxes) the mean density is correct, but the variance is reduced except in particle regions away from the interface. Extensions of the methodology to fluid mechanics applications are discussed.
Pushed beyond the brink: Allee effects, environmental stochasticity, and extinction
Roth, Gregory; Schreiber, Sebastian J.
2014-01-01
To understand the interplay between environmental stochasticity and Allee effects, we analyse persistence, asymptotic extinction, and conditional persistence for stochastic difference equations. Our analysis reveals that persistence requires that the geometric mean of fitness at low densities is greater than one. When this geometric mean is less than one, asymptotic extinction occurs with high probability for low initial population densities. Additionally, if the population only experiences positive density-dependent feedbacks, conditional persistence occurs provided the geometric mean of fitness at high population densities is greater than one. However, if the population experiences both positive and negative density-dependent feedbacks, conditional persistence only occurs if environmental fluctuations are sufficiently small. We illustrate counter-intuitively that environmental fluctuations can increase the probability of persistence when populations are initially at low densities, and can cause asymptotic extinction of populations experiencing intermediate predation rates despite conditional persistence occurring at higher predation rates. PMID:25275425
Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion
Del Razo, Mauricio J; Qian, Hong; Lin, Guang
2014-01-01
The currently existing theory of fluorescence correlation spectroscopy(FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems here are no closed solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Our results show that current linear FCS theory could be adequate ...
Stochastic Contraction in Riemannian Metrics
Pham, Quang-Cuong; Slotine, Jean-Jacques
2013-01-01
Stochastic contraction analysis is a recently developed tool for studying the global stability properties of nonlinear stochastic systems, based on a differential analysis of convergence in an appropriate metric. To date, stochastic contraction results and sharp associated performance bounds have been established only in the specialized context of state-independent metrics, which restricts their applicability. This paper extends stochastic contraction analysis to the case of general time- and...
Stochastically forced dislocation density distribution in plastic deformation
Chattopadhyay, Amit K
2016-01-01
The dynamical evolution of dislocations in plastically deformed metals is controlled by both deterministic factors arising out of applied loads and stochastic effects appearing due to fluctuations of internal stress. Such type of stochastic dislocation processes and the associated spatially inhomogeneous modes lead to randomness in the observed deformation structure. Previous studies have analyzed the role of randomness in such textural evolution but none of these models have considered the impact of a finite decay time (all previous models assumed instantaneous relaxation which is "unphysical") of the stochastic perturbations in the overall dynamics of the system. The present article bridges this knowledge gap by introducing a colored noise in the form of an Ornstein-Uhlenbeck noise in the analysis of a class of linear and nonlinear Wiener and Ornstein-Uhlenbeck processes that these structural dislocation dynamics could be mapped on to. Based on an analysis of the relevant Fokker-Planck model, our results sh...
Turning the resistive MHD into a stochastic field theory
Directory of Open Access Journals (Sweden)
M. Materassi
2008-08-01
Full Text Available Classical systems stirred by random forces of given statistics may be described via a path integral formulation in which their degrees of freedom are stochastic variables themselves, undergoing a multiple-history probabilistic evolution. This framework seems to be easily applicable to resistive Magneto-Hydro-Dynamics (MHD. Indeed, MHD equations form a dynamic system of classical variables in which the terms representing the density, the pressure and the conductivity of the plasma are irregular functions of space and time when turbulence occurs. By treating those irregular terms as random stirring forces, it is possible to introduce a Stochastic Field Theory which should represent correctly the impulsive phenomena caused by the spece- and time-irregularity of plasma turbulence. This work is motivated by the recent observational evidences of the crucial role played by stochastic fluctuations in space plasmas.
Fully nonlinear dynamics of stochastic thin-film dewetting.
Nesic, S; Cuerno, R; Moro, E; Kondic, L
2015-12-01
The spontaneous formation of droplets via dewetting of a thin fluid film from a solid substrate allows materials nanostructuring. Often, it is crucial to be able to control the evolution, and to produce patterns characterized by regularly spaced droplets. While thermal fluctuations are expected to play a role in the dewetting process, their relevance has remained poorly understood, particularly during the nonlinear stages of evolution that involve droplet formation. Within a stochastic lubrication framework, we show that thermal noise substantially influences the process of droplets formation. Stochastic systems feature a smaller number of droplets with a larger variability in size and space distribution, when compared to their deterministic counterparts. Finally, we discuss the influence of stochasticity on droplet coarsening for asymptotically long times. PMID:26764623
Fully nonlinear dynamics of stochastic thin-film dewetting
Nesic, S.; Cuerno, R.; Moro, E.; Kondic, L.
2015-12-01
The spontaneous formation of droplets via dewetting of a thin fluid film from a solid substrate allows materials nanostructuring. Often, it is crucial to be able to control the evolution, and to produce patterns characterized by regularly spaced droplets. While thermal fluctuations are expected to play a role in the dewetting process, their relevance has remained poorly understood, particularly during the nonlinear stages of evolution that involve droplet formation. Within a stochastic lubrication framework, we show that thermal noise substantially influences the process of droplets formation. Stochastic systems feature a smaller number of droplets with a larger variability in size and space distribution, when compared to their deterministic counterparts. Finally, we discuss the influence of stochasticity on droplet coarsening for asymptotically long times.
Regular and stochastic behavior of Parkinsonian pathological tremor signals
Yulmetyev, R M; Panischev, O Y; Hänggi, P; Timashev, S F; Vstovsky, G V; Yulmetyev, Renat M.; Demin, Sergey A.; Panischev, Oleg Yu.; H\\"anggi, Peter; Timashev, Serge F.; Vstovsky, Grigoriy V.
2006-01-01
Regular and stochastic behavior in the time series of Parkinsonian pathological tremor velocity is studied on the basis of the statistical theory of discrete non-Markov stochastic processes and flicker-noise spectroscopy. We have developed a new method of analyzing and diagnosing Parkinson's disease (PD) by taking into consideration discreteness, fluctuations, long- and short-range correlations, regular and stochastic behavior, Markov and non-Markov effects and dynamic alternation of relaxation modes in the initial time signals. The spectrum of the statistical non-Markovity parameter reflects Markovity and non-Markovity in the initial time series of tremor. The relaxation and kinetic parameters used in the method allow us to estimate the relaxation scales of diverse scenarios of the time signals produced by the patient in various dynamic states. The local time behavior of the initial time correlation function and the first point of the non-Markovity parameter give detailed information about the variation of p...
Backreaction and Stochastic Effects in Single Field Inflation
Levasseur, Laurence Perreault
2014-01-01
The formalism of Stochastic Inflation is a powerful tool for analyzing backreaction of cosmological perturbations, and making precise predictions for inflationary observables. We demonstrate this with the simple m^2phi^2 model of inflation, wherein we obtain an effective field theory for IR modes of the inflaton, which remains coupled to UV modes through a classical noise. We compute slow-roll corrections to the evolution of UV modes (i.e. quantum fluctuations), and track this effect from the UV theory to the IR theory, where it manifests as a correction to the classical noise. We compute the stochastic correction to the spectral index of primordial perturbations, finding a small effect, and discuss models in which this effect can become large. We extend our analysis to tensor modes, and demonstrate that the stochastic approach allows us to recover the standard tensor tilt $n_T$, plus corrections.
Alfonso, L.
2015-01-01
In cloud modeling studies, the time evolution of droplet size distributions due to collision–coalescence events is usually modeled with the Smoluchowski coagulation equation, also known as the kinetic collection equation (KCE). However, the KCE is a deterministic equation with no stochastic fluctuations or correlations. Therefore, the full stochastic description of cloud droplet growth in a coalescing system must be obtained from the solution of the multivariate master equat...
Stochastic thermodynamics in the quantum regime: From quantum measurement to quantum trajectories
Elouard, Cyril; Marti, David Herrera; Clusel, Maxime; Auffèves, Alexia
2016-01-01
This article sets up a new formalism to investigate stochastic thermodynamics of out-of-equilibrium quantum systems, where stochasticity primarily comes from quantum measurement. In the absence of any bath, we define a purely quantum component to heat exchange, that corresponds to energy fluctuations induced by measurement back-action. By providing a central position to quantum measurement, our formalism bridges the gap between quantum optics and quantum thermodynamics: Thermal signatures of ...
Linear response in stochastic mean-field theories and the onset of instabilities
International Nuclear Information System (INIS)
The small amplitude response of stochastic one-body theories, such as the Boltzmann-Langevin approach is studied. Whereas the two-time correlation function only describes the propagation of fluctuations initially present, the equal-time correlation function is related to the source of stochasticity. For stable systems it yields the Einstein relation, while for unstable systems it determines the growth of the instabilities. These features are illustrated for unstable nuclear matter in two dimensions. (author) 14 refs.; 5 figs
Non-equilibrium thermodynamics of stochastic systems with odd and even variables
Spinney, Richard E.; Ford, Ian J.
2012-01-01
The total entropy production of stochastic systems can be divided into three quantities. The first corresponds to the excess heat, whilst the second two comprise the house-keeping heat. We denote these two components the transient and generalised house-keeping heat and we obtain an integral fluctuation theorem for the latter, valid for all Markovian stochastic dynamics. A previously reported formalism is obtained when the stationary probability distribution is symmetric for all variables that...
Collaborative tracking and control in time-dependent stochastic dynamical systems
Forgoston, Eric; Hsieh, Ani; Schwartz, Ira; Yecko, Philip
2013-11-01
We consider the problem of stochastic prediction and control in a time-dependent stochastic environment, such as the ocean, where escape from an almost invariant region occurs due to random fluctuations. Lagrangian Coherent Structures (LCS) are found using collaborative tracking, and a control policy is formulated that utilizes knowledge of the LCS. The control strategy enables mobile sensors to autonomously maintain a desired distribution in the environment, and is evaluated with experimental data. Research supported by the Office of Naval Research.
Stochastic quantization: Stabilizing quantum models
International Nuclear Information System (INIS)
Osterwalder-Schrader positivity is shown to be fulfilled for stochastically quantized lattice gauge theories, spin models and P(phi) interactions bounded from below. Problems arising are discussed. A stochastic equation is derived to stabilize the quantum Einstein gravity. It is shown that the stochastic quantization of the Yang-Mills theory leads to a well-defined semiclassical expansion. (orig.)
Stochastic quantization of Proca field
International Nuclear Information System (INIS)
We discuss the complications that arise in the application of Nelson's stochastic quantization scheme to classical Proca field. One consistent way to obtain spin-one massive stochastic field is given. It is found that the result of Guerra et al on the connection between ground state stochastic field and the corresponding Euclidean-Markov field extends to the spin-one case. (author)
Stochastic effects on biodiversity in cyclic coevolutionary dynamics
Reichenbach, Tobias; Frey, Erwin
2008-01-01
Finite-size fluctuations arising in the dynamics of competing populations may have dramatic influence on their fate. As an example, in this article, we investigate a model of three species which dominate each other in a cyclic manner. Although the deterministic approach predicts (neutrally) stable coexistence of all species, for any finite population size, the intrinsic stochasticity unavoidably causes the eventual extinction of two of them.
An effective stochastic semiclassical theory for the gravitational field
Martin, Rosario; Verdaguer, Enric
1998-01-01
Assuming that the mechanism proposed by Gell-Mann and Hartle works as a mechanism for decoherence and classicalization of the metric field, we formally derive the form of an effective theory for the gravitational field in a semiclassical regime. This effective theory takes the form of the usual semiclassical theory of gravity, based on the semiclassical Einstein equation, plus a stochastic correction which accounts for the back reaction of the lowest order matter stress-energy fluctuations.
Electron density fluctuations accelerate the branching of streamer discharges in air
Luque, A
2011-01-01
Branching is an essential element of streamer discharge dynamics but today it is understood only qualitatively. The variability and irregularity observed in branched streamer trees suggest that stochastic terms are relevant for the description of streamer branching. We here consider electron density fluctuations due to the discrete particle number as a source of stochasticity in positive streamers in air at standard temperature and pressure. We derive a quantitative estimate for the branching distance that agrees within a factor of 2 with experimental values. As branching without noise would occur later, if at all, we conclude that stochastic particle noise is relevant for streamer branching in air at atmospheric pressure.
The stochastic quality calculus
DEFF Research Database (Denmark)
Zeng, Kebin; Nielson, Flemming; Nielson, Hanne Riis
We introduce the Stochastic Quality Calculus in order to model and reason about distributed processes that rely on each other in order to achieve their overall behaviour. The calculus supports broadcast communication in a truly concurrent setting. Generally distributed delays are associated with...
Stochastic Control - External Models
DEFF Research Database (Denmark)
Poulsen, Niels Kjølstad
2005-01-01
This note is devoted to control of stochastic systems described in discrete time. We are concerned with external descriptions or transfer function model, where we have a dynamic model for the input output relation only (i.e.. no direct internal information). The methods are based on LTI systems and...
Stochastic nonlinear beam equations
Czech Academy of Sciences Publication Activity Database
Brzezniak, Z.; Maslowski, Bohdan; Seidler, Jan
2005-01-01
Roč. 132, č. 1 (2005), s. 119-149. ISSN 0178-8051 R&D Projects: GA ČR(CZ) GA201/01/1197 Institutional research plan: CEZ:AV0Z10190503 Keywords : stochastic beam equation * stability Subject RIV: BA - General Mathematics Impact factor: 0.896, year: 2005
The stochastic quality calculus
DEFF Research Database (Denmark)
Zeng, Kebin; Nielson, Flemming; Nielson, Hanne Riis
2014-01-01
We introduce the Stochastic Quality Calculus in order to model and reason about distributed processes that rely on each other in order to achieve their overall behaviour. The calculus supports broadcast communication in a truly concurrent setting. Generally distributed delays are associated...
International Nuclear Information System (INIS)
Major headings in this review include: proton sources; antiproton production; antiproton sources and Liouville, the role of the Debuncher; transverse stochastic cooling, time domain; the accumulator; frequency domain; pickups and kickers; Fokker-Planck equation; calculation of constants in the Fokker-Planck equation; and beam feedback
Jiang, Yuming
2009-01-01
Network calculus, a theory dealing with queuing systems found in computer networks, focuses on performance guarantees. This title presents a comprehensive treatment for the stochastic service-guarantee analysis research and provides basic introductory material on the subject, as well as discusses the various researches in the area.
Focus on stochastic thermodynamics
Van den Broeck, Christian; Sasa, Shin-ichi; Seifert, Udo
2016-02-01
We introduce the thirty papers collected in this ‘focus on’ issue. The contributions explore conceptual issues within and around stochastic thermodynamics, use this framework for the theoretical modeling and experimental investigation of specific systems, and provide further perspectives on and for this active field.
