Cell-to-Cell stochastic fluctuations in apoptotic signaling can decide between life and death
Raychaudhuri, S; Nguyen, T; Khan, E M; Goldkorn, T
2007-01-01
Apoptosis, or genetically programmed cell death, is a crucial cellular process that maintains the balance between life and death in cells. The precise molecular mechanism of apoptosis signaling and how these two pathways are differentially activated under distinct apoptotic stimuli is poorly understood. We developed a Monte Carlo-based stochastic simulation model that can characterize distinct signaling behaviors in the two major pathways of apoptotic signaling using a novel probability distribution-based approach. Specifically, we show that for a weak death signal, such as low levels of death ligand Fas (CD95) binding or under stress conditions, the type 2 mitochondrial pathway dominates apoptotic signaling. Our results also show signaling in the type 2 pathway is stochastic, where the population average over many cells does not capture the cell-to-cell fluctuations in the time course (~1 - 10 hours) of downstream caspase-3 activation. On the contrary, the probability distribution of caspase-3 activation for...
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.
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.
Fluctuations and dissipations in stochastic energetic resonance
Institute of Scientific and Technical Information of China (English)
Xue Sheng-Hu; Lin Min; Meng Ying
2012-01-01
By analyzing the fluctuations and dissipations of a Brownian particle colliding with the molecules in a fluid,the work exchanged between the Brownian particle constrained in a bistable potential well and an external periodic force is investigated.Characters of the stochastic energetic resonance are found and studied at different intensities of fluctuations and dissipations.The microscopic mechanism of energy exchange between the Brownian particle and the external force is revealed.The method used in this study provides a novel way of controlling the stochastic energetic resonance.
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
Current fluctuations in stochastic lattice gases.
Bertini, L; De Sole, A; Gabrielli, D; Jona-Lasinio, G; Landim, C
2005-01-28
We study current fluctuations in lattice gases in the macroscopic limit extending the dynamic approach for density fluctuations developed in previous articles. More precisely, we establish a large deviation theory for the space-time fluctuations of the empirical current which include the previous results. We then estimate the probability of a fluctuation of the average current over a large time interval. It turns out that recent results by Bodineau and Derrida [Phys. Rev. Lett. 92, 180601 (2004)
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.
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; 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.
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.
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.
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.
Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity.
Qian, Hong; Shi, Pei-Zhe; Xing, Jianhua
2009-06-28
We present a simple, unifying theory for stochastic biochemical systems with multiple time-scale dynamics that exhibit noise-induced bistability in an open-chemical environment, while the corresponding macroscopic reaction is unistable. Nonlinear stochastic biochemical systems like these are fundamentally different from classical systems in equilibrium or near-equilibrium steady state whose fluctuations are unimodal following Einstein-Onsager-Lax-Keizer theory. We show that noise-induced bistability in general arises from slow fluctuations, and a pitchfork bifurcation occurs as the rate of fluctuations decreases. Since an equilibrium distribution, due to detailed balance, has to be independent of changes in time-scale, the bifurcation is necessarily a driven phenomenon. As examples, we analyze three biochemical networks of currently interest: self-regulating gene, stochastic binary decision, and phosphorylation-dephosphorylation cycle with fluctuating kinase. The implications of bistability to biochemical complexity are discussed.
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.
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...
Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes
Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti
2016-08-01
Dynamic co-operativity 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 co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.
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...
Five-dimensional scenario with a fluctuating three-brane an stochastic approach to gravity
Quirós, I
2001-01-01
A five-dimensional scenario with a non compact extra dimension of infinite extent is studied, in which a single three-brane is affected by small Gaussian fluctuations in the extra dimension. The average magnitude of the fluctuations is of order of the electro-weak length scale ($\\sigma\\sim m_{EW}^{-1}$). The model provides an stochastic approach to gravity that accounts for an alternative resolution of the mass hierarchy problem. The cosmological constant problem can be suitably treated as well. Surprisingly the Mach's principle finds a place in the model. It is argued that the Mach's principle, the mass hierarchy and the cosmological constant problem, are different aspects of a same property of gravity in this model: its stochastic character. Thin-brane scenarios are recovered in the "no-fluctuations" limit ($\\sigma\\to 0$).
Zhang, Yue; Zheng, Yan; Liu, Xi; Zhang, Qingling; Li, Aihua
2016-11-01
This study considers a class of differential algebraic stage-structured bio-economic models with stochastic fluctuations. The stochastic bio-economic model is simplified to an Itô equation using the stochastic averaging method. The stochastic stability, Hopf bifurcation, and P-bifurcation are discussed based on the singular boundary theory of the diffusion process for the system and the invariant measure theory of dynamic systems. Numerical simulations are presented to illustrate our main results.
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.
Institute of Scientific and Technical Information of China (English)
Shi-Qi Jiang; Bo Wu; Tian-Xiang Gu
2007-01-01
The stochastic resonance phenomenon in a harmonic oscillator with fluctuating intrinsic frequency by asymmetric dichotomous noise is investigated in this paper By using the random average method and ShapiroLoginov formula, the exact solution of the average output amplitude gain (OAG) is obtained. Numerical results show that OAG depends nonmonotonically on the noise characteristics: intensity, correlation time and asymmetry.The maximum OAG can be achieved by tuning the noise asymmetry and or the noise correlation time.
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...
Directory of Open Access Journals (Sweden)
Daniel Stockholm
Full Text Available BACKGROUND: In culture, isogenic mammalian cells typically display enduring phenotypic heterogeneity that arises from fluctuations of gene expression and other intracellular processes. This diversity is not just simple noise but has biological relevance by generating plasticity. Noise driven plasticity was suggested to be a stem cell-specific feature. RESULTS: Here we show that the phenotypes of proliferating tissue progenitor cells such as primary mononuclear muscle cells can also spontaneously fluctuate between different states characterized by the either high or low expression of the muscle-specific cell surface molecule CD56 and by the corresponding high or low capacity to form myotubes. Although this capacity is a cell-intrinsic property, the cells switch their phenotype under the constraints imposed by the highly heterogeneous microenvironment created by their own collective movement. The resulting heterogeneous cell population is characterized by a dynamic equilibrium between "high CD56" and "low CD56" phenotype cells with distinct spatial distribution. Computer simulations reveal that this complex dynamic is consistent with a context-dependent noise driven bistable model where local microenvironment acts on the cellular state by encouraging the cell to fluctuate between the phenotypes until the low noise state is found. CONCLUSIONS: These observations suggest that phenotypic fluctuations may be a general feature of any non-terminally differentiated cell. The cellular microenvironment created by the cells themselves contributes actively and continuously to the generation of fluctuations depending on their phenotype. As a result, the cell phenotype is determined by the joint action of the cell-intrinsic fluctuations and by collective cell-to-cell interactions.
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.
Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J. Andrew
2016-08-01
Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of
Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J Andrew
2016-08-01
Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of
Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J Andrew
2016-08-01
Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of
Experimental study of the stochastic heating of a single Brownian particle by charge fluctuations
Schmidt, Christian; Piel, Alexander
2016-08-01
The Brownian motion of a micro-particle, which is suspended in the sheath of a radio-frequency discharge, is studied by high-speed video microscopy. In this environment, stochastic heating by charge fluctuations is expected, which should lead to an anisotropic kinetic temperature of the particle with a preferential heating in the direction of the mean electric field in the sheath. The stochastic heating should become more effective at low gas pressures where cooling by the neutral gas becomes ineffective. Our refined experiments confirm the anisotropic heating and the temperature rise for diminishing pressure. Particle-in-cell simulations have guided us in modifying the gap width of the discharge and to specify the dependence of the plasma density on gas pressure as n i ∝ p 1 / 2 . Since the stochastic heating rate also depends on the life-time of charge fluctuations, a temperature scaling T kin ∝ p 3 / 2 results, which is in agreement with the experimental data. The experimental procedure to eliminate other spurious heating mechanisms is described in detail.
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
Energy Technology Data Exchange (ETDEWEB)
Mekkaoui, Abdessamad [IEK-4 Forschungszentrum Juelich 52428 (Germany)
2013-07-01
A method to derive stochastic differential equations for intermittent plasma density dynamics in magnetic fusion edge plasma is presented. It uses a measured first four moments (mean, variance, Skewness and Kurtosis) and the correlation time of turbulence to write a Pearson equation for the probability distribution function of fluctuations. The Fokker-Planck equation is then used to derive a Langevin equation for the plasma density fluctuations. A theoretical expectations are used as a constraints to fix the nonlinearity structure of the stochastic differential equation. In particular when the quadratically nonlinear dynamics is assumed, then it is shown that the plasma density is driven by a multiplicative Wiener process and evolves on the turbulence correlation time scale, while the linear growth is quadratically damped by the fluctuation level. Strong criteria for statistical discrimination of experimental time series are proposed as an alternative to the Kurtosis-Skewness scaling. This scaling is broadly used in contemporary literature to characterize edge turbulence, but it is inappropriate because a large family of distributions could share this scaling. Strong criteria allow us to focus on the relevant candidate distribution and approach a nonlinear structure of edge turbulence model.
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.
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.
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.
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.
Rojas, E. L.; Young, M. A.; Hysell, D. L.
2016-06-01
The phase speed saturation of Farley-Buneman waves is studied as an interaction with the random turbulent fluctuations in the background. We used the formalism of stochastic differential equations to model the complex interactions with a linearized system plus a stochastic term. Applying an averaging technique, we can obtain an augmented linear system that depends on the random behavior of the waves. The results show that following this approach we can obtain phase velocities that saturate close to the ion acoustic speed (Cs). This approach seems promising for the study of the influence of plasma turbulence generated by different kinds of instabilities on the mean state of the ionosphere.
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.
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...
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.
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.
Hill's Equation with Small Fluctuations: Cycle to Cycle Variations and Stochastic Processes
Adams, Fred C
2013-01-01
Hill's equations arise in a wide variety of physical problems, and are specified by a natural frequency, a periodic forcing function, and a forcing strength parameter. This classic problem is generalized here in two ways: [A] to Random Hill's equations which allow the forcing strength q_k, the oscillation frequency \\lambda_k, and the period \\tau_k of the forcing function to vary from cycle to cycle, and [B] to Stochastic Hill's equations which contain (at least) one additional term that is a stochastic process \\xi. This paper considers both random and stochastic Hill's equations with small parameter variations, so that p_k=q_k-, \\ell_k=\\lambda_k-, and \\xi are all O(\\epsilon), where \\epsilon<<1. We show that random Hill's equations and stochastic Hill's equations have the same growth rates when the parameter variations p_k and \\ell_k obey certain constraints given in terms of the moments of \\xi. For random Hill's equations, the growth rates for the solutions are given by the growth rates of a matrix tran...
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 ...
A Bayesian Approach Accounting for Stochastic Fluctuations in Stellar Cluster Properties
Fouesneau, M
2009-01-01
The integrated spectro-photometric properties of star clusters are subject to large cluster-to-cluster variations. They are distributed in non trivial ways around the average properties predicted by standard population synthesis models. This results from the stochastic mass distribution of the finite (small) number of luminous stars in each cluster, stars which may be either particularly blue or particularly red. The color distributions are broad and usually far from Gaussian, especially for young and intermediate age clusters, as found in interacting galaxies. When photometric measurements of clusters are used to estimate ages and masses in conjunction with standard models, biases are to be expected. We present a Bayesian approach that explicitly accounts for stochasticity when estimating ages and masses of star clusters that cannot be resolved into stars. Based on Monte-Carlo simulations, we are starting to explore the probability distributions of star cluster properties obtained given a set of multi-wavele...
Shnoll, S E
2006-01-01
Earlier we showed that the fine structure of the spectrum of amplitude variations in the results of measurements of the processes of different nature (in other words, the fine structure of the dispersion of results or the pattern of the corresponding histograms) is subject to macroscopic fluctuations, changing regularly with time. These changes indicate that the dispersion of results that remains after all artifacts are excluded inevitably accompanies any measurements and reflects very basic features of our world. In our research, we have come to the conclusion that this dispersion of results is the effect of space-time fluctuations, which, in their turn, are caused by the movement of the measured object in an anisotropic gravitational field. Among other things, this conclusion means that the examination of the detailed pattern of distributions obtained from the results of measurement of the dynamics of processes of different nature discovers laws, which cannot be revealed with traditional methods for the ana...
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.
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.
Stochastic Dynamics of Electrical Membrane with Voltage-Dependent Ion Channel Fluctuations
Qian, Hong; Qian, Min
2014-01-01
Brownian ratchet like stochastic theory for the electrochemical membrane system of Hodgkin-Huxley (HH) is developed. The system is characterized by a continuous variable $Q_m(t)$, representing mobile membrane charge density, and a discrete variable $K_t$ representing ion channel conformational dynamics. A Nernst-Planck-Nyquist-Johnson type equilibrium is obtained when multiple conducting ions have a common reversal potential. Detailed balance yields a previously unknown relation between the channel switching rates and membrane capacitance, bypassing Eyring-type explicit treatment of gating charge kinetics. From a molecular structural standpoint, membrane charge $Q_m$ is a more natural dynamic variable than potential $V_m$; our formalism treats $Q_m$-dependent conformational transition rates $\\lambda_{ij}$ as intrinsic parameters. Therefore in principle, $\\lambda_{ij}$ vs. $V_m$ is experimental protocol dependent,e.g., different from voltage or charge clamping measurements. For constant membrane capacitance pe...
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...
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; Cho, H. T.; Hu, Bei Lok
2016-09-01
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 Martín 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
Directory of Open Access Journals (Sweden)
Suzanne Gaudet
Full Text Available Stochastic fluctuations in gene expression give rise to cell-to-cell variability in protein levels which can potentially cause variability in cellular phenotype. For TRAIL (TNF-related apoptosis-inducing ligand variability manifests itself as dramatic differences in the time between ligand exposure and the sudden activation of the effector caspases that kill cells. However, the contribution of individual proteins to phenotypic variability has not been explored in detail. In this paper we use feature-based sensitivity analysis as a means to estimate the impact of variation in key apoptosis regulators on variability in the dynamics of cell death. We use Monte Carlo sampling from measured protein concentration distributions in combination with a previously validated ordinary differential equation model of apoptosis to simulate the dynamics of receptor-mediated apoptosis. We find that variation in the concentrations of some proteins matters much more than variation in others and that precisely which proteins matter depends both on the concentrations of other proteins and on whether correlations in protein levels are taken into account. A prediction from simulation that we confirm experimentally is that variability in fate is sensitive to even small increases in the levels of Bcl-2. We also show that sensitivity to Bcl-2 levels is itself sensitive to the levels of interacting proteins. The contextual dependency is implicit in the mathematical formulation of sensitivity, but our data show that it is also important for biologically relevant parameter values. Our work provides a conceptual and practical means to study and understand the impact of cell-to-cell variability in protein expression levels on cell fate using deterministic models and sampling from parameter distributions.
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.
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.
Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling
Directory of Open Access Journals (Sweden)
Sarah Filippi
2016-06-01
Full Text Available Cellular signaling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signaling systems remain poorly understood. Here, we measure the dynamics of phosphorylated MEK and ERK across cell populations and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modeling framework to show that extrinsic noise, particularly that from upstream MEK, is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. We furthermore show that without extrinsic noise in the core module, variable (including noisy signals would be faithfully reproduced downstream, but the within-module extrinsic variability distorts these signals and leads to a drastic reduction in the mutual information between incoming signal and ERK activity.
Regulated cell-to-cell variation in a cell-fate decision system.
Colman-Lerner, Alejandro; Gordon, Andrew; Serra, Eduard; Chin, Tina; Resnekov, Orna; Endy, Drew; Pesce, C Gustavo; Brent, Roger
2005-09-29
Here we studied the quantitative behaviour and cell-to-cell variability of a prototypical eukaryotic cell-fate decision system, the mating pheromone response pathway in yeast. We dissected and measured sources of variation in system output, analysing thousands of individual, genetically identical cells. Only a small proportion of total cell-to-cell variation is caused by random fluctuations in gene transcription and translation during the response ('expression noise'). Instead, variation is dominated by differences in the capacity of individual cells to transmit signals through the pathway ('pathway capacity') and to express proteins from genes ('expression capacity'). Cells with high expression capacity express proteins at a higher rate and increase in volume more rapidly. Our results identify two mechanisms that regulate cell-to-cell variation in pathway capacity. First, the MAP kinase Fus3 suppresses variation at high pheromone levels, while the MAP kinase Kss1 enhances variation at low pheromone levels. Second, pathway capacity and expression capacity are negatively correlated, suggesting a compensatory mechanism that allows cells to respond more precisely to pheromone in the presence of a large variation in expression capacity. PMID:16170311
DEFF Research Database (Denmark)
Neergaard, Jesper; Schieber, Jay D.
1999-01-01
A self-consistent reptation model that includes chain stretching, chain-length fluctuations, segment connectivity and constraint release is used to predict transient and steady flows. Quantitative comparisons are made with entangledsolution data. The model is able to capture quantitatively all...... for differentmolecular weight, the transient and steady-state behavior of the extinction angle, and the stress relaxation in cessation of steady shear flow....
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.
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.
Directory of Open Access Journals (Sweden)
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.
Quantifying Cell-to-Cell Variations in Lithium Ion Batteries
Directory of Open Access Journals (Sweden)
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.
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.
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
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.
Directory of Open Access Journals (Sweden)
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.
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...
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
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/.
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...
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.
CD81 is dispensable for hepatitis C virus cell-to-cell transmission in hepatoma cells.
