Fluctuations as stochastic deformation
Kazinski, P. O.
2008-04-01
A notion of stochastic deformation is introduced and the corresponding algebraic deformation procedure is developed. This procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation parameter (the Planck constant). This method is demonstrated on diverse relativistic and nonrelativistic models with finite and infinite degrees of freedom. It is shown that under stochastic deformation the model of a nonrelativistic particle interacting with the electromagnetic field on a curved background passes into the stochastic model described by the Fokker-Planck equation with the diffusion tensor being the inverse metric tensor. The first stochastic correction to the Newton equations for this system is found. The Klein-Kramers equation is also derived as the stochastic deformation of a certain classical model. Relativistic generalizations of the Fokker-Planck and Klein-Kramers equations are obtained by applying the procedure of stochastic deformation to appropriate relativistic classical models. The analog of the Fokker-Planck equation associated with the stochastic Lorentz-Dirac equation is derived too. The stochastic deformation of the models of a free scalar field and an electromagnetic field is investigated. It turns out that in the latter case the obtained stochastic model describes a fluctuating electromagnetic field in a transparent medium.
Work fluctuations and stochastic resonance
We study Brownian particle motion in a double-well potential driven by an ac force. This system exhibits the phenomenon of stochastic resonance. Distribution of work done on the system over a drive period in the time asymptotic regime has been calculated. We show that fluctuations in the input energy or work done dominate the mean value. The mean value of work done over a period as a function of noise strength can also be used to characterize stochastic resonance in the system. We also discuss the validity of steady state fluctuation theorems in this particular system
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
Marinov, Georgi K; Williams, Brian A; McCue, Ken; Schroth, Gary P; Gertz, Jason; Myers, Richard M; Wold, Barbara J
2014-03-01
Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30-100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states. PMID:24299736
Stochastic Einstein equations with fluctuating volume
Dzhunushaliev, Vladimir
2016-01-01
We develop a simple model to study classical fields on the background of a fluctuating spacetime volume. It is applied to formulate the stochastic Einstein equations with a perfect-fluid source. We investigate the particular case of a stochastic Friedmann-Lema\\^itre-Robertson-Walker cosmology, and show that the resulting field equations can lead to solutions which avoid the initial big bang singularity. By interpreting the fluctuations as the result of the presence of a quantum spacetime, we conclude that classical singularities can be avoided even within a stochastic model that include quantum effects in a very simple manner.
Density fluctuations in simple stochastic reactor models
A method to study density fluctuations in a nuclear reactor simultaneously taking into account intrinsic fluctuations usually modelled by a master equation and parametric noise usually modelled by stochastic kinetic equations is presented. The mean density and density-fluctuations variance are calculated for a simple point-reactor model in the presence of Gaussian white-noise fluctuations in the fission, capture and source event rates. They are also calculated in the case of dichotomous noise fluctuations in the source event rate. 'Crossed fluctuation' contributions to the density fluctuations are found that only appear when considering simultaneously intrinsic and parametric noise. These contributions allow distinction to be made between reactivity fluctuations due to fission-rate and capture-rate fluctuations. (author)
Stochastic game dynamics under demographic fluctuations.
Huang, Weini; Hauert, Christoph; Traulsen, Arne
2015-07-21
Frequency-dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency-dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model that naturally combines these two evolutionary ingredients by assuming frequency-dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population, and thus the population size, is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by deterministic competitive Lotka-Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. Because the population size is driven by fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size the population would thrive regardless of its average payoff. PMID:26150518
Thermal diffusion by stochastic electromagnetic fluctuations
A new simple systematic method has been developed to analytically evaluate the thermal diffusion coefficient of guiding center test particles brought by coexisting homogeneously stochastic electrostatic and electro-magnetic fluctuations. As a most simple case, thermal diffusion coefficients for electrons and ions are analytically obtained in a large aspect straight tokamak with a small gyro-radius and negligible magnetic shear and negligible equilibrium E vector x B vector flow shear. Those analytical formulae are applicable to the range beyond so-called quasi-linear limit: thermal diffusion coefficient are squarely (linearly) proportional to fluctuation amplitudes in the quasi-linear (beyond quasi-linear) region. It is shown that the thermal diffusion of electrons (ions) is mainly dominated by magnetic (electrostatic) fluctuations in the experimentally relevant situations, even if both magnetic and electrostatic fluctuations coexist. It is also shown that the resonant electrons do not diffuse when the electric field parallel to the unperturbed magnetic field lines is negligible, even if electrostatic and electromagnetic fluctuations coexist. (author)
Stochastically fluctuations of the modernized fast pulsed reactor IBR-2
Full Text : Stochastically fluctuations of the power of the IBR-2 reactor have been quite significant (20 percent), they affect the dynamics of the reactor, the process of regulation, starting on the work of the experimental equipment, etc. On the other hand, the presence of large fluctuations in power at the IBR-2M has had its advantages. Investigation of stochastic fluctuations has allowed to estimate some physical parameters of the nuclear reactor core, for example, the mean lifetime of prompt neutrons in the reactor, source of spontaneous neutrons, and absolute power of the reactor. The main results of the investigation impulse stochastically fluctuations of the IBR-2 periodic pulsed reactor after modernization have been presented. It has been shown that the experimental results have been close to the calculated ones
Stochastic thermodynamics of macrospins with fluctuating amplitude and direction.
Bandopadhyay, Swarnali; Chaudhuri, Debasish; Jayannavar, A M
2015-09-01
We consider stochastic energy balance and entropy production (EP) in a generalized Langevin dynamics of macrospins, allowing for both amplitude and direction fluctuations, under external magnetic field. EP is calculated using a Fokker-Planck equation, distinguishing between reversible and irreversible parts of probability currents. The system entropy increases due to irreversible non-equilibrium processes, and reduces as heat dissipates to the surrounding environment. Using path probability distributions of time-forward trajectories and conjugate trajectories under time reversal, we obtain fluctuation theorems (FT) for total stochastic EP. We show that the choice of conjugate trajectories is crucial in obtaining entropy-like quantities that obey FTs. PMID:26465462
Gravitational brainwaves, quantum fluctuations and stochastic quantization
Bar, D.
2007-01-01
It is known that the biological activity of the brain involves radiation of electric waves. These waves result from ionic currents and charges traveling among the brain's neurons. But it is obvious that these ions and charges are carried by their relevant masses which should give rise, according to the gravitational theory, to extremely weak gravitational waves. We use in the following the stochastic quantization (SQ) theory to calculate the probability to find a large ensemble of brains radi...
Gravitational brainwaves, quantum fluctuations and stochastic quantization
Bar, D
2007-01-01
It is known that the biological activity of the brain involves radiation of electric waves. These waves result from ionic currents and charges traveling among the brain's neurons. But it is obvious that these ions and charges are carried by their relevant masses which should give rise, according to the gravitational theory, to extremely weak gravitational waves. We use in the following the stochastic quantization (SQ) theory to calculate the probability to find a large ensemble of brains radiating similar gravitational waves. We also use this SQ theory to derive the equilibrium state related to the known Lamb shift.
Energy fluctuations induced by stochastic frequency changes in atom traps
We study the quantum description of energy fluctuations induced by stochastic changes in the frequency of atom traps. Using the connection between classical and quantum descriptions of parametric oscillators, the classical cumulant expansion method is used to obtain quantum results beyond standard perturbation theory. Both the case of static and time-dependent traps are explicitly worked out
Extreme fluctuations in stochastic network coordination with time delays
Hunt, D.; Molnár, F.; Szymanski, B. K.; Korniss, G.
2015-12-01
We study the effects of uniform time delays on the extreme fluctuations in stochastic synchronization and coordination problems with linear couplings in complex networks. We obtain the average size of the fluctuations at the nodes from the behavior of the underlying modes of the network. We then obtain the scaling behavior of the extreme fluctuations with system size, as well as the distribution of the extremes on complex networks, and compare them to those on regular one-dimensional lattices. For large complex networks, when the delay is not too close to the critical one, fluctuations at the nodes effectively decouple, and the limit distributions converge to the Fisher-Tippett-Gumbel density. In contrast, fluctuations in low-dimensional spatial graphs are strongly correlated, and the limit distribution of the extremes is the Airy density. Finally, we also explore the effects of nonlinear couplings on the stability and on the extremes of the synchronization landscapes.
Effective cosmological constant induced by stochastic fluctuations of Newton's constant
de Cesare, Marco; Sakellariadou, Mairi
2016-01-01
We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.
Effective cosmological constant induced by stochastic fluctuations of Newton's constant
de Cesare, Marco; Lizzi, Fedele; Sakellariadou, Mairi
2016-09-01
We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.
Stochastic Amplification of Fluctuations in Cortical Up-States
Hidalgo, Jorge; Seoane, Luís F.; Cortés, Jesús M.; Muñoz, Miguel A.
2012-01-01
Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow Hz oscillations which are widely known as transitions between Up and Down States. Despite a large number of studies on Up-Down transitions, deciphering its nature, mechanisms and function are still today challenging tasks. In this paper we focus on recent experimental evidence, showing that a class of spontaneous oscillations can emerge within the Up states. In particular, a non-trivial peak around Hz appears in their associated power-spectra, what produces an enhancement of the activity power for higher frequencies (in the Hz band). Moreover, this rhythm within Ups seems to be an emergent or collective phenomenon given that individual neurons do not lock to it as they remain mostly unsynchronized. Remarkably, similar oscillations (and the concomitant peak in the spectrum) do not appear in the Down states. Here we shed light on these findings by using different computational models for the dynamics of cortical networks in presence of different levels of physiological complexity. Our conclusion, supported by both theory and simulations, is that the collective phenomenon of “stochastic amplification of fluctuations” – previously described in other contexts such as Ecology and Epidemiology – explains in an elegant and parsimonious manner, beyond model-dependent details, this extra-rhythm emerging only in the Up states but not in the Downs. PMID:22879879
Stochastic cooling of bunched beams from fluctuation and kinetic theory
Chattopadhyay, S.
1982-09-01
A theoretical formalism for stochastic phase-space cooling of bunched beams in storage rings is developed on the dual basis of classical fluctuation theory and kinetic theory of many-body systems in phase-space. The physics is that of a collection of three-dimensional oscillators coupled via retarded nonconservative interactions determined by an electronic feedback loop. At the heart of the formulation is the existence of several disparate time-scales characterizing the cooling process. Both theoretical approaches describe the cooling process in the form of a Fokker-Planck transport equation in phase-space valid up to second order in the strength and first order in the auto-correlation of the cooling signal. With neglect of the collective correlations induced by the feedback loop, identical expressions are obtained in both cases for the coherent damping and Schottky noise diffusion coefficients. These are expressed in terms of Fourier coefficients in a harmonic decomposition in angle of the generalized nonconservative cooling force written in canonical action-angle variables of the particles in six-dimensional phase-space. Comparison of analytic results to a numerical simulation study with 90 pseudo-particles in a model cooling system is presented.
Stochastic cooling of bunched beams from fluctuation and kinetic theory
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
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.
We investigate the phenomenon that stochastic fluctuation induced the competition between tumor extinction and recurrence in the model of tumor growth derived from the catalytic Michaelis–Menten reaction. We analyze the probability transitions between the extinction state and the state of the stable tumor by the Mean First Extinction Time (MFET) and Mean First Return Time (MFRT). It is found that the positional fluctuations hinder the transition, but the environmental fluctuations, to a certain level, facilitate the tumor extinction. The observed behavior could be used as prior information for the treatment of cancer. -- Highlights: ► Stochastic fluctuation induced the competition between extinction and recurrence. ► The probability transitions are investigated. ► The positional fluctuations hinder the transition. ► The environmental fluctuations, to a certain level, facilitate the tumor extinction. ► The observed behavior can be used as prior information for the treatment of cancer.
Impulse power stochastically fluctuations of the modernized fast pulsed reactor IBR-2
Full text : Stochastically fluctuations of the power of the IBR-2 reactor have been quite significant, they affect the dynamics of the reactor, the process of regulation, starting on the work of the experimental equipment. On the other hand, the presence of large fluctuations in power at the IBR-2M has had its advantages. Investigation of stochastic fluctuations has allowed to estimate some physical parameters of the nuclear reactor core, for example, the mean lifetime of prompt neutrons in the reactor, source of spontaneous neutrons and absolute power of the reactor. The main results of the investigation impulse power stochastically fluctuations of the IBR-2 periodic pulsed reactor after modernization have been presented. It has been shown that the experimental results have been close to the calculated ones
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.
Li Dongxi, E-mail: lidongxi@mail.nwpu.edu.c [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China); Xu Wei; Guo, Yongfeng; Xu Yong [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China)
2011-01-31
We investigate a stochastic model of tumor growth derived from the catalytic Michaelis-Menten reaction with positional and environmental fluctuations under subthreshold periodic treatment. Firstly, the influences of environmental fluctuations on the treatable stage are analyzed numerically. Applying the standard theory of stochastic resonance derived from the two-state approach, we derive the signal-to-noise ratio (SNR) analytically, which is used to measure the stochastic resonance phenomenon. It is found that the weak environmental fluctuations could induce the extinction of tumor cells in the subthreshold periodic treatment. The positional stability is better in favor of the treatment of the tumor cells. Besides, the appropriate and feasible treatment intensity and the treatment cycle should be highlighted considered in the treatment of tumor cells.