Stochastic population oscillations in spatial predator-prey models
Energy Technology Data Exchange (ETDEWEB)
Taeuber, Uwe C, E-mail: tauber@vt.edu [Department of Physics, Virginia Tech, Blacksburg, VA 24061-0435 (United States)
2011-09-15
It is well-established that including spatial structure and stochastic noise in models for predator-prey interactions invalidates the classical deterministic Lotka-Volterra picture of neutral population cycles. In contrast, stochastic models yield long-lived, but ultimately decaying erratic population oscillations, which can be understood through a resonant amplification mechanism for density fluctuations. In Monte Carlo simulations of spatial stochastic predator-prey systems, one observes striking complex spatio-temporal structures. These spreading activity fronts induce persistent correlations between predators and prey. In the presence of local particle density restrictions (finite prey carrying capacity), there exists an extinction threshold for the predator population. The accompanying continuous non-equilibrium phase transition is governed by the directed-percolation universality class. We employ field-theoretic methods based on the Doi-Peliti representation of the master equation for stochastic particle interaction models to (i) map the ensuing action in the vicinity of the absorbing state phase transition to Reggeon field theory, and (ii) to quantitatively address fluctuation-induced renormalizations of the population oscillation frequency, damping, and diffusion coefficients in the species coexistence phase.
Pluralistic and stochastic gene regulation: examples, models and consistent theory.
Salas, Elisa N; Shu, Jiang; Cserhati, Matyas F; Weeks, Donald P; Ladunga, Istvan
2016-06-01
We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of transcription factors, variable DNA motifs, and bursts in gene expression. Stochastic regulation is also indicated by frequently subdued effects of knockout mutants of regulators, their evolutionary losses/gains and massive rewiring of regulatory sites. We report wide-spread pluralistic regulation in ≈800 000 tightly co-expressed pairs of diverse human genes. Typically, half of ≈50 observed regulators bind to both genes reproducibly, twice more than in independently expressed gene pairs. We also examine the largest set of co-expressed genes, which code for cytoplasmic ribosomal proteins. Numerous regulatory complexes are highly significant enriched in ribosomal genes compared to highly expressed non-ribosomal genes. We could not find any DNA-associated, strict sense master regulator. Despite major fluctuations in transcription factor binding, our machine learning model accurately predicted transcript levels using binding sites of 20+ regulators. Our pluralistic and stochastic theory is consistent with partially random binding patterns, redundancy, stochastic regulator binding, burst-like expression, degeneracy of binding motifs and massive regulatory rewiring during evolution. PMID:26823500
Directory of Open Access Journals (Sweden)
Elston Timothy C
2004-03-01
Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.
Directory of Open Access Journals (Sweden)
V.M. Loktev
2008-09-01
Full Text Available We analyze the spectral properties of a phenomenological model for a weakly doped two-dimensional antiferromagnet, in which the carriers move within one of the two sublattices where they were introduced. Such a constraint results in the free carrier spectra with the maxima at k=(± π/2 , ± π/2 observed in some cuprates. We consider the spectral properties of the model by taking into account fluctuations of the spins in the antiferromagnetic background. We show that such fluctuations lead to a non-pole-like structure of the single-hole Green's function and these fluctuations can be responsible for some anomalous "strange metal" properties of underdoped cuprates in the nonsuperconducting regime.
External noise control in inherently stochastic biological systems.
Zheng, Likun; Chen, Meng; Nie, Qing
2012-11-01
Biological systems are often subject to external noise from signal stimuli and environmental perturbations, as well as noises in the intracellular signal transduction pathway. Can different stochastic fluctuations interact to give rise to new emerging behaviors? How can a system reduce noise effects while still being capable of detecting changes in the input signal? Here, we study analytically and computationally the role of nonlinear feedback systems in controlling external noise with the presence of large internal noise. In addition to noise attenuation, we analyze derivatives of Fano factor to study systems' capability of differentiating signal inputs. We find effects of internal noise and external noise may be separated in one slow positive feedback loop system; in particular, the slow loop can decrease external noise and increase robustness of signaling with respect to fluctuations in rate constants, while maintaining the signal output specific to the input. For two feedback loops, we demonstrate that the influence of external noise mainly depends on how the fast loop responds to fluctuations in the input and the slow loop plays a limited role in determining the signal precision. Furthermore, in a dual loop system of one positive feedback and one negative feedback, a slower positive feedback always leads to better noise attenuation; in contrast, a slower negative feedback may not be more beneficial. Our results reveal interesting stochastic effects for systems containing both extrinsic and intrinsic noises, suggesting novel noise filtering strategies in inherently stochastic systems. PMID:23213267
Adaptive stochastic cellular automata: Applications
Qian, S.; Lee, Y. C.; Jones, R. D.; Barnes, C. W.; Flake, G. W.; O'Rourke, M. K.; Lee, K.; Chen, H. H.; Sun, G. Z.; Zhang, Y. Q.; Chen, D.; Giles, C. L.
1990-09-01
The stochastic learning cellular automata model has been applied to the problem of controlling unstable systems. Two example unstable systems studied are controlled by an adaptive stochastic cellular automata algorithm with an adaptive critic. The reinforcement learning algorithm and the architecture of the stochastic CA controller are presented. Learning to balance a single pole is discussed in detail. Balancing an inverted double pendulum highlights the power of the stochastic CA approach. The stochastic CA model is compared to conventional adaptive control and artificial neural network approaches.
Energy Technology Data Exchange (ETDEWEB)
Cao, Xiaobin
2011-01-15
The quasi-one-dimensional systems exhibit some unusual phenomenon, such as the Peierls instability, the pseudogap phenomena and the absence of a Fermi-Dirac distribution function line shape in the photoemission spectroscopy. Ever since the discovery of materials with highly anisotropic properties, it has been recognized that fluctuations play an important role above the three-dimensional phase transition. This regime where the precursor fluctuations are presented can be described by the so called fluctuating gap model (FGM) which was derived from the Froehlich Hamiltonian to study the low energy physics of the one-dimensional electron-phonon system. Not only is the FGM of great interest in the context of quasi-one-dimensional materials, liquid metal and spin waves above T{sub c} in ferromagnets, but also in the semiclassical approximation of superconductivity, it is possible to replace the original three-dimensional problem by a directional average over effectively one-dimensional problem which in the weak coupling limit is described by the FGM. In this work, we investigate the FGM in a wide temperature range with different statistics of the order parameter fluctuations. We derive a formally exact solution to this problem and calculate the density of states, the spectral function and the optical conductivity. In our calculation, we show that a Dyson singularity appears in the low energy density of states for Gaussian fluctuations in the commensurate case. In the incommensurate case, there is no such kind of singularity, and the zero frequency density of states varies differently as a function of the correlation lengths for different statistics of the order parameter fluctuations. Using the density of states we calculated with non-Gaussian order parameter fluctuations, we are able to calculate the static spin susceptibility which agrees with the experimental data very well. In the calculation of the spectral functions, we show that as the correlation increases, the
Fluctuations at low temperatures
International Nuclear Information System (INIS)
The London prize committee cites a number of my works under the common term 'fluctuations'. Research under the general heading of 'fluctuations' has followed a different course during different periods of my life. I am deeply indebted to many people who have contributed to and participated in the research projects that have been cited; among them there were my professors and my students. I would like to acknowledge them and to talk about these people in conjunction with the physical problems on which we worked, stressing that for me these people, their personality and my intellectual activities were inseparable. (orig.)
International Nuclear Information System (INIS)
The quasi-one-dimensional systems exhibit some unusual phenomenon, such as the Peierls instability, the pseudogap phenomena and the absence of a Fermi-Dirac distribution function line shape in the photoemission spectroscopy. Ever since the discovery of materials with highly anisotropic properties, it has been recognized that fluctuations play an important role above the three-dimensional phase transition. This regime where the precursor fluctuations are presented can be described by the so called fluctuating gap model (FGM) which was derived from the Froehlich Hamiltonian to study the low energy physics of the one-dimensional electron-phonon system. Not only is the FGM of great interest in the context of quasi-one-dimensional materials, liquid metal and spin waves above Tc in ferromagnets, but also in the semiclassical approximation of superconductivity, it is possible to replace the original three-dimensional problem by a directional average over effectively one-dimensional problem which in the weak coupling limit is described by the FGM. In this work, we investigate the FGM in a wide temperature range with different statistics of the order parameter fluctuations. We derive a formally exact solution to this problem and calculate the density of states, the spectral function and the optical conductivity. In our calculation, we show that a Dyson singularity appears in the low energy density of states for Gaussian fluctuations in the commensurate case. In the incommensurate case, there is no such kind of singularity, and the zero frequency density of states varies differently as a function of the correlation lengths for different statistics of the order parameter fluctuations. Using the density of states we calculated with non-Gaussian order parameter fluctuations, we are able to calculate the static spin susceptibility which agrees with the experimental data very well. In the calculation of the spectral functions, we show that as the correlation increases, the quasi
Energy Technology Data Exchange (ETDEWEB)
Silva, Milena Wollmann da; Vilhena, Marco Tullio M.B.; Bodmann, Bardo Ernst J.; Vasques, Richard, E-mail: milena.wollmann@ufrgs.br, E-mail: vilhena@mat.ufrgs.br, E-mail: bardobodmann@ufrgs.br, E-mail: richard.vasques@fulbrightmail.org [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Programa de Pos-Graduacao em Engenharia Mecanica
2015-07-01
The neutron point kinetics equation, which models the time-dependent behavior of nuclear reactors, is often used to understand the dynamics of nuclear reactor operations. It consists of a system of coupled differential equations that models the interaction between (i) the neutron population; and (II) the concentration of the delayed neutron precursors, which are radioactive isotopes formed in the fission process that decay through neutron emission. These equations are deterministic in nature, and therefore can provide only average values of the modeled populations. However, the actual dynamical process is stochastic: the neutron density and the delayed neutron precursor concentrations vary randomly with time. To address this stochastic behavior, Hayes and Allen have generalized the standard deterministic point kinetics equation. They derived a system of stochastic differential equations that can accurately model the random behavior of the neutron density and the precursor concentrations in a point reactor. Due to the stiffness of these equations, this system was numerically implemented using a stochastic piecewise constant approximation method (Stochastic PCA). Here, we present a study of the influence of stochastic fluctuations on the results of the neutron point kinetics equation. We reproduce the stochastic formulation introduced by Hayes and Allen and compute Monte Carlo numerical results for examples with constant and time-dependent reactivity, comparing these results with stochastic and deterministic methods found in the literature. Moreover, we introduce a modified version of the stochastic method to obtain a non-stiff solution, analogue to a previously derived deterministic approach. (author)
International Nuclear Information System (INIS)
The neutron point kinetics equation, which models the time-dependent behavior of nuclear reactors, is often used to understand the dynamics of nuclear reactor operations. It consists of a system of coupled differential equations that models the interaction between (i) the neutron population; and (II) the concentration of the delayed neutron precursors, which are radioactive isotopes formed in the fission process that decay through neutron emission. These equations are deterministic in nature, and therefore can provide only average values of the modeled populations. However, the actual dynamical process is stochastic: the neutron density and the delayed neutron precursor concentrations vary randomly with time. To address this stochastic behavior, Hayes and Allen have generalized the standard deterministic point kinetics equation. They derived a system of stochastic differential equations that can accurately model the random behavior of the neutron density and the precursor concentrations in a point reactor. Due to the stiffness of these equations, this system was numerically implemented using a stochastic piecewise constant approximation method (Stochastic PCA). Here, we present a study of the influence of stochastic fluctuations on the results of the neutron point kinetics equation. We reproduce the stochastic formulation introduced by Hayes and Allen and compute Monte Carlo numerical results for examples with constant and time-dependent reactivity, comparing these results with stochastic and deterministic methods found in the literature. Moreover, we introduce a modified version of the stochastic method to obtain a non-stiff solution, analogue to a previously derived deterministic approach. (author)
Extension of Nelson's stochastic quantization to finite temperature using thermo field dynamics
Kobayashi, K.; Yamanaka, Y.
2011-08-01
We present an extension of Nelson's stochastic quantum mechanics to finite temperature. Utilizing the formulation of Thermo Field Dynamics (TFD), we can show that Ito's stochastic equations for tilde and non-tilde particle positions reproduce the TFD-type Schrödinger equation which is equivalent to the Liouville-von Neumann equation. In our formalism, the drift terms in the Ito's stochastic equation have the temperature dependence and the thermal fluctuation is induced through the correlation of the non-tilde and tilde particles. We show that our formalism satisfies the position-momentum uncertainty relation at finite temperature.
Indian Academy of Sciences (India)
C. S. Leung; J. Y. Wei; T. Harko; Z. Kovacs
2011-03-01
In this paper, we introduce a simplified model for explaining the observations of optical intra-day variability (IDV) of the BL Lac Objects. We assume that the source of the IDV are the stochastic oscillations of an accretion disk around a supermassive black hole. The stochastic fluctuations on the vertical direction of the accretion disk are described by using a Langevin type equation with a damping term and a random, white noise type force. Furthermore, preliminary numerical simulation results are presented, which are based on the numerical analysis of the Langevin stochastic differential equation.
Stochastic model for aerodynamic force dynamics on wind turbine blades in unsteady wind inflow
Luhur, Muhammad Ramzan; Kühn, Martin; Wächter, Matthias
2015-01-01
The paper presents a stochastic approach to estimate the aerodynamic forces with local dynamics on wind turbine blades in unsteady wind inflow. This is done by integrating a stochastic model of lift and drag dynamics for an airfoil into the aerodynamic simulation software AeroDyn. The model is added as an alternative to the static table lookup approach in blade element momentum (BEM) wake model used by AeroDyn. The stochastic forces are obtained for a rotor blade element using full field turbulence simulated wind data input and compared with the classical BEM and dynamic stall models for identical conditions. The comparison shows that the stochastic model generates additional extended dynamic response in terms of local force fluctuations. Further, the comparison of statistics between the classical BEM, dynamic stall and stochastic models' results in terms of their increment probability density functions gives consistent results.
Stochastic processes in cell biology
Bressloff, Paul C
2014-01-01
This book develops the theory of continuous and discrete stochastic processes within the context of cell biology. A wide range of biological topics are covered including normal and anomalous diffusion in complex cellular environments, stochastic ion channels and excitable systems, stochastic calcium signaling, molecular motors, intracellular transport, signal transduction, bacterial chemotaxis, robustness in gene networks, genetic switches and oscillators, cell polarization, polymerization, cellular length control, and branching processes. The book also provides a pedagogical introduction to the theory of stochastic process – Fokker Planck equations, stochastic differential equations, master equations and jump Markov processes, diffusion approximations and the system size expansion, first passage time problems, stochastic hybrid systems, reaction-diffusion equations, exclusion processes, WKB methods, martingales and branching processes, stochastic calculus, and numerical methods. This text is primarily...
Ramsay, Malcolm; Harrowell, Peter
2016-04-01
The influence of an applied shear on the planar crystal-melt interface is modeled by a nonlinear stochastic partial differential equation of the interface fluctuations. A feature of this theory is the asymmetric destruction of interface fluctuations due to advection of the crystal protrusions on the liquid side of the interface only. We show that this model is able to qualitatively reproduce the nonequilibrium coexistence line found in simulations. The impact of shear on spherical clusters is also addressed.
Detectability of Space-Time Fluctuations in Ultra High Energy Cosmic Ray Experiments
R. AloisioINFN/LNGS; P. BlasiINAF Arcetri; A. GalanteUniv. L'Aquila; P. L. GhiaCNR and INFN Torino; A. F. GrilloINFN LNGS
2002-01-01
It is generally expected that quantum gravity affects the structure of space-time by introducing stochastic fluctuations in the geometry, and, ultimately, in the measurements of four-distances and four-momenta.These fluctuations may induce observable consequences on the propagation of ultra high energy particles, mainly in the range of energies of interest for cosmic ray physics, over large distances, leading to their detection or constraining the underlying quantum gravitat...