Witteveldt, Jeroen; Evans, Matthew J; Bitzegeio, Julia; Koutsoudakis, George; Owsianka, Ania M; Angus, Allan G N; Keck, Zhen-Yong; Foung, Steven K H; Pietschmann, Thomas; Rice, Charles M; Patel, Arvind H
2009-01-01
Hepatitis C virus (HCV) infects cells by the direct uptake of cell-free virus following virus engagement with specific cell receptors such as CD81. Recent data have shown that HCV is also capable of direct cell-to-cell transmission, although the role of CD81 in this process is disputed. Here, we generated cell culture infectious strain JFH1 HCV (HCVcc) genomes carrying an alanine substitution of E2 residues W529 or D535 that are critical for binding to CD81 and infectivity. Co-cultivation of these cells with naïve cells expressing enhanced green fluorescent protein (EGFP) resulted in a small number of cells co-expressing both EGFP and HCV NS5A, showing that the HCVcc mutants are capable of cell-to-cell spread. In contrast, no cell-to-cell transmission from JFH1(DeltaE1E2)-transfected cells occurred, indicating that the HCV glycoproteins are essential for this process. The frequency of cell-to-cell transmission of JFH1(W529A) was unaffected by the presence of neutralizing antibodies that inhibit E2-CD81 interactions. By using cell lines that expressed little or no CD81 and that were refractive to infection with cell-free virus, we showed that the occurrence of viral cell-to-cell transmission is not influenced by the levels of CD81 on either donor or recipient cells. Thus, our results show that CD81 plays no role in the cell-to-cell spread of HCVcc and that this mode of transmission is shielded from neutralizing antibodies. These data suggest that therapeutic interventions targeting the entry of cell-free HCV may not be sufficient in controlling an ongoing chronic infection, but need to be complemented by additional strategies aimed at disrupting direct cell-to-cell viral transmission. PMID:19088272
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.
Stochastic volatility and stochastic leverage
DEFF Research Database (Denmark)
Veraart, Almut; Veraart, Luitgard A. M.
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...... 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...
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
The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium
van Gestel, Jordi; Nowak, Martin A.; Tarnita, Corina E.
2012-01-01
Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation. However, over the last decades cell-to-cell communication has been found to be ubiquitous. By secreting molecular signals in the extracellular environment microorganisms can indirectly assess
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
Consistency of detrended fluctuation analysis
Løvsletten, Ola
2016-01-01
The scaling function $F(s)$ in detrended fluctuation analysis (DFA) scales as $F(s)\\sim s^{H}$ for stochastic processes with Hurst exponents $H$. We prove this scaling law for both stationary stochastic processes with $01$. As a final application of the new theory, we present an estimator $\\hat F(s)$ that can handle missing data in regularly sampled time series without the need for interpolation schemes. Under mild regularity conditions, $\\hat F(s)$ is equal in expectation to the fluctuation function $F(s)$ in the gap-free case.
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.
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...
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
Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa.
Pesci, E C; Milbank, J B; Pearson, J P; McKnight, S; Kende, A S; Greenberg, E P; Iglewski, B H
1999-09-28
Numerous species of bacteria use an elegant regulatory mechanism known as quorum sensing to control the expression of specific genes in a cell-density dependent manner. In Gram-negative bacteria, quorum sensing systems function through a cell-to-cell signal molecule (autoinducer) that consists of a homoserine lactone with a fatty acid side chain. Such is the case in the opportunistic human pathogen Pseudomonas aeruginosa, which contains two quorum sensing systems (las and rhl) that operate via the autoinducers, N-(3-oxododecanoyl)-L-homoserine lactone and N-butyryl-L-homoserine lactone. The study of these signal molecules has shown that they bind to and activate transcriptional activator proteins that specifically induce numerous P. aeruginosa virulence genes. We report here that P. aeruginosa produces another signal molecule, 2-heptyl-3-hydroxy-4-quinolone, which has been designated as the Pseudomonas quinolone signal. It was found that this unique cell-to-cell signal controlled the expression of lasB, which encodes for the major virulence factor, LasB elastase. We also show that the synthesis and bioactivity of Pseudomonas quinolone signal were mediated by the P. aeruginosa las and rhl quorum sensing systems, respectively. The demonstration that 2-heptyl-3-hydroxy-4-quinolone can function as an intercellular signal sheds light on the role of secondary metabolites and shows that P. aeruginosa cell-to-cell signaling is not restricted to acyl-homoserine lactones.
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.
Stochastic gravity: beyond semiclassical gravity
Energy Technology Data Exchange (ETDEWEB)
Verdaguer, E [Departament de Fisica Fonamental and CER en Astrofisica, Fisica de Particules i Cosmologia, Universitat de Barcelona, Av. Diagonal 647, 08028 Barcelona (Spain)
2007-05-15
The back-reaction of a classical gravitational field interacting with quantum matter fields is described by the semiclassical Einstein equation, which has the expectation value of the quantum matter fields stress tensor as a source. The semiclassical theory may be obtained from the quantum field theory of gravity interacting with N matter fields in the large N limit. This theory breaks down when the fields quantum fluctuations are important. Stochastic gravity goes beyond the semiclassical limit and allows for a systematic and self-consistent description of the metric fluctuations induced by these quantum fluctuations. The correlation functions of the metric fluctuations obtained in stochastic gravity reproduce the correlation functions in the quantum theory to leading order in an 1/N expansion. Two main applications of stochastic gravity are discussed. The first, in cosmology, to obtain the spectrum of primordial metric perturbations induced by the inflaton fluctuations, even beyond the linear approximation. The second, in black hole physics, to study the fluctuations of the horizon of an evaporating black hole.
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...
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
Zhang, Tongqian; Meng, Xinzhu; Zhang, Tonghua
2015-01-01
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. PMID:26504489
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.
Mihailović, Dragutin T.; Kostić, Vladimir R.; Balaž, Igor; Kapor, Darko
2016-10-01
We examine the threshold of the influence of the tunneling nanotubes (TNTs) on the cell-to-cell communication integrity. A deterministic model is introduced with the Michaelis-Menten dynamics and the intercellular exchange of substance. The influence of TNTs are considered as a functional perturbation of the main communication and treated as the matrix nearness problems. We analyze communication integrity in terms of the \\emph{pseudospectra} of the exchange, to find the \\emph{distance to instability}. The threshold of TNTs influence is computed for Newman-Gastner and Erd\\H{o}s-R\\'enyi gap junction (GJ) networks.
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.
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
Stochastic ice stream dynamics
Mantelli, Elisa; Bertagni, Matteo Bernard; Ridolfi, Luca
2016-08-01
Ice streams are narrow corridors of fast-flowing ice that constitute the arterial drainage network of ice sheets. Therefore, changes in ice stream flow are key to understanding paleoclimate, sea level changes, and rapid disintegration of ice sheets during deglaciation. The dynamics of ice flow are tightly coupled to the climate system through atmospheric temperature and snow recharge, which are known exhibit stochastic variability. Here we focus on the interplay between stochastic climate forcing and ice stream temporal dynamics. Our work demonstrates that realistic climate fluctuations are able to (i) induce the coexistence of dynamic behaviors that would be incompatible in a purely deterministic system and (ii) drive ice stream flow away from the regime expected in a steady climate. We conclude that environmental noise appears to be crucial to interpreting the past behavior of ice sheets, as well as to predicting their future evolution.
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 ...
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
Simmons, L. W.; Tomkins, J. L.; Kotiaho, J. S.; Hunt, J.
1999-01-01
A prominent paradigm in evolutionary biology over the last ten years has been the role of fluctuating asymmetry in sexual selection. Fluctuating asymmetry in bilaterally paired traits, and in particular sexual traits, has been proposed to be a reliable indicator of individual quality and the focus of selection through sexual competition and attractiveness. We surveyed the literature on fluctuating asymmetry and sexual selection and found a marked chronological decline in the proportion of stu...
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
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.
Directory of Open Access Journals (Sweden)
Ryan Chong
Full Text Available Intracellular bacterial pathogens, such as Listeria monocytogenes and Rickettsia conorii display actin-based motility in the cytosol of infected cells and spread from cell to cell through the formation of membrane protrusions at the cell cortex. Whereas the mechanisms supporting cytosolic actin-based motility are fairly well understood, it is unclear whether specific host factors may be required for supporting the formation and resolution of membrane protrusions. To address this gap in knowledge, we have developed high-throughput fluorescence microscopy and computer-assisted image analysis procedures to quantify pathogen spread in human epithelial cells. We used the approach to screen a siRNA library covering the human kinome and identified 7 candidate kinases whose depletion led to severe spreading defects in cells infected with L. monocytogenes. We conducted systematic validation procedures with redundant silencing reagents and confirmed the involvement of the serine/threonine kinases, CSNK1A1 and CSNK2B. We conducted secondary assays showing that, in contrast with the situation observed in CSNK2B-depleted cells, L. monocytogenes formed wild-type cytosolic tails and displayed wild-type actin-based motility in the cytosol of CSNK1A1-depleted cells. Furthermore, we developed a protrusion formation assay and showed that the spreading defect observed in CSNK1A1-depleted cells correlated with the formation of protrusion that did not resolve into double-membrane vacuoles. Moreover, we developed sending and receiving cell-specific RNAi procedures and showed that CSNK1A was required in the sending cells, but was dispensable in the receiving cells, for protrusion resolution. Finally, we showed that the observed defects were specific to Listeria monocytogenes, as Rickettsia conorii displayed wild-type cell-to-cell spread in CSNK1A1- and CSNK2B-depleted cells. We conclude that, in addition to the specific host factors supporting cytosolic actin
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.
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.
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.
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.
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...
Quantum Fluctuations Of The Stress Tensor
Wu, C
2002-01-01
Quantum fluctuations of the stress tensor are important in many branches of physics, including the study of the validity of semiclassical gravity and the backreaction problem in stochastic semiclassical gravity. The geometry fluctuations induced by stress tensor fluctuations are important to understand quantum gravity and the problem of lightcone fluctuations. Stress tensor fluctuations also hold the key to understand fundamental physical effects like quantum fluctuations of radiation pressure, and that is crucial to the sensitivity of interferometers and the limitations on the detection of gravitational waves. Even the wave-particle duality of light can be better understood by the study of quantum fluctuations of thermal radiation. It is well known in quantum field theory that the expectation value of the energy density, which contains quadratic field operators (e.g. E2 and B2 in the electromagnatic field case), is divergent and can be renormalized simply by normal ordering, which is subtracting out the vac...
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...
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 ...
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
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
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.
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
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.
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.
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 roots, indicating that plasmodesmata may be conduits for nucleotide (ATP and ADP) exchange between 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.
Li, Yi; Bao, Yi M; Wei, Chun H; Kang, Zhen S; Zhong, Yong W; Mao, Peng; Wu, Gang; Chen, Zhang L; Schiemann, Joachim; Nelson, Richard S
2004-05-01
Rice dwarf virus (RDV) is a member of the genus Phytoreovirus, which is composed of viruses with segmented double-stranded RNA genomes. Proteins that support the intercellular movement of these viruses in the host have not been identified. Microprojectile bombardment was used to determine which open reading frames (ORFs) support intercellular movement of a heterologous virus. A plasmid containing an infectious clone of Potato virus X (PVX) defective in cell-to-cell movement and expressing either beta-glucuronidase or green fluorescent protein (GFP) was used for cobombardment with plasmids containing ORFs from RDV gene segments S1 through S12 onto leaves of Nicotiana benthamiana. Cell-to-cell movement of the movement-defective PVX was restored by cobombardment with a plasmid containing S6. In the absence of S6, no other gene segment supported movement. Identical results were obtained with Nicotiana tabacum, a host that allows fewer viruses to infect and spread within its tissue. S6 supported the cell-to-cell movement of the movement-defective PVX in sink and source leaves of N. benthamiana. A mutant S6 lacking the translation start codon did not complement the cell-to-cell movement of the movement-defective PVX. An S6 protein product (Pns6)-enhanced GFP fusion was observed near or within cell walls of epidermal cells from N. tabacum. By immunocytochemistry, unfused Pns6 was localized to plasmodesmata in rice leaves infected with RDV. S6 thus encodes a protein with characteristics identical to those of other viral proteins required for the cell-to-cell movement of their genome and therefore is likely required for the cell-to-cell movement of RDV.
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.
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
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) ...
Modelling the Impact of Cell-To-Cell Transmission in Hepatitis B Virus
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
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
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
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...
Laboratory Evidence for Stochastic Plasma-Wave Growth
Austin, D. R.; Hole, M. J.; Robinson, P. A.; Cairns, Iver H.; Dallaqua, R.
2007-11-01
The first laboratory confirmation of stochastic growth theory is reported. Floating potential fluctuations are measured in a vacuum arc centrifuge using a Langmuir probe. Statistical analysis of the energy density reveals a lognormal distribution over roughly 2 orders of magnitude, with a high-field nonlinear cutoff whose spatial dependence is consistent with the predicted eigenmode profile. These results are consistent with stochastic growth and nonlinear saturation of a spatially extended eigenmode, the first evidence for stochastic growth of an extended structure.
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...
Reliability-based Dynamic Network Design with Stochastic Networks
Li, H.
2009-01-01
Transportation systems are stochastic and dynamic systems. The road capacities and the travel demand are fluctuating from time to time within a day and at the same time from day to day. For road users, the travel time and travel costs experienced over time and space are stochastic, thus desire relia
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
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
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.
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 statistica...
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.
Enhanced droplet spreading due to thermal fluctuations
Energy Technology Data Exchange (ETDEWEB)
Willis, A M; Freund, J B, E-mail: jbfreund@illinois.ed [Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, 1206 West Green Street, Urbana, IL 61801 (United States)
2009-11-18
The lubrication equation that governs the dynamics of thin liquid films can be augmented to account for stochastic stresses associated with the thermal fluctuations of the fluid. It has been suggested that under certain conditions the spreading rate of a liquid drop on a surface will be increased by these stochastic stresses. Here, an atomistic simulation of a spreading drop is designed to examine such a regime and provide a quantitative assessment of the stochastic lubrication equation for spreading. It is found that the atomistic drop does indeed spread faster than the standard lubrication equations would suggest and that the stochastic lubrication equation of Gruen et al (2006 J. Stat. Phys. 122 1261-91) predicts the spread rate.
Government Policy and Aggregate Fluctuations Government Policy and Aggregate Fluctuations
Directory of Open Access Journals (Sweden)
Ellen R. McGrattan
1991-03-01
Full Text Available Government Policy and Aggregate Fluctuations This paper investigates the effect of including fiscal and monetary variables in a simple real business cycle model. The starting point is the stochastic growth model with fuctuations driven by technological shocks. The growth model is first extended to include government spending and taxes on factors of production. A second extension imposes a cash-in-advance constraint on purchases of consumption goods. For the three models, equilibrium decision functions and predictions for second moments are compared.
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.
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...
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.
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.
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.
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.
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.
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...
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 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 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.
da Silva, Robert L; Krumholz, Mark R
2014-01-01
The integrated light of a stellar population, measured through photometric filters that are sensitive to the presence of young stars, is often used to infer the star formation rate (SFR) for that population. However, these techniques rely on an assumption that star formation is a continuous process, whereas in reality stars form in discrete spatially- and temporally-correlated structures. This discreteness causes the light output to undergo significant time-dependent fluctuations, which, if not accounted for, introduce errors and biases in the inferred SFRs. We use SLUG (a code that Stochastically Lights Up Galaxies) to simulate galaxies undergoing stochastic star formation. We then use these simulations to present a quantitative analysis of these effects and provide tools for calculating probability distribution functions of SFRs given a set of observations. We show that, depending on the SFR tracer used, stochastic fluctuations can produce non-trivial errors at SFRs as high as 1 Msun/yr, and we suggest meth...
Stochasticity in cell biology: Modeling across levels
Pedraza, Juan Manuel
2009-03-01
Effective modeling of biological processes requires focusing on a particular level of description, and this requires summarizing de details of lower levels into effective variables and properly accounting for the constrains that other levels impose. In the context of stochasticity in gene expression, I will show how the details of the stochastic process can be characterized by a few effective parameters, which facilitates modeling but complicates interpretation of current experiments. I will show how the resulting noise can provide advantageous or deleterious phenotypic fluctuation and how noise control in the copy number control system of plasmids can change the selective pressures. This system illustrates the direct connection between molecular dynamics and evolutionary dynamics.
Directory of Open Access Journals (Sweden)
Joachim Almquist
Full Text Available The last decade has seen a rapid development of experimental techniques that allow data collection from individual cells. These techniques have enabled the discovery and characterization of variability within a population of genetically identical cells. Nonlinear mixed effects (NLME modeling is an established framework for studying variability between individuals in a population, frequently used in pharmacokinetics and pharmacodynamics, but its potential for studies of cell-to-cell variability in molecular cell biology is yet to be exploited. Here we take advantage of this novel application of NLME modeling to study cell-to-cell variability in the dynamic behavior of the yeast transcription repressor Mig1. In particular, we investigate a recently discovered phenomenon where Mig1 during a short and transient period exits the nucleus when cells experience a shift from high to intermediate levels of extracellular glucose. A phenomenological model based on ordinary differential equations describing the transient dynamics of nuclear Mig1 is introduced, and according to the NLME methodology the parameters of this model are in turn modeled by a multivariate probability distribution. Using time-lapse microscopy data from nearly 200 cells, we estimate this parameter distribution according to the approach of maximizing the population likelihood. Based on the estimated distribution, parameter values for individual cells are furthermore characterized and the resulting Mig1 dynamics are compared to the single cell times-series data. The proposed NLME framework is also compared to the intuitive but limited standard two-stage (STS approach. We demonstrate that the latter may overestimate variabilities by up to almost five fold. Finally, Monte Carlo simulations of the inferred population model are used to predict the distribution of key characteristics of the Mig1 transient response. We find that with decreasing levels of post-shift glucose, the transient
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
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.