Optimal Stochastic Restart Renders Fluctuations in First Passage Times Universal
Reuveni, Shlomi
2016-04-01
Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT) processes seem to have very little in common but it is actually quite the other way around. Here we show that the relative standard deviation associated with the FPT of an optimally restarted process, i.e., one that is restarted at a constant (nonzero) rate which brings the mean FPT to a minimum, is always unity. We interpret, further generalize, and discuss this finding and the implications arising from it.
Environmental Fluctuations and Stochastic Resonance in Protein Folding.
Dave, Kapil; Davtyan, Aram; Papoian, Garegin A; Gruebele, Martin; Platkov, Max
2016-05-01
Stochastic resonance is a mechanism whereby a weak signal becomes detectable through the addition of noise. It is common in many macroscopic biological phenomena, but here we ask whether it can be observed in a microscopic biological phenomenon, protein folding. We investigate the folding kinetics of the protein VlsE, with a folding relaxation time of about 0.7 seconds at 38 °C in vitro. First we show that the VlsE unfolding/refolding reaction can be driven by a periodic thermal excitation above the reaction threshold. We detect the reaction by fluorescence from FRET labels on VlSE and show that accurate rate coefficients and activation barriers can be obtained from modulated kinetics. Then we weaken the periodic temperature modulation below the reaction threshold, and show that addition of artificial thermal noise speeds up the reaction from an undetectable to a detectable rate. We observe a maximum in the recovered signal as a function of thermal noise, a stochastic resonance. Simulation of a small model-protein, analysis in an accompanying theory paper, and our experimental result here all show that correlated noise is a physically and chemically plausible mechanism by which cells could modulate biomolecular dynamics during threshold processes such as signaling. PMID:26711088
A model for the optimal design of a supply chain network driven by stochastic fluctuations
Petridis, Kostas; Dey, Prasanta K
2015-01-01
Supply chain optimization schemes have more often than not underplayed the role of inherent stochastic fluctuations in the associated variables. The present article focuses on the associated reengagement and correlated renormalization of supply chain predictions now with the inclusion of stochasticity induced fluctuations in the structure. With a processing production plant in mind that involves stochastically varying production and transportation costs both from the site to the plant as well as from the plant to the customer base, this article proves that the producer may benefit through better outlay in the form of higher sale prices with lowered optimized production costs only through a suitable selective choice of producers whose production cost probability density function abides a Pareto distribution. Lower the Pareto exponent, better is the supply chain prediction for cost optimization. On the other hand, other symmetric (normal) and asymmetric (lognormal) distributions lead to upscaled costs both in t...
Black Hole Fluctuations and Backreaction in Stochastic Gravity
Sinha, S; Hu, B L; Sinha, Sukanya; Raval, Alpan
2003-01-01
We present a framework for analyzing black hole backreaction from the point of view of quantum open systems using influence functional formalism. We focus on the model of a black hole described by a radially perturbed quasi-static metric and Hawking radiation by a conformally coupled massless quantum scalar field. It is shown that the closed-time-path (CTP) effective action yields a non-local dissipation term as well as a stochastic noise term in the equation of motion, the Einstein-Langevin equation. Once the thermal Green's function in a Schwarzschild background becomes available to the required accuracy the strategy described here can be applied to obtain concrete results on backreaction. We also present an alternative derivation of the CTP effective action in terms of the Bogolyubov coefficients, thus making a connection with the interpretation of the noise term as measuring the difference in particle production in alternative histories.
Particle-density fluctuations and universality in the conserved stochastic sandpile
Dickman, Ronald; da Cunha, S. D.
2015-08-01
We examine fluctuations in particle density in the restricted-height, conserved stochastic sandpile (CSS). In this and related models, the global particle density is a temperaturelike control parameter. Thus local fluctuations in this density correspond to disorder; if this disorder is a relevant perturbation of directed percolation (DP), then the CSS should exhibit non-DP critical behavior. We analyze the scaling of the variance Vℓ of the number of particles in regions of ℓd sites in extensive simulations of the quasistationary state in one and two dimensions. Our results, combined with a Harris-like argument for the relevance of particle-density fluctuations, strongly suggest that conserved stochastic sandpiles belong to a universality class distinct from that of DP.
Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes
Kumar, Ashutosh; Nandi, Mintu; Dua, Arti
2016-01-01
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, how...
Effects of stochastic fluctuations at molecule–electrode contacts in transition voltage spectroscopy
Highlights: ► Work devoted to transition voltage spectroscopy, a hot topic in molecular electronics. ► First theoretical study on the physical origin of stochastic fluctuations in TVS. ► First theoretical study that considers effects of electron correlations on TVS. ► Supporting the idea that the transition voltage is a molecular signature. ► Validation of the Newns–Anderson model for molecular junctions of interest. - Abstract: The influence of the stochastic fluctuations at contacts on the electron transport through molecular junctions based on alkanedithiols is investigated theoretically. Results are presented, which demonstrate that the transition voltage Vt is insensitive to fluctuations in the electrode–molecule hopping integrals. By contrast, reasonably large fluctuations (δJ∼2eV) in the Coulomb contact interaction J, included via an extended Newns–Anderson model, lead to fluctuations in the molecular orbital energetic alignment ε0, which are consistent with the fluctuations in Vt observed experimentally. The impact of these J- (or ε0-) fluctuations on the conductance G is considerably stronger than on Vt. The G-fluctuations driven by δJ represent a substantial fraction of the fluctuations displayed by experimental conductance histograms. The electron system for J≠0 is correlated, i.e., it cannot be described within a single-particle (Landauer-based) picture. However, in the J-range of interest, the ratio Vt/ε0 turns out to be only weakly dependent on J. The weak impact of J on the ratio Vt/ε0 is important because it suggests that, even in the presence of realistically strong electron correlations, transition voltage spectroscopy can be a useful tool of investigation.
Altaner, Bernhard; Wachtel, Artur; Vollmer, Jürgen
2015-10-01
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational states of these biological macromolecules. A recently developed theoretical framework [A. Wachtel, J. Vollmer, and B. Altaner, Phys. Rev. E 92, 042132 (2015), 10.1103/PhysRevE.92.042132] provides a simple algorithm for the determination of macroscopic currents and correlation integrals of arbitrary fluctuating currents. Here we use it to discuss energy conversion and nonequilibrium response in different models for the molecular motor kinesin. Methodologically, our results demonstrate the effectiveness of the algorithm in dealing with parameter-dependent stochastic models. For the concrete biophysical problem our results reveal two interesting features in experimentally accessible parameter regions: the validity of a nonequilibrium Green-Kubo relation at mechanical stalling as well as a negative differential mobility for superstalling forces.
Space-time fluctuations and a stochastic Schr\\"odinger-Newton equation
Bera, Sayantani; Singh, Tejinder P
2016-01-01
We propose a stochastic modification of the Schr\\"{o}dinger-Newton equation which takes into account the effect of extrinsic spacetime fluctuations. We use this equation to demonstrate gravitationally induced decoherence of two gaussian wave-packets, and obtain a decoherence criterion similar to those obtained in the earlier literature in the context of effects of gravity on the Schr\\"{o}dinger equation.
A Stochastic Approach to Thermal Fluctuations during a First Order Electroweak Phase Transition
Illuminati, F.; Riotto, A.
1995-01-01
We investigate the role played by subcritical bubbles at the onset of the electroweak phase transition. Treating the configuration modelling the thermal fluctuations around the homogeneous zero configuration of the Higgs field as a stochastic variable, we describe its dynamics by a phenomenological Langevin equation. This approach allows to properly take into account both the effects of the thermal bath on the system: a systematic dyssipative force, which tends to erase out any initial subcri...
Rocha, Paulo; Raischel, Frank; Boto, João P.; Lind, Pedro G.
2016-05-01
We present a framework for describing the evolution of stochastic observables having a nonstationary distribution of values. The framework is applied to empirical volume-prices from assets traded at the New York Stock Exchange, about which several remarks are pointed out from our analysis. Using Kullback-Leibler divergence we evaluate the best model out of four biparametric models commonly used in the context of financial data analysis. In our present data sets we conclude that the inverse Γ distribution is a good model, particularly for the distribution tail of the largest volume-price fluctuations. Extracting the time series of the corresponding parameter values we show that they evolve in time as stochastic variables themselves. For the particular case of the parameter controlling the volume-price distribution tail we are able to extract an Ornstein-Uhlenbeck equation which describes the fluctuations of the highest volume-prices observed in the data. Finally, we discuss how to bridge the gap from the stochastic evolution of the distribution parameters to the stochastic evolution of the (nonstationary) observable and put our conclusions into perspective for other applications in geophysics and biology.
A stochastic approach to thermal fluctuations during a first order electroweak phase transition
Illuminati, F
1995-01-01
We investigate the role played by subcritical bubbles at the onset of the electroweak phase transition. Treating the configuration modelling the thermal fluctuations around the homogeneous zero configuration of the Higgs field as a stochastic variable, we describe its dynamics by a phenomenological Langevin equation. This approach allows to properly take into account both the effects of the thermal bath on the system: a systematic dyssipative force, which tends to erase out any initial subcritical configuration, and a random stochastic force responsible for the fluctuations. We show that the contribution to the variance \\lgh\\phi^2(t)\\rg_V in a given volume V from any initial subcritical configuration is quickly damped away and that, in the limit of long times, \\lgh\\phi^2(t)\\rg_V approaches its equilibrium value provided by the stochastic force and independent from the viscosity coefficient, as predicted by the fluctuation-dissipation theorem. In agreement with some recent claims, we conclude that thermal fluc...
Fluctuations of large-scale jets in the stochastic 2D Euler equation
Nardini, Cesare
2016-01-01
Two-dimensional turbulence in a rectangular domain self-organises into large-scale unidirectional jets. While several results are present to characterize the mean jets velocity profile, much less is known about the fluctuations. We study jets dynamics in the stochastically forced two-dimensional Euler equations. In the limit where the average jets velocity profile evolves slowly with respect to turbulent fluctuations, we employ a multi-scale (kinetic theory) approach, which relates jet dynamics to the statistics of Reynolds stresses. We study analytically the Gaussian fluctuations of Reynolds stresses and predict the spatial structure of the jets velocity covariance. Our results agree qualitatively well with direct numerical simulations, clearly showing that the jets velocity profile are enhanced away from the stationary points of the average velocity profile. A numerical test of our predictions at quantitative level seems out of reach at the present day.
Jansen, TL; Hayashi, T; Zhuang, W; Mukamel, S
2005-01-01
The effects of hydrogen-bond forming and breaking kinetics on the linear and coherent third-order infrared spectra of the OH stretch of HOD in D2O are described by Markovian, not necessarily Gaussian, fluctuations and simulated using the stochastic Liouville equations. Slow (0.5 ps) fluctuations are
QB1 - Stochastic Gene Regulation
Munsky, Brian [Los Alamos National Laboratory
2012-07-23
Summaries of this presentation are: (1) Stochastic fluctuations or 'noise' is present in the cell - Random motion and competition between reactants, Low copy, quantization of reactants, Upstream processes; (2) Fluctuations may be very important - Cell-to-cell variability, Cell fate decisions (switches), Signal amplification or damping, stochastic resonances; and (3) Some tools are available to mode these - Kinetic Monte Carlo simulations (SSA and variants), Moment approximation methods, Finite State Projection. We will see how modeling these reactions can tell us more about the underlying processes of gene regulation.
Petrosyan, K G
2014-01-01
We present a statistical physics framework for description of nonlinear non-equilibrium stochastic processes, modeled via chemical master equation, in the weak-noise limit. Using the Poisson representation approach and applying the large-deviation principle we first solve the master equation. Then we use the notion of the non-equilibrium free energy to derive an integral fluctuation relation for nonlinear non-equilibrium systems under feedback control. We point out that the free energy as well as some functionals can serve as non-equilibrium Lyapunov function which has an important property to decay to its minimal value monotonously at all times. The Poisson representation technique is illustrated via exact stochastic treatment of biophysical processes, such as bacterial chemosensing and molecular evolution.
Stochastic volatility of financial markets as the fluctuating rate of trading: an empirical study
Silva, A C; Yakovenko, Victor M.
2006-01-01
We present an empirical study of the subordination hypothesis for a stochastic time series of a stock price. The fluctuating rate of trading is identified with the stochastic variance of the stock price, as in the continuous-time random walk (CTRW) framework. The probability distribution of the stock price changes (log-returns) for a given number of trades N is found to be approximately Gaussian. The probability distribution of N for a given time interval Dt is non-Poissonian and has an exponential tail for large N and a sharp cutoff for small N. Combining these two distributions produces a nontrivial distribution of log-returns for a given time interval Dt, which has exponential tails and a Gaussian central part, in agreement with empirical observations.