Directory of Open Access Journals (Sweden)
Nicole L.K. Galloway
2015-09-01
Full Text Available The progressive depletion of CD4 T cells underlies clinical progression to AIDS in untreated HIV-infected subjects. Most dying CD4 T cells correspond to resting nonpermissive cells residing in lymphoid tissues. Death is due to an innate immune response against the incomplete cytosolic viral DNA intermediates accumulating in these cells. The viral DNA is detected by the IFI16 sensor, leading to inflammasome assembly, caspase-1 activation, and the induction of pyroptosis, a highly inflammatory form of programmed cell death. We now show that cell-to-cell transmission of HIV is obligatorily required for activation of this death pathway. Cell-free HIV-1 virions, even when added in large quantities, fail to activate pyroptosis. These findings underscore the infected CD4 T cells as the major killing units promoting progression to AIDS and highlight a previously unappreciated role for the virological synapse in HIV pathogenesis.
DEFF Research Database (Denmark)
Shang, Yunlong; Zhang, Chenghui; Cui, Naxin;
2015-01-01
In conventional equalizers, the facts of bulky size and high cost are widespread. Particularly, the zero switching loss and zero-voltage gap (ZVG) between cells are difficult to implement due to the high-frequency hard switching and the voltage drop across power devices. To overcome...... these difficulties, an innovative direct cell-to-cell battery equalizer based on quasi-resonant LC converter (QRLCC) and boost DC-DC converter (BDDC) is proposed. The QRLCC is employed to gain zero-current switching (ZCS), leading to a reduction of power losses. The BDDC is employed to enhance the equalization...... voltage gap for large balancing current and ZVG between cells. Instead of a dedicated equalizer for each cell, only one balancing converter is employed and shared by all cells, reducing the size and implementation cost. Moreover, the equalization current can be regulated as needed by controlling the duty...
Kuhn, Dagmar A.; Hartmann, Raimo; Fytianos, Kleanthis; Petri-Fink, Alke; Rothen-Rutishauser, Barbara; Parak, Wolfgang J.
2015-06-01
Polyelectrolyte multilayer microcapsules around 3.4 micrometers in diameter were added to epithelial cells, monocyte-derived macrophages, and dendritic cells in vitro and their uptake kinetics were quantified. All three cell types were combined in a triple co-culture model, mimicking the human epithelial alveolar barrier. Hereby, macrophages were separated in a three-dimensional model from dendritic cells by a monolayer of epithelial cells. While passing of small nanoparticles has been demonstrated from macrophages to dendritic cells across the epithelial barrier in previous studies, for the micrometer-sized capsules, this process could not be observed in a significant amount. Thus, this barrier is a limiting factor for cell-to-cell transfer of micrometer-sized particles.
Broken detailed balance in active fluctuations of semiflexible filaments
Gladrow, Jannes; Fakhri, Nikta; Mackintosh, Fred C.; Schmidt, Christoph F.; Broedersz, Chase P.
2015-03-01
Non-equilibrium microscopic force generation in cells often results in stochastic steady-state fluctuations. In the cell cytoskeleton, for example, cytoplasmic myosins can drive vigorous conformational fluctuations of actin filaments and microtubules. We here present an analytical and numerical analysis of randomly driven shape fluctuations of semiflexible filaments in a viscoelastic environment. To detect and quantify non-equilibrium dynamics, we focus on the breaking of detailed balance in a conformational phase space subtended by eigenmodes of the beam equation. Molecular dynamics simulations reveal a non-zero circulatory flux in phase space induced by motor activity. Furthermore, we derived an analytical expression of nonequilibrium mode correlations that allows us to predict temporal effects of active molecular motors.
Energy fluctuations in a biharmonically driven nonlinear system
Indian Academy of Sciences (India)
Navinder Singh; Sourabh Lahiri; A M Jayannavar
2010-03-01
We study the fluctuations of work done and dissipated heat of a Brownian particle in a symmetric double well system. The system is driven by two periodic input signals that rock the potential simultaneously. Confinement in one preferred well can be achieved by modulating the relative phase between the drives. We show that in the presence of pumping the stochastic resonance signal is enhanced when analysed in terms of the average work done on the system per cycle. This is in contrast with the case when pumping is achieved by applying an external static bias, which degrades resonance. We analyse the nature of work and heat fluctuations and show that the steady state fluctuation theorem holds in this system.
Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations.
Poitevin, Frédéric; Delarue, Marc; Orland, Henri
2016-07-01
We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin-like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counterions. PMID:27075231
Fluctuations in the multifragmentation
International Nuclear Information System (INIS)
The method of scaled factorial moments, which measure dynamical fluctuations without the influence of Poissonian noise, is presented. Its application for the analysis of the multiparticle (multifragment) densities at small scales is also discussed. (K.A.) 39 refs., 5 figs
FLUCTUATION RESULTS FRO PHENIX.
Energy Technology Data Exchange (ETDEWEB)
MITCHELL, J.T.
2005-04-21
The PHENIX Experiment at the Relativistic Heavy Ion Collider has made measurements of event-by-event fluctuations in the net charge, the mean transverse momentum, and the charged particle multiplicity as a function of collision energy, centrality, and transverse momentum in heavy ion collisions. The results of these measurements will be reviewed and discussed.
Diagnostics for fluctuation measurements
Donne, A. J. H.
2000-01-01
Transport of particles and heat in magnetic confinement devices is largely attributed to the presence of microscopic instabilities. To better understand the physical mechanisms underlying plasma transport processes it is necessary to diagnose the fluctuations in the various quantities along with the
International Nuclear Information System (INIS)
Highlights: • We studied the interaction between tumor cells and fibroblasts in ameloblastoma. • AM-3 ameloblastoma cells secreted significantly high IL-1α levels. • IL-1α derived from AM-3 cells promoted IL-6 and IL-8 secretion of fibroblasts. • IL-6 and IL-8 activated the cellular motility and proliferation of AM-3 cells. - Abstract: Ameloblastoma is an odontogenic benign tumor that occurs in the jawbone, which invades bone and reoccurs locally. This tumor is treated by wide surgical excision and causes various problems, including changes in facial countenance and mastication disorders. Ameloblastomas have abundant tumor stroma, including fibroblasts and immune cells. Although cell-to-cell interactions are considered to be involved in the pathogenesis of many diseases, intercellular communications in ameloblastoma have not been fully investigated. In this study, we examined interactions between tumor cells and stromal fibroblasts via soluble factors in ameloblastoma. We used a human ameloblastoma cell line (AM-3 ameloblastoma cells), human fibroblasts (HFF-2 fibroblasts), and primary-cultured fibroblasts from human ameloblastoma tissues, and analyzed the effect of ameloblastoma-associated cell-to-cell communications on gene expression, cytokine secretion, cellular motility and proliferation. AM-3 ameloblastoma cells secreted higher levels of interleukin (IL)-1α than HFF-2 fibroblasts. Treatment with conditioned medium from AM-3 ameloblastoma cells upregulated gene expression and secretion of IL-6 and IL-8 of HFF-2 fibroblasts and primary-cultured fibroblast cells from ameloblastoma tissues. The AM3-stimulated production of IL-6 and IL-8 in fibroblasts was neutralized by pretreatment of AM-3 cells with anti-IL-1α antibody and IL-1 receptor antagonist. Reciprocally, cellular motility of AM-3 ameloblastoma cells was stimulated by HFF-2 fibroblasts in IL-6 and IL-8 dependent manner. In conclusion, ameloblastoma cells and stromal fibroblasts behave
Energy Technology Data Exchange (ETDEWEB)
Fuchigami, Takao [Department of Biochemistry and Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Department of Oral and Maxillofacial Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Kibe, Toshiro [Department of Oral and Maxillofacial Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Koyama, Hirofumi; Kishida, Shosei; Iijima, Mikio [Department of Biochemistry and Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Nishizawa, Yoshiaki [Kagoshima University Faculty of Medicine, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Hijioka, Hiroshi; Fujii, Tomomi [Department of Oral and Maxillofacial Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Ueda, Masahiro [Natural Science Centre for Research and Education, Kagoshima University, 1-21-24 Koorimoto, Kagoshima 890-8580 (Japan); Nakamura, Norifumi [Department of Oral and Maxillofacial Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Kiyono, Tohru [Department of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuouku, Tokyo 104-0045 (Japan); Kishida, Michiko, E-mail: kmichiko@m2.kufm.kagoshima-u.ac.jp [Department of Biochemistry and Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan)
2014-09-05
Highlights: • We studied the interaction between tumor cells and fibroblasts in ameloblastoma. • AM-3 ameloblastoma cells secreted significantly high IL-1α levels. • IL-1α derived from AM-3 cells promoted IL-6 and IL-8 secretion of fibroblasts. • IL-6 and IL-8 activated the cellular motility and proliferation of AM-3 cells. - Abstract: Ameloblastoma is an odontogenic benign tumor that occurs in the jawbone, which invades bone and reoccurs locally. This tumor is treated by wide surgical excision and causes various problems, including changes in facial countenance and mastication disorders. Ameloblastomas have abundant tumor stroma, including fibroblasts and immune cells. Although cell-to-cell interactions are considered to be involved in the pathogenesis of many diseases, intercellular communications in ameloblastoma have not been fully investigated. In this study, we examined interactions between tumor cells and stromal fibroblasts via soluble factors in ameloblastoma. We used a human ameloblastoma cell line (AM-3 ameloblastoma cells), human fibroblasts (HFF-2 fibroblasts), and primary-cultured fibroblasts from human ameloblastoma tissues, and analyzed the effect of ameloblastoma-associated cell-to-cell communications on gene expression, cytokine secretion, cellular motility and proliferation. AM-3 ameloblastoma cells secreted higher levels of interleukin (IL)-1α than HFF-2 fibroblasts. Treatment with conditioned medium from AM-3 ameloblastoma cells upregulated gene expression and secretion of IL-6 and IL-8 of HFF-2 fibroblasts and primary-cultured fibroblast cells from ameloblastoma tissues. The AM3-stimulated production of IL-6 and IL-8 in fibroblasts was neutralized by pretreatment of AM-3 cells with anti-IL-1α antibody and IL-1 receptor antagonist. Reciprocally, cellular motility of AM-3 ameloblastoma cells was stimulated by HFF-2 fibroblasts in IL-6 and IL-8 dependent manner. In conclusion, ameloblastoma cells and stromal fibroblasts behave
Beilby, Mary J
2016-01-01
The morphology of characean algae could be mistaken for a higher plant: stem-like axes with leaf-like branchlets anchored in the soil by root-like rhizoids. However, all of these structures are made up of giant multinucleate cells separated by multicellular nodal complexes. The excised internodal cells survive long enough for the nodes to give rise to new thallus. The size of the internodes and their thick cytoplasmic layer minimize impalement injury and allow specific micro-electrode placement. The cell structure can be manipulated by centrifugation, perfusion of cell contents or creation of cytoplasmic droplets, allowing access to both vacuolar and cytoplasmic compartments and both sides of the cell membranes. Thousands of electrical measurements on intact or altered cells and cytoplasmic droplets laid down basis to modern plant electrophysiology. Furthermore, the giant internodal cells and whole thalli facilitate research into many other plant properties. As nutrients have to be transported from rhizoids to growing parts of the thallus and hormonal signals need to pass from cell to cell, Characeae possess very fast cytoplasmic streaming. The mechanism was resolved in the characean model. Plasmodesmata between the internodal cells and nodal complexes facilitate transport of ions, nutrients and photosynthates across the nodes. The internal structure was found to be similar to those of higher plants. Recent experiments suggest a strong circadian influence on metabolic pathways producing indole-3-acetic acid (IAA) and serotonin/melatonin. The review will discuss the impact of the characean models arising from fragments of cells, single cells, cell-to-cell transport or whole thalli on understanding of plant evolution and physiology. PMID:27504112
Multiplane 3D superresolution optical fluctuation imaging
Geissbuehler, Stefan; Godinat, Aurélien; Bocchio, Noelia L; Dubikovskaya, Elena A; Lasser, Theo; Leutenegger, Marcel
2013-01-01
By switching fluorophores on and off in either a deterministic or a stochastic manner, superresolution microscopy has enabled the imaging of biological structures at resolutions well beyond the diffraction limit. Superresolution optical fluctuation imaging (SOFI) provides an elegant way of overcoming the diffraction limit in all three spatial dimensions by computing higher-order cumulants of image sequences of blinking fluorophores acquired with a conventional widefield microscope. So far, three-dimensional (3D) SOFI has only been demonstrated by sequential imaging of multiple depth positions. Here we introduce a versatile imaging scheme which allows for the simultaneous acquisition of multiple focal planes. Using 3D cross-cumulants, we show that the depth sampling can be increased. Consequently, the simultaneous acquisition of multiple focal planes reduces the acquisition time and hence the photo-bleaching of fluorescent markers. We demonstrate multiplane 3D SOFI by imaging the mitochondria network in fixed ...
Queues and Lévy fluctuation theory
Dębicki, Krzysztof
2015-01-01
The book provides an extensive introduction to queueing models driven by Lévy-processes as well as a systematic account of the literature on Lévy-driven queues. The objective is to make the reader familiar with the wide set of probabilistic techniques that have been developed over the past decades, including transform-based techniques, martingales, rate-conservation arguments, change-of-measure, importance sampling, and large deviations. On the application side, it demonstrates how Lévy traffic models arise when modelling current queueing-type systems (as communication networks) and includes applications to finance. Queues and Lévy Fluctuation Theory will appeal to graduate/postgraduate students and researchers in mathematics, computer science, and electrical engineering. Basic prerequisites are probability theory and stochastic processes.
Binary Fingerprints at Fluctuation-Enhanced Sensing
Chang, Hung-Chih; King, Maria D; Kwan, Chiman
2009-01-01
We developed a simple way to generate binary patterns based on spectral slopes in different frequency ranges at fluctuation-enhanced sensing. Such patterns can be considered as binary "fingerprints" of odors. The method has experimentally been demonstrated with a commercial semiconducting metal oxide (Taguchi) sensor exposed to bacterial odors (Escherichia coli and Anthrax-surrogate Bacillus subtilis) and processing their stochastic signals. With a single Taguchi sensor, the situations of empty chamber, tryptic soy agar (TSA) medium, or TSA with bacteria could be distinguished with 100% reproducibility. The bacterium numbers were in the range of 25 thousands to 1 million. To illustrate the relevance for ultra-low power consumption, we show that this new type of signal processing and pattern recognition task can be implemented by a simple analog circuitry and a few logic gates with total power consumption in the microWatts range.
Maximum entropy distribution of stock price fluctuations
Bartiromo, Rosario
2013-04-01
In this paper we propose to use the principle of absence of arbitrage opportunities in its entropic interpretation to obtain the distribution of stock price fluctuations by maximizing its information entropy. We show that this approach leads to a physical description of the underlying dynamics as a random walk characterized by a stochastic diffusion coefficient and constrained to a given value of the expected volatility, in this way taking into account the information provided by the existence of an option market. The model is validated by a comprehensive comparison with observed distributions of both price return and diffusion coefficient. Expected volatility is the only parameter in the model and can be obtained by analysing option prices. We give an analytic formulation of the probability density function for price returns which can be used to extract expected volatility from stock option data.