Dando, Robin; Roper, Stephen D
2009-12-15
Isolated taste cells, taste buds and strips of lingual tissue from taste papillae secrete ATP upon taste stimulation. Taste bud receptor (Type II) cells have been identified as the source of ATP secretion. Based on studies on isolated taste buds and single taste cells, we have postulated that ATP secreted from receptor cells via pannexin 1 hemichannels acts within the taste bud to excite neighbouring presynaptic (Type III) cells. This hypothesis, however, remains to be tested in intact tissues. In this report we used confocal Ca(2+) imaging and lingual slices containing intact taste buds to test the hypothesis of purinergic signalling between taste cells in a more integral preparation. Incubating lingual slices with apyrase reversibly blocked cell-to-cell communication between receptor cells and presynaptic cells, consistent with ATP being the transmitter. Inhibiting pannexin 1 gap junction hemichannels with CO(2)-saturated buffer or probenecid significantly reduced cell-cell signalling between receptor cells and presynaptic cells. In contrast, anandamide, a blocker of connexin gap junction channels, had no effect of cell-to-cell communication in taste buds. These findings are consistent with the model for peripheral signal processing via ATP and pannexin 1 hemichannels in mammalian taste buds.
Giant natural fluctuation models and anthropogenic warming
Lovejoy, S.; Rio Amador, L.; Hébert, R.; Lima, I.
2016-08-01
Explanations for the industrial epoch warming are polarized around the hypotheses of anthropogenic warming (AW) and giant natural fluctuations (GNFs). While climate sceptics have systematically attacked AW, up until now they have only invoked GNFs. This has now changed with the publication by D. Keenan of a sample of 1000 series from stochastic processes purporting to emulate the global annual temperature since 1880. While Keenan's objective was to criticize the International Panel on Climate Change's trend uncertainty analysis (their assumption that residuals are only weakly correlated), for the first time it is possible to compare a stochastic GNF model with real data. Using Haar fluctuations, probability distributions, and other techniques of time series analysis, we show that his model has unrealistically strong low-frequency variability so that even mild extrapolations imply ice ages every ≈1000 years. Helped by statistics, the GNF model can easily be scientifically rejected.
Hosaka, Tadaaki; Ohira, Toru; Lucian, Christian; Milton, John
2005-03-01
Time-delayed feedback control becomes problematic in situations in which the time constant of the system is fast compared to the feedback reaction time. In particular, when perturbations are unpredictable, traditional feedback or feed-forward control schemes can be insufficient. Nonethless a human can balance a stick at their fingertip in the presence of fluctuations that occur on time scales shorter than their neural reaction times. Here we study a simple model of a repulsive delayed random walk and demonstrate that the interplay between noise and delay can transiently stabilize an unstable fixed-point. This observation leads to the concept of ``delayed stochastic control,'' i.e. stabilization of tasks, such as stick balancing at the fingertip, by optimally tuning the noise level with respect to the feedback delay time. References:(1)J.L.Cabrera and J.G.Milton, PRL 89 158702 (2002);(2) T. Ohira and J.G.Milton, PRE 52 3277 (1995);(3)T.Hosaka, T.Ohira, C.Lucian, J.L.Cabrera, and J.G.Milton, Prog. Theor. Phys. (to appear).
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...
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.
Cosmological fluctuations of a random field and radiation fluid
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Bastero-Gil, Mar [Departamento de Física Teórica y del Cosmos, Campus de Fuentenueva, Universidad de Granada, Granada, 18071 (Spain); Berera, Arjun [SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ (United Kingdom); Moss, Ian G. [School of Mathematics and Statistics, Newcastlle University, Newcastle upon Tyne, NE1 7RU (United Kingdom); Ramos, Rudnei O., E-mail: mbg@ugr.es, E-mail: ab@ph.ed.ac.uk, E-mail: ian.moss@ncl.ac.uk, E-mail: rudnei@uerj.br [Departamento de Física Teórica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, 20550-013 Brazil (Brazil)
2014-05-01
A generalization of the random fluid hydrodynamic fluctuation theory due to Landau and Lifshitz is applied to describe cosmological fluctuations in systems with radiation and scalar fields. The viscous pressures, parametrized in terms of the bulk and shear viscosity coefficients, and the respective random fluctuations in the radiation fluid are combined with the stochastic and dissipative scalar evolution equation. This results in a complete set of equations describing the perturbations in both scalar and radiation fluids. These derived equations are then studied, as an example, in the context of warm inflation. Similar treatments can be done for other cosmological early universe scenarios involving thermal or statistical fluctuations.
General Analysis of Type I Planetary Migration with Stochastic Perturbations
Adams, Fred C
2009-01-01
This paper presents a generalized treatment of Type I planetary migration in the presence of stochastic perturbations. In many planet-forming disks, the Type I migration mechanism, driven by asymmetric torques, acts on a short time scale and compromises planet formation. If the disk also supports MHD instabilities, however, the corresponding turbulent fluctuations produce additional stochastic torques that modify the steady inward migration scenario. This work studies the migration of planetary cores in the presence of stochastic fluctuations using complementary methods, including a Fokker-Planck approach and iterative maps. Stochastic torques have two main effects: [1] Through outward diffusion, a small fraction of the planetary cores can survive in the face of Type I inward migration. [2] For a given starting condition, the result of any particular realization of migration is uncertain, so that results must be described in terms of the distributions of outcomes. In addition to exploring different regimes of...
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...
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
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.
Asymmetric stochastic switching driven by intrinsic molecular noise.
Directory of Open Access Journals (Sweden)
David Frigola
Full Text Available 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 inherently state-dependent, drive asymmetric switching. These theoretical results are consistent with experimental data that have been reported for the bistable system of the gallactose signaling network in yeast. Our study unravels that intrinsic fluctuations, while not required to describe bistability, are fundamental to understand stochastic switching and the dynamical relative stability of multiple states.
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...
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 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...
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.
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
Directory of Open Access Journals (Sweden)
Chia Yin Lee
2011-12-01
Full Text Available Chikungunya virus (CHIKV is an alphavirus responsible for numerous epidemics throughout Africa and Asia, causing infectious arthritis and reportedly linked with fatal infections in newborns and elderly. Previous studies in animal models indicate that humoral immunity can protect against CHIKV infection, but despite the potential efficacy of B-cell-driven intervention strategies, there are no virus-specific vaccines or therapies currently available. In addition, CHIKV has been reported to elicit long-lasting virus-specific IgM in humans, and to establish long-term persistence in non-human primates, suggesting that the virus might evade immune defenses to establish chronic infections in man. However, the mechanisms of immune evasion potentially employed by CHIKV remain uncharacterized. We previously described two human monoclonal antibodies that potently neutralize CHIKV infection. In the current report, we have characterized CHIKV mutants that escape antibody-dependent neutralization to identify the CHIKV E2 domain B and fusion loop "groove" as the primary determinants of CHIKV interaction with these antibodies. Furthermore, for the first time, we have also demonstrated direct CHIKV cell-to-cell transmission, as a mechanism that involves the E2 domain A and that is associated with viral resistance to antibody-dependent neutralization. Identification of CHIKV sub-domains that are associated with human protective immunity, will pave the way for the development of CHIKV-specific sub-domain vaccination strategies. Moreover, the clear demonstration of CHIKV cell-to-cell transmission and its possible role in the establishment of CHIKV persistence, will also inform the development of future anti-viral interventions. These data shed new light on CHIKV-host interactions that will help to combat human CHIKV infection and inform future studies of CHIKV pathogenesis.
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...
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...
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.
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.
Stochastic single-molecule dynamics of synaptic membrane protein domains
Kahraman, Osman; Haselwandter, Christoph A
2016-01-01
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.
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.
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)
Michelle Hawkins
2013-11-01
Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.
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.
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...
Fundamentals of Stochastic Networks
Ibe, Oliver C
2011-01-01
An interdisciplinary approach to understanding queueing and graphical networks In today's era of interdisciplinary studies and research activities, network models are becoming increasingly important in various areas where they have not regularly been used. Combining techniques from stochastic processes and graph theory to analyze the behavior of networks, Fundamentals of Stochastic Networks provides an interdisciplinary approach by including practical applications of these stochastic networks in various fields of study, from engineering and operations management to communications and the physi
Singular stochastic differential equations
Cherny, Alexander S
2005-01-01
The authors introduce, in this research monograph on stochastic differential equations, a class of points termed isolated singular points. Stochastic differential equations possessing such points (called singular stochastic differential equations here) arise often in theory and in applications. However, known conditions for the existence and uniqueness of a solution typically fail for such equations. The book concentrates on the study of the existence, the uniqueness, and, what is most important, on the qualitative behaviour of solutions of singular stochastic differential equations. This is done by providing a qualitative classification of isolated singular points, into 48 possible types.
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...
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.
Mean, fluctuations and predictability in biological dispersal
Giometto, A.; Altermatt, F.; Carrara, F.; Rinaldo, A.
2013-12-01
Dispersal is a key ecological phenomenon, fundamental to the understanding of the dynamics of invasive species, spread of epidemics and range shifts due to climate or environmental change. Additionally, organisms' spread drives species distribution and affects their coexistence. Despite its relevance, replicated experimentation on biological dispersal is inconclusive to date and current assessments point at inherent limitations to predictability owing to large fluctuations even in the simplest ecological settings. In contrast, we show by replicated experimentation on the spread of the ciliate Tetrahymena sp. in linear landscapes, that information on local unconstrained movement and reproduction of individuals allows to predict reliably the existence and speed of traveling waves of invasion at the macroscopic scale. Furthermore, a theoretical approach introducing demographic stochasticity in the Fisher-Kolmogorov framework of reaction-diffusion processes is shown to capture both the mean and the observed fluctuations in range expansions between replicated invasions. Thus, the predictability of the phenomenon overcomes the inherent stochasticity. Notably, predictions on the spread of organisms are based on local, short-time and independent observations of the two processes affecting dispersal, namely individuals' movement and reproduction. Our results establish a causal link from the short-term individual level to the long-term, broad-scale population patterns and may be generalized to sort whether the variability observed in nature or in experimental ensembles might be accounted for by systematic differences between landscapes or by stochasticity affecting basic vital rates of the organisms involved.
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.
Directory of Open Access Journals (Sweden)
Masashi Fujita
Full Text Available In the two-cell stage embryos of Caenorhabditis elegans, the contact surface of the two blastomeres forms a curve that bulges from the AB blastomere to the P₁ blastomere. This curve is a consequence of the high intracellular hydrostatic pressure of AB compared with that of P₁. However, the higher pressure in AB is intriguing because AB has a larger volume than P₁. In soap bubbles, which are a widely used model of cell shape, a larger bubble has lower pressure than a smaller bubble. Here, we reveal that the higher pressure in AB is mediated by its higher cortical tension. The cell fusion experiments confirmed that the curvature of the contact surface is related to the pressure difference between the cells. Chemical and genetic interferences showed that the pressure difference is mediated by actomyosin. Fluorescence imaging indicated that non-muscle myosin is enriched in the AB cortex. The cell killing experiments provided evidence that AB but not P₁ is responsible for the pressure difference. Computer simulation clarified that the cell-to-cell heterogeneity of cortical tensions is indispensable for explaining the pressure difference. This study demonstrates that heterogeneity in surface tension results in significant deviations of cell behavior compared to simple soap bubble models, and thus must be taken into consideration in understanding cell shape within embryos.
Fujita, Masashi; Onami, Shuichi
2012-01-01
In the two-cell stage embryos of Caenorhabditis elegans, the contact surface of the two blastomeres forms a curve that bulges from the AB blastomere to the P₁ blastomere. This curve is a consequence of the high intracellular hydrostatic pressure of AB compared with that of P₁. However, the higher pressure in AB is intriguing because AB has a larger volume than P₁. In soap bubbles, which are a widely used model of cell shape, a larger bubble has lower pressure than a smaller bubble. Here, we reveal that the higher pressure in AB is mediated by its higher cortical tension. The cell fusion experiments confirmed that the curvature of the contact surface is related to the pressure difference between the cells. Chemical and genetic interferences showed that the pressure difference is mediated by actomyosin. Fluorescence imaging indicated that non-muscle myosin is enriched in the AB cortex. The cell killing experiments provided evidence that AB but not P₁ is responsible for the pressure difference. Computer simulation clarified that the cell-to-cell heterogeneity of cortical tensions is indispensable for explaining the pressure difference. This study demonstrates that heterogeneity in surface tension results in significant deviations of cell behavior compared to simple soap bubble models, and thus must be taken into consideration in understanding cell shape within embryos. PMID:22253922
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.
Agbo, Solomon N.; Merdzhanova, Tsvetelina; Yu, Shicheng; Tempel, Hermann; Kungl, Hans; Eichel, Rüdiger-A.; Rau, Uwe; Astakhov, Oleksandr
2016-09-01
This work focuses on the potentials of monolithic integrated thin-film silicon solar cell and lithium ion cell in a simple cell-to-cell integration without any control electronics as a compact power solution for portable electronic devices. To demonstrate this we used triple-junction thin-film silicon solar cell connected directly to a lithium ion battery cell to charge the battery and in turn discharge the battery through the solar cell. Our results show that with appropriate voltage matching the solar cell provides efficient charging for lab-scale lithium ion storage cell. Despite the absence of any control electronics the discharge rate of the Li-ion cell through the non-illuminated solar cell can be much lower than the charging rate when the current voltage (IV) characteristics of the solar cell is matched properly to the charge-discharge characteristics of the battery. This indicates good sustainability of the ultimately simple integrated device. At the maximum power point, solar energy-to-battery charging efficiency of 8.5% which is nearly the conversion efficiency of the solar cell was obtained indicating potential for loss-free operation of the photovoltaic (PV)-battery integration. For the rest of the charging points, an average of 8.0% charging efficiency was obtained.
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.
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...
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)
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.
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...
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)
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...
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
Bible, Amber; Russell, Matthew H; Alexandre, Gladys
2012-07-01
The Che1 chemotaxis-like pathway of Azospirillum brasilense contributes to chemotaxis and aerotaxis, and it has also been found to contribute to regulating changes in cell surface adhesive properties that affect the propensity of cells to clump and to flocculate. The exact contribution of Che1 to the control of chemotaxis and flocculation in A. brasilense remains poorly understood. Here, we show that Che1 affects reversible cell-to-cell clumping, a cellular behavior in which motile cells transiently interact by adhering to one another at their nonflagellated poles before swimming apart. Clumping precedes and is required for flocculation, and both processes appear to be independently regulated. The phenotypes of a ΔaerC receptor mutant and of mutant strains lacking cheA1, cheY1, cheB1, or cheR1 (alone or in combination) or with che1 deleted show that Che1 directly mediates changes in the flagellar swimming velocity and that this behavior directly modulates the transient nature of clumping. Our results also suggest that an additional receptor(s) and signaling pathway(s) are implicated in mediating other Che1-independent changes in clumping identified in the present study. Transient clumping precedes the transition to stable clump formation, which involves the production of specific extracellular polysaccharides (EPS); however, production of these clumping-specific EPS is not directly controlled by Che1 activity. Che1-dependent clumping may antagonize motility and prevent chemotaxis, thereby maintaining cells in a metabolically favorable niche.
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.
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.
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
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.
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.
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.
Applications of Little's Law to stochastic models of gene expression
Elgart, Vlad; Kulkarni, Rahul V
2010-01-01
The intrinsic stochasticity of gene expression can lead to large variations in protein levels across a population of cells. To explain this variability, different sources of mRNA fluctuations ('Poisson' and 'Telegraph' processes) have been proposed in stochastic models of gene expression. Both Poisson and Telegraph scenario models explain experimental observations of noise in protein levels in terms of 'bursts' of protein expression. Correspondingly, there is considerable interest in establishing relations between burst and steady-state protein distributions for general stochastic models of gene expression. In this work, we address this issue by considering a mapping between stochastic models of gene expression and problems of interest in queueing theory. By applying a general theorem from queueing theory, Little's Law, we derive exact relations which connect burst and steady-state distribution means for models with arbitrary waiting-time distributions for arrival and degradation of mRNAs and proteins. The de...
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...
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...
DEFF Research Database (Denmark)
Shang, Yunlong; Zhang, Chenghui; Cui, Naxin;
2015-01-01
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...
Taoka, Ken-ichiro; Ham, Byung-Kook; Xoconostle-Cázares, Beatriz; Rojas, Maria R.; Lucas, William J.
2007-01-01
In plants, cell-to-cell trafficking of non-cell-autonomous proteins (NCAPs) involves protein–protein interactions, and a role for posttranslational modification has been implicated. In this study, proteins contained in pumpkin (Cucurbita maxima cv Big Max) phloem sap were used as a source of NCAPs to further explore the molecular basis for selective NCAP trafficking. Protein overlay assays and coimmunoprecipitation experiments established that phosphorylation and glycosylation, on both Nicotiana tabacum NON-CELL-AUTONOMOUS PATHWAY PROTEIN1 (Nt-NCAPP1) and the phloem NCAPs, are essential for their interaction. Detailed molecular analysis of a representative phloem NCAP, Cm-PP16-1, identified the specific residues on which glycosylation and phosphorylation must occur for effective binding to NCAPP1. Microinjection studies confirmed that posttranslational modification on these residues is essential for cell-to-cell movement of Cm-PP16-1. Lastly, a glutathione S-transferase (GST)–Cm-PP16-1 fusion protein system was employed to test whether the peptide region spanning these residues was required for cell-to-cell movement. These studies established that a 36–amino acid peptide was sufficient to impart cell-to-cell movement capacity to GST, a normally cell-autonomous protein. These findings are consistent with the hypothesis that a phosphorylation-glycosylation recognition motif functions to control the binding of a specific subset of phloem NCAPs to NCAPP1 and their subsequent transport through plasmodesmata. PMID:17601822
As, van H.