We investigate a stochastic heat engine based on an over-damped particle diffusing on the positive real axis in an externally driven time-periodic log-harmonic potential. The periodic driving is composed of two isothermal and two adiabatic branches. Within our specific setting we verify the recent universal results regarding efficiency at maximum power and discuss properties of the optimal protocol. Namely, we show that for certain fixed parameters the optimal protocol maximizes not only the output power but also the efficiency. Moreover, we calculate the variance of the output work and discuss the possibility of minimizing fluctuations of the output power. (paper)
Stochastic resonance in a groundwater-dependent plant ecosystem with fluctuations and time delay
We numerically investigate the stochastic resonance (SR) pheno menon in a groundwater-dependent plant ecosystem under the combined influence of environmental fluctuations, seasonal rainfall oscillation, and time delay. The effects of time delay and intrinsic and extrinsic fluctuations on the output signal-to-noise ratio (SNR) of the system are analyzed. The results indicate that the SNR exhibits a maximum as a function of the intensities of the intrinsic and extrinsic noises, identifying the occurrence of the SR effect. An increase of the delay time always suppresses the SR effect, while an increase of correlation strength between noises may suppress or enhance it. The SNR also shows a resonant behavior as a function of the correlation strength between noises, and it can be weakened by the time delay. (paper)
Charmet, Jérôme; Michaels, Thomas C. T.; Daly, Ronan; Prasad, Abhinav; Thiruvenkathanathan, Pradyumna; Langley, Robin S.; Knowles, Tuomas P. J.; Seshia, Ashwin A.
2016-06-01
Recent advances in micro- and nanotechnology have enabled the development of ultrasensitive sensors capable of detecting small numbers of species. In general, however, the response induced by the random adsorption of a small number of objects onto the surface of such sensors results in significant fluctuations due to the heterogeneous sensitivity inherent to many such sensors coupled to statistical fluctuations in the particle number. At present, this issue is addressed by considering either the limit of very large numbers of analytes, where fluctuations vanish, or the converse limit, where the sensor response is governed by individual analytes. Many cases of practical interest, however, fall between these two limits and remain challenging to analyze. Here, we address this limitation by deriving a general theoretical framework for quantifying measurement variations on mechanical resonators resulting from statistical-number fluctuations of analyte species. Our results provide insights into the stochastic processes in the sensing environment and offer opportunities to improve the performance of mechanical-resonator-based sensors. This metric can be used, among others, to aid in the design of robust sensor platforms to reach ultrahigh-resolution measurements using an array of sensors. These concepts, illustrated here in the context of biosensing, are general and can therefore be adapted and extended to other sensors with heterogeneous sensitivity.
We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications
Leonard, T.; Lander, B.; Seifert, U. [II. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Speck, T. [Institut für Theoretische Physik II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany)
2013-11-28
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for the work still hold albeit for a different, apparent, change of free energy.
A simple stochastic model for dipole moment fluctuations in numerical dynamo simulations
Domenico G. eMeduri
2016-04-01
Full Text Available Earth's axial dipole field changes in a complex fashion on many differenttime scales ranging from less than a year to tens of million years.Documenting, analysing, and replicating this intricate signalis a challenge for data acquisition, theoretical interpretation,and dynamo modelling alike. Here we explore whether axial dipole variationscan be described by the superposition of a slow deterministic driftand fast stochastic fluctuations, i.e. by a Langevin-type system.The drift term describes the time averaged behaviour of the axial dipole variations,whereas the stochastic part mimics complex flow interactions over convective time scales.The statistical behaviour of the system is described by a Fokker-Planck equation whichallows useful predictions, including the average rates of dipole reversals and excursions.We analyse several numerical dynamo simulations, most of which havebeen integrated particularly long in time, and also the palaeomagneticmodel PADM2M which covers the past 2 Myr.The results show that the Langevin description provides a viable statistical modelof the axial dipole variations on time scales longer than about 1 kyr.For example, the axial dipole probability distribution and the average reversalrate are successfully predicted.The exception is PADM2M where the stochastic model reversal rate seems too low.The dependence of the drift on the axial dipolemoment reveals the nonlinear interactions that establish thedynamo balance. A separate analysis of inductive and diffusive magnetic effectsin three dynamo simulations suggests that the classical quadraticquenching of induction predicted by mean-field theory seems at work.
Out-of-equilibrium fluctuations in stochastic long-range interacting systems
Gupta, Shamik; Dauxois, Thierry; Ruffo, Stefano
2016-03-01
For a many-particle system with long-range interactions and evolving under stochastic dynamics, we study for the first time the out-of-equilibrium fluctuations of the work done on the system by a time-dependent external force. For equilibrium initial conditions, the work distributions for a given protocol of variation of the force in time and the corresponding time-reversed protocol exhibit a remarkable scaling and a symmetry when expressed in terms of the average and the standard deviation of the work. The distributions of the work per particle predict, by virtue of the Crooks fluctuation theorem, the equilibrium free-energy density of the system. For a large number N of particles, the latter is in excellent agreement with the value computed by considering the Langevin dynamics of a single particle in a self-consistent mean field generated by its interaction with other particles. The agreement highlights the effective mean-field nature of the original many-particle dynamics for large N. For initial conditions in non-equilibrium stationary states (NESSs), we study the distribution of a quantity similar to dissipated work that satisfies the non-equilibrium generalization of the Clausius inequality, namely, the Hatano-Sasa equality, for transitions between NESSs. Besides illustrating the validity of the equality, we show that the distribution has exponential tails that decay differently on the left and on the right.
Schunck, M.; Hegmann, M.; Sedlmayr, E.
2007-01-01
We investigate the effects of stochastic density fluctuations on the dust temperatures and the resulting infrared (IR) emission spectra of interstellar clouds as an extension of preceding investigations by Hegmann & Kegel. We consider absorption and scattering by dust grains in spherical clouds which are, on average, homogeneous but have a fluctuating density. The spatial variation of the density is described by means of a Markov process. This clump model introduces two parameters: the correlation length ln and the Gaussian width σn of the density fluctuations. As the intensity Iλ,n inherits the randomness of the density n, the ordinary radiative transfer equation has to be replaced by a generalized transfer equation of Fokker-Planck type. In the first part, we investigate the influence of our model parameters on the radiative transport in the ultraviolet (UV) and use the results to calculate the dust temperature in radiative equilibrium. Afterwards, the IR emission of the dust is modelled for the same set of clump parameters. We find that the presence of clumps decreases the effective extinction and therefore leads to substantial differences in UV illumination and dust temperatures, compared with the homogeneous case. Because of the distribution of dust temperatures, the presence of clumps also affects the IR emission and thus possible observations. In the second part, we use a fit with two blackbody spectra to determine the cloud dust mass from our synthetic IR fluxes. It is shown that in a clumpy environment the overall dust mass is generally underestimated. This effect correlates with the degree of cloud fragmentation.
Listening to the noise: random fluctuations reveal gene network parameters
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2009-01-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations show cell-to-cell variability that can manifest significant phenotypic differences. Noise-induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far...
Highlights: ► Solar radiation data for European cities follow the Extreme Value or Weibull distribution. ► Simulation model for the sizing of SAPV systems based on energy balance and stochastic analysis. ► Simulation of PV Generator-Loads-Battery Storage System performance for all months. ► Minimum peak power and battery capacity required for reliable SAPV sizing for various European cities. ► Peak power and battery capacity reduced by more than 30% for operation 95% success rate. -- Abstract: The large fluctuations observed in the daily solar radiation profiles affect highly the reliability of the PV system sizing. Increasing the reliability of the PV system requires higher installed peak power (Pm) and larger battery storage capacity (CL). This leads to increased costs, and makes PV technology less competitive. This research paper presents a new stochastic simulation model for stand-alone PV systems, developed to determine the minimum installed Pm and CL for the PV system to be energy independent. The stochastic simulation model developed, makes use of knowledge acquired from an in-depth statistical analysis of the solar radiation data for the site, and simulates the energy delivered, the excess energy burnt, the load profiles and the state of charge of the battery system for the month the sizing is applied, and the PV system performance for the entire year. The simulation model provides the user with values for the autonomy factor d, simulating PV performance in order to determine the minimum Pm and CL depending on the requirements of the application, i.e. operation with critical or non-critical loads. The model makes use of NASA’s Surface meteorology and Solar Energy database for the years 1990–2004 for various cities in Europe with a different climate. The results obtained with this new methodology indicate a substantial reduction in installed peak power and battery capacity, both for critical and non-critical operation, when compared to
Colucci, Paul John
A methodology termed the "filtered density function" (FDF) is developed and implemented for large eddy simulation (LES) of chemically reacting turbulent flows. In this methodology, the effects of the unresolved scalar fluctuations are taken into account by considering the probability density function (PDF) of the subgrid scale (SGS) scalar quantities. The transport equation governing the evolution of the FDF is derived in which the effect of chemical reaction appears in a closed form. The influences of scalar mixing and convection within the subgrid are modeled. The generalization to variable density flows is made through consideration of the filtered mass density function (FMDF). The FDF and FMDF transport equations are solved numerically via a Lagrangian Monte Carlo scheme in which the solutions of equivalent stochastic differential equations (SDEs) are obtained. The consistency of the approach, the convergence of the Monte Carlo solution, and the performance of the closures employed in the FDF and FMDF transport equations are assessed by comparisons with results obtained by direct numerical simulation (DNS) and by conventional LES procedures in which the first two SGS scalar moments are obtained by a finite difference method (LES-FD). In non-reacting flows, the Monte Carlo solution yields results similar to those via LES-FD for the first two SGS moments. The advantage of the methodology is demonstrated by its use in LES of reacting flows. In the absence of a closure for the SGS scalar fluctuations, the LES-FD results are significantly different from those based on DNS. Comparatively, the FDF and FMDF yield much better agreement with filtered DNS results. The methodology is also tested by comparative assessments against experimental data for a heat releasing hydrogen-fluorine reacting mixing layer.
Zhang, Yue; Zhang, Qingling; Yan, Xing-Gang
2014-06-01
In this paper, a class of singular Leslie-Gower predator-prey bioeconomic models with environment fluctuations and time delays is investigated. Local stability analysis of the model reveals that there is a phenomenon of singularity induced bifurcation due to variation of economic interest of harvesting. By choosing the delay as a bifurcation parameter, it is shown that the Hopf bifurcations can occur as the delay crosses some critical values. Then, the effect of a fluctuating environment on the singular stochastic delayed predator-prey bioeconomic model is discussed. Finally numerical simulations demonstrate that the amplitude of oscillation for population is enhanced when compared with the oscillation observed in the deterministic environment.
Hong, Dawei; Man, Shushuang; Martin, Joseph V
2016-01-21
There are two functionally important factors in signal propagation in a brain structural network: the very first synaptic delay-a time delay about 1ms-from the moment when signals originate to the moment when observation on the signal propagation can begin; and rapid random fluctuations in membrane potentials of every individual neuron in the network at a timescale of microseconds. We provide a stochastic analysis of signal propagation in a general setting. The analysis shows that the two factors together result in a stochastic mechanism for the signal propagation as described below. A brain structural network is not a rigid circuit rather a very flexible framework that guides signals to propagate but does not guarantee success of the signal propagation. In such a framework, with the very first synaptic delay, rapid random fluctuations in every individual neuron in the network cause an "alter-and-concentrate effect" that almost surely forces signals to successfully propagate. By the stochastic mechanism we provide analytic evidence for the existence of a force behind signal propagation in a brain structural network caused by rapid random fluctuations in every individual neuron in the network at a timescale of microseconds with a time delay of 1ms. PMID:26555846
Rocha, Paulo; Boto, João P; Lind, Pedro G
2015-01-01
We present a framework for describing the evolution of stochastic observables having a non-stationary distribution of values. The framework is applied to empirical volume-prices from assets traded at the New York stock exchange. Using Kullback-Leibler divergence we evaluate the best model out from four biparametric models standardly used in the context of financial data analysis. In our present data sets we conclude that the inverse $\\Gamma$-distribution is a good model, particularly for the distribution tail of the largest volume-price fluctuations. Extracting the time-series of the corresponding parameter values we show that they evolve in time as stochastic variables themselves. For the particular case of the parameter controlling the volume-price distribution tail we are able to extract an Ornstein-Uhlenbeck equation which describes the fluctuations of the largest volume-prices observed in the data. Finally, we discuss how to bridge from the stochastic evolution of the distribution parameters to the stoch...
Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver
2013-01-01
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulatio...
Kim, Won Kyu; 10.1063/1.4746118
2012-01-01
Within the cell, biopolymers are often situated in constrained, fluid environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is of paramount importance to understand quantitatively how they, utilizing their flexibility, optimally respond to a minute signal, which is, in general, temporally fluctuating far away from equilibrium. To this end, we analytically study viscoelastic response and associated stochastic resonance in a stretched single semi-flexible chain to an oscillatory force or electric field. Including hydrodynamic interactions between chain segments, we evaluate dynamics of the polymer extension in coherent response to the force or field. We find power amplification factor of the response at a noise-strength (temperature) can attain the maximum that grows as the chain length increases, indicative of an entropic stochastic resonance (ESR). In particular for a charged chain under an electric field, we find that the maximum also occurs at an optimal chain length, a new feature of E...
Garcia, O. E.; Kube, R.; Theodorsen, A.; Pécseli, H. L.