Fluctuation and dissipation in de Sitter space
Fischler, Willy; Pedraza, Juan F; Tangarife, Walter
2014-01-01
In this paper we study some thermal properties of quantum field theories in de Sitter space by means of holographic techniques. We focus on the static patch of de Sitter and assume that the quantum fields are in the standard Bunch-Davies vacuum. More specifically, we follow the stochastic motion of a massive charged particle due to its interaction with Hawking radiation. The process is described in terms of the theory of Brownian motion in inhomogeneous media and its associated Langevin dynamics. At late times, we find that the particle undergoes a regime of slow diffusion and never reaches the horizon, in stark contrast to the usual random walk behavior at finite temperature. Nevertheless, the fluctuation-dissipation theorem is found to hold at all times.
Fluctuations and Linear Response in Supercooled Liquids
DEFF Research Database (Denmark)
Nielsen, Johannes K.
Fluctuation dissipation theorems are derived for thermodynamic properties like frequency dependent specific heat and compressibility. First the case where a systems dynamics are restricted by constant volume and energy is considered. The dynamic linear response to a heat pulse and a volume change...... the external thermodynamic system parameters. In thermodynamic response theory equivalence between ensembles is broken, but time correlation functions sampled in different ensembles are connected through the Maxwell relations of thermodynamics generalized to the frequency domain. Different...... applications of the theory in the field of supercooled liquids are showed. First the full frequency dependent thermodynamic response matrix is extracted from simulations of a binary Lennard Jones liquid. Secondly some simple stochastic models of supercooled liquids are analysed in the framework of linear...
Fluctuations in type IV pilus retraction
Linden, M; Jonsson, A B; Wallin, M; Linden, Martin; Johansson, Emil; Jonsson, Ann-Beth; Wallin, Mats
2005-01-01
The type IV pilus retraction motor is found in many important bacterial pathogens. It is the strongest known linear motor protein and is required for bacterial infectivity. We characterize the dynamics of type IV pilus retraction in terms of a stochastic chemical reaction model. We find that a two state model can describe the experimental force velocity relation and qualitative dependence of ATP concentration. The results indicate that the dynamics is limited by an ATP-dependent step at low load and a force-dependent step at high load, and that at least one step is effectively irreversible in the measured range of forces. The irreversible nature of the sub-step(s) lead to interesting predictions for future experiments: We find different parameterizations with mathematically identical force velocity relations but different fluctuations (diffusion constant). We also find a longer elementary step compared to an earlier analysis, which agrees better with known facts about the structure of the pilus filament and e...
Measurement of magnetic fluctuation-induced heat transport in tokamaks and RFP
International Nuclear Information System (INIS)
It has long been recognized that fluctuations in the magnetic field are a potent mechanism for the anomalous transport of energy in confined plasmas. The energy transport process originates from particle motion along magnetic fields, which have a fluctuating component in the radial direction (perpendicular to the confining equilibrium magnetic surfaces). A key feature is that the transport can be large even if the fluctuation amplitude is small. If the fluctuations are resonant with the equilibrium magnetic field (i.e., the fluctuation amplitude is constant along an equilibrium field line) then a small fluctuation can introduce stochasticity to the field line trajectories. Particles following the chaotically wandering field lines can rapidly carry energy across the plasma
Testing the Propagating Fluctuations Model with a Long, Global Accretion Disk Simulation
Hogg, J Drew
2015-01-01
The broad-band variability of many accreting systems displays characteristic structure; log-normal flux distributions, RMS-flux relations, and long inter-band lags. These characteristics are usually interpreted as inward propagating fluctuations in an accretion disk driven by stochasticity of the angular momentum transport mechanism. We present the first analysis of propagating fluctuations in a long-duration, high-resolution, global three-dimensional magnetohydrodynamic (MHD) simulation of a geometrically-thin ($h/r\\approx0.1$) accretion disk around a black hole. While the dynamical-timescale turbulent fluctuations in the Maxwell stresses are too rapid to drive radially-coherent fluctuations in the accretion rate, we find that the low-frequency quasi-periodic dynamo action introduces low-frequency fluctuations in the Maxwell stresses which then drive the propagating fluctuations. Examining both the mass accretion rate and emission proxies, we recover log-normality, linear RMS-flux relations, and radial coher...
Charge fluctuations and their effect on conduction in biological ion channels
Luchinsky, D G; Kaufman, I; McClintock, P V E; Eisenberg, R S
2008-01-01
The effect of fluctuations on the conductivity of ion channels is investigated. It is shown that modulation of the potential barrier at the selectivity site due to electrostatic amplification of charge fluctuations at the channel mouth exerts a leading-order effect on the channel conductivity. A Brownian dynamical model of ion motion in a channel is derived that takes into account both fluctuations at the channel mouth and vibrational modes of the wall. The charge fluctuations are modeled as a short noise flipping the height of the potential barrier. The wall fluctuations are introduced as a slow vibrational mode of protein motion that modulates ion conductance both stochastically and periodically. The model is used to estimate the contribution of the electrostatic amplification of charge fluctuations to the conductivity of ion channels.
Terrestrial Gravity Fluctuations
Directory of Open Access Journals (Sweden)
Jan Harms
2015-12-01
Full Text Available Different forms of fluctuations of the terrestrial gravity field are observed by gravity experiments. For example, atmospheric pressure fluctuations generate a gravity-noise foreground in measurements with super-conducting gravimeters. Gravity changes caused by high-magnitude earthquakes have been detected with the satellite gravity experiment GRACE, and we expect high-frequency terrestrial gravity fluctuations produced by ambient seismic fields to limit the sensitivity of ground-based gravitational-wave (GW detectors. Accordingly, terrestrial gravity fluctuations are considered noise and signal depending on the experiment. Here, we will focus on ground-based gravimetry. This field is rapidly progressing through the development of GW detectors. The technology is pushed to its current limits in the advanced generation of the LIGO and Virgo detectors, targeting gravity strain sensitivities better than 10^–23 Hz^–1/2 above a few tens of a Hz. Alternative designs for GW detectors evolving from traditional gravity gradiometers such as torsion bars, atom interferometers, and superconducting gradiometers are currently being developed to extend the detection band to frequencies below 1 Hz. The goal of this article is to provide the analytical framework to describe terrestrial gravity perturbations in these experiments. Models of terrestrial gravity perturbations related to seismic fields, atmospheric disturbances, and vibrating, rotating or moving objects, are derived and analyzed. The models are then used to evaluate passive and active gravity noise mitigation strategies in GW detectors, or alternatively, to describe their potential use in geophysics. The article reviews the current state of the field, and also presents new analyses especially with respect to the impact of seismic scattering on gravity perturbations, active gravity noise cancellation, and time-domain models of gravity perturbations from atmospheric and seismic point sources. Our
Terrestrial Gravity Fluctuations
Harms, Jan
2015-12-01
Different forms of fluctuations of the terrestrial gravity field are observed by gravity experiments. For example, atmospheric pressure fluctuations generate a gravity-noise foreground in measurements with super-conducting gravimeters. Gravity changes caused by high-magnitude earthquakes have been detected with the satellite gravity experiment GRACE, and we expect high-frequency terrestrial gravity fluctuations produced by ambient seismic fields to limit the sensitivity of ground-based gravitational-wave (GW) detectors. Accordingly, terrestrial gravity fluctuations are considered noise and signal depending on the experiment. Here, we will focus on ground-based gravimetry. This field is rapidly progressing through the development of GW detectors. The technology is pushed to its current limits in the advanced generation of the LIGO and Virgo detectors, targeting gravity strain sensitivities better than 10^-23 Hz^-1/2 above a few tens of a Hz. Alternative designs for GW detectors evolving from traditional gravity gradiometers such as torsion bars, atom interferometers, and superconducting gradiometers are currently being developed to extend the detection band to frequencies below 1 Hz. The goal of this article is to provide the analytical framework to describe terrestrial gravity perturbations in these experiments. Models of terrestrial gravity perturbations related to seismic fields, atmospheric disturbances, and vibrating, rotating or moving objects, are derived and analyzed. The models are then used to evaluate passive and active gravity noise mitigation strategies in GW detectors, or alternatively, to describe their potential use in geophysics. The article reviews the current state of the field, and also presents new analyses especially with respect to the impact of seismic scattering on gravity perturbations, active gravity noise cancellation, and time-domain models of gravity perturbations from atmospheric and seismic point sources. Our understanding of
Patterns of temporal scaling of groundwater level fluctuation
Yu, Xue; Ghasemizadeh, Reza; Padilla, Ingrid Y.; Kaeli, David; Alshawabkeh, Akram
2016-05-01
We studied the fractal scaling behavior of groundwater level fluctuation for various types of aquifers in Puerto Rico using the methods of (1) detrended fluctuation analysis (DFA) to examine the monofractality and (2) wavelet transform maximum modulus (WTMM) to analyze the multifractality. The DFA results show that fractals exist in groundwater fluctuations of all the aquifers with scaling patterns that are anti-persistent (1 1.5; 1.62 ± 0.07, 4 wells). The multifractal analysis confirmed the need to characterize these highly complex processes with multifractality, which originated from the stochastic distribution of the irregularly-shaped fluctuations. The singularity spectra of the fluctuation processes in each well were site specific. We found a general elevational effect with smaller fractal scaling coefficients in the shallower wells, except for the Northern Karst Aquifer Upper System. High spatial variability of fractal scaling of groundwater level fluctuations in the karst aquifer is due to the coupled effects of anthropogenic perturbations, precipitation, elevation and particularly the high heterogeneous hydrogeological conditions.
Fluctuations, temperature, and detailed balance in classical nucleation theory
Energy Technology Data Exchange (ETDEWEB)
McGraw, R. [Environmental Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973 (United States); LaViolette, R.A. [Idaho National Engineering Laboratory, P.O. Box 1625, Idaho Falls, Idaho 83415 (United States)
1995-06-08
The role of temperature in classical nucleation theory is examined. It is shown that while even small clusters are assigned a temperature in the classical theory, this must be a fluctuating quantity. Stochastic simulations of cluster evaporation and growth are presented to track the temperature fluctuations in time. The relation {l_angle}{vert_bar}{delta}{ital T}{vert_bar}{sup 2}{r_angle}={ital kT}{sup @2}{ital d}0/{ital C}{sub {nu}} for the mean square temperature fluctuation is confirmed, where {ital k} is the Boltzmann constant, {ital C}{sub {nu}} is the cluster heat capacity, and {ital T}{sub 0} is the bath temperature. For small capillary drops (50--100 molecules), the resulting rms temperature fluctuations of 10{degree}--20{degree} might be expected to have a significant effect on the nucleation rate. However, the simulations reveal a cluster temperature distribution that is centered several degrees below {ital T}{sub 0}. A theory is presented to explain this effect. To first order, which includes Gaussian fluctuations of the cluster temperature {ital T}, we find that the effective temperature for cluster evaporation is {ital T}{minus}{ital h}/2{ital C}{sub {nu}}, where {ital h} is the latent heat. This temperature correction is precisely that required by detailed balance and results both in a centering of the cluster temperature distribution on {ital T}{sub 0} and a cancellation of any significant effect of temperature fluctuations on the nucleation rate.
Concentration fluctuations in gas releases by industrial accidents. Final report
Energy Technology Data Exchange (ETDEWEB)
Nielsen, M.; Chatwin, P.C.; Joergensen, H.E.; Mole, N.; Munro, R.J.; Ott, S.
2002-05-01
The COFIN project studied existing remote-sensing Lidar data on concentration fluctuations in atmospheric dispersion from continuous sources at ground level. Fluctuations are described by stochastic models developed by a combination of statistical analyses and surface-layer scaling. The statistical moments and probability density distribution of the fluctuations are most accurately determined in a frame of reference following the instantaneous plume centreline. The spatial distribution of these moments is universal with a gaussian core and exponential tails. The instantaneous plume width is fluctuating with a log-normal distribution. The position of the instantaneous plume centre-line is modelled by a normal distribution and a Langevin equation, by which the meander effect on the time-averaged plume width is predicted. Fixed-frame statistics are modelled by convolution of moving-frame statistics and the probability distribution for the plume centreline. The distance-neighbour function generalized for higher-order statistics has a universal exponential shape. Simulation tools for concentration fluctuations have been developed for either multiple correlated time series or multi-dimensional fields. These tools are based on Karhunen-Loeve expansion and Fourier transformations using iterative or correlation-distortion techniques. The input to the simulation is the probability distribution of the individual processes, assumed stationary, and the cross-correlations of all signal combinations. The use in practical risk assessment is illustrated by implementation of a typical heavy-gas dispersion model, enhanced for prediction and simulation of concentration fluctuations. (au)
Directory of Open Access Journals (Sweden)
William Margulies
2004-11-01
Full Text Available In this paper, we study a specific stochastic differential equation depending on a parameter and obtain a representation of its probability density function in terms of Jacobi Functions. The equation arose in a control problem with a quadratic performance criteria. The quadratic performance is used to eliminate the control in the standard Hamilton-Jacobi variational technique. The resulting stochastic differential equation has a noise amplitude which complicates the solution. We then solve Kolmogorov's partial differential equation for the probability density function by using Jacobi Functions. A particular value of the parameter makes the solution a Martingale and in this case we prove that the solution goes to zero almost surely as time tends to infinity.
Multistage stochastic optimization
Pflug, Georg Ch
2014-01-01
Multistage stochastic optimization problems appear in many ways in finance, insurance, energy production and trading, logistics and transportation, among other areas. They describe decision situations under uncertainty and with a longer planning horizon. This book contains a comprehensive treatment of today’s state of the art in multistage stochastic optimization. It covers the mathematical backgrounds of approximation theory as well as numerous practical algorithms and examples for the generation and handling of scenario trees. A special emphasis is put on estimation and bounding of the modeling error using novel distance concepts, on time consistency and the role of model ambiguity in the decision process. An extensive treatment of examples from electricity production, asset liability management and inventory control concludes the book
Samuelson, P A
1971-02-01
Because a commodity like wheat can be carried forward from one period to the next, speculative arbitrage serves to link its prices at different points of time. Since, however, the size of the harvest depends on complicated probability processes impossible to forecast with certainty, the minimal model for understanding market behavior must involve stochastic processes. The present study, on the basis of the axiom that it is the expected rather than the known-for-certain prices which enter into all arbitrage relations and carryover decisions, determines the behavior of price as the solution to a stochastic-dynamic-programming problem. The resulting stationary time series possesses an ergodic state and normative properties like those often observed for real-world bourses. PMID:16591903
Stochastic calculus and applications
Cohen, Samuel N
2015-01-01
Completely revised and greatly expanded, the new edition of this text takes readers who have been exposed to only basic courses in analysis through the modern general theory of random processes and stochastic integrals as used by systems theorists, electronic engineers and, more recently, those working in quantitative and mathematical finance. Building upon the original release of this title, this text will be of great interest to research mathematicians and graduate students working in those fields, as well as quants in the finance industry. New features of this edition include: End of chapter exercises; New chapters on basic measure theory and Backward SDEs; Reworked proofs, examples and explanatory material; Increased focus on motivating the mathematics; Extensive topical index. "Such a self-contained and complete exposition of stochastic calculus and applications fills an existing gap in the literature. The book can be recommended for first-year graduate studies. It will be useful for all who intend to wo...