2007-01-01
Water content and hydraulic conductivity, including transport within cells, over membranes, cell-to-cell, and long-distance xylem and phloem transport, are strongly affected by plant water stress. By being able to measure these transport processes non-invasely in the intact plant situation in relati
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.
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.
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
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.
Stochastic behavior of nanoscale dielectric wall buckling
Friedman, Lawrence H.; Levin, Igor; Cook, Robert F.
2016-01-01
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. PMID:27330220
Hydrodynamics of charge fluctuations and balance functions
Ling, B; Stephanov, M
2013-01-01
We apply stochastic hydrodynamics to the study of charge density fluctuations in QCD matter undergoing Bjorken expansion. We find that the charge density correlations are given by a time integral over the history of the system, with the dominant contribution coming from the QCD crossover region where the change of susceptibility per entropy, chi T/s, is most significant. We study the rapidity and azimuthal angle dependence of the resulting charge balance function using a simple analytic model of heavy-ion collision evolution. Our results are in agreement with experimental measurements, indicating that hydrodynamic fluctuations contribute significantly to the measured charge correlations in high energy heavy-ion collisions. The sensitivity of the balance function to the value of the charge diffusion coefficient D allows us to estimate the typical value of this coefficient in the crossover region to be rather small, of the order of 1/(2pi T), characteristic of a strongly coupled plasma.
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 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.
Studies of Fluctuation Processes in Nuclear Collisions
Energy Technology Data Exchange (ETDEWEB)
Ayik, Sakir [Tennessee Technological Univ., Cookeville, TN (United States). Dept. of Physics
2016-04-14
fluctuation mechanism do not play an important role at low energies and the mean-field fluctuations provide the dominant mechanism. The PI developed a stochastic mean-field (SMF) approach for nuclear dynamics by incorporating zero-point and thermal fluctuations of the initial state. This improvement provides an approximate description of quantal fluctuations of the collective motion, which was missing in the standard mean-field approach. We carried out a number of applications of the SMF approach for dynamics of spinodal instabilities in nuclear matter and the nucleon exchange mechanism in the quasi fission reactions. Further applications of the approach are currently in progress.
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.
Frédéric, Pierret
2014-01-01
The equations of celestial mechanics that govern the variation of the orbital elements are completely derived for stochastic perturbation which generalized the classic perturbation equations which are used since Gauss, starting from Newton's equation and it's solution. The six most understandable orbital element, the semi-major axis, the eccentricity, the inclination, the longitude of the ascending node, the pericenter angle and the mean motion are express in term of the angular momentum vector $\\textbf{H}$ per unit of mass and the energy $E$ per unit of mass. We differentiate those expressions using It\\^o's theory of differential equations due to the stochastic nature of the perturbing force. The result is applied to the two-body problem perturbed by a stochastic dust cloud and also perturbed by a stochastic dynamical oblateness of the central body.
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 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
Geometric Stochastic Resonance
Ghosh, Pulak Kumar; Savel'ev, Sergey E; Nori, Franco
2015-01-01
A Brownian particle moving across a porous membrane subject to an oscillating force exhibits stochastic resonance with properties which strongly depend on the geometry of the confining cavities on the two sides of the membrane. Such a manifestation of stochastic resonance requires neither energetic nor entropic barriers, and can thus be regarded as a purely geometric effect. The magnitude of this effect is sensitive to the geometry of both the cavities and the pores, thus leading to distinctive optimal synchronization conditions.
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...
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 ...
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.
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.
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.
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).
Enhancement of Ambipolar Diffusion Rates through Field Fluctuations
Fatuzzo, M; Fatuzzo, Marco; Adams, Fred C.
2002-01-01
Previous treatments of ambipolar diffusion in star-forming molecular clouds do not consider the effects of fluctuations in the fluid fields about their mean values. This paper generalizes the ambipolar diffusion problem in molecular cloud layers to include such fluctuations. Because magnetic diffusion is a nonlinear process, fluctuations can lead to an enhancement of the ambipolar diffusion rate. In addition, the stochastic nature of the process makes the ambipolar diffusion time take on a distribution of different values. In this paper, we focus on the case of long wavelength fluctuations and find that the rate of ambipolar diffusion increases by a significant factor $\\Lambda \\sim 1 - 10$. The corresponding decrease in the magnetic diffusion time helps make ambipolar diffusion more consistent with observations.
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...
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.
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...
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.
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.
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...
Messenger RNA Fluctuations and Regulatory RNAs Shape the Dynamics of Negative Feedback Loop
Martínez, María Rodríguez; Tlusty, Tsvi; Pilpel, Yitzhak; Furman, Itay; 10.1103/PhysRevE.81.031924
2010-01-01
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while individual cells may show sustained oscillations in the concentrations of some proteins, such oscillations may appear damped in the population average. In this paper we investigate the role of RNA stochastic fluctuations as a leading force to produce a sustained excitatory behavior at the single cell level. Opposed to some previous models, we build a fully stochastic model of a negative feedback loop that explicitly takes into account the RNA stochastic dynamics. We find that messenger RNA random fluctuations can be amplified during translation and produce sustained pulses of protein expression. Motivated by the recent appreciation of the importance of non--coding regulatory RNAs in post--transcription regulation, we also consider the possibility that a regulatory RNA transcri...
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 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
Pierret, Frédéric
2016-02-01
We derived the equations of Celestial Mechanics governing the variation of the orbital elements under a stochastic perturbation, thereby generalizing the classical Gauss equations. Explicit formulas are given for the semimajor axis, the eccentricity, the inclination, the longitude of the ascending node, the pericenter angle, and the mean anomaly, which are expressed in term of the angular momentum vector H per unit of mass and the energy E per unit of mass. Together, these formulas are called the stochastic Gauss equations, and they are illustrated numerically on an example from satellite dynamics.
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.
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...
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 entrainment of a stochastic oscillator.
Wang, Guanyu; Peskin, Charles S
2015-01-01
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.
Gaussian fluctuations of singleeigenvalues intime-dependent GUE
Schön, Victor
2013-01-01
This thesis investigates the fluctuations of the eigenvalues of the Gaussian Unitary Ensemble on the basis of numerical simulations performed in the programming environment MATLAB. As is well known: if a Wiener process is defined on the space of Hermitian matrices then the eigenvalues describe a stochastic process known as Dyson Brownian motion. Thus, given a realisation of Dyson Brownian motion, the aim of this thesis is to investigate the distribution of a certain random vector pertaining t...
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...
Diffusion in fluctuating media: first passage time problem
Energy Technology Data Exchange (ETDEWEB)
Revelli, Jorge A.; Budde, Carlos E.; Wio, Horacio S
2002-12-30
We study the actual and important problem of Mean First Passage Time (MFPT) for diffusion in fluctuating media. We exploit van Kampen's technique of composite stochastic processes, obtaining analytical expressions for the MFPT for a general system, and focus on the two state case where the transitions between the states are modelled introducing both Markovian and non-Markovian processes. The comparison between the analytical and simulations results show an excellent agreement.
Stochastic integrals: a combinatorial approach
Rota, Gian-Carlo; Wallstrom, Timothy C.
1997-01-01
A combinatorial definition of multiple stochastic integrals is given in the setting of random measures. It is shown that some properties of such stochastic integrals, formerly known to hold in special cases, are instances of combinatorial identities on the lattice of partitions of a set. The notion of stochastic sequences of binomial type is introduced as a generalization of special polynomial sequences occuring in stochastic integration, such as Hermite, Poisson–Charlier an...
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...
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.
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 ...
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
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.
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.
Turning the resistive MHD into a stochastic field theory
Materassi, M.; Consolini, G.
2008-08-01
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.
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...
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...
Stochastic heart-rate model can reveal pathologic cardiac dynamics
Kuusela, Tom
2004-03-01
A simple one-dimensional Langevin-type stochastic difference equation can simulate the heart-rate fluctuations in a time scale from minutes to hours. The model consists of a deterministic nonlinear part and a stochastic part typical of Gaussian noise, and both parts can be directly determined from measured heart-rate data. Data from healthy subjects typically exhibit the deterministic part with two or more stable fixed points. Studies of 15 congestive heart-failure subjects reveal that the deterministic part of pathologic heart dynamics has no clear stable fixed points. Direct simulations of the stochastic model for normal and pathologic cases can produce statistical parameters similar to those of real subjects. Results directly indicate that pathologic situations simplify the heart-rate control system.
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.
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...
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...
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 ...
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.
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,...
D.F. Schrager
2006-01-01
We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing m
Energy Technology Data Exchange (ETDEWEB)
Tollestrup, A.V.; Dugan, G
1983-12-01
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. (GHT)
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.
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.
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.
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.
Directory of Open Access Journals (Sweden)
Rika Etchuuya
Full Text Available Escherichia coli is not assumed to be naturally transformable. However, several recent reports have shown that E. coli can express modest genetic competence in certain conditions that may arise in its environment. We have shown previously that spontaneous lateral transfer of non-conjugative plasmids occurs in a colony biofilm of mixed E. coli strains (a set of a donor strain harbouring a plasmid and a plasmid-free recipient strain. In this study, with high-frequency combinations of strains and a plasmid, we constructed the same lateral plasmid transfer system in liquid culture. Using this system, we demonstrated that this lateral plasmid transfer was DNase-sensitive, indicating that it is a kind of transformation in which DNase-accessible extracellular naked DNA is essential. However, this transformation did not occur with purified plasmid DNA and required a direct supply of plasmid from co-existing donor cells. Based on this feature, we have termed this transformation type as 'cell-to-cell transformation'. Analyses using medium conditioned with the high-frequency strain revealed that this strain released a certain factor(s that promoted cell-to-cell transformation and arrested growth of the other strains. This factor is heat-labile and protease-sensitive, and its roughly estimated molecular mass was between ∼9 kDa and ∼30 kDa, indicating that it is a polypeptide factor. Interestingly, this factor was effective even when the conditioned medium was diluted 10(-5-10(-6, suggesting that it acts like a pheromone with high bioactivity. Based on these results, we propose that cell-to-cell transformation is a novel natural transformation mechanism in E. coli that requires cell-derived DNA and is promoted by a peptide pheromone. This is the first evidence that suggests the existence of a peptide pheromone-regulated transformation mechanism in E. coli and in Gram-negative bacteria.
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
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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.
Balint, Richard; Richardson, Stephen M; Cartmell, Sarah H
2015-10-01
Numerous scientific studies and clinical trials are carried out each year exploring the use of mesenchymal stromal cells in regenerative medicine and tissue engineering. However, the effective and reliable expansion of this very important cell type remains a challenge. In this study the importance of cell-to-cell contact during expansion has been explored on the proliferation and differentiation potential of the produced cells. Cells were cultured up to passage 5 under conditions where cell-to-cell contact was either probable (40-70% confluence; see supporting information, Protocol A) or where it was unlikely (10-50% confluence; see supporting information, Protocol B). The effect of the two different conditions on expansion efficiency; proliferation rate and tri-lineage differentiation potential was assessed. Differences in immunophenotype, cell size and senescence were also investigated. Protocol B cultures expanded twice as fast as those cultured with Protocol A. In passage 5 experiments low confluence expanded cells displayed a 10% higher overall proliferation rate, and produced 23% more cells in growth, 12% more in osteogenic, 77% more in adipogenic, but 27% less in chondrogenic medium. Differentiation potential wasn't decisively affected at the mRNA level. However, Protocol B favoured bone and cartilage differentiation at the secretional level. Protocol A populations showed reduced purity, expressing CD105 in only 76% compared to the 96.7% in Protocol B cultures. Protocol A populations also contained significantly more (+4.2%) senescent cells, however, no difference was found in cell size between the two protocols. The findings of this study suggest that cell-to-cell contact, and therefore high confluence levels, is detrimental to MSC quality.
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.
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
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.
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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.
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...
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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)
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.
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.
Wei, Katy; Moinat, Maxim; Maarleveld, Timo R; Bruggeman, Frank J
2014-07-29
Signal transduction by prokaryotes almost exclusively relies on two-component systems for sensing and responding to (extracellular) signals. Here, we use stochastic models of two-component systems to better understand the impact of stochasticity on the fidelity and robustness of signal transmission, the outcome of autoregulatory gene expression and the influence of cell growth and division. We report that two-component systems are remarkably robust against copy number fluctuations of the signalling proteins they are composed of, which enhances signal transmission fidelity. Furthermore, we find that due to stochasticity these systems can get locked in an active state for extended time periods when (initially high) signal levels drop to zero. This behaviour can contribute to a bet-hedging adaptation strategy, aiding survival in fluctuating environments. Additionally, autoregulatory gene expression can cause two-component systems to become bistable at realistic parameter values. As a result, two sub-populations of cells can co-exist-active and inactive cells, which contributes to fitness in unpredictable environments. Bistability proved robust with respect to cell growth and division, and is tunable by the growth rate. In conclusion, our results indicate how single cells can cope with the inevitable stochasticity occurring in the activity of their two-component systems. They are robust to disadvantageous fluctuations that scramble signal transduction and they exploit beneficial stochasticity that generates fitness-enhancing heterogeneity across an isogenic population of cells.
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
Predicting evolutionary rescue via evolving plasticity in stochastic environments.
Ashander, Jaime; Chevin, Luis-Miguel; Baskett, Marissa L
2016-09-28
Phenotypic plasticity and its evolution may help evolutionary rescue in a novel and stressful environment, especially if environmental novelty reveals cryptic genetic variation that enables the evolution of increased plasticity. However, the environmental stochasticity ubiquitous in natural systems may alter these predictions, because high plasticity may amplify phenotype-environment mismatches. Although previous studies have highlighted this potential detrimental effect of plasticity in stochastic environments, they have not investigated how it affects extinction risk in the context of evolutionary rescue and with evolving plasticity. We investigate this question here by integrating stochastic demography with quantitative genetic theory in a model with simultaneous change in the mean and predictability (temporal autocorrelation) of the environment. We develop an approximate prediction of long-term persistence under the new pattern of environmental fluctuations, and compare it with numerical simulations for short- and long-term extinction risk. We find that reduced predictability increases extinction risk and reduces persistence because it increases stochastic load during rescue. This understanding of how stochastic demography, phenotypic plasticity, and evolution interact when evolution acts on cryptic genetic variation revealed in a novel environment can inform expectations for invasions, extinctions, or the emergence of chemical resistance in pests. PMID:27655762
Demography of Verreaux's sifaka in a stochastic rainfall environment.
Lawler, Richard R; Caswell, Hal; Richard, Alison F; Ratsirarson, Joelisoa; Dewar, Robert E; Schwartz, Marion
2009-09-01
In this study, we use deterministic and stochastic models to analyze the demography of Verreaux's sifaka (Propithecus verreauxi verreauxi) in a fluctuating rainfall environment. The model is based on 16 years of data from Beza Mahafaly Special Reserve, southwest Madagascar. The parameters in the stage-classified life cycle were estimated using mark-recapture methods. Statistical models were evaluated using information-theoretic techniques and multi-model inference. The highest ranking model is time-invariant, but the averaged model includes rainfall-dependence of survival and breeding. We used a time-series model of rainfall to construct a stochastic demographic model. The time-invariant model and the stochastic model give a population growth rate of about 0.98. Bootstrap confidence intervals on the growth rates, both deterministic and stochastic, include 1. Growth rates are most elastic to changes in adult survival. Many demographic statistics show a nonlinear response to annual rainfall but are depressed when annual rainfall is low, or the variance in annual rainfall is high. Perturbation analyses from both the time-invariant and stochastic models indicate that recruitment and survival of older females are key determinants of population growth rate.
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.
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
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.
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.
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...
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.
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...
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
Stochastic modelling of turbulence
DEFF Research Database (Denmark)
Sørensen, Emil Hedevang Lohse
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...... turbine operates in the turbulent atmospheric boundary layer. In this respect, three regimes are of particular interest: modelling the turbulent wind before it interacts with the wind turbine (e.g. to be used in load simulations), modelling of the interaction of the wind with the wind turbine (e.......g. to extract information about a wind turbine's production of power), and modelling the wake generated by the wind turbine so that its influence on other wind turbines further downstream in turn can be modelled (e.g. to be used in load simulations). The thesis makes the contributions listed below. A spatial...
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 porous media equations
Barbu, Viorel; Röckner, Michael
2016-01-01
Focusing on stochastic porous media equations, this book places an emphasis on existence theorems, asymptotic behavior and ergodic properties of the associated transition semigroup. Stochastic perturbations of the porous media equation have reviously been considered by physicists, but rigorous mathematical existence results have only recently been found. The porous media equation models a number of different physical phenomena, including the flow of an ideal gas and the diffusion of a compressible fluid through porous media, and also thermal propagation in plasma and plasma radiation. Another important application is to a model of the standard self-organized criticality process, called the "sand-pile model" or the "Bak-Tang-Wiesenfeld model". The book will be of interest to PhD students and researchers in mathematics, physics and biology.
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.
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...
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.
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)
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.
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...
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.
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 ...
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.
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...
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.
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
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.