2016-05-01
A stochastic model is presented for intermittent fluctuations in the scrape-off layer of magnetically confined plasmas. The fluctuations in the plasma density are modeled by a super-position of uncorrelated pulses with fixed shape and duration, describing radial motion of blob-like structures. In the case of an exponential pulse shape and exponentially distributed pulse amplitudes, predictions are given for the lowest order moments, probability density function, auto-correlation function, level crossings, and average times for periods spent above and below a given threshold level. Also, the mean squared errors on estimators of sample mean and variance for realizations of the process by finite time series are obtained. These results are discussed in the context of single-point measurements of fluctuations in the scrape-off layer, broad density profiles, and implications for plasma-wall interactions due to the transient transport events in fusion grade plasmas. The results may also have wide applications for modelling fluctuations in other magnetized plasmas such as basic laboratory experiments and ionospheric irregularities.
Considering a damped linear oscillator model subjected to a white noise with an inherent angular frequency and a periodic external driving force, we derive the analytic expression of the first moment of output response, and study the stochastic resonance phenomenon in a system. The results show that the output response of this system behaves as a simple harmonic vibration, of which the frequency is the same as the external driving frequency, and the variations of amplitude with the driving frequency and the inherent frequency present a bona fide stochastic resonance. (general)
Zhang Ling-Ying; Jin Guo-Xiang; Cao Li; Wang Zhi-Yun
2012-01-01
Considering a damped linear oscillator model subjected to a white noise with an inherent angular frequency and a periodic external driving force,we derive the analytic expression of the first moment of output response,and study the stochastic resonance phenomenon in a system.The results show that the output response of this system behaves as a simple harmonic vibration,of which the frequency is the same as the external driving frequency,and the variations of amplitude with the driving frequency and the inherent frequency present a bona fide stochastic resonance.
Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver
2013-10-22
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host-parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5 °C) and permissive (23 °C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645
Duncan, Alison B.; Gonzalez, Andrew; Kaltz, Oliver
2013-01-01
Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645
EFT Beyond the Horizon: Stochastic Inflation and How Primordial Quantum Fluctuations Go Classical
Burgess, C P; Tasinato, G; Williams, M
2015-01-01
We identify the effective theory describing inflationary super-Hubble scales and show it to be a special case of effective field theories appropriate to open systems. Open systems allow information to be exchanged between the degrees of freedom of interest and those that are integrated out, such as for particles moving through a fluid. Strictly speaking they cannot in general be described by an effective lagrangian; rather the appropriate `low-energy' limit is instead a Lindblad equation describing the evolution of the density matrix of the slow degrees of freedom. We derive the equation relevant to super-Hubble modes of quantum fields in near-de Sitter spacetimes and derive two implications. We show the evolution of the diagonal density-matrix elements quickly approaches the Fokker-Planck equation of Starobinsky's stochastic inflationary picture. This provides an alternative first-principles derivation of this picture's stochastic noise and drift, as well as its leading corrections. (An application computes ...
Determinants of Cell-to-Cell Variability in Protein Kinase Signaling
Matthias Jeschke; Stephan Baumgärtner; Stefan Legewie
2013-01-01
Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds ('pathway sensitivity') and the maximal act...
Wen, Xing-Chun; He, Ling-Yun
2015-08-01
There is a bitter controversy over what drives the housing price in China in the existing literature. In this paper, we investigate the underlying driving force behind housing price fluctuations in China, especially focusing on the role of housing demand shock with that of money supply shock in explaining housing price movements, by a new Keynesian dynamic stochastic general equilibrium model. Empirical results suggest that it is housing demand, instead of money supply, that mainly drives China's housing price movements. Relevant policy implication is further discussed, namely, whether to consider the housing price fluctuations in the conduct of monetary policy. By means of the policy simulations, we find that a real house price-augmented money supply rule is a better monetary policy for China's economy stabilization. 1. Investment refers to fixed capital investment. 2. Housing price refers to national average housing price. Quarterly data on housing price during the period of our work are not directly available. However, monthly data of the value of sales on housing and sale volume on housing can be directly obtained from National Bureau of Statistics of China. We add up the monthly data and calculate one quarter's housing price by dividing the value of housing sales by its sale volume in one quarter. 3. M2 means the broad money supply in China.
Bouzat, Sebastián
2016-01-01
One-dimensional models coupling a Langevin equation for the cargo position to stochastic stepping dynamics for the motors constitute a relevant framework for analyzing multiple-motor microtubule transport. In this work we explore the consistence of these models focusing on the effects of the thermal noise. We study how to define consistent stepping and detachment rates for the motors as functions of the local forces acting on them in such a way that the cargo velocity and run-time match previously specified functions of the external load, which are set on the base of experimental results. We show that due to the influence of the thermal fluctuations this is not a trivial problem, even for the single-motor case. As a solution, we propose a motor stepping dynamics which considers memory on the motor force. This model leads to better results for single-motor transport than the approaches previously considered in the literature. Moreover, it gives a much better prediction for the stall force of the two-motor case, highly compatible with the experimental findings. We also analyze the fast fluctuations of the cargo position and the influence of the viscosity, comparing the proposed model to the standard one, and we show how the differences on the single-motor dynamics propagate to the multiple motor situations. Finally, we find that the one-dimensional character of the models impede an appropriate description of the fast fluctuations of the cargo position at small loads. We show how this problem can be solved by considering two-dimensional models. PMID:26871095
Absorptive and dispersive optical profiles in fluctuating environments: A stochastic model
In this study, we determined the absorptive and dispersive optical profiles of a molecular system coupled with a thermal bath. Solvent effects were explicitly considered by modelling the non-radiative interaction with the solute as a random variable. The optical stochastical Bloch equations (OSBE) were solved using a time-ordered cumulant expansion with white noise as a correlation function. We found a solution for the Fourier component of coherence at the third order of perturbation for the nonlinear Four-wave mixing signal and produced analytical expressions for the optical responses of the system. Finally, we examined the behaviour of these properties with respect to the noise parameter, frequency detuning of the dynamic perturbation, and relaxation times.
Fluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics
Wachtel, Artur; Vollmer, Jürgen; Altaner, Bernhard
2015-10-01
Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication.
Stochasticity in the yeast mating pathway
We report stochastic simulations of the yeast mating signal transduction pathway. The effects of intrinsic and external noise, the influence of cell-to-cell difference in the pathway capacity, and noise propagation in the pathway have been examined. The stochastic temporal behaviour of the pathway is found to be robust to the influence of inherent fluctuations, and intrinsic noise propagates in the pathway in a uniform pattern when the yeasts are treated with pheromones of different stimulus strengths and of varied fluctuations. In agreement with recent experimental findings, extrinsic noise is found to play a more prominent role than intrinsic noise in the variability of proteins. The occurrence frequency for the reactions in the pathway are also examined and a more compact network is obtained by dropping most of the reactions of least occurrence
Stochastic fluctuations and distributed control of gene expression impact cellular memory.
Guillaume Corre
Full Text Available Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.
Conformally-related Einstein-Langevin equations for metric fluctuations in stochastic gravity
Satin, Seema; Hu, Bei Lok
2016-01-01
For a conformally-coupled scalar field we obtain the conformally-related Einstein-Langevin equations, using appropriate transformations for all the quantities in the equations between two conformally-related spacetimes. In particular, we analyze the transformations of the influence action, the stress energy tensor, the noise kernel and the dissipation kernel. In due course the fluctuation-dissipation relation is also discussed. The analysis in this paper thereby facilitates a general solution to the Einstein-Langevin equation once the solution of the equation in a simpler, conformally-related spacetime is known. For example, from the Minkowski solution of Martin and Verdaguer, those of the Einstein-Langevin equations in conformally-flat spacetimes, especially for spatially-flat Friedmann-Robertson-Walker models, can be readily obtained.
Wetland Ecohydrology: stochastic description of water level fluctuations across the soil surface
Tamea, S.; Muneepeerakul, R.; Laio, F.; Ridolfi, L.; Rodriguez-Iturbe, I.
2009-12-01
Wetlands provide a suite of social and ecological critical functions such as being habitats of disease-carrying vectors, providing buffer zones against hurricanes, controlling sediment transport, filtering nutrients and contaminants, and a repository of great biological diversity. More recently, wetlands have also been recognized as crucial for carbon storage in the context of global climate change. Despite such importance, quantitative approaches to many aspects of wetlands are far from adequate. Therefore, improving our quantitative understanding of wetlands is necessary to our ability to maintain, manage, and restore these invaluable environments. In wetlands, hydrologic factors and ecosystem processes interplay and generate unique characteristics and a delicate balance between biotic and abiotic elements. The main hydrologic driver of wetland ecosystems is the position of the water level that, being above or below ground, determines the submergence or exposure of soil. When the water level is above the soil surface, soil saturation and lack of oxygen causes hypoxia, anaerobic functioning of microorganisms and anoxic stress in plants, that might lead to the death of non-adapted organisms. When the water level lies below the soil surface, the ecosystem becomes groundwater-dependent, and pedological and physiological aspects play their role in the soil water balance. We propose here a quantitative description of wetland ecohydrology, through a stochastic process-based water balance, driven by a marked compound Poisson noise representing rainfall events. The model includes processes such as rainfall infiltration, evapotranspiration, capillary rise, and the contribution of external water bodies, which are quantified in a simple yet realistic way. The semi-analytical steady-state probability distributions of water level spanning across the soil surface are validated with data from the Everglades (Florida, USA). The model and its results allow for a quantitative
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
Shnoll S. E.
2006-04-01
Full Text Available This is a survey of the fine structure stochastic distributions in measurements obtained by me over 50 years. It is shown: (1 The forms of the histograms obtained at each geographic point (at each given moment of time are similar with high probability, even if we register phenomena of completely different nature --- from biochemical reactions to the noise in a gravitational antenna, or alpha-decay. (2 The forms of the histograms change with time. The iterations of the same form have the periods of the stellar day (1.436 min, the solar day (1.440 min, the calendar year (365 solar days, and the sidereal year (365 solar days plus 6 hours and 9 min. (3 At the same instants of the local time, at different geographic points, the forms of the histograms are the same, with high probability. (4 The forms of the histograms depend on the locations of the Moon and the Sun with respect to the horizon. (5 All the facts are proof of the dependance of the form of the histograms on the location of the measured objects with respect to stars, the Sun, and the Moon. (6 At the instants of New Moon and the maxima of solar eclipses there are specific forms of the histograms. (7 It is probable that the observed correlations are not connected to flow power changes (the changes of the gravity force --- we did not find the appropriate periods in changes in histogram form. (8 A sharp anisotropy of space was discovered, registered by alpha-decay detectors armed with collimators. Observations at 54 North (the collimator was pointed at the Pole Star showed no day-long periods, as was also the case for observations at 82 North, near the Pole. Histograms obtained by observations with an Easterly-directed collimator were determined every 718 minutes (half stellar day and with observations using a Westerly-directed collimator. (9 Collimators rotating counter-clockwise, in parallel with the celestial equator, gave the probability of changes in histograms as the number of the
Reyes, Luz Marina; Aguilar, Jose Edgar Madriz; Bellini, Mauricio
2010-01-01
We develop a stochastic approach to study scalar field fluctuations of the inflaton field in an early inflationary universe with a black-hole (BH), which is described by an effective 4D SdS metric. Considering a 5D Ricci-flat SdS static metric, we implement a planar coordinate transformation, in order to obtain a 5D cosmological metric, from which the effective 4D SdS metric can be induced on a 4D hypersurface. We found that at the end of inflation, the squared fluctuations of the inflaton fi...
Hu, B. L. (Bei-Lok)
1999-01-01
We give a summary of the status of current research in stochastic semiclassical gravity and suggest directions for further investigations. This theory generalizes the semiclassical Einstein equation to an Einstein-Langevin equation with a stochastic source term arising from the fluctuations of the energy-momentum tensor of quantum fields. We mention recent efforts in applying this theory to the study of black hole fluctuations and backreaction problems, linear response of hot flat space, and ...
Modulating cell-to-cell variability and sensitivity to death ligands by co-drugging
Flusberg, Deborah A.; Sorger, Peter K.
2013-06-01
TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) holds promise as an anti-cancer therapeutic but efficiently induces apoptosis in only a subset of tumor cell lines. Moreover, even in clonal populations of responsive lines, only a fraction of cells dies in response to TRAIL and individual cells exhibit cell-to-cell variability in the timing of cell death. Fractional killing in these cell populations appears to arise not from genetic differences among cells but rather from differences in gene expression states, fluctuations in protein levels and the extent to which TRAIL-induced death or survival pathways become activated. In this study, we ask how cell-to-cell variability manifests in cell types with different sensitivities to TRAIL, as well as how it changes when cells are exposed to combinations of drugs. We show that individual cells that survive treatment with TRAIL can regenerate the sensitivity and death-time distribution of the parental population, demonstrating that fractional killing is a stable property of cell populations. We also show that cell-to-cell variability in the timing and probability of apoptosis in response to treatment can be tuned using combinations of drugs that together increase apoptotic sensitivity compared to treatment with one drug alone. In the case of TRAIL, modulation of cell-to-cell variability by co-drugging appears to involve a reduction in the threshold for mitochondrial outer membrane permeabilization.