Stochastic flights of propellers
Pan, Margaret; Chiang, Eugene; Evans, Steven N
2012-01-01
Kilometer-sized moonlets in Saturn's A ring create S-shaped wakes called "propellers" in surrounding material. The Cassini spacecraft has tracked the motions of propellers for several years and finds that they deviate from Keplerian orbits having constant semimajor axes. The inferred orbital migration is known to switch sign. We show using a statistical test that the time series of orbital longitudes of the propeller Bl\\'eriot is consistent with that of a time-integrated Gaussian random walk. That is, Bl\\'eriot's observed migration pattern is consistent with being stochastic. We further show, using a combination of analytic estimates and collisional N-body simulations, that stochastic migration of the right magnitude to explain the Cassini observations can be driven by encounters with ring particles 10-20 m in radius. That the local ring mass is concentrated in decameter-sized particles is supported on independent grounds by occultation analyses.
Dynamic stochastic optimization
Ermoliev, Yuri; Pflug, Georg
2004-01-01
Uncertainties and changes are pervasive characteristics of modern systems involving interactions between humans, economics, nature and technology. These systems are often too complex to allow for precise evaluations and, as a result, the lack of proper management (control) may create significant risks. In order to develop robust strategies we need approaches which explic itly deal with uncertainties, risks and changing conditions. One rather general approach is to characterize (explicitly or implicitly) uncertainties by objec tive or subjective probabilities (measures of confidence or belief). This leads us to stochastic optimization problems which can rarely be solved by using the standard deterministic optimization and optimal control methods. In the stochastic optimization the accent is on problems with a large number of deci sion and random variables, and consequently the focus ofattention is directed to efficient solution procedures rather than to (analytical) closed-form solu tions. Objective an...
Fluctuating hyperfine interactions: an updated computational implementation
Energy Technology Data Exchange (ETDEWEB)
Zacate, M. O., E-mail: zacatem1@nku.edu [Northern Kentucky University, Department of Physics and Geology (United States); Evenson, W. E. [Utah Valley University, Department of Physics (United States)
2015-04-15
The stochastic hyperfine interactions modeling library (SHIML) is a set of routines written in the C programming language designed to assist in the analysis of stochastic models of hyperfine interactions. The routines read a text-file description of the model, set up the Blume matrix, upon which the evolution operator of the quantum mechanical system depends, and calculate the eigenvalues and eigenvectors of the Blume matrix, from which theoretical spectra of experimental techniques can be calculated. The original version of SHIML constructs Blume matrices applicable for methods that measure hyperfine interactions with only a single nuclear spin state. In this paper, we report an extension of the library to provide support for methods such as Mössbauer spectroscopy and nuclear resonant scattering of synchrotron radiation, which are sensitive to interactions with two nuclear spin states. Examples will be presented that illustrate the use of this extension of SHIML to generate Mössbauer spectra for polycrystalline samples under a number of fluctuating hyperfine field models.
Stochastic Volatility Demand Systems
Apostolos Serletis; Maksim Isakin
2014-01-01
We address the estimation of stochastic volatility demand systems. In particular, we relax the homoscedasticity assumption and instead assume that the covariance matrix of the errors of demand systems is time-varying. Since most economic and fiÂ…nancial time series are nonlinear, we achieve superior modeling using parametric nonlinear demand systems in which the unconditional variance is constant but the conditional variance, like the conditional mean, is also a random variable depending on c...
Stochastic Overall Equipment Effectiveness
Zammori, Francesco Aldo; Braglia, Marcello; Frosolini, Marco
2011-01-01
Abstract This paper focuses on the Overall Equipment Effectiveness (OEE), a key performance indicator typically adopted to support Lean Manufacturing and Total Productive Maintenance. Unfortunately, being a deterministic metric, the OEE only provides a static representation of a process, but fails to capture the real variability of manufacturing performances. To take into account the stochastic nature of the OEE, an approximated procedure based on the application of the Central Lim...
Stochastic resonance and computation
Torres, José-Leonel; Trainor, Lynn
1997-09-01
Stochastic resonance (SR) occurs in bistable nonlinear systems subject to noise, as the entrainment of their output by a weak periodic modulation added to the input. Electronic computation involves switching of memory elements between two states that correspond to 1 and 0, respectively. The possibility of switching errors due to SR in memory elements is considered, showing that it represents a negligible danger to reliable computation.
Stochastic reconstruction of sandstones
Manwart, C.; Torquato, S.; Hilfer, R.
2000-01-01
A simulated annealing algorithm is employed to generate a stochastic model for a Berea and a Fontainebleau sandstone with prescribed two-point probability function, lineal path function, and ``pore size'' distribution function, respectively. We find that the temperature decrease of the annealing has to be rather quick to yield isotropic and percolating configurations. A comparison of simple morphological quantities indicates good agreement between the reconstructions and the original sandston...
Identifiability in stochastic models
1992-01-01
The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.
Decentralized stochastic control
Mahajan, Aditya; Mannan, Mehnaz
2013-01-01
Decentralized stochastic control refers to the multi-stage optimization of a dynamical system by multiple controllers that have access to different information. Decentralization of information gives rise to new conceptual challenges that require new solution approaches. In this expository paper, we use the notion of an \\emph{information-state} to explain the two commonly used solution approaches to decentralized control: the person-by-person approach and the common-information approach.
Stochastic Weighted Fractal Networks
Carletti, Timoteo
2010-01-01
In this paper we introduce new models of complex weighted networks sharing several properties with fractal sets: the deterministic non-homogeneous weighted fractal networks and the stochastic weighted fractal networks. Networks of both classes can be completely analytically characterized in terms of the involved parameters. The proposed algorithms improve and extend the framework of weighted fractal networks recently proposed in (T. Carletti & S. Righi, in press Physica A, 2010)
Periodic and stochastic thermal modulation of protein folding kinetics.
Platkov, Max; Gruebele, Martin
2014-07-21
Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude. PMID:25053342
Isolating intrinsic noise sources in a stochastic genetic switch
International Nuclear Information System (INIS)
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule that binds to the promotor of the other gene. When the repressor is bound to a promotor, the corresponding gene is not transcribed and no protein is produced. Either one of the promotors can be repressed at any given time or both can be unrepressed, leaving three possible promotor states. This model is analysed in its bistable regime in which the deterministic limit exhibits two stable fixed points and an unstable saddle, and the case of small noise is considered. On small timescales, the stochastic process fluctuates near one of the stable fixed points, and on large timescales, a metastable transition can occur, where fluctuations drive the system past the unstable saddle to the other stable fixed point. To explore how different intrinsic noise sources affect these transitions, fluctuations in protein production and degradation are eliminated, leaving fluctuations in the promotor state as the only source of noise in the system. The process without protein noise is then compared to the process with weak protein noise using perturbation methods and Monte Carlo simulations. It is found that some significant differences in the random process emerge when the intrinsic noise source is removed. (paper)
Periodic and stochastic thermal modulation of protein folding kinetics
International Nuclear Information System (INIS)
Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude
Stochasticity Modeling in Memristors
Naous, Rawan
2015-10-26
Diverse models have been proposed over the past years to explain the exhibiting behavior of memristors, the fourth fundamental circuit element. The models varied in complexity ranging from a description of physical mechanisms to a more generalized mathematical modeling. Nonetheless, stochasticity, a widespread observed phenomenon, has been immensely overlooked from the modeling perspective. This inherent variability within the operation of the memristor is a vital feature for the integration of this nonlinear device into the stochastic electronics realm of study. In this paper, experimentally observed innate stochasticity is modeled in a circuit compatible format. The model proposed is generic and could be incorporated into variants of threshold-based memristor models in which apparent variations in the output hysteresis convey the switching threshold shift. Further application as a noise injection alternative paves the way for novel approaches in the fields of neuromorphic engineering circuits design. On the other hand, extra caution needs to be paid to variability intolerant digital designs based on non-deterministic memristor logic.
Detrended fluctuation analysis made flexible to detect range of cross-correlated fluctuations
Kwapień, Jarosław; Oświecimka, Paweł; DroŻdŻ, Stanisław
2015-11-01
The detrended cross-correlation coefficient ρDCCA has recently been proposed to quantify the strength of cross-correlations on different temporal scales in bivariate, nonstationary time series. It is based on the detrended cross-correlation and detrended fluctuation analyses (DCCA and DFA, respectively) and can be viewed as an analog of the Pearson coefficient in the case of the fluctuation analysis. The coefficient ρDCCA works well in many practical situations but by construction its applicability is limited to detection of whether two signals are generally cross-correlated, without the possibility to obtain information on the amplitude of fluctuations that are responsible for those cross-correlations. In order to introduce some related flexibility, here we propose an extension of ρDCCA that exploits the multifractal versions of DFA and DCCA: multifractal detrended fluctuation analysis and multifractal detrended cross-correlation analysis, respectively. The resulting new coefficient ρq not only is able to quantify the strength of correlations but also allows one to identify the range of detrended fluctuation amplitudes that are correlated in two signals under study. We show how the coefficient ρq works in practical situations by applying it to stochastic time series representing processes with long memory: autoregressive and multiplicative ones. Such processes are often used to model signals recorded from complex systems and complex physical phenomena like turbulence, so we are convinced that this new measure can successfully be applied in time-series analysis. In particular, we present an example of such application to highly complex empirical data from financial markets. The present formulation can straightforwardly be extended to multivariate data in terms of the q -dependent counterpart of the correlation matrices and then to the network representation.
Majorana approach to the stochastic theory of line shapes
Komijani, Yashar; Coleman, Piers
2016-08-01
Motivated by recent Mössbauer experiments on strongly correlated mixed-valence systems, we revisit the Kubo-Anderson stochastic theory of spectral line shapes. Using a Majorana representation for the nuclear spin we demonstrate how to recast the classic line-shape theory in a field-theoretic and diagrammatic language. We show that the leading contribution to the self-energy can reproduce most of the observed line-shape features including splitting and line-shape narrowing, while the vertex and the self-consistency corrections can be systematically included in the calculation. This approach permits us to predict the line shape produced by an arbitrary bulk charge fluctuation spectrum providing a model-independent way to extract the local charge fluctuation spectrum of the surrounding medium. We also derive an inverse formula to extract the charge fluctuation from the measured line shape.
Stochastic and non-stochastic effects - a conceptual analysis
International Nuclear Information System (INIS)
The attempt to divide radiation effects into stochastic and non-stochastic effects is discussed. It is argued that radiation or toxicological effects are contingently related to radiation or chemical exposure. Biological effects in general can be described by general laws but these laws never represent a necessary connection. Actually stochastic effects express contingent, or empirical, connections while non-stochastic effects represent semantic and non-factual connections. These two expressions stem from two different levels of discourse. The consequence of this analysis for radiation biology and radiation protection is discussed. (author)
Institute of Scientific and Technical Information of China (English)
郑忠华; 张瑜
2015-01-01
This paper establishes a dynamic stochastic general equilibrium model of multi -departmentcontains a heterogeneous family,enterprise,retailers,commercial bank,etc.The borrowing behaviors of enterprises and borrowing households make the economic impacts on enterprise production and even the entire supply field by corporate borrowing behavior. Through the influences on consumption savings by household borrowing, important subject of transmission of economic fluctuation is composed of real estate market and banking system. Accordingly,the model portrays a variety of shocks (including the preference of real estate ) on dynamic impacts of macroeconomic variables. The results of the model show that the increase in real estate demand to some extent will bring economic recession,The impact of monetary policy through the banking system to economic fluctuations,different expression form the main body of the real estate market,the bank to business, personalfinance,in China,the bank system China's economic fluctuation is the subject of transmission can not be ignored.%本文建立了一个包含异质性家庭、企业、零售商、商业银行、中央银行等多部门的动态随机一般均衡模型。模型中企业以房地产抵押向银行借贷，普通家庭通过银行借款提前消费房地产，将房地产市场与银行体系引入模型，两者构成模型中经济波动传导的主体。我们模拟了各种冲击（包括房地产偏好、存款准备金率、通胀等）对宏观经济变量的动态影响，模拟的一些结果和现实中国经济反应非常一致。模拟结果表明：房地产需求的增加会在一定程度上引发经济衰退，影响经济最重要的变量是央行的存款准备金率和通胀冲击，银行体系将外生冲击分散传导，导致经济主体在冲击下形成其不同经济表现，在我国，银行体系是我国经济波动不可忽视的传导途径。
Stochastic Model for Power Grid Dynamics
Anghel, M; Werley, K A; Anghel, Marian; Motter, Adilson E.; Werley, Kenneth A.
2006-01-01
We introduce a stochastic model that describes the quasi-static dynamics of an electric transmission network under perturbations introduced by random load fluctuations, random removing of system components from service, random repair times for the failed components, and random response times to implement optimal system corrections for removing line overloads in a damaged or stressed transmission network. We use a linear approximation to the network flow equations and apply linear programming techniques that optimize the dispatching of generators and loads in order to eliminate the network overloads associated with a damaged system. We also provide a simple model for the operator's response to various contingency events that is not always optimal due to either failure of the state estimation system or due to the incorrect subjective assessment of the severity associated with these events. This further allows us to use a game theoretic framework for casting the optimization of the operator's response into the c...
Supercomputer optimizations for stochastic optimal control applications
Chung, Siu-Leung; Hanson, Floyd B.; Xu, Huihuang
1991-01-01
Supercomputer optimizations for a computational method of solving stochastic, multibody, dynamic programming problems are presented. The computational method is valid for a general class of optimal control problems that are nonlinear, multibody dynamical systems, perturbed by general Markov noise in continuous time, i.e., nonsmooth Gaussian as well as jump Poisson random white noise. Optimization techniques for vector multiprocessors or vectorizing supercomputers include advanced data structures, loop restructuring, loop collapsing, blocking, and compiler directives. These advanced computing techniques and superconducting hardware help alleviate Bellman's curse of dimensionality in dynamic programming computations, by permitting the solution of large multibody problems. Possible applications include lumped flight dynamics models for uncertain environments, such as large scale and background random aerospace fluctuations.
Stochastic Electrodynamics and the Compton effect
International Nuclear Information System (INIS)
Some of the main qualitative features of the Compton effect are tried to be described within the realm of Classical Stochastic Electrodynamics (SED). It is found indications that the combined action of the incident wave (frequency ω), the radiation reaction force and the zero point fluctuating electromagnetic fields of SED, are able to given a high average recoil velocity v/c=α/(1+α) to the charged particle. The estimate of the parameter α gives α ∼ ℎω/mc2 where 2Πℎ is the constant and mc2 is the rest energy of the particle. It is verified that this recoil is just that necessary to explain the frequency shift, observed in the scattered radiation as due to a classical double Doppler shift. The differential cross section for the radiation scattered by the recoiling charge using classical electromagnetism also calculated. The same expression as obtained by Compton in his fundamental work of 1923 is found. (author)
Discrete stochastic modeling of calcium channel dynamics
Baer, M E; Levine, H; Tsimring, L S; Baer, Markus; Falcke, Martin; Levine, Herbert; Tsimring, Lev S.