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
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.
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.
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.
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...
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)
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.
Superfluid phase transition with activated velocity fluctuations: Renormalization group approach.
Dančo, Michal; Hnatič, Michal; Komarova, Marina V; Lučivjanský, Tomáš; Nalimov, Mikhail Yu
2016-01-01
A quantum field model that incorporates Bose-condensed systems near their phase transition into a superfluid phase and velocity fluctuations is proposed. The stochastic Navier-Stokes equation is used for a generation of the velocity fluctuations. As such this model generalizes model F of critical dynamics. The field-theoretic action is derived using the Martin-Siggia-Rose formalism and path integral approach. The regime of equilibrium fluctuations is analyzed within the perturbative renormalization group method. The double (ε,δ)-expansion scheme is employed, where ε is a deviation from space dimension 4 and δ describes scaling of velocity fluctuations. The renormalization procedure is performed to the leading order. The main corollary gained from the analysis of the thermal equilibrium regime suggests that one-loop calculations of the presented models are not sufficient to make a definite conclusion about the stability of fixed points. We also show that critical exponents are drastically changed as a result of the turbulent background and critical fluctuations are in fact destroyed by the developed turbulence fluctuations. The scaling exponent of effective viscosity is calculated and agrees with expected value 4/3.
Fluctuating hyperfine interactions: an updated computational implementation
Zacate, M. O.; Evenson, W. E.
2015-04-01
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.
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.
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.
Lyapunov exponents of stochastic systems—from micro to macro
Laffargue, Tanguy; Tailleur, Julien; van Wijland, Frédéric
2016-03-01
Lyapunov exponents of dynamical systems are defined from the rates of divergence of nearby trajectories. For stochastic systems, one typically assumes that these trajectories are generated under the ‘same noise realization’. The purpose of this work is to critically examine what this expression means. For Brownian particles, we consider two natural interpretations of the noise: intrinsic to the particles or stemming from the fluctuations of the environment. We show how they lead to different distributions of the largest Lyapunov exponent as well as different fluctuating hydrodynamics for the collective density field. We discuss, both at microscopic and macroscopic levels, the limits in which these noise prescriptions become equivalent. We close this paper by providing an estimate of the largest Lyapunov exponent and of its fluctuations for interacting particles evolving with Dean-Kawasaki dynamics.
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...
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
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...
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)
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...
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.
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.
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.
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。
Nomura, Fumimasa; Kaneko, Tomoyuki; Hamada, Tomoyo; Hattori, Akihiro; Yasuda, Kenji
2013-06-01
To predict the risk of fatal arrhythmia induced by cardiotoxicity in the highly complex human heart system, we have developed a novel quasi-in vivo electrophysiological measurement assay, which combines a ring-shaped human cardiomyocyte network and a set of two electrodes that form a large single ring-shaped electrode for the direct measurement of irregular cell-to-cell conductance occurrence in a cardiomyocyte network, and a small rectangular microelectrode for forced pacing of cardiomyocyte beating and for acquiring the field potential waveforms of cardiomyocytes. The advantages of this assay are as follows. The electrophysiological signals of cardiomyocytes in the ring-shaped network are superimposed directly on a single loop-shaped electrode, in which the information of asynchronous behavior of cell-to-cell conductance are included, without requiring a set of huge numbers of microelectrode arrays, a set of fast data conversion circuits, or a complex analysis in a computer. Another advantage is that the small rectangular electrode can control the position and timing of forced beating in a ring-shaped human induced pluripotent stem cell (hiPS)-derived cardiomyocyte network and can also acquire the field potentials of cardiomyocytes. First, we constructed the human iPS-derived cardiomyocyte ring-shaped network on the set of two electrodes, and acquired the field potential signals of particular cardiomyocytes in the ring-shaped cardiomyocyte network during simultaneous acquisition of the superimposed signals of whole-cardiomyocyte networks representing cell-to-cell conduction. Using the small rectangular electrode, we have also evaluated the response of the cell network to electrical stimulation. The mean and SD of the minimum stimulation voltage required for pacing (VMin) at the small rectangular electrode was 166+/-74 mV, which is the same as the magnitude of amplitude for the pacing using the ring-shaped electrode (179+/-33 mV). The results showed that the
Stochastic population dynamics in astrochemistry and aerosol science
Losert-Valiente Kroon, C. M.
Classical, non-equilibrium systems of diffusing species or entities undergoing depletion, evaporation and reaction processes are at the heart of many problems in Physics, Chemistry, Biology and Financial Mathematics. It is well known that fluctuations and correlations in statistical systems can have a profound influence on the macroscopic properties of the system. However, the traditional rate equations that describe the evolution of mean populations in time and space do not incorporate statistical fluctuations. This becomes an issue of great importance when population densities are low. In order to develop a stochastic description of birth-and-death processes beyond the mean field approximation I employ techniques in classical many-body Physics in a manner analogous to the treatment of quantum systems. I obtain promising results to understand and quantify the exact circumstances of the failure of the mean-field approximation in specific problems in Astrophysics, namely heterogeneous chemical reactions in interstellar clouds, and in Aerosol Science, namely heterogeneous nucleation processes, and deliver the means to manipulate the alternative stochastic framework according to the Doi-Peliti formalism. In this framework the mean population of a species is given by the average of a solution to a set of constraint equations over all realisations of the stochastic noise. The constraint equations are inhomogeneous stochastic partial differential equations with multiplicative real or complex Gaussian noise. In general, these equations cannot be solved analytically. Therefore I resort to the numerical implementation of the Doi-Peliti formalism. The main code is written in the GNU C language, some algebraic calculations are performed by means of the MapleV package. In the case of large population densities the stochastic framework renders the same results as the mean field approximation whereas for low population densities its predictions differ substantially from the
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.
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.
Stochastic synchronization of genetic oscillator networks
Directory of Open Access Journals (Sweden)
Chen Luonan
2007-01-01
Full Text Available Abstract Background The study of synchronization among genetic oscillators is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. Genetic networks are intrinsically noisy due to natural random intra- and inter-cellular fluctuations. Therefore, it is important to study the effects of noise perturbation on the synchronous dynamics of genetic oscillators. From the synthetic biology viewpoint, it is also important to implement biological systems that minimizing the negative influence of the perturbations. Results In this paper, based on systems biology approach, we provide a general theoretical result on the synchronization of genetic oscillators with stochastic perturbations. By exploiting the specific properties of many genetic oscillator models, we provide an easy-verified sufficient condition for the stochastic synchronization of coupled genetic oscillators, based on the Lur'e system approach in control theory. A design principle for minimizing the influence of noise is also presented. To demonstrate the effectiveness of our theoretical results, a population of coupled repressillators is adopted as a numerical example. Conclusion In summary, we present an efficient theoretical method for analyzing the synchronization of genetic oscillator networks, which is helpful for understanding and testing the synchronization phenomena in biological organisms. Besides, the results are actually applicable to general oscillator networks.
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
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...
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...
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.
Petukhov, B. V.
2016-04-01
The dynamics of kink solitons is very sensitive to random irregularities of the potential relief. The evolution of kinks after their generation is essentially modified by strong fluctuations of the potential. The stochastic nature of such modification is taken into account by the theory of extreme deviations on a random walk.
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
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.
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.
Galloway, Nicole L K; Doitsh, Gilad; Monroe, Kathryn M; Yang, Zhiyuan; Muñoz-Arias, Isa; Levy, David N; Greene, Warner C
2015-09-01
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.
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 quadratic costs. We will start with the basic minimal variance problem and then move on to more complex and applicable strategies such as GMV, GPC and LQG control. These methods can be regarded as extension to the basic minimal variance strategy and have all a close relation to prediction. Consequently...... a section on that topic can be found in appendix....
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 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.
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...... with the outputs and at the same time the inputs impose constraints on the waiting times. Consequently, the expected inputs may not be available when needed and therefore the calculus allows to express the absence of data.The communication delays are expressed by general distributions and the resulting semantics...
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.
Lemaire, Morgane; Masquelier, Cécile; Beraud, Cyprien; Rybicki, Arkadiusz; Servais, Jean-Yves; Iserentant, Gilles; Schmit, Jean-Claude; Seguin-Devaux, Carole; Perez Bercoff, Danielle
2016-01-01
The cytoplasmic tail (gp41CT) of the HIV-1 envelope (Env) mediates Env incorporation into virions and regulates Env intracellular trafficking. Little is known about the functional impact of variability in this domain. To address this issue, we compared the replication of recombinant virus pairs carrying the full Env (Env viruses) or the Env ectodomain fused to the gp41CT of NL4.3 (EnvEC viruses) (12 subtype C and 10 subtype B pairs) in primary CD4+ T-cells and monocyte-derived-macrophages (MDMs). In CD4+ T-cells, replication was as follows: B-EnvEC = B-Env>C-EnvEC>C-Env, indicating that the gp41CT of subtype C contributes to the low replicative capacity of this subtype. In MDMs, in contrast, replication capacity was comparable for all viruses regardless of subtype and of gp41CT. In CD4+ T-cells, viral entry, viral release and viral gene expression were similar. However, infectivity of free virions and cell-to-cell transmission of C-Env viruses released by CD4+ T-cells was lower, suggestive of lower Env incorporation into virions. Subtype C matrix only minimally rescued viral replication and failed to restore infectivity of free viruses and cell-to-cell transmission. Taken together, these results show that polymorphisms in the gp41CT contribute to viral replication capacity and suggest that the number of Env spikes per virion may vary across subtypes. These findings should be taken into consideration in the design of vaccines. PMID:27598717
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
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
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.
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...
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.
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.
A Mechanistic Stochastic Ricker Model: Analytical and Numerical Investigations
Gadrich, Tamar; Katriel, Guy
The Ricker model is one of the simplest and most widely-used ecological models displaying complex nonlinear dynamics. We study a discrete-time population model, which is derived from simple assumptions concerning individual organisms’ behavior, using the “site-based” approach, developed by Brännström, Broomhead, Johansson and Sumpter. In the large-population limit the model converges to the Ricker model, and can thus be considered a mechanistic version of the Ricker model, derived from basic ecological principles, and taking into account the demographic stochasticity inherent to finite populations. We employ several analytical and precise numerical methods to study the model, showing how each approach contributes to understanding the model’s dynamics. Expressing the model as a Markov chain, we employ the concept of quasi-stationary distributions, which are computed numerically, and used to examine the interaction between complex deterministic dynamics and demographic stochasticity, as well as to calculate mean times to extinction. A Gaussian Markov chain approximation is used to obtain quantitative asymptotic approximations for the size of fluctuations of the stochastic model’s time series around the deterministic trajectory, and for the correlations between successive fluctuations. Results of these approximations are compared to results obtained from quasi-stationary distributions and from direct simulations, and are shown to be in good agreement.
Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion
Energy Technology Data Exchange (ETDEWEB)
Del Razo, Mauricio; Pan, Wenxiao; Qian, Hong; Lin, Guang
2014-05-30
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 [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there 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. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.
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.
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 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.
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...
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.
Recursive Concurrent Stochastic Games
Etessami, Kousha
2008-01-01
We study Recursive Concurrent Stochastic Games (RCSGs), extending our recent analysis of recursive simple stochastic games [16,17] to a concurrent setting where the two players choose moves simultaneously and independently at each state. For multi-exit games, our earlier work already showed undecidability for basic questions like termination, thus we focus on the important case of single-exit RCSGs (1-RCSGs). We first characterize the value of a 1-RCSG termination game as the least fixed point solution of a system of nonlinear minimax functional equations, and use it to show PSPACE decidability for the quantitative termination problem. We then give a strategy improvement technique, which we use to show that player 1 (maximizer) has \\epsilon-optimal randomized Stackless & Memoryless (r-SM) strategies for all \\epsilon > 0, while player 2 (minimizer) has optimal r-SM strategies. Thus, such games are r-SM-determined. These results mirror and generalize in a strong sense the randomized memoryless determinacy r...
AA, stochastic precooling pickup
1980-01-01
The freshly injected antiprotons were subjected to fast stochastic "precooling". In this picture of a precooling pickup, the injection orbit is to the left, the stack orbit to the far right. After several seconds of precooling with the system's kickers (in momentum and in the vertical plane), the precooled antiprotons were transferred, by means of RF, to the stack tail, where they were subjected to further stochastic cooling in momentum and in both transverse planes, until they ended up, deeply cooled, in the stack core. During precooling, a shutter near the central orbit shielded the pickups from the signals emanating from the stack-core, whilst the stack-core was shielded from the violent action of the precooling kickers by a shutter on these. All shutters were opened briefly during transfer of the precooled antiprotons to the stack tail. Here, the shutter is not yet mounted. Precooling pickups and kickers had the same design, except that the kickers had cooling circuits and the pickups had none. Peering th...
Stochastic Blind Motion Deblurring
Xiao, Lei
2015-05-13
Blind motion deblurring from a single image is a highly under-constrained problem with many degenerate solutions. A good approximation of the intrinsic image can therefore only be obtained with the help of prior information in the form of (often non-convex) regularization terms for both the intrinsic image and the kernel. While the best choice of image priors is still a topic of ongoing investigation, this research is made more complicated by the fact that historically each new prior requires the development of a custom optimization method. In this paper, we develop a stochastic optimization method for blind deconvolution. Since this stochastic solver does not require the explicit computation of the gradient of the objective function and uses only efficient local evaluation of the objective, new priors can be implemented and tested very quickly. We demonstrate that this framework, in combination with different image priors produces results with PSNR values that match or exceed the results obtained by much more complex state-of-the-art blind motion deblurring algorithms.
Stochastic ferromagnetism analysis and numerics
Brzezniak, Zdzislaw; Neklyudov, Mikhail; Prohl, Andreas
2013-01-01
This monograph examines magnetization dynamics at elevated temperatures which can be described by the stochastic Landau-Lifshitz-Gilbert equation (SLLG). Comparative computational studies with the stochastic model are included. Constructive tools such as e.g. finite element methods are used to derive the theoretical results, which are then used for computational studies.
On stochastic finite difference schemes
Gyongy, Istvan
2013-01-01
Finite difference schemes in the spatial variable for degenerate stochastic parabolic PDEs are investigated. Sharp results on the rate of $L_p$ and almost sure convergence of the finite difference approximations are presented and results on Richardson extrapolation are established for stochastic parabolic schemes under smoothness assumptions.
Stochastic Pi-calculus Revisited
DEFF Research Database (Denmark)
Cardelli, Luca; Mardare, Radu Iulian
2013-01-01
We develop a version of stochastic Pi-calculus with a semantics based on measure theory. We dene the behaviour of a process in a rate environment using measures over the measurable space of processes induced by structural congruence. We extend the stochastic bisimulation to include the concept of...
Alternative Asymmetric Stochastic Volatility Models
M. Asai (Manabu); M.J. McAleer (Michael)
2010-01-01
textabstractThe stochastic volatility model usually incorporates asymmetric effects by introducing the negative correlation between the innovations in returns and volatility. In this paper, we propose a new asymmetric stochastic volatility model, based on the leverage and size effects. The model is
Anticipated backward stochastic differential equations
Peng, Shige; Yang, Zhe
2009-01-01
In this paper we discuss new types of differential equations which we call anticipated backward stochastic differential equations (anticipated BSDEs). In these equations the generator includes not only the values of solutions of the present but also the future. We show that these anticipated BSDEs have unique solutions, a comparison theorem for their solutions, and a duality between them and stochastic differential delay equations.
International Nuclear Information System (INIS)
The behavior of neutrons and gamma rays in a nuclear reactor or configuration of fissile material can be represented as a stochastic process. The observation of this stochastic process is usually achieved by measuring the fluctuations of the neutron and gamma ray population on the system. The general theory of the stochastic neutron field has been developed to a high degree. However, the theory of the stochastic nature of the gamma rays and neutrons couples the two processes. The generalized probability balances are developed from which the first and higher moments of the neutron and gamma rays fields are obtained. The paper also provides a description of the probability generating functions for both photon and neutron detectors that are the foundations for measurements of the fluctuations. The formalism developed in this paper for the representation of the statistical descriptors of the neutron-photon coupled field is applicable for many neutron noise analysis measurements
Variance decomposition in stochastic simulators
Le Maître, O. P.; Knio, O. M.; Moraes, A.
2015-06-01
This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.
Variance decomposition in stochastic simulators
Le Maître, O. P.
2015-06-28
This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.
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...
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.
Institute of Scientific and Technical Information of China (English)
Feng Lin; Jiu Li Luo; Nan Rong Zhao
2011-01-01
By means of a stochastic model suggested in this paper for the systems with local non-equilibrium excited thermal fluctuations, the famous Shannon entropy is extended to include the heat conduction processes controlled externally by boundary constraints of constant temperature gradients at two sides. Meanwhile, using the description of master equation for the continuous Markov processes a balance equation of stochastic entropy production valid for one dimension gaseous heat conduction systems with high values of Prandtl number has been also established. Based on it, a general expression for both the stochastic entropy production and the entropy production of fluctuations have been further deduced by the O-expansions. In this formalism, all kinds of stochastic contributions to the dissipation from the non-equilibrium thermal fluctuation and internal noise turn explicit.
Zamorano, Nelson; Gómez, Alfredo
2013-04-01
The existence of a fluctuating torque generates a wide variety of possible orbits. This situation contrasts with those examples where the torque vanishes and the angular momentum remains constant. Here we study a two dimensional example with a logarithmic effective potential V(x,y)= 12,,^2o,[ x^2 + (y/b)^2], with a small deviation from the axis symmetry given by the constant b with b propose it as a good pedagogical tool for reviewing the main concepts of newtonian dynamics.