Cell-to-cell movement of mitochondria in plants
Gurdon, Csanad; Svab, Zora; Feng, Yaping; Kumar, Dibyendu; Maliga, Pal
2016-01-01
We report cell-to-cell movement of mitochondria through a graft junction of two tobacco species, Nicotiana tabacum and Nicotiana sylvestris. The flowers of the N. tabacum line we used are male sterile due to a sterility-causing mitochondrial genome, whereas the N. sylvestris flowers are fertile. Grafting created an opportunity for organelle movement during the healing process when cell-to-cell connections at the graft junction were restored. We recognized N. sylvestris mitochondrial DNA trans...
Determinants of cell-to-cell variability in protein kinase signaling.
Matthias Jeschke
Full Text Available Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds ('pathway sensitivity' and the maximal activation level upon strong stimulation. Minimal kinase cascades with gradual dose-response behavior show strong variability, because the pathway sensitivity and the maximal activation level cannot be simultaneously invariant. Negative feedback regulation resolves this trade-off and coordinately reduces fluctuations in the pathway sensitivity and maximal activation. Feedbacks acting at different levels in the cascade control different aspects of the dose-response curve, thereby synergistically reducing the variability. We also investigated more complex, ultrasensitive signaling cascades capable of switch-like decision making, and found that these can be inherently robust to protein concentration fluctuations. We describe how the cell-to-cell variability of ultrasensitive signaling systems can be actively regulated, e.g., by altering the expression of phosphatase(s or by feedback/feedforward loops. Our calculations reveal that slow transcriptional negative feedback loops allow for variability suppression while maintaining switch-like decision making. Taken together, we describe design principles of signaling cascades that promote robustness. Our results may explain why certain signaling cascades like the yeast pheromone pathway show switch-like decision making with little cell-to-cell variability.
Reyes, Luz Marina; Bellini, Mauricio
2010-01-01
We develop a stochastic approach to study scalar field fluctuations of the inflaton field in an early inflationary universe with a Black-Hole (BH), which is described by an effective 4D SdS metric. The extended cosmological metric is obtained after make a planar coordinate transformation on a 5D Ricci-flat Schwarzschild-de Sitter (SdS) static metric. We found that at the end of inflation the spectrum of the squared field fluctuations of the inflaton field depends on the mass $M$ of the BH, but, in the limit of very small BH's mass, this spectrum agrees with whole obtained in standard inflation for a de Sitter expansion.
Listening to the noise: random fluctuations reveal gene network parameters.
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2009-01-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations show cell-to-cell variability that can manifest significant phenotypic differences. Noise-induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We show that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. This establishes a potentially powerful approach for the identification of gene networks and offers a new window into the workings of these networks. PMID:19888213
Cell-to-cell movement of mitochondria in plants.
Gurdon, Csanad; Svab, Zora; Feng, Yaping; Kumar, Dibyendu; Maliga, Pal
2016-03-22
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer fromNicotiana sylvestrisintoNicotiana tabacumcells. The alloplasmicN. tabacumline we used carriesNicotiana undulatacytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer fromN. sylvestristoN. tabacumcould be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility toorf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation. PMID:26951647
Cell-to-cell communication within intact human skin.
Salomon, D.; Saurat, J. H.; Meda, P.
1988-01-01
We have characterized cell-to-cell communication (coupling) within intact human skin by microinjecting single keratinocytes with a gap junction-permeant tracer (Lucifer Yellow). 25-50 keratinocytes from different layers of the epidermis were seen to be coupled after most injections (n = 31). A few noncommunicating cells were also microinjected (n = 3) or observed within large territories of coupled keratinocytes. Microinjections of dermal fibroblasts demonstrated an extensive coupling (greate...
Tetherin restricts productive HIV-1 cell-to-cell transmission.
Nicoletta Casartelli
Full Text Available The IFN-inducible antiviral protein tetherin (or BST-2/CD317/HM1.24 impairs release of mature HIV-1 particles from infected cells. HIV-1 Vpu antagonizes the effect of tetherin. The fate of virions trapped at the cell surface remains poorly understood. Here, we asked whether tetherin impairs HIV cell-to-cell transmission, a major means of viral spread. Tetherin-positive or -negative cells, infected with wild-type or DeltaVpu HIV, were used as donor cells and cocultivated with target lymphocytes. We show that tetherin inhibits productive cell-to-cell transmission of DeltaVpu to targets and impairs that of WT HIV. Tetherin accumulates with Gag at the contact zone between infected and target cells, but does not prevent the formation of virological synapses. In the presence of tetherin, viruses are then mostly transferred to targets as abnormally large patches. These viral aggregates do not efficiently promote infection after transfer, because they accumulate at the surface of target cells and are impaired in their fusion capacities. Tetherin, by imprinting virions in donor cells, is the first example of a surface restriction factor limiting viral cell-to-cell spread.
Regulation of cell-to-cell variability in divergent gene expression
Yan, Chao; Wu, Shuyang; Pocetti, Christopher; Bai, Lu
2016-03-01
Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically `leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs.
Matsakos, T; Stehlé, C; González, M; Ibgui, L; de Sá, L; Lanz, T; Orlando, S; Bonito, R; Argiroffi, C; Reale, F; Peres, G
2013-01-01
Context. Theoretical arguments and numerical simulations of radiative shocks produced by the impact of the accreting gas onto young stars predict quasi-periodic oscillations in the emitted radiation. However, observational data do not show evidence of such periodicity. Aims. We investigate whether physically plausible perturbations in the accretion column or in the chromosphere could disrupt the shock structure influencing the observability of the oscillatory behavior. Methods. We performed local 2D magneto-hydrodynamical simulations of an accretion shock impacting a chromosphere, taking optically thin radiation losses and thermal conduction into account. We investigated the effects of several perturbation types, such as clumps in the accretion stream or chromospheric fluctuations, and also explored a wide range of plasma-\\beta values. Results. In the case of a weak magnetic field, the post-shock region shows chaotic motion and mixing, smoothing out the perturbations and retaining a global periodic signature....
We show that the general two-variable Langevin equations with inhomogeneous noise and friction can generate many different forms of power-law distributions. By solving the corresponding stationary Fokker–Planck equation, we can obtain a condition under which these power-law distributions are accurately created in a system away from equilibrium. This condition is an energy-dependent relation between the diffusion coefficient and the friction coefficient and thus it provides a fluctuation-dissipation relation for nonequilibrium systems with power-law distributions. Further, we study the specific forms of the Fokker–Planck equation that correctly lead to such power-law distributions, and then present a possible generalization of the Klein–Kramers equation and the Smoluchowski equation to a complex system, whose stationary-state solutions are exactly a Tsallis distribution
Quantifying Cell-to-Cell Variations in Lithium Ion Batteries
Shriram Santhanagopalan
2012-01-01
Full Text Available Lithium ion batteries have conventionally been manufactured in small capacities but large volumes for consumer electronics applications. More recently, the industry has seen a surge in the individual cell capacities, as well as the number of cells used to build modules and packs. Reducing cell-to-cell and lot-to-lot variations has been identified as one of the major means to reduce the rejection rate when building the packs as well as to improve pack durability. The tight quality control measures have been passed on from the pack manufactures to the companies building the individual cells and in turn to the components. This paper identifies a quantitative procedure utilizing impedance spectroscopy, a commonly used tool, to determine the effects of material variability on the cell performance, to compare the relative importance of uncertainties in the component properties, and to suggest a rational procedure to set quality control specifications for the various components of a cell, that will reduce cell-to-cell variability, while preventing undue requirements on uniformity that often result in excessive cost of manufacturing but have a limited impact on the cells' performance.
Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission
Christine Gross
2016-03-01
Full Text Available The tumorvirus human T-cell lymphotropic virus type 1 (HTLV-1, a member of the delta-retrovirus family, is transmitted via cell-containing body fluids such as blood products, semen, and breast milk. In vivo, HTLV-1 preferentially infects CD4+ T-cells, and to a lesser extent, CD8+ T-cells, dendritic cells, and monocytes. Efficient infection of CD4+ T-cells requires cell-cell contacts while cell-free virus transmission is inefficient. Two types of cell-cell contacts have been described to be critical for HTLV-1 transmission, tight junctions and cellular conduits. Further, two non-exclusive mechanisms of virus transmission at cell-cell contacts have been proposed: (1 polarized budding of HTLV-1 into synaptic clefts; and (2 cell surface transfer of viral biofilms at virological synapses. In contrast to CD4+ T-cells, dendritic cells can be infected cell-free and, to a greater extent, via viral biofilms in vitro. Cell-to-cell transmission of HTLV-1 requires a coordinated action of steps in the virus infectious cycle with events in the cell-cell adhesion process; therefore, virus propagation from cell-to-cell depends on specific interactions between cellular and viral proteins. Here, we review the molecular mechanisms of HTLV-1 transmission with a focus on the HTLV-1-encoded proteins Tax and p8, their impact on host cell factors mediating cell-cell contacts, cytoskeletal remodeling, and thus, virus propagation.
Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission.
Gross, Christine; Thoma-Kress, Andrea K
2016-01-01
The tumorvirus human T-cell lymphotropic virus type 1 (HTLV-1), a member of the delta-retrovirus family, is transmitted via cell-containing body fluids such as blood products, semen, and breast milk. In vivo, HTLV-1 preferentially infects CD4⁺ T-cells, and to a lesser extent, CD8⁺ T-cells, dendritic cells, and monocytes. Efficient infection of CD4⁺ T-cells requires cell-cell contacts while cell-free virus transmission is inefficient. Two types of cell-cell contacts have been described to be critical for HTLV-1 transmission, tight junctions and cellular conduits. Further, two non-exclusive mechanisms of virus transmission at cell-cell contacts have been proposed: (1) polarized budding of HTLV-1 into synaptic clefts; and (2) cell surface transfer of viral biofilms at virological synapses. In contrast to CD4⁺ T-cells, dendritic cells can be infected cell-free and, to a greater extent, via viral biofilms in vitro. Cell-to-cell transmission of HTLV-1 requires a coordinated action of steps in the virus infectious cycle with events in the cell-cell adhesion process; therefore, virus propagation from cell-to-cell depends on specific interactions between cellular and viral proteins. Here, we review the molecular mechanisms of HTLV-1 transmission with a focus on the HTLV-1-encoded proteins Tax and p8, their impact on host cell factors mediating cell-cell contacts, cytoskeletal remodeling, and thus, virus propagation. PMID:27005656
Stochastic Physicochemical Dynamics
Tsekov, Roumen
2001-01-01
The monograph considers thermodynamic relaxation in quantum systems, stochastic dynamics of gas molecules, fluctuation stability of thin liquid films, resonant diffusion in modulated solid structures and catalytic kinetics of chemical dissociation.
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.
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.
Gaëtan Gruel
Full Text Available Most studies that aim to understand the interactions between different types of photon radiation and cellular DNA assume homogeneous cell irradiation, with all cells receiving the same amount of energy. The level of DNA damage is therefore generally determined by averaging it over the entire population of exposed cells. However, evaluating the molecular consequences of a stochastic phenomenon such as energy deposition of ionizing radiation by measuring only an average effect may not be sufficient for understanding some aspects of the cellular response to this radiation. The variance among the cells associated with this average effect may also be important for the behaviour of irradiated tissue. In this study, we accurately estimated the distribution of the number of radiation-induced γH2AX foci (RIF per cell nucleus in a large population of endothelial cells exposed to 3 macroscopic doses of gamma rays from 60Co. The number of RIF varied significantly and reproducibly from cell to cell, with its relative standard deviation ranging from 36% to 18% depending on the macroscopic dose delivered. Interestingly, this relative cell-to-cell variability increased as the dose decreased, contrary to the mean RIF count per cell. This result shows that the dose effect, in terms of the number of DNA lesions indicated by RIF is not as simple as a purely proportional relation in which relative SD is constant with dose. To analyse the origins of this observed variability, we calculated the spread of the specific energy distribution for the different target volumes and subvolumes in which RIF can be generated. Variances, standard deviations and relative standard deviations all changed similarly from dose to dose for biological and calculated microdosimetric values. This similarity is an important argument that supports the hypothesis of the conservation of the association between the number of RIF per nucleus and the specific energy per DNA molecule. This
Eichhorn, Ralf; Aurell, Erik
2014-04-01
'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response
Johnson, Philip R.; Hu, B. L.
2000-01-01
We apply the open systems concept and the influence functional formalism introduced in Paper I to establish a stochastic theory of relativistic moving spinless particles in a quantum scalar field. The stochastic regime resting between the quantum and semi-classical captures the statistical mechanical attributes of the full theory. Applying the particle-centric world-line quantization formulation to the quantum field theory of scalar QED we derive a time-dependent (scalar) Abraham-Lorentz-Dira...