1999-01-01
We propose a simple discrete stochastic model for calcium dynamics in living cells. Specifically, the calcium concentration distribution is assumed to give rise to a set of probabilities for the opening/closing of channels which release calcium thereby changing those probabilities. We study this model in one dimension, analytically in the mean-field limit of large number of channels per site N, and numerically for small N. As the number of channels per site is increased, the transition from a non-propagating region of activity to a propagating one changes in nature from one described by directed percolation to that of deterministic depinning in a spatially discrete system. Also, for a small number of channels a propagating calcium wave can leave behind a novel fluctuation-driven state, in a parameter range where the limiting deterministic model exhibits only single pulse propagation.
Discrete Stochastic Modeling of Calcium Channel Dynamics
International Nuclear Information System (INIS)
We propose a discrete stochastic model for calcium dynamics in living cells. A set of probabilities for the opening/closing of calcium channels is assumed to depend on the calcium concentration. We study this model in one dimension, analytically in the limit of a large number of channels per site N , and numerically for small N . As the number of channels per site is increased, the transition from a nonpropagating region of activity to a propagating one changes from one described by directed percolation to that of deterministic depinning in a spatially discrete system. Also, for a small number of channels a propagating calcium wave can leave behind a novel fluctuation-driven state. (c) 2000 The American Physical Society
Wandering bumps in stochastic neural fields
Kilpatrick, Zachary P
2012-01-01
We study the effects of noise on stationary pulse solutions (bumps) in spatially extended neural fields. The dynamics of a neural field is described by an integrodifferential equation whose integral term characterizes synaptic interactions between neurons in different spatial locations of the network. Translationally symmetric neural fields support a continuum of stationary bump solutions, which may be centered at any spatial location. Random fluctuations are introduced by modeling the system as a spatially extended Langevin equation whose noise term we take to be multiplicative or additive. For nonzero noise, these bumps are shown to wander about the domain in a purely diffusive way. We can approximate the effective diffusion coefficient using a small noise expansion. Upon breaking the (continuous) translation symmetry of the system using a spatially heterogeneous inputs or synapses, bumps in the stochastic neural field can become temporarily pinned to a finite number of locations in the network. In the case...
Mixing properties of stochastic quantum Hamiltonians
Onorati, E; Kliesch, M; Brown, W; Werner, A H; Eisert, J
2016-01-01
Random quantum processes play a central role both in the study of fundamental mixing processes in quantum mechanics related to equilibration, thermalisation and fast scrambling by black holes, as well as in quantum process design and quantum information theory. In this work, we present a framework describing the mixing properties of continuous-time unitary evolutions originating from local Hamiltonians having time-fluctuating terms, reflecting a Brownian motion on the unitary group. The induced stochastic time evolution is shown to converge to a unitary design. As a first main result, we present bounds to the mixing time. By developing tools in representation theory, we analytically derive an expression for a local k-th moment operator that is entirely independent of k, giving rise to approximate unitary k-designs and quantum tensor product expanders. As a second main result, we introduce tools for proving bounds on the rate of decoupling from an environment with random quantum processes. By tying the mathema...
Physics of Fashion Fluctuations
Donangelo, Raul; Hansen, Alex; Sneppen, Kim; Souza, Sergio R.
2000-01-01
We consider a market where many agents trade many different types of products with each other. We model development of collective modes in this market, and quantify these by fluctuations that scale with time with a Hurst exponent of about 0.7. We demonstrate that individual products in the model occationally become globally accepted means of exchange, and simultaneously become very actively traded. Thus collective features similar to money spontaneously emerge, without any a priori reason.
Fluctuations in quantum devices
Directory of Open Access Journals (Sweden)
H.Haken
2004-01-01
Full Text Available Logical gates can be formalized by Boolean algebra whose elementary operations can be realized by devices that employ the interactions of macroscopic numbers of elementary excitations such as electrons, holes, photons etc. With increasing miniaturization to the nano scale and below, quantum fluctuations become important and can no longer be ignored. Based on Heisenberg equations of motion for the creation and annihilation operators of elementary excitations, I determine the noise sources of composite quantum systems.
Fluctuations in quantum devices
Haken, H.
2004-01-01
Logical gates can be formalized by Boolean algebra whose elementary operations can be realized by devices that employ the interactions of macroscopic numbers of elementary excitations such as electrons, holes, photons etc. With increasing miniaturization to the nano scale and below, quantum fluctuations become important and can no longer be ignored. Based on Heisenberg equations of motion for the creation and annihilation operators of elementary excitations, I determine the noise sources of c...
Fluctuations of Entropy Production in Partially Masked Electric Circuits: Theoretical Analysis
Chiang, K. -H.; Chou, C.-W.; Lee, C. -L.; Lai, P. -Y.; Chen, Y. -F.
2016-01-01
In this work we perform theoretical analysis about a coupled RC circuit with constant driven currents. Starting from stochastic differential equations, where voltages are subject to thermal noises, we derive time-correlation functions, steady-state distributions and transition probabilities of the system. The validity of the fluctuation theorem (FT) is examined for scenarios with complete and incomplete descriptions.
A dynamic aggregate model for the simulation of short term power fluctuations
De Tommasi, L.; Gibescu, M.; Brand, A.J.
2012-01-01
An important aspect related to wind energy integration into the electrical power system is the fluctuation of the generated power due to the stochastic variations of the wind speed across the area where wind turbines are installed. Simulation models are useful tools to evaluate the impact of the win
Stochastic Nature in Cellular Processes
Institute of Scientific and Technical Information of China (English)
刘波; 刘圣君; 王祺; 晏世伟; 耿轶钊; SAKATA Fumihiko; GAO Xing-Fa
2011-01-01
The importance of stochasticity in cellular processes is increasingly recognized in both theoretical and experimental studies. General features of stochasticity in gene regulation and expression are briefly reviewed in this article, which include the main experimental phenomena, classification, quantization and regulation of noises. The correlation and transmission of noise in cascade networks are analyzed further and the stochastic simulation methods that can capture effects of intrinsic and extrinsic noise are described.
Stochastic Analysis of Cylindrical Shell
Directory of Open Access Journals (Sweden)
Grzywiński Maksym
2014-06-01
Full Text Available The paper deals with some chosen aspects of stochastic structural analysis and its application in the engineering practice. The main aim of the study is to apply the generalized stochastic perturbation techniques based on classical Taylor expansion with a single random variable for solution of stochastic problems in structural mechanics. The study is illustrated by numerical results concerning an industrial thin shell structure modeled as a 3-D structure.
Some stochastic aspects of quantization
Indian Academy of Sciences (India)
Ichiro Ohba
2002-08-01
From the advent of quantum mechanics, various types of stochastic-dynamical approach to quantum mechanics have been tried. We discuss how to utilize Nelson’s stochastic quantum mechanics to analyze the tunneling phenomena, how to derive relativistic ﬁeld equations via the Poisson process and how to describe a quantum dynamics of open systems by the use of quantum state diffusion, or the stochastic Schrödinger equation.
Sidharth, B G
1998-01-01
We examine conservation laws, typically the conservation of linear momentum, in the light of a recent successful formulation of fermions as Kerr-Newman type Black Holes, which are created fluctuationally from a background Zero Point Field. We conclude that these conservation laws are to be taken in the spirit of thermodynamic laws.
Exploiting intrinsic fluctuations to identify model parameters.
Zimmer, Christoph; Sahle, Sven; Pahle, Jürgen
2015-04-01
Parameterisation of kinetic models plays a central role in computational systems biology. Besides the lack of experimental data of high enough quality, some of the biggest challenges here are identification issues. Model parameters can be structurally non-identifiable because of functional relationships. Noise in measured data is usually considered to be a nuisance for parameter estimation. However, it turns out that intrinsic fluctuations in particle numbers can make parameters identifiable that were previously non-identifiable. The authors present a method to identify model parameters that are structurally non-identifiable in a deterministic framework. The method takes time course recordings of biochemical systems in steady state or transient state as input. Often a functional relationship between parameters presents itself by a one-dimensional manifold in parameter space containing parameter sets of optimal goodness. Although the system's behaviour cannot be distinguished on this manifold in a deterministic framework it might be distinguishable in a stochastic modelling framework. Their method exploits this by using an objective function that includes a measure for fluctuations in particle numbers. They show on three example models, immigration-death, gene expression and Epo-EpoReceptor interaction, that this resolves the non-identifiability even in the case of measurement noise with known amplitude. The method is applied to partially observed recordings of biochemical systems with measurement noise. It is simple to implement and it is usually very fast to compute. This optimisation can be realised in a classical or Bayesian fashion. PMID:26672148
Hybrid stochastic simplifications for multiscale gene networks
Directory of Open Access Journals (Sweden)
Debussche Arnaud
2009-09-01
Full Text Available Abstract Background Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. Results We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion 123 which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. Conclusion Hybrid simplifications can be used for onion-like (multi-layered approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.
Stochastic Analysis with Financial Applications
Kohatsu-Higa, Arturo; Sheu, Shuenn-Jyi
2011-01-01
Stochastic analysis has a variety of applications to biological systems as well as physical and engineering problems, and its applications to finance and insurance have bloomed exponentially in recent times. The goal of this book is to present a broad overview of the range of applications of stochastic analysis and some of its recent theoretical developments. This includes numerical simulation, error analysis, parameter estimation, as well as control and robustness properties for stochastic equations. This book also covers the areas of backward stochastic differential equations via the (non-li
Stochastic modeling of thermal fatigue crack growth
Radu, Vasile
2015-01-01
The book describes a systematic stochastic modeling approach for assessing thermal-fatigue crack-growth in mixing tees, based on the power spectral density of temperature fluctuation at the inner pipe surface. It shows the development of a frequency-temperature response function in the framework of single-input, single-output (SISO) methodology from random noise/signal theory under sinusoidal input. The frequency response of stress intensity factor (SIF) is obtained by a polynomial fitting procedure of thermal stress profiles at various instants of time. The method, which takes into account the variability of material properties, and has been implemented in a real-world application, estimates the probabilities of failure by considering a limit state function and Monte Carlo analysis, which are based on the proposed stochastic model. Written in a comprehensive and accessible style, this book presents a new and effective method for assessing thermal fatigue crack, and it is intended as a concise and practice-or...
Stochastic basins of attraction for metastable states
Serdukova, Larissa; Zheng, Yayun; Duan, Jinqiao; Kurths, Jürgen
2016-07-01
Basin of attraction of a stable equilibrium point is an effective concept for stability analysis in deterministic systems; however, it does not contain information on the external perturbations that may affect it. Here we introduce the concept of stochastic basin of attraction (SBA) by incorporating a suitable probabilistic notion of basin. We define criteria for the size of the SBA based on the escape probability, which is one of the deterministic quantities that carry dynamical information and can be used to quantify dynamical behavior of the corresponding stochastic basin of attraction. SBA is an efficient tool to describe the metastable phenomena complementing the known exit time, escape probability, or relaxation time. Moreover, the geometric structure of SBA gives additional insight into the system's dynamical behavior, which is important for theoretical and practical reasons. This concept can be used not only in models with small noise intensity but also with noise whose amplitude is proportional or in general is a function of an order parameter. As an application of our main results, we analyze a three potential well system perturbed by two types of noise: Brownian motion and non-Gaussian α-stable Lévy motion. Our main conclusions are that the thermal fluctuations stabilize the metastable system with an asymmetric three-well potential but have the opposite effect for a symmetric one. For Lévy noise with larger jumps and lower jump frequencies ( α = 0.5 ) metastability is enhanced for both symmetric and asymmetric potentials.
Diffusive processes in a stochastic magnetic field
International Nuclear Information System (INIS)
The statistical representation of a fluctuating (stochastic) magnetic field configuration is studied in detail. The Eulerian correlation functions of the magnetic field are determined, taking into account all geometrical constraints: these objects form a nondiagonal matrix. The Lagrangian correlations, within the reasonable Corrsin approximation, are reduced to a single scalar function, determined by an integral equation. The mean square perpendicular deviation of a geometrical point moving along a perturbed field line is determined by a nonlinear second-order differential equation. The separation of neighboring field lines in a stochastic magnetic field is studied. We find exponentiation lengths of both signs describing, in particular, a decay (on the average) of any initial anisotropy. The vanishing sum of these exponentiation lengths ensures the existence of an invariant which was overlooked in previous works. Next, the separation of a particle's trajectory from the magnetic field line to which it was initially attached is studied by a similar method. Here too an initial phase of exponential separation appears. Assuming the existence of a final diffusive phase, anomalous diffusion coefficients are found for both weakly and strongly collisional limits. The latter is identical to the well known Rechester-Rosenbluth coefficient, which is obtained here by a more quantitative (though not entirely deductive) treatment than in earlier works
Stochastic properties of strongly coupled plasmas.
Morozov, I V; Norman, G E; Valuev, A A
2001-03-01
Stochastic properties of equilibrium strongly coupled plasmas are investigated by a molecular dynamics method. The Krylov-Kolmogorov entropy K and the dynamical memory time t(m) are calculated both for electrons and ions with mass ratios 10-10(5). Two values of K entropy for ions are discovered corresponding to electron and ion time scales. The dependence of the K entropy on the number of particles, the nonideality parameter, and the form of the interaction potential is investigated. The problem of the accuracy of molecular dynamics simulations is discussed. A universal relation between Kt(m) and the fluctuation of the total energy of the system is obtained. The relation does not depend on the numerical integration scheme, temperature, density, and the interparticle interaction potential, so that it may be applied to arbitrary dynamic systems. Transition from dynamic to stochastic correlation is treated for both electron and ion velocity autocorrelation functions, for Langmuir and ion-sound plasma wave dynamic structure factors. We point to quantum uncertainty as a physical reason which limits dynamic (Newton) correlation for times greater than t(m). PMID:11308773
Net charge fluctuations in Au + Au interactions at sqrt[s(NN)]=130 GeV.