[Symmetry is beauty - or is it? The rise and fall of fluctuating asymmetry].
Debat, Vincent
Fluctuating asymmetry is the stochastic, minor deviation from perfect symmetry in bilaterally symmetrical organisms. It reflects the limit of developmental precision. Such a precision can be influenced by various factors, both internal (genetic mutations, stochastic variation at every levels of development) and external (environmental influences). Fluctuating asymmetry has receive an extreme attention for the past few decades, that culminated in the 90s: it has been used as an estimator of heterozygosity, fitness, environmental stress, and widely applied to human biology, sociobiology and psychology before being more or less discredited in the early 2000s. The reasons for such an extreme popularity and then disgrace are discussed here. Far from suggesting to abandon the study of fluctuating asymmetry, we indicate some of the most promising research avenues. ‡.
Fluctuation Induced Structure in Chemical Reaction with Small Number of Molecules
Suzuki, Yasuhiro
We investigate the behaviors of chemical reactions of the Lotka-Volterra model with small number of molecules; hence the occurrence of random fluctuations modifies the deterministic behavior and the law of mass action is replaced by a stochastic model. We model it by using Abstract Rewriting System on Multisets, ARMS; ARMS is a stochastic method of simulating chemical reactions and it is based on the reaction rate equation. We confirmed that the magnitude of fluctuations on periodicity of oscillations becomes large, as the number of involved molecules is getting smaller; and these fluctuations induce another structure, which have not observed in the reactions with large number of molecules. We show that the underling mechanism through investigating the coarse grained phase space of ARMS.
[Symmetry is beauty - or is it? The rise and fall of fluctuating asymmetry].
Debat, Vincent
Fluctuating asymmetry is the stochastic, minor deviation from perfect symmetry in bilaterally symmetrical organisms. It reflects the limit of developmental precision. Such a precision can be influenced by various factors, both internal (genetic mutations, stochastic variation at every levels of development) and external (environmental influences). Fluctuating asymmetry has receive an extreme attention for the past few decades, that culminated in the 90s: it has been used as an estimator of heterozygosity, fitness, environmental stress, and widely applied to human biology, sociobiology and psychology before being more or less discredited in the early 2000s. The reasons for such an extreme popularity and then disgrace are discussed here. Far from suggesting to abandon the study of fluctuating asymmetry, we indicate some of the most promising research avenues. ‡. PMID:27615188
System Entropy Measurement of Stochastic Partial Differential Systems
Directory of Open Access Journals (Sweden)
Bor-Sen Chen
2016-03-01
Full Text Available System entropy describes the dispersal of a system’s energy and is an indication of the disorder of a physical system. Several system entropy measurement methods have been developed for dynamic systems. However, most real physical systems are always modeled using stochastic partial differential dynamic equations in the spatio-temporal domain. No efficient method currently exists that can calculate the system entropy of stochastic partial differential systems (SPDSs in consideration of the effects of intrinsic random fluctuation and compartment diffusion. In this study, a novel indirect measurement method is proposed for calculating of system entropy of SPDSs using a Hamilton–Jacobi integral inequality (HJII-constrained optimization method. In other words, we solve a nonlinear HJII-constrained optimization problem for measuring the system entropy of nonlinear stochastic partial differential systems (NSPDSs. To simplify the system entropy measurement of NSPDSs, the global linearization technique and finite difference scheme were employed to approximate the nonlinear stochastic spatial state space system. This allows the nonlinear HJII-constrained optimization problem for the system entropy measurement to be transformed to an equivalent linear matrix inequalities (LMIs-constrained optimization problem, which can be easily solved using the MATLAB LMI-toolbox (MATLAB R2014a, version 8.3. Finally, several examples are presented to illustrate the system entropy measurement of SPDSs.
Stochastic analysis of response functions in environmental modeling
Energy Technology Data Exchange (ETDEWEB)
Tumeo, M.A.
1988-01-01
Development of a new mathematical technique to include stochasticity in environmental models used of resource management and public health risk analysis is reported. The technique is based on the expansion of basic governing equations to include stochastic terms. The stochastic terms are then separated from the non-fluctuating terms, and the resulting set of equations solved simultaneously. The solutions of this set of equations are used to calculate the moments of the output variables. In addition, the moments are used in conjunction with the Fokker-Planck Equation to produce an analytical solution for the probability density functions of the dependent variables. The technique is applied in two examples. The first example is an application to the Streeter-Phelps BOD-OD Equations. Results of the analysis are compared to field data as well as to results of a Monte Carlo model and to moments derived using a Stochastic Differential Equations approach. The second application involves analysis of health risks associated with waterborne diseases. Results are compared to the results of a Monte Carlo simulation of a similar system of equations.
Persistence for stochastic difference equations: A mini-review
Schreiber, Sebastian J
2011-01-01
Understanding under what conditions populations, whether they be plants, animals, or viral particles, persist is an issue of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations are key factors that can facilitate or disrupt persistence. One approach to examining the interplay between these deterministic and stochastic forces is the construction and analysis of stochastic difference equations $X_{t+1}=F(X_t,\\xi_{t+1})$ where $X_t \\in \\R^k$ represents the state of the populations and $\\xi_1,\\xi_2,...$ is a sequence of random variables representing environmental stochasticity. In the analysis of these stochastic models, many theoretical population biologists are interested in whether the models are bounded and persistent. Here, boundedness asserts that asymptotically $X_t$ tends to remain in compact sets. In contrast, persistence requires that $X_t$ tends to be "repelled" by some "extinction set" $S_0\\subset \\R^k$. Here, results on both of these pro...
Localized Spectral Analysis of Fluctuating Power Generation from Solar Energy Systems
Directory of Open Access Journals (Sweden)
Johan Nijs
2007-01-01
Full Text Available Fluctuations in solar irradiance are a serious obstacle for the future large-scale application of photovoltaics. Occurring regularly with the passage of clouds, they can cause unexpected power variations and introduce voltage dips to the power distribution system. This paper proposes the treatment of such fluctuating time series as realizations of a stochastic, locally stationary, wavelet process. Its local spectral density can be estimated from empirical data by means of wavelet periodograms. The wavelet approach allows the analysis of the amplitude of fluctuations per characteristic scale, hence, persistence of the fluctuation. Furthermore, conclusions can be drawn on the frequency of occurrence of fluctuations of different scale. This localized spectral analysis was applied to empirical data of two successive years. The approach is especially useful for network planning and load management of power distribution systems containing a high density of photovoltaic generation units.
Fitness in fluctuating environments
Tanase Nicola, Sorin; Nemenman, Ilya
2011-03-01
Often environments change faster than the time needed to evolve optimal phenotypes through cycles of mutation and selection. We focus on this case, but assume that environmental oscillations are slower than an individual's lifetime. This is relevant, for example, for bacterial populations confronted with daily environmental changes. We analyze a resource-limited competition between a mutant phenotype and the ancestor. Environmental dynamics is represented by periodically varying, off-phase parameters of the corresponding Lotka-Volterra model. For the very slow dynamics (but still faster than the fixation time scale) the strength and the sign of selection are functions of the birth/death rates averaged over all of the environmental states and independent of the period of the fluctuations. For faster fluctuations, selection depends on the particular sequence of the successive environmental states. In particular, a time reversal of the environmental dynamics can change the sign of the selection. We conclude that the fittest phenotype in a changing environment can be very different from both the optimal phenotype in the average environment, and the phenotype with the largest average fitness.
Riedler, Martin G; Wainrib, Gilles
2011-01-01
In the present paper we present limit theorems for a sequence of Piecewise Deterministic Markov Processes taking values in Hilbert spaces. This class of processes provides a rigorous framework for stochastic spatial models in which discrete random events are globally coupled with continuous space-dependent variables solving partial differential equations, e.g., stochastic hybrid models of excitable membranes. We derive a law of large numbers which establishes a connection to deterministic macroscopic models and a martingale central limit theorem which connects the stochastic fluctuations to diffusion processes. As a prerequisite we carry out a thorough discussion of Hilbert space valued martingales associated to the PDMPs. Furthermore, these limit theorems provide the basis for a general Langevin approximation to PDMPs, i.e., certain stochastic partial differential equations that are expected to be similar in their dynamics to PDMPs. We apply these results to compartmental-type models of spatially extended ne...
Klyatskin, Valery I
2015-01-01
This monograph set presents a consistent and self-contained framework of stochastic dynamic systems with maximal possible completeness. Volume 1 presents the basic concepts, exact results, and asymptotic approximations of the theory of stochastic equations on the basis of the developed functional approach. This approach offers a possibility of both obtaining exact solutions to stochastic problems for a number of models of fluctuating parameters and constructing various asymptotic buildings. Ideas of statistical topography are used to discuss general issues of generating coherent structures from chaos with probability one, i.e., almost in every individual realization of random parameters. The general theory is illustrated with certain problems and applications of stochastic mathematical physics in various fields such as mechanics, hydrodynamics, magnetohydrodynamics, acoustics, optics, and radiophysics.
Analysis of the deterministic and stochastic SIRS epidemic models with nonlinear incidence
Liu, Qun; Chen, Qingmei
2015-06-01
In this paper, the deterministic and stochastic SIRS epidemic models with nonlinear incidence are introduced and investigated. For deterministic system, the basic reproductive number R0 is obtained. Furthermore, if R0 ≤ 1, then the disease-free equilibrium is globally asymptotically stable and if R0 > 1, then there is a unique endemic equilibrium which is globally asymptotically stable. For stochastic system, to begin with, we verify that there is a unique global positive solution starting from the positive initial value. Then when R0 > 1, we prove that stochastic perturbations may lead the disease to extinction in scenarios where the deterministic system is persistent. When R0 ≤ 1, a result on fluctuation of the solution around the disease-free equilibrium of deterministic model is obtained under appropriate conditions. At last, if the intensity of the white noise is sufficiently small and R0 > 1, then there is a unique stationary distribution to stochastic system.
Energy Technology Data Exchange (ETDEWEB)
Li, Xiao, E-mail: lixiao1228@163.com; Ji, Guanghua, E-mail: ghji@bnu.edu.cn; Zhang, Hui, E-mail: hzhang@bnu.edu.cn
2015-02-15
We use the stochastic Cahn–Hilliard equation to simulate the phase transitions of the macromolecular microsphere composite (MMC) hydrogels under a random disturbance. Based on the Flory–Huggins lattice model and the Boltzmann entropy theorem, we develop a reticular free energy suit for the network structure of MMC hydrogels. Taking the random factor into account, with the time-dependent Ginzburg-Landau (TDGL) mesoscopic simulation method, we set up a stochastic Cahn–Hilliard equation, designated herein as the MMC-TDGL equation. The stochastic term in the equation is constructed appropriately to satisfy the fluctuation-dissipation theorem and is discretized on a spatial grid for the simulation. A semi-implicit difference scheme is adopted to numerically solve the MMC-TDGL equation. Some numerical experiments are performed with different parameters. The results are consistent with the physical phenomenon, which verifies the good simulation of the stochastic term.
The stochastic dance of circling sperm cells: sperm chemotaxis in the plane
Energy Technology Data Exchange (ETDEWEB)
Friedrich, B M; Juelicher, F [Max Planck Institute for the Physics of Complex Systems, Noethnitzer Strasse 38, 01187 Dresden (Germany)], E-mail: ben@pks.mpg.de, E-mail: julicher@pks.mpg.de
2008-12-15
Biological systems such as single cells must function in the presence of fluctuations. It has been shown in a two-dimensional experimental setup that sea urchin sperm cells move toward a source of chemoattractant along planar trochoidal swimming paths, i.e. drifting circles. In these experiments, a pronounced variability of the swimming paths is observed. We present a theoretical description of sperm chemotaxis in two dimensions which takes fluctuations into account. We derive a coarse-grained theory of stochastic sperm swimming paths in a concentration field of chemoattractant. Fluctuations enter as multiplicative noise in the equations for the sperm swimming path. We discuss the stochastic properties of sperm swimming and predict a concentration-dependence of the effective diffusion constant of sperm swimming which could be tested in experiments.
The stochastic dance of circling sperm cells: sperm chemotaxis in the plane
International Nuclear Information System (INIS)
Biological systems such as single cells must function in the presence of fluctuations. It has been shown in a two-dimensional experimental setup that sea urchin sperm cells move toward a source of chemoattractant along planar trochoidal swimming paths, i.e. drifting circles. In these experiments, a pronounced variability of the swimming paths is observed. We present a theoretical description of sperm chemotaxis in two dimensions which takes fluctuations into account. We derive a coarse-grained theory of stochastic sperm swimming paths in a concentration field of chemoattractant. Fluctuations enter as multiplicative noise in the equations for the sperm swimming path. We discuss the stochastic properties of sperm swimming and predict a concentration-dependence of the effective diffusion constant of sperm swimming which could be tested in experiments.
Stochastic variability of large-scale oceanic flows above topography anomalies
Venaille, Antoine; Molines, J -M; Barnier, B
2011-01-01
Large-scale oceanic currents show large fluctuations at decadal, centennial and even millennial time scales. Here, we describe a new stochastic variability mechanism which is genuinely internal to the ocean, i.e. not due to fluctuations in atmospheric forcing. The key ingredient is the existence of closed contours of bottom topography surrounded by a stirring region of enhanced eddy activity. This configuration leads to the formation of a robust but highly variable vortex above the topography anomaly. The vortex dynamics integrates the white noise forcing of oceanic eddies into a red noise signal for the large scale volume transport of the vortex. The fluctuations of the transport of the Zapiola anticyclone (100 Sv) in the Argentine basin are argued to be an example of such eddy-driven stochastic variability, on the basis of a 310 years long simulation of a comprehensive ocean model run driven by a repeated-year forcing.
Bunched beam stochastic cooling
Energy Technology Data Exchange (ETDEWEB)
Wei, Jie
1992-09-01
The scaling laws for bunched-beam stochastic cooling has been derived in terms of the optimum cooling rate and the mixing condition. In the case that particles occupy the entire sinusoidal rf bucket, the optimum cooling rate of the bunched beam is shown to be similar to that predicted from the coasting-beam theory using a beam of the same average density and mixing factor. However, in the case that particles occupy only the center of the bucket, the optimum rate decrease in proportion to the ratio of the bunch area to the bucket area. The cooling efficiency can be significantly improved if the synchrotron side-band spectrum is effectively broadened, e.g. by the transverse tune spread or by using a double rf system.
Bunched beam stochastic cooling
Energy Technology Data Exchange (ETDEWEB)
Wei, Jie.
1992-01-01
The scaling laws for bunched-beam stochastic cooling has been derived in terms of the optimum cooling rate and the mixing condition. In the case that particles occupy the entire sinusoidal rf bucket, the optimum cooling rate of the bunched beam is shown to be similar to that predicted from the coasting-beam theory using a beam of the same average density and mixing factor. However, in the case that particles occupy only the center of the bucket, the optimum rate decrease in proportion to the ratio of the bunch area to the bucket area. The cooling efficiency can be significantly improved if the synchrotron side-band spectrum is effectively broadened, e.g. by the transverse tune spread or by using a double rf system.
Stochastic Programming with Probability
Andrieu, Laetitia; Vázquez-Abad, Felisa
2007-01-01
In this work we study optimization problems subject to a failure constraint. This constraint is expressed in terms of a condition that causes failure, representing a physical or technical breakdown. We formulate the problem in terms of a probability constraint, where the level of "confidence" is a modelling parameter and has the interpretation that the probability of failure should not exceed that level. Application of the stochastic Arrow-Hurwicz algorithm poses two difficulties: one is structural and arises from the lack of convexity of the probability constraint, and the other is the estimation of the gradient of the probability constraint. We develop two gradient estimators with decreasing bias via a convolution method and a finite difference technique, respectively, and we provide a full analysis of convergence of the algorithms. Convergence results are used to tune the parameters of the numerical algorithms in order to achieve best convergence rates, and numerical results are included via an example of ...
Stochastic population theories
Ludwig, Donald
1974-01-01
These notes serve as an introduction to stochastic theories which are useful in population biology; they are based on a course given at the Courant Institute, New York, in the Spring of 1974. In order to make the material. accessible to a wide audience, it is assumed that the reader has only a slight acquaintance with probability theory and differential equations. The more sophisticated topics, such as the qualitative behavior of nonlinear models, are approached through a succession of simpler problems. Emphasis is placed upon intuitive interpretations, rather than upon formal proofs. In most cases, the reader is referred elsewhere for a rigorous development. On the other hand, an attempt has been made to treat simple, useful models in some detail. Thus these notes complement the existing mathematical literature, and there appears to be little duplication of existing works. The authors are indebted to Miss Jeanette Figueroa for her beautiful and speedy typing of this work. The research was supported by the Na...
Stochastic reconstruction of sandstones
Manwart; Torquato; Hilfer
2000-07-01
A simulated annealing algorithm is employed to generate a stochastic model for a Berea sandstone and a Fontainebleau sandstone, with each a 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 sandstones. Also, the mean survival time of a random walker in the pore space is reproduced with good accuracy. However, a more detailed investigation by means of local porosity theory shows that there may be significant differences of the geometrical connectivity between the reconstructed and the experimental samples.
Stochasticity in processes fundamentals and applications to chemistry and biology
Schuster, Peter
2016-01-01
This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed t...
Environmental versus demographic variability in stochastic predator-prey models
Dobramysl, U.; Täuber, U. C.