Ahmet, Kara
2015-01-01
This paper presents a simple model of the provision of higher educational services that considers and exemplifies nonlinear, stochastic, and potentially chaotic processes. I use the methods of system dynamics to simulate these processes in the context of a particular sociologically interesting case, namely that of the Turkish higher education…
Nieto-Vesperinas, Manuel
2014-01-01
The mechanical action on matter of the electromagnetic field emitted by a fluctuating source is governed by its statistics. In particular, thermal sources and vacuum fluctuations exert on bodies those well-known Casimir (C) and Van der Waals (VdW) forces. However, we have recently demonstrated that partially coherent random electromagnetic fields emitted by tailored optical sources, induce a photonic force on particles which, in particular, may be equivalent to those of Van der Waals and Casimir.
Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters
Munsky, Brian; Trinh, Brooke; Khammash, Mustafa
2010-03-01
The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations exhibit cell-to-cell variability that can manifest significant prototypical differences. Noise induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified using flow cytometry, single molecule fluorescence in situ hybridization, time lapse fluorescence microscopy and other single cell and single molecule measurement techniques. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. We use theoretical investigations to establish experimental guidelines for the identification of gene regulatory networks, and we apply these guideline to experimentally identify predictive models for different regulatory mechanisms in bacteria and yeast.
Protease inhibitors effectively block cell-to-cell spread of HIV-1 between T cells
Titanji, Boghuma; Aasa-Chapman, Marlen; Pillay, Deenan; Jolly, Clare
2013-01-01
Background; The Human Immunodeficiency Virus type-1 (HIV-1) spreads by cell-free diffusion and by direct cell-to-cell transfer, the latter being a significantly more efficient mode of transmission. Recently it has been suggested that cell-to-cell spread may permit ongoing virus replication in the presence of antiretroviral therapy (ART) based on studies performed using Reverse Transcriptase Inhibitors (RTIs). Protease Inhibitors (PIs) constitute an important component of ART; however whether ...
Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan
2016-01-01
Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911
Stochastic TDHF and the Boltzman-Langevin equation
Outgoing from a time-dependent theory of correlations, we present a stochastic differential equation for the propagation of ensembles of Slater determinants, called Stochastic Time-Dependent Hartree-Fock (Stochastic TDHF). These ensembles are allowed to develop large fluctuations in the Hartree-Fock mean fields. An alternative stochastic differential equation, the Boltzmann-Langevin equation, can be derived from Stochastic TDHF by averaging over subensembles with small fluctuations
Stochastic volatility and stochastic leverage
Veraart, Almut; Veraart, Luitgard A. M.
2009-01-01
This paper proposes the new concept of stochastic leverage in stochastic volatility models.Stochastic leverage refers to a stochastic process which replaces the classical constant correlationparameter between the asset return and the stochastic volatility process. We provide a systematictreatment of stochastic leverage and propose to model the stochastic leverage effect explicitly,e.g. by means of a linear transformation of a Jacobi process. Such models are both analyticallytractable and allo...
On the stochastic stability of MHD equilibria
The stochastic stability in the large of stationary equilibria of ideal and dissipative magnetohydrodynamics under the influence of stationary random fluctuations is studied using the direct Liapunov method. Sufficient and necessary conditions for stability of the linearized Euler-Lagrangian systems are given. The destabilizing effect of stochastic fluctuations is demonstrated. (orig.)
Role of Exosome Shuttle RNA in Cell-to-Cell Communication.
Zhang, Wei; Peng, Peng; Shen, Keng
2016-08-01
There are several ways that transpire in cell-to-cell communication,with or without cell contact. Exosomes play an important role in cell-to-cell communication,which do not need cell contact,as that can result in a relatively long-distance influence. Exosome contains RNA components including mRNA and micro-RNA,which are protected by exosomes rigid membranes. This allows those components be passed long distance through the circulatory system. The mRNA components are far different from their donor cells,and the micro-RNA components may reflect the cell they originated. In this article we review the role of exosomes in cell-to-cell communication,with particular focus on their potentials in both diagnostic and therapeutic applications. PMID:27594165
Influence of viral genes on the cell-to-cell spread of RNA silencing
Zhou, Yu; Ryabov, Eugene; Zhang, Xuemei; Hong, Yiguo
2008-01-01
The turnip crinkle virus-based vector TCV–GFPΔCP had been devised previously to study cell-to-cell and long-distance spread of virus-induced RNA silencing. TCV–GFPΔCP, which had been constructed by replacing the coat protein (CP) gene with a green fluorescent protein (GFP) coding sequence, was able to induce RNA silencing in single epidermal cells, from which RNA silencing spread from cell-to-cell. Using this unique local silencing assay together with mutagenesis analysis, two TCV genes, p8 a...
Measuring and modelling cell-to-cell variation in uptake of gold nanoparticles
Jeynes, JCG; Jeynes, C.; Merchant, MJ; Kirkby, KJ
2013-01-01
The cell-to-cell variation of gold nanoparticle (GNP) uptake is important for therapeutic applications. We directly counted the GNPs in hundreds of individual cells, and showed that the large variation from cell-to-cell could be directly modelled by assuming log-normal distributions of both cell mass and GNP rate of uptake. This was true for GNPs non-specifically bound to fetal bovine serum or conjugated to a cell penetrating peptide. Within a population of cells, GNP content varied naturally...
A recurrent stochastic binary network
赵杰煜
2001-01-01
Stochastic neural networks are usually built by introducing random fluctuations into the network. A natural method is to use stochastic connections rather than stochastic activation functions. We propose a new model in which each neuron has very simple functionality but all the connections are stochastic. It is shown that the stationary distribution of the network uniquely exists and it is approximately a Boltzmann-Gibbs distribution. The relationship between the model and the Markov random field is discussed. New techniques to implement simulated annealing and Boltzmann learning are proposed. Simulation results on the graph bisection problem and image recognition show that the network is powerful enough to solve real world problems.
Gambling with Superconducting Fluctuations
Foltyn, Marek; Zgirski, Maciej
2015-08-01
Josephson junctions and superconducting nanowires, when biased close to superconducting critical current, can switch to a nonzero voltage state by thermal or quantum fluctuations. The process is understood as an escape of a Brownian particle from a metastable state. Since this effect is fully stochastic, we propose to use it for generating random numbers. We present protocol for obtaining random numbers and test the experimentally harvested data for their fidelity. Our work is prerequisite for using the Josephson junction as a tool for stochastic (probabilistic) determination of physical parameters such as magnetic flux, temperature, and current.
MEMS-based dynamic cell-to-cell culture platforms using electrochemical surface modifications
MEMS-based biological platforms with the capability of both spatial placements and time releases of living cells for cell-to-cell culture experiments have been designed and demonstrated utilizing electrochemical surface modification effects. The spatial placement is accomplished by electrochemical surface modification of substrate surfaces to be either adhesive or non-adhesive for living cells. The time control is achieved by the electrical activation of the selective indium tin oxide co-culture electrode to allow the migration of living cells onto the electrode to start the cell-to-cell culture studies. Prototype devices have a three-electrode design with an electrode size of 50 × 50 µm2 and the separation gaps of 2 µm between them. An electrical voltage of −1.5 V has been used to activate the electrodes independently and sequentially to demonstrate the dynamic cell-to-cell culture experiments of NIH 3T3 fibroblast and Madin Darby canine kidney cells. As such, this MEMS platform could be a basic yet versatile tool to characterize transient cell-to-cell interactions
The Arabidopsis synaptotagmin SYTA regulates the cell-to-cell movement of diverse plant viruses
Asako eUchiyama
2014-11-01
Full Text Available Synaptotagmins are a large gene family in animals that have been extensively characterized due to their role as calcium sensors to regulate synaptic vesicle exocytosis and endocytosis in neurons, and dense core vesicle exocytosis for hormone secretion from neuroendocrine cells. Thought to be exclusive to animals, synaptotagmins have recently been characterized in Arabidopsis thaliana, in which they comprise a five gene family. Using infectivity and leaf-based functional assays, we have shown that Arabidopsis SYTA regulates endocytosis and marks an endosomal vesicle recycling pathway to regulate movement protein-mediated trafficking of the Begomovirus Cabbage leaf curl virus (CaLCuV and the Tobamovirus Tobacco mosaic virus (TMV through plasmodesmata (Lewis and Lazarowitz, 2010. To determine whether SYTA has a central role in regulating the cell-to-cell trafficking of a wider range of diverse plant viruses, we extended our studies here to examine the role of SYTA in the cell-to-cell movement of additional plant viruses that employ different modes of movement, namely the Potyvirus Turnip mosaic virus (TuMV, the Caulimovirus Cauliflower mosaic virus (CaMV and the Tobamovirus Turnip vein clearing virus (TVCV, which in contrast to TMV does efficiently infect Arabidopsis. We found that both TuMV and TVCV systemic infection, and the cell-to-cell trafficking of the their movement proteins, were delayed in the Arabidopsis Col-0 syta-1 knockdown mutant. In contrast, CaMV systemic infection was not inhibited in syta-1. Our studies show that SYTA is a key regulator of plant virus intercellular movement, being necessary for the ability of diverse cell-to-cell movement proteins encoded by Begomoviruses (CaLCuV MP, Tobamoviruses (TVCV and TMV 30K protein and Potyviruses (TuMV P3N-PIPO to alter PD and thereby mediate virus cell-to-cell spread.
Stochastic volatility and stochastic leverage
Veraart, Almut; Veraart, Luitgard A. M.
models which allow for a stochastic leverage effect: the generalised Heston model and the generalised Barndorff-Nielsen & Shephard model. We investigate the impact of a stochastic leverage effect in the risk neutral world by focusing on implied volatilities generated by option prices derived from our new......This paper proposes the new concept of stochastic leverage in stochastic volatility models. Stochastic leverage refers to a stochastic process which replaces the classical constant correlation parameter between the asset return and the stochastic volatility process. We provide a systematic...... treatment of stochastic leverage and propose to model the stochastic leverage effect explicitly, e.g. by means of a linear transformation of a Jacobi process. Such models are both analytically tractable and allow for a direct economic interpretation. In particular, we propose two new stochastic volatility...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread
Czuczman, Mark A.; Fattouh, Ramzi; van Rijn, Jorik; Canadien, Veronica; Osborne, Suzanne; Aleixo M Muise; Kuchroo, Vijay K.; Higgins, Darren E.; Brumell, John H.
2014-01-01
Efferocytosis, the process by which dying/dead cells are removed by phagocytosis, plays an important role in development, tissue homeostasis and innate immunity 1 . Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes (Lm), can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can esca...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread
Czuczman, Mark A.; Fattouh, Ramzi; van Rijn, Jorik; Canadien, Veronica; Osborne, Suzanne; Aleixo M Muise; Kuchroo, Vijay K.; Higgins, Darren E.; Brumell, John H.
2014-01-01
Efferocytosis, the process by which dying/dead cells are removed by phagocytosis, plays an important role in development, tissue homeostasis and innate immunity1. Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes (Lm), can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can escape...
The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks.
Chevalier, Michael; Venturelli, Ophelia; El-Samad, Hana
2015-10-01
Stochastic fluctuations in signaling and gene expression limit the ability of cells to sense the state of their environment, transfer this information along cellular pathways, and respond to it with high precision. Mutual information is now often used to quantify the fidelity with which information is transmitted along a cellular pathway. Mutual information calculations from experimental data have mostly generated low values, suggesting that cells might have relatively low signal transmission fidelity. In this work, we demonstrate that mutual information calculations might be artificially lowered by cell-to-cell variability in both initial conditions and slowly fluctuating global factors across the population. We carry out our analysis computationally using a simple signaling pathway and demonstrate that in the presence of slow global fluctuations, every cell might have its own high information transmission capacity but that population averaging underestimates this value. We also construct a simple synthetic transcriptional network and demonstrate using experimental measurements coupled to computational modeling that its operation is dominated by slow global variability, and hence that its mutual information is underestimated by a population averaged calculation. PMID:26484538
Bible, Amber N.; Khalsa-Moyers, Gurusahai K.; Mukherjee, Tanmoy; Green, Calvin S.; Mishra, Priyanka; Purcell, Alicia; Aksenova, Anastasia; Hurst, Gregory B.
2015-01-01
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists. PMID:26407887
Enhancement of Chemotactic Cell Aggregation by Haptotactic Cell-To-Cell Interaction.
Tae-Goo Kwon
Full Text Available The crawling of biological cell is a complex phenomenon involving various biochemical and mechanical processes. Some of these processes are intrinsic to individual cells, while others pertain to cell-to-cell interactions and to their responses to extrinsically imposed cues. Here, we report an interesting aggregation dynamics of mathematical model cells, when they perform chemotaxis in response to an externally imposed global chemical gradient while they influence each other through a haptotaxis-mediated social interaction, which confers intriguing trail patterns. In the absence of the cell-to-cell interaction, the equilibrium population density profile fits well to that of a simple Keller-Segal population dynamic model, in which a chemotactic current density [Formula: see text] competes with a normal diffusive current density [Formula: see text], where p and ρ refer to the concentration of chemoattractant and population density, respectively. We find that the cell-to-cell interaction confers a far more compact aggregation resulting in a much higher peak equilibrium cell density. The mathematical model system is applicable to many biological systems such as swarming microglia and neutrophils or accumulating ants towards a localized food source.