Adcox, K; Adler, S S; Ajitanand, N N; Akiba, Y; Alexander, J; Aphecetche, L; Arai, Y; Aronson, S H; Averbeck, R; Awes, T C; Barish, K N; Barnes, P D; Barrette, J; Bassalleck, B; Bathe, S; Baublis, V; Bazilevsky, A; Belikov, S; Bellaiche, F G; Belyaev, S T; Bennett, M J; Berdnikov, Y; Botelho, S; Brooks, M L; Brown, D S; Bruner, N; Bucher, D; Buesching, H; Bumazhnov, V; Bunce, G; Burward-Hoy, J; Butsyk, S; Carey, T A; Chand, P; Chang, J; Chang, W C; Chavez, L L; Chernichenko, S; Chi, C Y; Chiba, J; Chiu, M; Choudhury, R K; Christ, T; Chujo, T; Chung, M S; Chung, P; Cianciolo, V; Cole, B A; D'Enterria, D G; David, G; Delagrange, H; Denisov, A; Deshpande, A; Desmond, E J; Dietzsch, O; Dinesh, B V; Drees, A; Durum, A; Dutta, D; Ebisu, K; Efremenko, Y V; El Chenawi, K; En'yo, H; Esumi, S; Ewell, L; Ferdousi, T; Fields, D E; Fokin, S L; Fraenkel, Z; Franz, A; Frawley, A D; Fung, S-Y; Garpman, S; Ghosh, T K; Glenn, A; Godoi, A L; Goto, Y; Greene, S V; Grosse Perdekamp, M; Gupta, S K; Guryn, W; Gustafsson, H-A; Haggerty, J S; Hamagaki, H; Hansen, A G; Hara, H; Hartouni, E P; Hayano, R; Hayashi, N; He, X; Hemmick, T K; Heuser, J M; Hibino, M; Hill, J C; Ho, D S; Homma, K; Hong, B; Hoover, A; Ichihara, T; Imai, K; Ippolitov, M S; Ishihara, M; Jacak, B V; Jang, W Y; Jia, J; Johnson, B M; Johnson, S C; Joo, K S; Kametani, S; Kang, J H; Kann, M; Kapoor, S S; Kelly, S; Khachaturov, B; Khanzadeev, A; Kikuchi, J; Kim, D J; Kim, H J; Kim, S Y; Kim, Y G; Kinnison, W W; Kistenev, E; Kiyomichi, A; Klein-Boesing, C; Klinksiek, S; Kochenda, L; Kochetkov, V; Koehler, D; Kohama, T; Kotchetkov, D; Kozlov, A; Kroon, P J; Kurita, K; Kweon, M J; Kwon, Y; Kyle, G S; Lacey, R; Lajoie, J G; Lauret, J; Lebedev, A; Lee, D M; Leitch, M J; Li, X H; Li, Z; Lim, D J; Liu, M X; Liu, X; Liu, Z; Maguire, C F; Mahon, J; Makdisi, Y I; Manko, V I; Mao, Y; Mark, S K; Markacs, S; Martinez, G; Marx, M D; Masaike, A; Matathias, F; Matsumoto, T; McGaughey, P L; Melnikov, E; Merschmeyer, M; Messer, F; Messer, M; Miake, Y; Miller, T E; Milov, A; Mioduszewski, S; Mischke, R E; Mishra, G C; Mitchell, J T; Mohanty, A K; Morrison, D P; Moss, J M; Mühlbacher, F; Muniruzzaman, M; Murata, J; Nagamiya, S; Nagasaka, Y; Nagle, J L; Nakada, Y; Nandi, B K; Newby, J; Nikkinen, L; Nilsson, P; Nishimura, S; Nyanin, A S; Nystrand, J; O'Brien, E; Ogilvie, C A; Ohnishi, H; Ojha, I D; Ono, M; Onuchin, V; Oskarsson, A; Osterman, L; Otterlund, I; Oyama, K; Paffrath, L; Palounek, A P T; Pantuev, V S; Papavassiliou, V; Pate, S F; Peitzmann, T; Petridis, A N; Pinkenburg, C; Pisani, R P; Pitukhin, P; Plasil, F; Pollack, M; Pope, K; Purschke, M L; Ravinovich, I; Read, K F; Reygers, K; Riabov, V; Riabov, Y; Rosati, M; Rose, A A; Ryu, S S; Saito, N; Sakaguchi, A; Sakaguchi, T; Sako, H; Sakuma, T; Samsonov, V; Sangster, T C; Santo, R; Sato, H D; Sato, S; Sawada, S; Schlei, B R; Schutz, Y; Semenov, V; Seto, R; Shea, T K; Shein, I; Shibata, T-A; Shigaki, K; Shiina, T; Shin, Y H; Sibiriak, I G; Silvermyr, D; Sim, K S; Simon-Gillo, J; Singh, C P; Singh, V; Sivertz, M; Soldatov, A; Soltz, R A; Sorensen, S; Stankus, P W; Starinsky, N; Steinberg, P; Stenlund, E; Ster, A; Stoll, S P; Sugioka, M; Sugitate, T; Sullivan, J P; Sumi, Y; Sun, Z; Suzuki, M; Takagui, E M; Taketani, A; Tamai, M; Tanaka, K H; Tanaka, Y; Taniguchi, E; Tannenbaum, M J; Thomas, J; Thomas, J H; Thomas, T L; Tian, W; Tojo, J; Torii, H; Towell, R S; Tserruya, I; Tsuruoka, H; Tsvetkov, A A; Tuli, S K; Tydesjö, H; Tyurin, N; Ushiroda, T; van Hecke, H W; Velissaris, C; Velkovska, J; Velkovsky, M; Vinogradov, A A; Volkov, M A; Vorobyov, A; Vznuzdaev, E; Wang, H; Watanabe, Y; White, S N; Witzig, C; Wohn, F K; Woody, C L; Xie, W; Yagi, K; Yokkaichi, S; Young, G R; Yushmanov, I E; Zajc, W A; Zhang, Z; Zhou, S
2002-08-19
Data from Au + Au interactions at sqrt[s(NN)]=130 GeV, obtained with the PHENIX detector at the Relativistic Heavy-Ion Collider, are used to investigate local net charge fluctuations among particles produced near midrapidity. According to recent suggestions, such fluctuations may carry information from the quark-gluon plasma. This analysis shows that the fluctuations are dominated by a stochastic distribution of particles, but are also sensitive to other effects, like global charge conservation and resonance decays. PMID:12190459
Approaching complexity by stochastic methods: From biological systems to turbulence
Energy Technology Data Exchange (ETDEWEB)
Friedrich, Rudolf [Institute for Theoretical Physics, University of Muenster, D-48149 Muenster (Germany); Peinke, Joachim [Institute of Physics, Carl von Ossietzky University, D-26111 Oldenburg (Germany); Sahimi, Muhammad [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089-1211 (United States); Reza Rahimi Tabar, M., E-mail: mohammed.r.rahimi.tabar@uni-oldenburg.de [Department of Physics, Sharif University of Technology, Tehran 11155-9161 (Iran, Islamic Republic of); Institute of Physics, Carl von Ossietzky University, D-26111 Oldenburg (Germany); Fachbereich Physik, Universitaet Osnabrueck, Barbarastrasse 7, 49076 Osnabrueck (Germany)
2011-09-15
This review addresses a central question in the field of complex systems: given a fluctuating (in time or space), sequentially measured set of experimental data, how should one analyze the data, assess their underlying trends, and discover the characteristics of the fluctuations that generate the experimental traces? In recent years, significant progress has been made in addressing this question for a class of stochastic processes that can be modeled by Langevin equations, including additive as well as multiplicative fluctuations or noise. Important results have emerged from the analysis of temporal data for such diverse fields as neuroscience, cardiology, finance, economy, surface science, turbulence, seismic time series and epileptic brain dynamics, to name but a few. Furthermore, it has been recognized that a similar approach can be applied to the data that depend on a length scale, such as velocity increments in fully developed turbulent flow, or height increments that characterize rough surfaces. A basic ingredient of the approach to the analysis of fluctuating data is the presence of a Markovian property, which can be detected in real systems above a certain time or length scale. This scale is referred to as the Markov-Einstein (ME) scale, and has turned out to be a useful characteristic of complex systems. We provide a review of the operational methods that have been developed for analyzing stochastic data in time and scale. We address in detail the following issues: (i) reconstruction of stochastic evolution equations from data in terms of the Langevin equations or the corresponding Fokker-Planck equations and (ii) intermittency, cascades, and multiscale correlation functions.
Hydrodynamics, flow, and flow fluctuations
International Nuclear Information System (INIS)
The matter formed in heavy-ion collisions has been shown to interact so strongly that it behaves like a relativistic fluid during its expansion. I show that initial-state fluctuations, due to the nucleonic structure of incoming nuclei, have a large effect of flow observables. I argue that these fluctuations do not reduce to eccentricity fluctuations. (author)
A Model for Lightcone Fluctuations due to Stress Tensor Fluctuations
Bessa, C H G; Ford, L H; Ribeiro, C C H
2016-01-01
We study a model for quantum lightcone fluctuations in which vacuum fluctuations of the electric field and of the squared electric field in a nonlinear dielectric material produce variations in the flight times of probe pulses. When this material has a non-zero third order polarizability, the flight time variations arise from squared electric field fluctuations, and are analogous to effects expected when the stress tensor of a quantized field drives passive spacetime geometry fluctuations. We also discuss the dependence of the squared electric field fluctuations upon the geometry of the material, which in turn determines a sampling function for averaging the squared electric field along the path of the pulse. This allows us to estimate the probability of especially large fluctuations, which is a measure of the probability distribution for quantum stress tensor fluctuations.
Stochastic conditional intensity processes
DEFF Research Database (Denmark)
Bauwens, Luc; Hautsch, Nikolaus
2006-01-01
model allows for a wide range of (cross-)autocorrelation structures in multivariate point processes. The model is estimated by simulated maximum likelihood (SML) using the efficient importance sampling (EIS) technique. By modeling price intensities based on NYSE trading, we provide significant evidence......In this article, we introduce the so-called stochastic conditional intensity (SCI) model by extending Russell’s (1999) autoregressive conditional intensity (ACI) model by a latent common dynamic factor that jointly drives the individual intensity components. We show by simulations that the proposed...... for a joint latent factor and show that its inclusion allows for an improved and more parsimonious specification of the multivariate intensity process...
Structured Stochastic Linear Bandits
Johnson, Nicholas; Sivakumar, Vidyashankar; Banerjee, Arindam
2016-01-01
The stochastic linear bandit problem proceeds in rounds where at each round the algorithm selects a vector from a decision set after which it receives a noisy linear loss parameterized by an unknown vector. The goal in such a problem is to minimize the (pseudo) regret which is the difference between the total expected loss of the algorithm and the total expected loss of the best fixed vector in hindsight. In this paper, we consider settings where the unknown parameter has structure, e.g., spa...
Stochastic thermodynamics of resetting
Fuchs, Jaco; Goldt, Sebastian; Seifert, Udo
2016-03-01
Stochastic dynamics with random resetting leads to a non-equilibrium steady state. Here, we consider the thermodynamics of resetting by deriving the first and second law for resetting processes far from equilibrium. We identify the contributions to the entropy production of the system which arise due to resetting and show that they correspond to the rate with which information is either erased or created. Using Landauer's principle, we derive a bound on the amount of work that is required to maintain a resetting process. We discuss different regimes of resetting, including a Maxwell demon scenario where heat is extracted from a bath at constant temperature.
Stochastic cooling for beginners
International Nuclear Information System (INIS)
These two lectures have been prepared to give a simple introduction to the principles. In Part I we try to explain stochastic cooling using the time-domain picture which starts from the pulse response of the system. In Part II the discussion is repeated, looking more closely at the frequency-domain response. An attempt is made to familiarize the beginners with some of the elementary cooling equations, from the 'single particle case' up to equations which describe the evolution of the particle distribution. (orig.)
Stochastic ontogenetic growth model
West, B. J.; West, D.
2012-02-01
An ontogenetic growth model (OGM) for a thermodynamically closed system is generalized to satisfy both the first and second law of thermodynamics. The hypothesized stochastic ontogenetic growth model (SOGM) is shown to entail the interspecies allometry relation by explicitly averaging the basal metabolic rate and the total body mass over the steady-state probability density for the total body mass (TBM). This is the first derivation of the interspecies metabolic allometric relation from a dynamical model and the asymptotic steady-state distribution of the TBM is fit to data and shown to be inverse power law.
Casimir bag energy in the stochastic approximation to the pure QCD vacuum
Fosco, C D
2007-01-01
We study the Casimir contribution to the bag energy coming from gluon field fluctuations, within the context of the stochastic vacuum model (SVM) of pure QCD. After formulating the problem in terms of the generating functional of field strength cumulants, we argue that the resulting predictions about the Casimir energy are compatible with the phenomenologically required bag energy term.
Wind power integration studies using a multi-stage stochastic electricity system model
DEFF Research Database (Denmark)
Meibom, Peter; Barth, R.; Brand, H.; Weber, C.
A large share of integrated wind power causes technical and financial impacts on the operation of the existing electricity system due to the fluctuating behaviour and unpredictability of wind power. The presented stochastic electricity market model optimises the unit commitment considering four k...
Carpentier, Pierre; Cohen, Guy; De Lara, Michel
2015-01-01
The focus of the present volume is stochastic optimization of dynamical systems in discrete time where - by concentrating on the role of information regarding optimization problems - it discusses the related discretization issues. There is a growing need to tackle uncertainty in applications of optimization. For example the massive introduction of renewable energies in power systems challenges traditional ways to manage them. This book lays out basic and advanced tools to handle and numerically solve such problems and thereby is building a bridge between Stochastic Programming and Stochastic Control. It is intended for graduates readers and scholars in optimization or stochastic control, as well as engineers with a background in applied mathematics.
Experimental scaling of fluctuations and confinement with Lundquist number in the RFP
International Nuclear Information System (INIS)
The scaling of the magnetic and velocity fluctuations with Lundquist number (S) is examined experimentally over a range of values from 7 x 104 to 106 in a reversed field pinch (RFP) plasma. Magnetic fluctuations do not scale uniquely with the Lundquist number. At high (relative) density, fluctuations scale as b∝S-0.18, and fluctuations are almost independent of S at low relative density, b∝S-0.07; however both exponents fall in the range of theoretical and numerical predictions. At high relative density, the scaling of the energy confinement time follows expectations for transport in a stochastic magnetic field. A confinement scaling law (nτE∝β4/5T-7/10A-3/5Iφ2) is derived assuming the persistent dominance of stochastic magnetic diffusion in the RFP and on the measured scaling of magnetic fluctuations. The peak velocity fluctuations during a sawtooth cycle scale marginally stronger than magnetic fluctuations but weaker than a simple Ohm's law prediction. The sawtooth period is determined by a resistive-Alfvenic hybrid time (Tsaw∝√(τRτAlf)) rather than a purely resistive time
Stochastic Runge-Kutta Software Package for Stochastic Differential Equations
Gevorkyan, M N; Korolkova, A V; Kulyabov, D S; Sevastyanov, L A
2016-01-01
As a result of the application of a technique of multistep processes stochastic models construction the range of models, implemented as a self-consistent differential equations, was obtained. These are partial differential equations (master equation, the Fokker--Planck equation) and stochastic differential equations (Langevin equation). However, analytical methods do not always allow to research these equations adequately. It is proposed to use the combined analytical and numerical approach studying these equations. For this purpose the numerical part is realized within the framework of symbolic computation. It is recommended to apply stochastic Runge--Kutta methods for numerical study of stochastic differential equations in the form of the Langevin. Under this approach, a program complex on the basis of analytical calculations metasystem Sage is developed. For model verification logarithmic walks and Black--Scholes two-dimensional model are used. To illustrate the stochastic "predator--prey" type model is us...
Modelling Meso-Scale Diffusion Processes in Stochastic Fluid Bio-Membranes
Rafii-Tabar, H
1999-01-01
The space-time dynamics of rigid inhomogeneities (inclusions) free to move in a randomly fluctuating fluid bio-membrane is derived and numerically simulated as a function of the membrane shape changes. Both vertically placed (embedded) inclusions and horizontally placed (surface) inclusions are considered. The energetics of the membrane, as a two-dimensional (2D) meso-scale continuum sheet, is described by the Canham-Helfrich Hamiltonian, with the membrane height function treated as a stochastic process. The diffusion parameter of this process acts as the link coupling the membrane shape fluctuations to the kinematics of the inclusions. The latter is described via Ito stochastic differential equation. In addition to stochastic forces, the inclusions also experience membrane-induced deterministic forces. Our aim is to simulate the diffusion-driven aggregation of inclusions and show how the external inclusions arrive at the sites of the embedded inclusions. The model has potential use in such emerging fields as...