2013-10-01
In contrast to the neutral population cycles of the deterministic mean-field Lotka-Volterra rate equations, including spatial structure and stochastic noise in models for predator-prey interactions yields complex spatio-temporal structures associated with long-lived erratic population oscillations. Environmental variability in the form of quenched spatial randomness in the predation rates results in more localized activity patches. Our previous study showed that population fluctuations in rare favorable regions in turn cause a remarkable increase in the asymptotic densities of both predators and prey. Very intriguing features are found when variable interaction rates are affixed to individual particles rather than lattice sites. Stochastic dynamics with demographic variability in conjunction with inheritable predation efficiencies generate non-trivial time evolution for the predation rate distributions, yet with overall essentially neutral optimization.
Stochastic dynamics of active swimmers in linear flows
Sandoval, Mario; Subramanian, Ganesh; Lauga, Eric
2014-01-01
Most classical work on the hydrodynamics of low-Reynolds-number swimming addresses deterministic locomotion in quiescent environments. Thermal fluctuations in fluids are known to lead to a Brownian loss of the swimming direction. As most cells or synthetic swimmers are immersed in external flows, we consider theoretically in this paper the stochastic dynamics of a model active particle (a self-propelled sphere) in a steady general linear flow. The stochasticity arises both from translational diffusion in physical space, and from a combination of rotary diffusion and run-and-tumble dynamics in orientation space. We begin by deriving a general formulation for all components of the long-time mean square displacement tensor for a swimmer with a time-dependent swimming velocity and whose orientation decorrelates due to rotary diffusion alone. This general framework is applied to obtain the convectively enhanced mean-squared displacements of a steadily-swimming particle in three canonical linear flows (extension, s...
Stochastic Models of Vesicular Sorting in Cellular Organelles
Vagne, Quentin
2016-01-01
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...
Fluctuations from dissipation in a hot non-Abelian plasma
Litim, Daniel F; Litim, Daniel F.; Manuel, Cristina
2000-01-01
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 a hot non-Abelian (classical or quantum) plasma, the resulting spectral functions agree with earlier findings obtained from the microscopic theory. As a by-product, it follows that theorem.
Introduction to stochastic dynamic programming
Ross, Sheldon M; Lukacs, E
1983-01-01
Introduction to Stochastic Dynamic Programming presents the basic theory and examines the scope of applications of stochastic dynamic programming. The book begins with a chapter on various finite-stage models, illustrating the wide range of applications of stochastic dynamic programming. Subsequent chapters study infinite-stage models: discounting future returns, minimizing nonnegative costs, maximizing nonnegative returns, and maximizing the long-run average return. Each of these chapters first considers whether an optimal policy need exist-providing counterexamples where appropriate-and the
Stochastic dynamic equations on general time scales
Martin Bohner; Olexandr M. Stanzhytskyi; Anastasiia O. Bratochkina
2013-01-01
In this article, we construct stochastic integral and stochastic differential equations on general time scales. We call these equations stochastic dynamic equations. We provide the existence and uniqueness theorem for solutions of stochastic dynamic equations. The crucial tool of our construction is a result about a connection between the time scales Lebesgue integral and the Lebesgue integral in the common sense.
An introduction to probability and stochastic processes
Melsa, James L
2013-01-01
Geared toward college seniors and first-year graduate students, this text is designed for a one-semester course in probability and stochastic processes. Topics covered in detail include probability theory, random variables and their functions, stochastic processes, linear system response to stochastic processes, Gaussian and Markov processes, and stochastic differential equations. 1973 edition.
Primordial Fluctuations within Teleparallelism
Wu, Yi-Peng
2011-01-01
To study the primordial fluctuations for gravity within teleparallelism, we perform a 3+1 decomposition of the vierbein field which makes the metric tensor identical to the ADM formulation. The torsion scalar is differ by a total divergence from the Ricci scalar under this representation as a consistent result. Using the unitary gauge of the scalar field, we obtain the same quadratic actions for both scalar and tensor perturbations as the standard ones in the minimal torsion scalar coupling. When the same scenario is applied to the higher-order action, $f(T)$ gravity, we find that the scalar-tensor coupling in the Einstein frame becomes a total divergence. Consequently, the cosmological perturbations are the same for $f(T)$ and $f(R)$ gravity theories in the earlier universe although the behaviors of the late time cosmic acceleration are apparently different.
Directory of Open Access Journals (Sweden)
Masanori Kaido
2014-11-01
Full Text Available The formation of virus movement protein (MP-containing punctate structures on the cortical endoplasmic reticulum is required for efficient intercellular movement of Red clover necrotic mosaic virus (RCNMV, a bipartite positive-strand RNA plant virus. We found that these cortical punctate structures constitute a viral replication complex (VRC in addition to the previously reported aggregate structures that formed adjacent to the nucleus. We identified host proteins that interacted with RCNMV MP in virus-infected Nicotiana benthamiana leaves using a tandem affinity purification method followed by mass spectrometry. One of these host proteins was glyceraldehyde 3-phosphate dehydrogenase-A (NbGAPDH-A, which is a component of the Calvin-Benson cycle in chloroplasts. Virus-induced gene silencing of NbGAPDH-A reduced RCNMV multiplication in the inoculated leaves, but not in the single cells, thereby suggesting that GAPDH-A plays a positive role in cell-to-cell movement of RCNMV. The fusion protein of NbGAPDH-A and green fluorescent protein localized exclusively to the chloroplasts. In the presence of RCNMV RNA1, however, the protein localized to the cortical VRC as well as the chloroplasts. Bimolecular fluorescence complementation assay and GST pulldown assay confirmed in vivo and in vitro interactions, respectively, between the MP and NbGAPDH-A. Furthermore, gene silencing of NbGAPDH-A inhibited MP localization to the cortical VRC. We discuss the possible roles of NbGAPDH-A in the RCNMV movement process.
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.
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.
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.
Stochastic analysis of laminated composite plate considering stochastic homogenization problem
Institute of Scientific and Technical Information of China (English)
S. SAKATA; K. OKUDA; K. IKEDA
2015-01-01
This paper discusses a multiscale stochastic analysis of a laminated composite plate consisting of unidirectional fiber reinforced composite laminae. In particular, influence of a microscopic random variation of the elastic properties of component materials on mechanical properties of the laminated plate is investigated. Laminated composites are widely used in civil engineering, and therefore multiscale stochastic analysis of laminated composites should be performed for reliability evaluation of a composite civil structure. This study deals with the stochastic response of a laminated composite plate against the microscopic random variation in addition to a random variation of fiber orientation in each lamina, and stochastic properties of the mechanical responses of the laminated plate is investigated. Halpin-Tsai formula and the homogenization theory-based finite element analysis are employed for estimation of effective elastic properties of lamina, and the classical laminate theory is employed for analysis of a laminated plate. The Monte-Carlo simulation and the first-order second moment method with sensitivity analysis are employed for the stochastic analysis. From the numerical results, importance of the multiscale stochastic analysis for reliability evaluation of a laminated composite structure and applicability of the sensitivity-based approach are discussed.
Fluctuations assisted stationary entanglement in driven quantum systems
Angelakis, Dimitris G
2011-01-01
We analyze the possible quantum correlations between two coupled dimer systems in the presence of independent losses and driven by a fluctuating field. For the case of the interaction being of a Heisenberg exchange type, we first analytically show the possibility for robust stationary entanglement for realistic values of the dissipation rates and then analyze its robustness as a function of the noise to signal ratio of the pump. We find that for a common fluctuating driving field, a stochastic resonance effect appears as function of the ratio between field strength and noise strength. The effect disappears in the case of uncorrelated or separate pumps. Our result is general and could be applied to different quantum systems ranging from electron spins in solid state, to ions trap technologies and cold atom set ups.
The Measure-theoretic Identity Underlying Transient Fluctuation Theorems
Shargel, Benjamin Hertz
2010-01-01
We prove a measure-theoretic identity that underlies all transient fluctuation theorems (TFTs) for entropy production and dissipated work in inhomogeneous deterministic and stochastic processes, including those of Evans and Searles, Crooks, and Seifert. The identity is used to deduce a tautological physical interpretation of TFTs in terms of the arrow of time, and its generality reveals that the self-inverse nature of the various trajectory and process transformations historically relied upon to prove TFTs, while necessary for these theorems from a physical standpoint, is not necessary from a mathematical one. The moment generating functions of thermodynamic variables appearing in the identity are shown to converge in general only in a vertical strip in the complex plane, with the consequence that a TFT that holds over arbitrary timescales may fail to give rise to an asymptotic fluctuation theorem for any possible speed of the corresponding large deviation principle. The case of strongly biased birth-death ch...
Extreme reaction times determine fluctuation scaling in human color vision
Medina, José M.; Díaz, José A.
2016-11-01
In modern mental chronometry, human reaction time defines the time elapsed from stimulus presentation until a response occurs and represents a reference paradigm for investigating stochastic latency mechanisms in color vision. Here we examine the statistical properties of extreme reaction times and whether they support fluctuation scaling in the skewness-kurtosis plane. Reaction times were measured for visual stimuli across the cardinal directions of the color space. For all subjects, the results show that very large reaction times deviate from the right tail of reaction time distributions suggesting the existence of dragon-kings events. The results also indicate that extreme reaction times are correlated and shape fluctuation scaling over a wide range of stimulus conditions. The scaling exponent was higher for achromatic than isoluminant stimuli, suggesting distinct generative mechanisms. Our findings open a new perspective for studying failure modes in sensory-motor communications and in complex networks.
Unifying three perspectives on information processing in stochastic thermodynamics.
Barato, A C; Seifert, U
2014-03-01
So far, feedback-driven systems have been discussed using (i) measurement and control, (ii) a tape interacting with a system, or (iii) by identifying an implicit Maxwell demon in steady-state transport. We derive the corresponding second laws from one master fluctuation theorem and discuss their relationship. In particular, we show that both the entropy production involving mutual information between system and controller and the one involving a Shannon entropy difference of an information reservoir like a tape carry an extra term different from the usual current times affinity. We, thus, generalize stochastic thermodynamics to the presence of an information reservoir. PMID:24655235
Diffusive dynamics and stochastic models of turbulent axisymmetric wakes
Rigas, G; Brackston, R D; Morrison, J F
2015-01-01
A modelling methodology to reproduce the experimental measurements of a turbulent flow under the presence of symmetry is presented. The flow is a three-dimensional wake generated by an axisymmetric body. We show that the dynamics of the turbulent wake- flow can be assimilated by a nonlinear two-dimensional Langevin equation, the deterministic part of which accounts for the broken symmetries which occur at the laminar and transitional regimes at low Reynolds numbers and the stochastic part of which accounts for the turbulent fluctuations. Comparison between theoretical and experimental results allows the extraction of the model parameters.
The importance of stochastic transitions for the origin of life.
Higgs, Paul G; Wu, Meng
2012-10-01
We discuss the origin of life in terms of an RNA World scenario in which the creation of autocatalytic sequences is the key step. Our computational models illustrate that life arises by a rare stochastic event that occurs due to spatially localized concentration fluctuations. This allows the chemical system to jump from a non-living state with very low ribozyme concentration to a living state that is controlled by ribozymes. Once the living state is established locally, it can spread deterministically through the rest of the system. These are generic features also possessed by more complex models with a greater degree of chemical realism.
Stochastic pumping of heat: approaching the Carnot efficiency.
Segal, Dvira
2008-12-31
Random noise can generate a unidirectional heat current across asymmetric nano-objects in the absence (or against) a temperature gradient. We present a minimal model for a molecular-level stochastic heat pump that may operate arbitrarily close to the Carnot efficiency. The model consists a fluctuating molecular unit coupled to two solids characterized by distinct phonon spectral properties. Heat pumping persists for a broad range of system and bath parameters. Furthermore, by filtering the reservoirs' phonons the pump efficiency can approach the Carnot limit.
Large amplitude motion with a stochastic mean-field approach
Directory of Open Access Journals (Sweden)
Yilmaz Bulent
2012-12-01
Full Text Available In the stochastic mean-field approach, an ensemble of initial conditions is considered to incorporate correlations beyond the mean-field. Then each starting point is propagated separately using the Time-Dependent Hartree-Fock equation of motion. This approach provides a rather simple tool to better describe fluctuations compared to the standard TDHF. Several illustrations are presented showing that this theory can be rather effective to treat the dynamics close to a quantum phase transition. Applications to fusion and transfer reactions demonstrate the great improvement in the description of mass dispersion.
Statistical Characteristics of the Received Signal for Stochastic Surface Models
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
This paper describes the stochastic model of the scattered electromagnetic field.Unlike common-used functional-determined models the proposed is characterised by amplitude/phase fluctuation of the received signal.This paper derives the statistical characteristic of the input signal and describes algorithm for its estimation in post-processing and real-time processing modes.Achieved characteristics allow the mapping and estimation of the surface models more accurate,moreover,such processing increase space resolution of synthetic aperture radar.
Fluctuating pulled fronts and Pomerons
International Nuclear Information System (INIS)
I present a pedagogical discussion of the influence of particle number fluctuations on the high energy evolution in QCD. I emphasize the event-by-event description, and the correspondence with the problem of 'fluctuating pulled fronts' in statistical physics. I explain that the correlations generated by fluctuations reduce the phase-space for BFKL evolution up to saturation. Because of that, the evolution 'slows down', and the rate for the energy increase of the saturation momentum is considerably decreased. I also discuss the diagrammatic interpretation of the particle number fluctuations in terms of Pomeron loops
Detecting Stochastic Information of Electrocardiograms
Gutíerrez, R M; Guti'errez, Rafael M.; Sandoval, Luis A.
2003-01-01
In this work we present a method to detect, identify and characterize stochastic information contained in an electrocardiogram (ECG). We assume, as it is well known, that the ECG has information corresponding to many different processes related to the cardiac activity. We analyze scaling and Markov processes properties of the detected stochastic information using the power spectrum of the ECG and the Fokker-Planck equation respectively. The detected stochastic information is then characterized by three measures. First, the slope of the power spectrum in a particular range of frequencies as a scaling parameter. Second, an empirical estimation of the drift and diffusion coefficients of the Fokker-Planck equation through the Kramers-Moyal coefficients which define the evolution of the probability distribution of the detected stochastic information.
Stochastic Climate Theory and Modelling
Franzke, Christian L E; Berner, Judith; Williams, Paul D; Lucarini, Valerio
2014-01-01
Stochastic methods are a crucial area in contemporary climate research and are increasingly being used in comprehensive weather and climate prediction models as well as reduced order climate models. Stochastic methods are used as subgrid-scale parameterizations as well as for model error representation, uncertainty quantification, data assimilation and ensemble prediction. The need to use stochastic approaches in weather and climate models arises because we still cannot resolve all necessary processes and scales in comprehensive numerical weather and climate prediction models. In many practical applications one is mainly interested in the largest and potentially predictable scales and not necessarily in the small and fast scales. For instance, reduced order models can simulate and predict large scale modes. Statistical mechanics and dynamical systems theory suggest that in reduced order models the impact of unresolved degrees of freedom can be represented by suitable combinations of deterministic and stochast...
Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.
Tiana, Guido; Amitai, Assaf; Pollex, Tim; Piolot, Tristan; Holcman, David; Heard, Edith; Giorgetti, Luca
2016-03-29
Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and thus to be properly regulated. Understanding the cell-to-cell and temporal variability of the chromatin fiber within TADs, and what determines them, is thus of great importance to better understand transcriptional regulation. We recently described an equilibrium polymer model that can accurately predict cell-to-cell variation of chromosome conformation within single TADs, from chromosome conformation capture-based data. Here we further analyze the conformational and energetic properties of our model. We show that the chromatin fiber within TADs can easily fluctuate between several conformational states, which are hierarchically organized and are not separated by important free energy barriers, and that this is facilitated by the fact that the chromatin fiber within TADs is close to the onset of the coil-globule transition. We further show that in this dynamic state the properties of the chromatin fiber, and its contact probabilities in particular, are determined in a nontrivial manner not only by site-specific interactions between strongly interacting loci along the fiber, but also by nonlocal correlations between pairs of contacts. Finally, we use live-cell experiments to measure the dynamics of the chromatin fiber in mouse embryonic stem cells, in combination with dynamical simulations, and predict that conformational changes within one TAD are likely to occur on timescales that are much shorter than the duration of one cell cycle. This suggests that genes and their regulatory elements may come together and disassociate several times during a cell cycle. These results have important implications for transcriptional
Pathwise construction of stochastic integrals
Nutz, Marcel
2012-01-01
We propose a method to construct the stochastic integral simultaneously under a non-dominated family of probability measures. Path-by-path, and without referring to a probability measure, we construct a sequence of Lebesgue-Stieltjes integrals whose medial limit coincides with the usual stochastic integral under essentially any probability measure such that the integrator is a semimartingale. This method applies to any predictable integrand.
Stochastic quantization and gauge theories
International Nuclear Information System (INIS)
Stochastic quantization is presented taking the Flutuation-Dissipation Theorem as a guide. It is shown that the original approach of Parisi and Wu to gauge theories fails to give the right results to gauge invariant quantities when dimensional regularization is used. Although there is a simple solution in an abelian theory, in the non-abelian case it is probably necessary to start from a BRST invariant action instead of a gauge invariant one. Stochastic regularizations are also discussed. (author)
The dynamics of stochastic processes
DEFF Research Database (Denmark)
Basse-O'Connor, Andreas
In the present thesis the dynamics of stochastic processes is studied with a special attention to the semimartingale property. This is mainly motivated by the fact that semimartingales provide the class of the processes for which it is possible to define a reasonable stochastic calculus due to the...... result is obtained and applied. Moreover, martingales indexed by the whole real line is studied and characterized and the thesis is concluded with a study of stationary solutions of the Langevin equation....