Bible, Amber N; Khalsa-Moyers, Gurusahai K; Mukherjee, Tanmoy; Green, Calvin S; Mishra, Priyanka; Purcell, Alicia; Aksenova, Anastasia; Hurst, Gregory B; Alexandre, Gladys
2015-12-01
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists. PMID:26407887
Phenomenology of Space Time Fluctuations
Aloisio, R.; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); Grillo, A. F.
2004-01-01
Quantum gravitational effects may induce stochastic fluctuations in the structure of space-time, to produce a characteristic foamy structure. It has been known for some time now that these fluctuations may have observable consequences for the propagation of cosmic ray particles over cosmological distances. While invoked as a possible explanation for the detection of the puzzling cosmic rays with energies in excess of the threshold for photopion production (the so-called super-GZK particles), ...
Listeria monocytogenes exploits efferocytosis to promote cell-to-cell spread.
Czuczman, Mark A; Fattouh, Ramzi; van Rijn, Jorik M; Canadien, Veronica; Osborne, Suzanne; Muise, Aleixo M; Kuchroo, Vijay K; Higgins, Darren E; Brumell, John H
2014-05-01
Efferocytosis, the process by which dying or dead cells are removed by phagocytosis, has an important role in development, tissue homeostasis and innate immunity. Efferocytosis is mediated, in part, by receptors that bind to exofacial phosphatidylserine (PS) on cells or cellular debris after loss of plasma membrane asymmetry. Here we show that a bacterial pathogen, Listeria monocytogenes, can exploit efferocytosis to promote cell-to-cell spread during infection. These bacteria can escape the phagosome in host cells by using the pore-forming toxin listeriolysin O (LLO) and two phospholipase C enzymes. Expression of the cell surface protein ActA allows L. monocytogenes to activate host actin regulatory factors and undergo actin-based motility in the cytosol, eventually leading to formation of actin-rich protrusions at the cell surface. Here we show that protrusion formation is associated with plasma membrane damage due to LLO's pore-forming activity. LLO also promotes the release of bacteria-containing protrusions from the host cell, generating membrane-derived vesicles with exofacial PS. The PS-binding receptor TIM-4 (encoded by the Timd4 gene) contributes to efficient cell-to-cell spread by L. monocytogenes in macrophages in vitro and growth of these bacteria is impaired in Timd4(-/-) mice. Thus, L. monocytogenes promotes its dissemination in a host by exploiting efferocytosis. Our results indicate that PS-targeted therapeutics may be useful in the fight against infections by L. monocytogenes and other bacteria that use similar strategies of cell-to-cell spread during infection. PMID:24739967
Initial activation of EpCAM cleavage via cell-to-cell contact
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
Tongqian Zhang
2015-01-01
Full Text Available The cure effect of a virus model with both cell-to-cell transmission and cell-to-virus transmission is studied. By the method of next generation matrix, the basic reproduction number is obtained. The locally asymptotic stability of the virus-free equilibrium and the endemic equilibrium is considered by investigating the characteristic equation of the model. The globally asymptotic stability of the virus-free equilibrium is proved by constructing suitable Lyapunov function, and the sufficient condition for the globally asymptotic stability of the endemic equilibrium is obtained by constructing suitable Lyapunov function and using LaSalle invariance principal.
Zhong, Peng; Agosto, Luis M.; Ilinskaya, Anna; Dorjbal, Batsukh; Truong, Rosaline; Derse, David; Uchil, Pradeep D; Heidecker, Gisela; Mothes, Walther
2013-01-01
Virus transmission can occur either by a cell-free mode through the extracellular space or by cell-to-cell transmission involving direct cell-to-cell contact. The factors that determine whether a virus spreads by either pathway are poorly understood. Here, we assessed the relative contribution of cell-free and cell-to-cell transmission to the spreading of the human immunodeficiency virus (HIV). We demonstrate that HIV can spread by a cell-free pathway if all the steps of the viral replication...
Ohira, Toru
2006-01-01
We present a simple dynamical model to address the question of introducing a stochastic nature in a time variable. This model includes noise in the time variable but not in the "space" variable, which is opposite to the normal description of stochastic dynamics. The notable feature is that these models can induce a "resonance" with varying noise strength in the time variable. Thus, they provide a different mechanism for stochastic resonance, which has been discussed within the normal context ...
Jennifer S. Liu
2012-11-01
Full Text Available Variability in signaling pathway activation between neighboring epithelial cells can arise from local differences in the microenvironment, noisy gene expression, or acquired genetic changes. To investigate the consequences of this cell-to-cell variability in signaling pathway activation on coordinated multicellular processes such as morphogenesis, we use DNA-programmed assembly to construct three-dimensional MCF10A microtissues that are mosaic for low-level expression of activated H-Ras. We find two emergent behaviors in mosaic microtissues: cells with activated H-Ras are basally extruded or lead motile multicellular protrusions that direct the collective motility of their wild-type neighbors. Remarkably, these behaviors are not observed in homogeneous microtissues in which all cells express the activated Ras protein, indicating that heterogeneity in Ras activity, rather than the total amount of Ras activity, is critical for these processes. Our results directly demonstrate that cell-to-cell variability in pathway activation within local populations of epithelial cells can drive emergent behaviors during epithelial morphogenesis.
Relation between radio-adaptive response and cell to cell communication
Ionizing radiation has been considered to cause severe damages to DNA and do harm to cells in proportion to the dose, however low it might be. In 1984, Wolff et al. showed that human peripheral lymphocytes adapted to the low-dose radiation from 3H-TdR added in culture medium and became resistant to the subsequent irradiation with high-doses of X-rays. This response, which is called radio-adaptive response, is also induced by X-rays and gamma-rays in human lymphocytes and Chinese hamster V79 cells. However, the mechanisms of and conditions for adaptive responses to radiation have not been clarified. With an objective of clarifying the conditions for adaptive responses of cells to radiation, we examined how the cell to cell communication is involved in the adaptive responses. We irradiated normal human embryo-derived (HE) cells and cancer cells (HeLa) in culture at high density with low-dose X-ray and examined their radio-adaptive responses by measuring the changes in sensitivity to subsequent high-dose X-ray irradiation using the Trypan Blue dye-exclusion test method. We also conducted experiments to examine the effects of Ca2+ ions and Phorbol 12-Myristate 13-Acetate (TPA) which are supposed to be involved in cell to cell communication. (author)
Jacob, Christian L; Lamorte, Louie; Sepulveda, Eliud; Lorenz, Ivo C; Gauthier, Annick; Franti, Michael
2013-09-01
Infection with human cytomegalovirus (CMV) during pregnancy is the most common cause of congenital disorders, and can lead to severe life-long disabilities with associated high cost of care. Since there is no vaccine or effective treatment, current efforts are focused on identifying potent neutralizing antibodies. A panel of CMV monoclonal antibodies identified from patent applications, was synthesized and expressed in order to reproduce data from the literature showing that anti-glycoprotein B antibodies neutralized virus entry into all cell types and that anti-pentameric complex antibodies are highly potent in preventing virus entry into epithelial cells. It had not been established whether antibodies could prevent subsequent rounds of infection that are mediated primarily by direct cell-to-cell transmission. A thorough validation of a plaque reduction assay to monitor cell-to-cell spread led to the conclusion that neutralizing antibodies do not significantly inhibit plaque formation or reduce plaque size when they are added post-infection. PMID:23849792
Staggered Schemes for Fluctuating Hydrodynamics
Balboa, F; Delgado-Buscalioni, R; Donev, A; Fai, T; Griffith, B; Peskin, C S
2011-01-01
We develop numerical schemes for solving the isothermal compressible and incompressible equations of fluctuating hydrodynamics on a grid with staggered momenta. We develop a second-order accurate spatial discretization of the diffusive, advective and stochastic fluxes that satisfies a discrete fluctuation-dissipation balance, and construct temporal discretizations that are at least second-order accurate in time deterministically and in a weak sense. Specifically, the methods reproduce the correct equilibrium covariances of the fluctuating fields to third (compressible) and second (incompressible) order in the time step, as we verify numerically. We apply our techniques to model recent experimental measurements of giant fluctuations in diffusively mixing fluids in a micro-gravity environment [A. Vailati et. al., Nature Communications 2:290, 2011]. Numerical results for the static spectrum of non-equilibrium concentration fluctuations are in excellent agreement between the compressible and incompressible simula...
Notes on Black Hole Fluctuations and Backreaction
Hu, B. L.; Raval, Alpan; Sinha, Sukanya
1999-01-01
In these notes we prepare the ground for a systematic investigation into the issues of black hole fluctuations and backreaction by discussing the formulation of the problem, commenting on possible advantages and shortcomings of existing works, and introducing our own approach via a stochastic semiclassical theory of gravity based on the Einstein-Langevin equation and the fluctuation-dissipation relation for a self-consistent description of metric fluctuations and dissipative dynamics of the b...
Notes on Black Hole Fluctuations and Backreaction
Hu, B L; Sinha, S; Raval, Alpan; Sinha, Sukanya
1999-01-01
In these notes we prepare the ground for a systematic investigation into the issues of black hole fluctuations and backreaction by discussing the formulation of the problem, commenting on possible advantages and shortcomings of existing works, and introducing our own approach via a stochastic semiclassical theory of gravity based on the Einstein-Langevin equation and the fluctuation-dissipation relation for a self-consistent description of metric fluctuations and dissipative dynamics of the black hole with backreaction of its Hawking radiance.
Small RNA Control of Cell-to-Cell Communication in Vibrio Harveyi and Vibrio Cholerae
Svenningsen, Sine Lo
Quorum sensing is a process of cell-to-cell communication, by which bacteria coordinate gene expression and behavior on a population-wide scale. Quorum sensing is accomplished through production, secretion, and subsequent detection of chemical signaling molecules termed autoinducers. The human pathogen Vibrio cholerae and the marine bioluminescent bacterium Vibrio harveyi incorporate information from multiple autoinducers, and also environmental signals and metabolic cues into their quorum-sensing pathways. At the core of these pathways lie several homologous small regulatory RNA molecules, the Quorum Regulatory RNAs. Small noncoding RNAs have emerged throughout the bacterial and eukaryotic kingdoms as key regulators of behavioral and developmental processes. Here, I review our present understanding of the role of the Qrr small RNAs in integrating quorum-sensing signals and in regulating the individual cells response to this information.
HidetadaHirakawa
2013-05-01
Full Text Available Bacteria use a cell-to-cell communication activity termed “Quorum sensing” to coordinate group behaviors in a cell-density dependent manner. Quorum sensing influences the expression profile of diverse genes, including antibiotic tolerance and virulence determinants, via specific chemical compounds called “Auto-inducers”. During quorum sensing, Gram-negative bacteria typically use an acylated homoserine lactone (AHL called auto-inducer 1 (AI-1. Since the first discovery of quorum sensing in a marine bacterium, it has been recognized that more than 100 species possess this mechanism of cell-to-cell communication. In addition to being of interest from a biological standpoint, quorum sensing is a potential target for antimicrobial chemotherapy. This unique concept of antimicrobial control relies on reducing the burden of virulence rather than killing the bacteria. It is believed that this approach will not only suppress the development of antibiotic resistance, but will also improve the treatment of refractory infections triggered by multi-drug resistant (MDR pathogens. In this paper, we review and track recent progress in studies on AHL inhibitors/modulators from a biological standpoint. It has been discovered that both natural and synthetic compounds can disrupt quorum sensing by a variety of means, such as jamming signal transduction, inhibition of signal production and break-down and trapping of signal compounds. We also focus on the regulatory elements that attenuate quorum sensing activities and discuss their unique properties. Understanding the biological roles of regulatory elements might be useful in developing inhibitor applications and understanding how quorum sensing is controlled.
Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells
Research highlights: → TGP52 cells display enhanced functionality in pseudoislet form. → Somatostatin content was reduced, but secretion increased in high glucose conditions. → Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mM glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.
Damodaran, Shima P; Eberhard, Stephan; Boitard, Laurent; Rodriguez, Jairo Garnica; Wang, Yuxing; Bremond, Nicolas; Baudry, Jean; Bibette, Jérôme; Wollman, Francis-André
2015-01-01
To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes. PMID:25760649
Shima P Damodaran
Full Text Available To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers and a significant subpopulation of slowly dividing cells (slow-growers. These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes.
Turbulent response in a stochastic regime
The theory for the non-linear, turbulent response in a system with intrinsic stochasticity is considered. It is argued that perturbative Eulerian theories, such as the Direct Interaction Approximation (DIA), are inherently unsuited to describe such a system. The exponentiation property that characterizes stochasticity appears in the Lagrangian picture and cannot even be defined in the Eulerian representation. An approximation for stochastic systems - the Normal Stochastic Approximation - is developed and states that the perturbed orbit functions (Lagrangian fluctuations) behave as normally distributed random variables. This is independent of the Eulerian statistics and, in fact, we treat the Eulerian fluctuations as fixed. A simple model problem (appropriate for the electron response in the drift wave) is subjected to a series of computer experiments. To within numerical noise the results are in agreement with the Normal Stochastic Approximation. The predictions of the DIA for this mode show substantial qualitative and quantitative departures from the observations
Dynamics of stochastic systems
Klyatskin, Valery I
2005-01-01
Fluctuating parameters appear in a variety of physical systems and phenomena. They typically come either as random forces/sources, or advecting velocities, or media (material) parameters, like refraction index, conductivity, diffusivity, etc. The well known example of Brownian particle suspended in fluid and subjected to random molecular bombardment laid the foundation for modern stochastic calculus and statistical physics. Other important examples include turbulent transport and diffusion of particle-tracers (pollutants), or continuous densities (''''oil slicks''''), wave propagation and scattering in randomly inhomogeneous media, for instance light or sound propagating in the turbulent atmosphere.Such models naturally render to statistical description, where the input parameters and solutions are expressed by random processes and fields.The fundamental problem of stochastic dynamics is to identify the essential characteristics of system (its state and evolution), and relate those to the input parameters of ...