Stochastic modelling of conjugate heat transfer in near-wall turbulence
Energy Technology Data Exchange (ETDEWEB)
Pozorski, Jacek [Institute of Fluid-Flow Machinery, Polish Academy of Sciences, Fiszera 14, 80952 Gdansk (Poland)]. E-mail: jp@imp.gda.pl; Minier, Jean-Pierre [Research and Development Division, Electricite de France, 6 quai Watier, 78400 Chatou (France)
2006-10-15
The paper addresses the conjugate heat transfer in turbulent flows with temperature assumed to be a passive scalar. The Lagrangian approach is applied and the heat transfer is modelled with the use of stochastic particles. The intensity of thermal fluctuations in near-wall turbulence is determined from the scalar probability density function (PDF) with externally provided dynamical statistics. A stochastic model for the temperature field in the wall material is proposed and boundary conditions for stochastic particles at the solid-fluid interface are formulated. The heated channel flow with finite-thickness walls is considered as a validation case. Computation results for the mean temperature profiles and the variance of thermal fluctuations are presented and compared with available DNS data.
A stochastic SIRS epidemic model with infectious force under intervention strategies
Cai, Yongli; Kang, Yun; Banerjee, Malay; Wang, Weiming
2015-12-01
In this paper, we extend a classical SIRS epidemic model with the infectious forces under intervention strategies from a deterministic framework to a stochastic differential equation (SDE) one through introducing random fluctuations. The value of our study lies in two aspects. Mathematically, by using the Markov semigroups theory, we prove that the reproduction number R0S can be used to govern the stochastic dynamics of SDE model. If R0S 1, under mild extra conditions, it has an endemic stationary distribution which leads to the stochastical persistence of the disease. Epidemiologically, we find that random fluctuations can suppress disease outbreak, which can provide us some useful control strategies to regulate disease dynamics.
On a theory of stability for nonlinear stochastic chemical reaction networks
International Nuclear Information System (INIS)
We present elements of a stability theory for small, stochastic, nonlinear chemical reaction networks. Steady state probability distributions are computed with zero-information (ZI) closure, a closure algorithm that solves chemical master equations of small arbitrary nonlinear reactions. Stochastic models can be linearized around the steady state with ZI-closure, and the eigenvalues of the Jacobian matrix can be readily computed. Eigenvalues govern the relaxation of fluctuation autocorrelation functions at steady state. Autocorrelation functions reveal the time scales of phenomena underlying the dynamics of nonlinear reaction networks. In accord with the fluctuation-dissipation theorem, these functions are found to be congruent to response functions to small perturbations. Significant differences are observed in the stability of nonlinear reacting systems between deterministic and stochastic modeling formalisms
A non-equilibrium, stochastic model for codon translation time statistics
Caniparoli, Luca
2013-01-01
Protein translation is one of the most important processes in cell life but, despite being well understood biochemically, the implications of its intrinsic stochastic nature have not been fully elucidated. In this paper we develop a microscopic and stochastic model for a ribosome translating a protein, which explicitly takes into consideration tRNA recharging dynamics, spatial inhomogeneity and stochastic fluctuations in the number of charged tRNAs around the ribosome. By analyzing this non-equilibrium system we are able to derive the statistical distribution of the intervals between subsequent translation events, and to show that it deviates from an exponential due to the coupling between the fluctuations of charged and uncharged populations of tRNA.
Stochastic lag time in nucleated linear self-assembly
Tiwari, Nitin S.; van der Schoot, Paul
2016-06-01
Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise on account of the small system size at the cellular scale. We study the nucleated reversible self-assembly of monomeric building blocks into polymer-like aggregates using the method of kinetic Monte Carlo. Kinetic Monte Carlo, being inherently stochastic, allows us to study the impact of fluctuations on the polymerization reactions. One of the most important characteristic features in this kind of problem is the existence of a lag phase before self-assembly takes off, which is what we focus attention on. We study the associated lag time as a function of system size and kinetic pathway. We find that the leading order stochastic contribution to the lag time before polymerization commences is inversely proportional to the system volume for large-enough system size for all nine reaction pathways tested. Finite-size corrections to this do depend on the kinetic pathway.
Orlandi, Chiara; Flinko, Robin; Lewis, George K.
2016-01-01
Several lines of evidence indicate that antibody-dependent cellular cytotoxicity (Wren et al., 2013) is important in the pathogenesis of HIV-1 infection. Namely, ADCC is induced during natural HIV-1 infection or in HIV-1 vaccine studies, the latter demonstrated by the RV144 vaccine trial. To expedite the assessment of ADCC in studies of HIV, we have developed a high throughput assay. We have optimized the rapid fluorometric antibody-mediated cytotoxicity assay (RFADCC) by transfecting the EGFP-CEM-NKr cell line to constitutively express SNAP-tagged CCR5. This cell line can then serve as a source of HIV-specific targets when coated with monomeric gp120, spinoculated with inactivated intact virions, infected by cell-free viral diffusion or infected by cell-to-cell transmission of virus. The optimized strategy has two significant advantages over the original RFADCC method: First, the preparation of detectable target cells is less labor intensive and faster as it does not rely on multiple staining and washing steps for target cells. Second, because the target cell markers GFP and SNAP are constitutively expressed, the assay provides highly reproducible data. These strengths make the optimized RFADCC assay suitable not only for studies of HIV-1 specific cytotoxicity but also for studies of cell–cell transmission of virus. In conclusion, this assay provides a new generation T cell line that can expedite large clinical studies as well as research studies in humans or non-human primates. PMID:26969387
Permanyer, Marc; Pauls, Eduardo; Badia, Roger; Esté, José A; Ballana, Ester
2013-01-01
Memory CD4+ T cells are preferentially infected by HIV-1 compared to naïve cells. HIV-1 fusion and entry is a dynamic process in which the cytoskeleton plays an important role by allowing virion internalization and uncoating. Here, we evaluate the role of the cortical actin in cell-to-cell transfer of virus antigens and infection of target CD4+ T cells. Using different actin remodeling compounds we demonstrate that efficiency of HIV-internalization was proportional to the actin polymerization of the target cell. Naïve (CD45RA+) and memory (CD45RA-) CD4+ T cells could be phenotypically differentiated by the degree of cortical actin density and their capacity to capture virus. Thus, the higher cortical actin density of memory CD4+ T cells was associated to increased efficiency of HIV-antigen internalization and the establishment of a productive infection. Conversely, the lower cortical actin density in naïve CD4+ T cells restricted viral antigen transfer and consequently HIV-1 infection. In conclusion, the cortical actin density differentially affects the susceptibility to HIV-1 infection in naïve and memory CD4+ T cells by modulating the efficiency of HIV antigen internalization. PMID:24244453
De Logu, A; Loy, G; Pellerano, M L; Bonsignore, L; Schivo, M L
2000-12-01
The essential oil obtained in toto from Santolina insularis was investigated for its antiviral activity on herpes simplex type 1 (HSV-1) and type 2 (HSV-2) in vitro. The IC(50) values, determined by plaque reduction assays, were 0.88 and 0.7 microg/ml for HSV-1 and HSV-2, respectively, while the CC(50) determined by the MTT test on Vero cells was 112 microg/ml, indicating a CC(50)/IC(50) ratio of 127 for HSV-1 and 160 for HSV-2. Results obtained by plaque reduction assays also indicated that the antiviral activity of S. insularis was principally due to direct virucidal effects. Antiviral activity against HSV-1 and HSV-2 was not observed in a post-attachment assay, and attachment assays indicated that virus adsorption was not inhibited. Up to 80% inhibition of HSV-1 was achieved at the concentration of 40 microg/ml by yield reduction assay. Furthermore, reduction of plaque formation assays also showed that S. insularis essential oil inhibits cell-to-cell transmission of both HSV-1 and HSV-2. PMID:11164504
Kaido, Masanori; Inoue, Yosuke; Takeda, Yoshika; Sugiyama, Kazuhiko; Takeda, Atsushi; Mori, Masashi; Tamai, Atsushi; Meshi, Tetsuo; Okuno, Tetsuro; Mise, Kazuyuki
2007-06-01
The 3a movement protein (MP) plays a central role in the movement of the RNA plant virus, Brome mosaic virus (BMV). To identify host factor genes involved in viral movement, a cDNA library of Nicotiana benthamiana, a systemic host for BMV, was screened with far-Western blotting using a recombinant BMV MP as probe. One positive clone encoded a protein with sequence similarity to the alpha chain of nascent-polypeptide-associated complex from various organisms, which is proposed to contribute to the fidelity of translocation of newly synthesized proteins. The orthologous gene from N. benthamiana was designated NbNACa1. The binding of NbNACa1 to BMV MP was confirmed in vivo with an agroinfiltration-immunoprecipitation assay. To investigate the involvement of NbNACa1 in BMV multiplication, NbNACa1-silenced (GSNAC) transgenic N. benthamiana plants were produced. Downregulation of NbNACa1 expression reduced virus accumulation in inoculated leaves but not in protoplasts. A microprojectile bombardment assay to monitor BMV-MP-assisted viral movement demonstrated reduced virus spread in GSNAC plants. The localization to the cell wall of BMV MP fused to green fluorescent protein was delayed in GSNAC plants. From these results, we propose that NbNACa1 is involved in BMV cell-to-cell movement through the regulation of BMV MP localization to the plasmodesmata. PMID:17555275
Directory of Open Access Journals (Sweden)
Clare Jolly
2011-09-01
Full Text Available Direct cell-cell spread of Human Immunodeficiency Virus type-1 (HIV-1 at the virological synapse (VS is an efficient mode of dissemination between CD4(+ T cells but the mechanisms by which HIV-1 proteins are directed towards intercellular contacts is unclear. We have used confocal microscopy and electron tomography coupled with functional virology and cell biology of primary CD4(+ T cells from normal individuals and patients with Chediak-Higashi Syndrome and report that the HIV-1 VS displays a regulated secretion phenotype that shares features with polarized secretion at the T cell immunological synapse (IS. Cell-cell contact at the VS re-orientates the microtubule organizing center (MTOC and organelles within the HIV-1-infected T cell towards the engaged target T cell, concomitant with polarization of viral proteins. Directed secretion of proteins at the T cell IS requires specialized organelles termed secretory lysosomes (SL and we show that the HIV-1 envelope glycoprotein (Env localizes with CTLA-4 and FasL in SL-related compartments and at the VS. Finally, CD4(+ T cells that are disabled for regulated secretion are less able to support productive cell-to-cell HIV-1 spread. We propose that HIV-1 hijacks the regulated secretory pathway of CD4(+ T cells to enhance its dissemination.
Directory of Open Access Journals (Sweden)
Frédéric Landmann
2012-04-01
Parasitic filarial nematodes that belong to the Onchocercidae family live in mutualism with Wolbachia endosymbionts. We developed whole-mount techniques to follow the segregation patterns of Wolbachia through the somatic and germline lineages of four filarial species. These studies reveal multiple evolutionarily conserved mechanisms that are required for Wolbachia localization to the germline. During the initial embryonic divisions, Wolbachia segregate asymmetrically such that they concentrate in the posteriorly localized P2 blastomere, a precursor to the adult germline and hypodermal lineages. Surprisingly, in the next division they are excluded from the germline precursor lineage. Rather, they preferentially segregate to the C blastomere, a source of posterior hypodermal cells. Localization to the germline is accomplished by a distinct mechanism in which Wolbachia invade first the somatic gonadal cells close to the ovarian distal tip cell, the nematode stem cell niche, from the hypodermis. This tropism is associated with a cortical F-actin disruption, suggesting an active engulfment. Significantly, germline invasion occurs only in females, explaining the lack of Wolbachia in the male germline. Once in the syncytial environment of the ovaries, Wolbachia rely on the rachis to multiply and disperse into the germ cells. The utilization of cell-to-cell invasion for germline colonization may indicate an ancestral mode of horizontal transfer that preceded the acquisition of the mutualism.
International Nuclear Information System (INIS)
To clarify the radio-adaptive response of normal cells to low-dose radiation, we irradiated human embryonic cells and HeLa cells with low-dose X-ray and examined the changes in sensitivity to subsequent high-dose X-irradiation. The results obtained were as follows; (1) When HE cells were irradiated by a high-dose of 200 cGy, the growth ratio of the living cells five days after the irradiation decreased to 37% of that of the cells which received no X-irradiation. When the cells received a preliminary irradiation of 10 to 20 cGy four hours before the irradiation of 200 cGy, the relative growth ratios increased significantly to 45-53%. (2) This preliminary irradiation effect was not observed in HeLa cells, being cancer cells. (3) When the HE cells suspended in a Ca2+ iron-free medium or TPA added medium while receiving the preliminary irradiation of 13 cGy, the effect of the preliminary irradiation in increasing the relative growth ratio of living cells was not observed. (4) This indicates that normal cells shows an adaptive response to low-dose radiation and become more radioresistant. This phenomenon is considered to involve cell-to-cell communication maintained in normal cells and intracellular signal transduction in which Ca2+ ion plays a role. (author)
Ding, Chuanlin; Cai, Yihua; Marroquin, Jose; Ildstad, Suzanne T.; Yan, Jun
2012-01-01
Plasmacytoid dendritic cells (pDCs) are specialized type I IFN producers, which play an important role in pathogenesis of autoimmune disorders. Dysregulated autoreactive B cell activation is a hallmark in most autoimmune diseases. This study was undertaken to investigate interactions between pDCs and autoreactive B cells. After co-culture of autoreactive B cells that recognize self-Ag small nuclear ribonucleoprotein particles with activated pDCs, we found that pDCs significantly enhance autoreactive B cell proliferation, autoAb production, and survival in response to toll-like receptor (TLR) and BCR stimulation. Neutralization of IFN-α/β and IL-6 abrogated partially pDC-mediated enhancement of autoreactive B cell activation. Transwell studies demonstrated that pDCs could provide activation signals to autoreactive B cells via cell-to-cell contact manner. The involvement of the ICAM-1-LFA-1 pathway was revealed as contributing to this effect. This in vitro enhancement effect was further demonstrated by an in vivo B cell adoptive transfer experiment, which showed that autoreactive B cell proliferation and activation were significantly decreased in MyD-88-deficient mice compared to WT mice. These data suggest the dynamic interplay between pDCs and B cells is required for full activation of autoreactive B cells upon TLR or BCR stimulation. PMID:19890051
Dynamic density functional theory with hydrodynamic interactions and fluctuations
Energy Technology Data Exchange (ETDEWEB)
Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States)
2014-06-21
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
Dynamic density functional theory with hydrodynamic interactions and fluctuations
International Nuclear Information System (INIS)
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions
Dynamic density functional theory with hydrodynamic interactions and fluctuations
Donev, Aleksandar; Vanden-Eijnden, Eric
2014-06-01
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, "Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps," Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, "A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law," J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
Atzberger, P. J.
2007-01-01
In this paper a direct correspondence is made between the effective stochastic dynamics of elastic structures of an Immersed Boundary Method incorporating thermal fluctuations and Stokesian-Browman Dynamics. The correspondence is made in the limit of small Reynolds number, in which the fluid relaxes rapidly on the time scale of the motion of the immersed structures, by performing an averaging procedure directly on the stochastic equations of the Immersed Boundary Method. It is found that the...