Stochastic optimization: beyond mathematical programming
CERN. Geneva
2015-01-01
Stochastic optimization, among which bio-inspired algorithms, is gaining momentum in areas where more classical optimization algorithms fail to deliver satisfactory results, or simply cannot be directly applied. This presentation will introduce baseline stochastic optimization algorithms, and illustrate their efficiency in different domains, from continuous non-convex problems to combinatorial optimization problem, to problems for which a non-parametric formulation can help exploring unforeseen possible solution spaces.
Abstractions of stochastic hybrid systems
Bujorianu, L.M.; Lygeros, J.; Bujorianu, M.C.
2005-01-01
Many control systems have large, infinite state space that can not be easily abstracted. One method to analyse and verify these systems is reachability analysis. It is frequently used for air traffic control and power plants. Because of lack of complete information about the environment or unpredicted changes, the stochastic approach is a viable alternative. In this paper, different ways of introducing rechability under uncertainty are presented. A new concept of stochastic bisimulation is in...
Stochastic roots of growth phenomena
De Lauro, E.; De Martino, S.; De Siena, S.; Giorno, V.
2014-05-01
We show that the Gompertz equation describes the evolution in time of the median of a geometric stochastic process. Therefore, we induce that the process itself generates the growth. This result allows us further to exploit a stochastic variational principle to take account of self-regulation of growth through feedback of relative density variations. The conceptually well defined framework so introduced shows its usefulness by suggesting a form of control of growth by exploiting external actions.
Stochastic comparisons of nonhomogeneous processes
Belzunce, Félix; Lillo, Rosa E.; Ruiz, José M.; Shaked, Moshe
2000-01-01
The purpose of this paper is to describe various conditions on the parameters of pairs of nonhomogeneous Poisson or birth processes under which the corresponding epoch or inter-epoch times are stochastically ordered in various senses. We derive results involving the usual stochastic order, the multivariate hazard rate order, the multivariate likelihood ratio order, and the multivariate mean residual life order. A sample of applications involving generalized Yule processes, load-sharing models...
Foliated stochastic calculus: Harmonic measures
Catuogno, Pedro J; Ruffino, Paulo R
2010-01-01
In this article we present an intrinsec construction of foliated Brownian motion via stochastic calculus adapted to foliation. The stochastic approach together with a proposed foliated vector calculus provide a natural method to work on harmonic measures. Other results include a decomposition of the Laplacian in terms of the foliated and basic Laplacians, a characterization of totally invariant measures and a differential equation for the density of harmonic measures.
Steganalysis of stochastic modulation steganography
Institute of Scientific and Technical Information of China (English)
HE Junhui; HUANG Jiwu
2006-01-01
Stochastic modulation steganography embeds secret message within the cover image by adding stego-noise with a specific probabilistic distribution. No method is known to be applicable to the estimation of stochastic modulation steganography. By analyzing the distributions of the horizontal pixel difference of images before and after stochastic modulation embedding, we present a new steganalytic approach to accurately estimate the length of secret message in stochastic modulation steganography. The proposed method first establishes a model describing the statistical relationship among the differences of the cover image, stego-image and stego-noise. In the case of stego- image-only steganalysis, rough estimate of the distributional parameters of the cover image's pixel difference is obtained with the use of the provided stego-image. And grid search and Chi-square goodness of fit test are exploited to estimate the length of the secret message embedded with stochastic modulation steganography. The experimental results demonstrate that our new approach is effective for steganalyzing stochastic modulation steganography and accurately estimating the length of the secret message.
Stochastic group selection model for the evolution of altruism
Silva, A T C; Silva, Ana T. C.
1999-01-01
We study numerically and analytically a stochastic group selection model in which a population of asexually reproducing individuals, each of which can be either altruist or non-altruist, is subdivided into $M$ reproductively isolated groups (demes) of size $N$. The cost associated with being altruistic is modelled by assigning the fitness $1- \\tau$, with $\\tau \\in [0,1]$, to the altruists and the fitness 1 to the non-altruists. In the case that the altruistic disadvantage $\\tau$ is not too large, we show that the finite $M$ fluctuations are small and practically do not alter the deterministic results obtained for $M \\to \\infty$. However, for large $\\tau$ these fluctuations greatly increase the instability of the altruistic demes to mutations. These results may be relevant to the dynamics of parasite-host systems and, in particular, to explain the importance of mutation in the evolution of parasite virulence.
Turbulence and Stochastic Processes
Celani, Antonio; Mazzino, Andrea; Pumir, Alain
sec:08-1In 1931 the monograph Analytical Methods in Probability Theory appeared, in which A.N. Kolmogorov laid the foundations for the modern theory of Markov processes [1]. According to Gnedenko: "In the history of probability theory it is difficult to find other works that changed the established points of view and basic trends in research work in such a decisive way". Ten years later, his article on fully developed turbulence provided the framework within which most, if not all, of the subsequent theoretical investigations have been conducted [2] (see e.g. the review by Biferale et al. in this volume [3]. Remarkably, the greatest advances made in the last few years towards a thorough understanding of turbulence developed from the successful marriage between the theory of stochastic processes and the phenomenology of turbulent transport of scalar fields. In this article we will summarize these recent developments which expose the direct link between the intermittency of transported fields and the statistical properties of particle trajectories advected by the turbulent flow (see also [4], and, for a more thorough review, [5]. We also discuss the perspectives of the Lagrangian approach beyond passive scalars, especially for the modeling of hydrodynamic turbulence.
AA, stochastic precooling kicker
1980-01-01
The freshly injected antiprotons were subjected to fast stochastic "precooling", while a shutter shielded the deeply cooled antiproton stack from the violent action of the precooling kicker. In this picture, the injection orbit is to the left, the stack orbit to the far right, the separating shutter is in open position. After several seconds of precooling (in momentum and in the vertical plane), the shutter was opened briefly, so that by means of RF the precooled antiprotons could be transferred to the stack tail, where they were subjected to further cooling in momentum and both transverse planes, until they ended up, deeply cooled, in the stack core. The fast shutter, which had to open and close in a fraction of a second was an essential item of the cooling scheme and a mechanical masterpiece. Here the shutter is in the open position. The precooling pickups were of the same design, with the difference that the kickers had cooling circuits and the pickups not. 8401150 shows a precooling pickup with the shutte...
Adaptation in stochastic environments
Clark, Colib
1993-01-01
The classical theory of natural selection, as developed by Fisher, Haldane, and 'Wright, and their followers, is in a sense a statistical theory. By and large the classical theory assumes that the underlying environment in which evolution transpires is both constant and stable - the theory is in this sense deterministic. In reality, on the other hand, nature is almost always changing and unstable. We do not yet possess a complete theory of natural selection in stochastic environ ments. Perhaps it has been thought that such a theory is unimportant, or that it would be too difficult. Our own view is that the time is now ripe for the development of a probabilistic theory of natural selection. The present volume is an attempt to provide an elementary introduction to this probabilistic theory. Each author was asked to con tribute a simple, basic introduction to his or her specialty, including lively discussions and speculation. We hope that the book contributes further to the understanding of the roles of "Cha...
Stochastic interpenetration of fluids
Energy Technology Data Exchange (ETDEWEB)
Steinkamp, M.J.; Clark, T.T.; Harlow, F.H.
1995-11-01
We describe a spectral approach to the investigation of fluid instability, generalized turbulence, and the interpenetration of fluids across an interface. The technique also applies to a single fluid with large variations in density. Departures of fluctuating velocity components from the local mean are far subsonic, but the mean Mach number can be large. Validity of the description is demonstrated by comparisons with experiments on turbulent mixing due to the late stages of Rayleigh-Taylor instability, when the dynamics become approximately self-similar in response to a constant body force. Generic forms for anisotropic spectral structure are described and used as a basis for deriving spectrally integrated moment equations that can be incorporated into computer codes for scientific and engineering analyses.
Basti, Gianfranco; Castiglione, Patrizia; Casolino, Marco; Perrone, Antonio L.; Picozza, Piergiorgio
1993-08-01
Usually, to discriminate among particle tracks in high energy physics a set of discriminating parameters is used. To cope with the different particle behaviors these parameters are connected by the human observer with boolean operators. We tested successfully an automatic method for particle recognition using a stochastic method to pre-process the input to a back propagation algorithm. The test was made using raw experimental data of electrons and negative pions taken at CERN laboratories (Geneva). From the theoretical standpoint, the stochastic pre-processing of a back propagation algorithm can be interpreted as finding the optimal fuzzy membership function notwithstanding high fluctuating (noisy) input data.
Effects of Demographic Noise on the Synchronization of a Metapopulation in a Fluctuating Environment
Lai, Yi Ming
2011-09-08
We use the theory of noise-induced phase synchronization to analyze the effects of demographic noise on the synchronization of a metapopulation of predator-prey systems within a fluctuating environment (Moran effect). Treating each local predator-prey population as a stochastic urn model, we derive a Langevin equation for the stochastic dynamics of the metapopulation. Assuming each local population acts as a limit cycle oscillator in the deterministic limit, we use phase reduction and averaging methods to derive the steady-state probability density for pairwise phase differences between oscillators, which is then used to determine the degree of synchronization of the metapopulation. © 2011 American Physical Society.
Charge Fluctuations in Nanoscale Capacitors
Limmer, D.T.; Merlet, C.; Salanne, M.; Chandler, D.; Madden, P.A.; van Roij, R.H.H.G.; Rotenberg, B.
2013-01-01
The fluctuations of the charge on an electrode contain information on the microscopic correlations within the adjacent fluid and their effect on the electronic properties of the interface. We investigate these fluctuations using molecular dynamics simulations in a constant-potential ensemble with hi
Soltani, Mohammad; Vargas-Garcia, Cesar A.; Antunes, Duarte; Singh, Abhyudai
2016-01-01
Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. Moreover, as many mRNA/protein species are expressed at low-copy numbers, errors incurred in partitioning of molecules between two daughter cells are significant. We derive analytical formulas for the total noise in protein levels when the cell-cycle duration follows a general class of probability distributions. Using a novel hybrid approach the total noise is decomposed into components arising from i) stochastic expression; ii) partitioning errors at the time of cell division and iii) random cell-division events. These formulas reveal that random cell-division times not only generate additional extrinsic noise, but also critically affect the mean protein copy numbers and intrinsic noise components. Counter intuitively, in some parameter regimes, noise in protein levels can decrease as cell-division times become more stochastic. Computations are extended to consider genome duplication, where transcription rate is increased at a random point in the cell cycle. We systematically investigate how the timing of genome duplication influences different protein noise components. Intriguingly, results show that noise contribution from stochastic expression is minimized at an optimal genome-duplication time. Our theoretical results motivate new experimental methods for decomposing protein noise levels from synchronized and asynchronized single-cell expression data. Characterizing the contributions of individual noise mechanisms will lead to precise estimates of gene expression parameters and techniques for altering stochasticity to change phenotype of individual cells. PMID:27536771
Directory of Open Access Journals (Sweden)
Saravanan Ayyadurai
Full Text Available PepT1 is a member of the proton-oligopeptide cotransporter family SLC15, which mediates the transport of di/tripeptides from intestinal lumen into epithelial cells. MicroRNAs (miRNAs, a small noncoding RNAs (21-23 nucleotides, post-transcriptionally regulate gene expression by binding to the 3'-untranslated regions (UTRs of their target mRNAs. Although the role of most miRNAs remains elusive, they have been implicated in vital cellular functions such as intestinal epithelial cells differentiation, proliferation, and apoptosis. In the present study, we investigated the effect of intestinal epithelial PepT1 expression on microRNA (miRNA expression/secretion in the colons of control mice and in mice with experimentally induced colonic inflammation (colitis. The colonic miRNA expression was deregulated in both colitis and control mice but the deregulation of miRNA expression/secretion was specific to colonic tissue and did not affect other tissues such as spleen and liver. Intestinal epithelial PepT1-dependent deregulation of colonic miRNA expression not only affects epithelial cells but also other cell types, such as intestinal macrophages. Importantly, we found the miRNA 23b which was known to be involved in inflammatory bowel disease was secreted and transported between cells to impose a gene-silencing effect on recipient intestinal macrophages. Based on our data, we may conclude that the expression of a specific protein, PepT1, in the intestine affects local miRNA expression/secretion in the colon on a tissue specific manner and may play an important role during the induction and progression of colitis. Colonic miRNA expression/secretion, regulated by intestinal epithelial PepT1, could play a crucial role in cell-to-cell communication during colitis.
Directory of Open Access Journals (Sweden)
Luisa Salvatori
Full Text Available An increasing number of malignancies has been shown to be initiated and propelled by small subpopulations of cancer stem cells (CSC. However, whether tumor aggressiveness is driven by CSC and by what extent this property may be relevant within the tumor mass is still unsettled. To address this issue, we isolated a rare tumor cell population on the basis of its CD44(+CD24(- phenotype from the human androgen-independent prostate carcinoma cell line DU145 and established its CSC properties. The behavior of selected CSC was investigated with respect to the bulk DU145 cells. The injection of CSC in nude mice generated highly vascularized tumors infiltrating the adjacent tissues, showing high density of neuroendocrine cells and expressing low levels of E-cadherin and β-catenin as well as high levels of vimentin. On the contrary, when a comparable number of unsorted DU145 cells were injected the resulting tumors were less aggressive. To investigate the different features of tumors in vivo, the influence of differentiated tumor cells on CSC was examined in vitro by growing CSC in the absence or presence of conditioned medium from DU145 cells. CSC grown in permissive conditions differentiated into cell populations with features similar to those of cells held in aggressive tumors generated from CSC injection. Differently, conditioned medium induced CSC to differentiate into a cell phenotype comparable to cells of scarcely aggressive tumors originated from bulk DU145 cell injection. These findings show for the first time that CSC are able to generate differentiated cells expressing either highly or scarcely aggressive phenotype, thus influencing prostate cancer progression. The fate of CSC was determined by signals released from tumor environment. Moreover, using microarray analysis we selected some molecules which could be involved in this cell-to-cell signaling, hypothesizing their potential value for prognostic or therapeutic applications.
Frequency fluctuations in silicon nanoresonators
Sansa, Marc; Sage, Eric; Bullard, Elizabeth C.; Gély, Marc; Alava, Thomas; Colinet, Eric; Naik, Akshay K.; Villanueva, Luis Guillermo; Duraffourg, Laurent; Roukes, Michael L.; Jourdan, Guillaume; Hentz, Sébastien
2016-06-01
Frequency stability is key to the performance of nanoresonators. This stability is thought to reach a limit with the resonator's ability to resolve thermally induced vibrations. Although measurements and predictions of resonator stability usually disregard fluctuations in the mechanical frequency response, these fluctuations have recently attracted considerable theoretical interest. However, their existence is very difficult to demonstrate experimentally. Here, through a literature review, we show that all studies of frequency stability report values several orders of magnitude larger than the limit imposed by thermomechanical noise. We studied a monocrystalline silicon nanoresonator at room temperature and found a similar discrepancy. We propose a new method to show that this was due to the presence of frequency fluctuations, of unexpected level. The fluctuations were not due to the instrumentation system, or to any other of the known sources investigated. These results challenge our current understanding of frequency fluctuations and call for a change in practices.
Wind power integration studies using a multi-stage stochastic electricity system model
DEFF Research Database (Denmark)
Meibom, Peter; Barth, R.; Brand, H.;
2007-01-01
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...... kinds of electricity markets (e.g. a spot and balancing market) and taking into account the stochastic behaviour of the wind power generation and of the prediction error. It can be used for the evaluation of varying electricity prices and system costs due to wind power integration...
Stochastic Hard-Sphere Dynamics for Hydrodynamics of Non-Ideal Fluids
Energy Technology Data Exchange (ETDEWEB)
Donev, A; Alder, B J; Garcia, A L
2008-02-26
A novel stochastic fluid model is proposed with a nonideal structure factor consistent with compressibility, and adjustable transport coefficients. This stochastic hard-sphere dynamics (SHSD) algorithm is a modification of the direct simulation Monte Carlo algorithm and has several computational advantages over event-driven hard-sphere molecular dynamics. Surprisingly, SHSD results in an equation of state and a pair correlation function identical to that of a deterministic Hamiltonian system of penetrable spheres interacting with linear core pair potentials. The fluctuating hydrodynamic behavior of the SHSD fluid is verified for the Brownian motion of a nanoparticle suspended in a compressible solvent.
Driving a macroscopic oscillator with the stochastic motion of a hydrogen molecule.
Lotze, Christian; Corso, Martina; Franke, Katharina J; von Oppen, Felix; Pascual, Jose Ignacio
2012-11-01
Energy harvesting from noise is a paradigm proposed by the theory of stochastic resonances. We demonstrate that the random switching of a hydrogen (H(2)) molecule can drive the oscillation of a macroscopic mechanical resonator. The H(2) motion was activated by tunneling electrons and caused fluctuations of the forces sensed by the tip of a noncontact atomic force microscope. The stochastic molecular noise and the periodic oscillation of the tip were coupled in a concerted dynamic that drives the system into self-oscillation. This phenomenon could be a way for enhancing the transfer of energy from incoherent sources into coherent dynamics of a molecular engine. PMID:23139328
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
Directory of Open Access Journals (Sweden)
Kaznessis Yiannis N
2006-02-01
Full Text Available Abstract Background Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Results Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users
DEFF Research Database (Denmark)
Kemsawasd, Varongsiri; Branco, Patrícia; Almeida, Maria Gabriela;
2015-01-01
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 ...