Multivariate fluctuation relations for currents
This paper is devoted to multivariate fluctuation relations for all the currents flowing across an open system in contact with several reservoirs at different temperatures and chemical potentials, or driven by time-independent external mechanical forces. After some transient behavior, the open system is supposed to reach a nonequilibrium steady state that is controlled by the thermodynamic and mechanical forces, called the affinities. The time-reversal symmetry of the underlying Hamiltonian dynamics implies symmetry relations among the statistical properties of the fluctuating currents, depending on the values of the affinities. These multivariate fluctuation relations are not only compatible with the second law of thermodynamics, but they also imply remarkable relations between the linear or nonlinear response coefficients and the cumulants of the fluctuating currents. These relations include the Onsager and Casimir reciprocity relations, as well as their generalizations beyond linear response. Methods to deduce multivariate fluctuation relations are presented for classical, stochastic and quantum systems. In this way, multivariate fluctuation relations are obtained for energy or particle transport in the effusion of an ideal gas, heat transport in Hamiltonian systems coupled by Langevin stochastic forces to heat reservoirs, driven Brownian motion of an electrically charged particle subjected to an external magnetic field, and quantum electron transport in multi-terminal mesoscopic circuits where the link to the scattering approach is established. (paper)
Parzen, Emanuel
2015-01-01
Well-written and accessible, this classic introduction to stochastic processes and related mathematics is appropriate for advanced undergraduate students of mathematics with a knowledge of calculus and continuous probability theory. The treatment offers examples of the wide variety of empirical phenomena for which stochastic processes provide mathematical models, and it develops the methods of probability model-building.Chapter 1 presents precise definitions of the notions of a random variable and a stochastic process and introduces the Wiener and Poisson processes. Subsequent chapters examine
Simulated microgravity allows to demonstrate cell-to-cell communication in bacteria
Mastroleo, Felice; van Houdt, Rob; Mergeay, Max; Hendrickx, Larissa; Wattiez, Ruddy; Leys, Natalie
Through the MELiSSA project, the European Space Agency aims to develop a closed life support system for oxygen, water and food production to support human life in space in forth-coming long term space exploration missions. This production is based on the recycling of the missions organic waste, including CO2 and minerals. The photosynthetic bacterium Rhodospir-illum rubrum S1H is used in MELiSSA to degrade organics with light energy and is the first MELiSSA organism that has been studied in space related environmental conditions (Mastroleo et al., 2009). It was tested in actual space flight to the International Space Station (ISS) as well as in ground simulations of ISS-like ionizing radiation and microgravity. In the present study, R. rubrum S1H was cultured in liquid medium in 2 devices simulating microgravity conditions, i.e. the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM). The re-sponse of the bacterium was evaluated at both the transcriptomic and proteomic levels using respectively a dedicated whole-genome microarray and high-throughput gel-free quantitative proteomics. Both at transcriptomic and proteomic level, the bacterium showed a significant response to cultivation in simulated microgravity. The response to low fluid shear modeled microgravity in RWV was different than to randomized microgravity in RPM. Nevertheless, both tests pointed out a change in and a likely interrelation between cell-to-cell communica-tion (i.e. quorum sensing) and cell pigmentation (i.e. photosynthesis) for R. rubrum S1H in microgravity conditions. A new type of cell-to-cell communication molecule in R. rubrum S1H was discovered and characterized. It is hypothised that the lack of convection currents and the fluid quiescence in (simulated) microgravity limits communications molecules to be spread throughout the medium. Cultivation in this new artificial environment of simulated micro-gravity has showed new properties of this well know bacterium
Schneider, Johannes J
2007-01-01
This book addresses stochastic optimization procedures in a broad manner. The first part offers an overview of relevant optimization philosophies; the second deals with benchmark problems in depth, by applying a selection of optimization procedures. Written primarily with scientists and students from the physical and engineering sciences in mind, this book addresses a larger community of all who wish to learn about stochastic optimization techniques and how to use them.
The Potato virus X TGBp3 protein associates with the ER network for virus cell-to-cell movement
Krishnamurthy, Konduru; Heppler, Marty; Mitra, Ruchira; Blancaflor, Elison; Payton, Mark; Nelson, Richard S.; Verchot-Lubicz, Jeanmarie
2003-01-01
Potato virus X (PVX) TGBp3 is required for virus cell-to-cell movement. Cell-to-cell movement of TGBp3 was studied using biolistic bombardment of plasmids expressing GFP:TGBp3. TGBp3 moves between cells in Nicotiana benthamiana, but requires TGBp1 to move in N. tabacum leaves. In tobacco leaves GFP:TGBp3 accumulated in a pattern resembling the endoplasmic reticulum (ER). To determine if the ER network is important for GFP:TGBp3 and for PVX cell-to-cell movement, a single mutation inhibiting membrane binding of TGBp3 was introduced into GFP:TGBp3 and into PVX. This mutation disrupted movement of GFP:TGBp3 and PVX. Brefeldin A, which disrupts the ER network, also inhibited GFP:TGBp3 movement in both Nicotiana species. Two deletion mutations, that do not affect membrane binding, hindered GFP:TGBp3 and PVX cell-to-cell movement. Plasmids expressing GFP:TGBp2 and GFP:TGBp3 were bombarded to several other PVX hosts and neither protein moved between adjacent cells. In most hosts, TGBp2 or TGBp3 cannot move cell-to-cell.
Can Cell to Cell Thermal Runaway Propagation be Prevented in a Li-ion Battery Module?
Jeevarajan, Judith; Lopez, Carlos; Orieukwu, Josephat
2014-01-01
Increasing cell spacing decreased adjacent cell damage center dotElectrically connected adjacent cells drained more than physically adjacent cells center dotRadiant barrier prevents propagation when fully installed between BP cells center dotBP cells vent rapidly and expel contents at 100% SOC -Slower vent with flame/smoke at 50% -Thermal runaway event typically occurs at 160 degC center dotLG cells vent but do not expel contents -Thermal runaway event typically occurs at 200 degC center dotSKC LFP modules did not propagate; fuses on negative terminal of cell may provide a benefit in reducing cell to cell damage propagation. New requirement in NASA-Battery Safety Requirements document: JSC 20793 Rev C 5.1.5.1 Requirements - Thermal Runaway Propagation a. For battery designs greater than a 80-Wh energy employing high specific energy cells (greater than 80 watt-hours/kg, for example, lithium-ion chemistries) with catastrophic failure modes, the battery shall be evaluated to ascertain the severity of a worst-case single-cell thermal runaway event and the propensity of the design to demonstrate cell-to-cell propagation in the intended application and environment. NASA has traditionally addressed the threat of thermal runaway incidents in its battery deployments through comprehensive prevention protocols. This prevention-centered approach has included extensive screening for manufacturing defects, as well as robust battery management controls that prevent abuse-induced runaway even in the face of multiple system failures. This focused strategy has made the likelihood of occurrence of such an event highly improbable. b. The evaluation shall include all necessary analysis and test to quantify the severity (consequence) of the event in the intended application and environment as well as to identify design modifications to the battery or the system that could appreciably reduce that severity. In addition to prevention protocols, programs developing battery designs with
Stochastic Simulation of Turing Patterns
FU Zheng-Ping; XU Xin-Hang; WANG Hong-Li; OUYANG Qi
2008-01-01
@@ We investigate the effects of intrinsic noise on Turing pattern formation near the onset of bifurcation from the homogeneous state to Turing pattern in the reaction-diffusion Brusselator. By performing stochastic simulations of the master equation and using Gillespie's algorithm, we check the spatiotemporal behaviour influenced by internal noises. We demonstrate that the patterns of occurrence frequency for the reaction and diffusion processes are also spatially ordered and temporally stable. Turing patterns are found to be robust against intrinsic fluctuations. Stochastic simulations also reveal that under the influence of intrinsic noises, the onset of Turing instability is advanced in comparison to that predicted deterministically.
Plasmodesmal-mediated cell-to-cell transport in wheat roots is modulated by anaerobic stress
Cleland, R. E.; Fujiwara, T.; Lucas, W. J.
1994-01-01
Cell-to-cell transport of small molecules and ions occurs in plants through plasmodesmata. Plant roots are frequently subjected to localized anaerobic stress, with a resultant decrease in ATP. In order to determine the effect of this stress on plasmodesmal transport, fluorescent dyes of increasing molecular weight (0.46 to 1OkDa) were injected into epidermal and cortical cells of 3-day-old wheat roots, and their movement into neighboring cells was determined by fluorescence microscopy. Anaerobiosis was generated by N2 gas or simulated by the presence of sodium azide, both of which reduced the ATP levels in the tissue by over 80%. In the absence of such stress, the upper limit for movement, or size exclusion limit (SEL), of cortical plasmodesmata was cells. Upon imposition of stress, the SEL rose to between 5 and 10 kDa. This response of plasmodesmata to a decrease in the level of ATP suggests that they are constricted by an ATP-dependent process so as to maintain a restricted SEL. When roots are subjected to anaerobic stress, an increase in SEL may permit enhanced delivery of sugars to the affected cells of the root where anaerobic respiration could regenerate the needed ATP.
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.
G. Natale
2013-03-01
Full Text Available Formation, aggregation and transmission of abnormal proteins are common features in neurodegenerative disorders including Parkinson’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis, and Huntington’s disease. The mechanisms underlying protein alterations in neurodegenerative diseases remain controversial. Novel findings highlighted altered protein clearing systems as common biochemical pathways which generate protein misfolding, which in turn causes protein aggregation and protein spreading. In fact, proteinaceous aggregates are prone to cell-to-cell propagation. This is reminiscent of what happens in prion disorders, where the prion protein misfolds thus forming aggregates which spread to neighbouring cells. For this reason, the term prionoids is currently used to emphasize how several misfolded proteins are transmitted in neurodegenerative diseases following this prion-like pattern. Histochemical techniques including the use of specific antibodies covering both light and electron microscopy offer a powerful tool to describe these phenomena and investigate specific molecular steps. These include: prion like protein alterations; glycation of prion-like altered proteins to form advanced glycation end-products (AGEs; mechanisms of extracellular secretion; interaction of AGEs with specific receptors placed on neighbouring cells (RAGEs. The present manuscript comments on these phenomena aimed to provide a consistent scenario of the available histochemical approaches to dissect each specific step.
Khang, Chang Hyun; Berruyer, Romain; Giraldo, Martha C; Kankanala, Prasanna; Park, Sook-Young; Czymmek, Kirk; Kang, Seogchan; Valent, Barbara
2010-04-01
Knowledge remains limited about how fungal pathogens that colonize living plant cells translocate effector proteins inside host cells to regulate cellular processes and neutralize defense responses. To cause the globally important rice blast disease, specialized invasive hyphae (IH) invade successive living rice (Oryza sativa) cells while enclosed in host-derived extrainvasive hyphal membrane. Using live-cell imaging, we identified a highly localized structure, the biotrophic interfacial complex (BIC), which accumulates fluorescently labeled effectors secreted by IH. In each newly entered rice cell, effectors were first secreted into BICs at the tips of the initially filamentous hyphae in the cell. These tip BICs were left behind beside the first-differentiated bulbous IH cells as the fungus continued to colonize the host cell. Fluorescence recovery after photobleaching experiments showed that the effector protein PWL2 (for prevents pathogenicity toward weeping lovegrass [Eragrostis curvula]) continued to accumulate in BICs after IH were growing elsewhere. PWL2 and BAS1 (for biotrophy-associated secreted protein 1), BIC-localized secreted proteins, were translocated into the rice cytoplasm. By contrast, BAS4, which uniformly outlines the IH, was not translocated into the host cytoplasm. Fluorescent PWL2 and BAS1 proteins that reached the rice cytoplasm moved into uninvaded neighbors, presumably preparing host cells before invasion. We report robust assays for elucidating the molecular mechanisms that underpin effector secretion into BICs, translocation to the rice cytoplasm, and cell-to-cell movement in rice. PMID:20435900
Rudnicka, Dominika; Feldmann, Jérôme; Porrot, Françoise; Wietgrefe, Steve; Guadagnini, Stéphanie; Prévost, Marie-Christine; Estaquier, Jérôme; Haase, Ashley T.; Sol-Foulon, Nathalie; Schwartz, Olivier
2009-01-01
Human immunodeficiency virus type 1 (HIV-1) efficiently propagates through cell-to-cell contacts, which include virological synapses (VS), filopodia, and nanotubes. Here, we quantified and characterized further these diverse modes of contact in lymphocytes. We report that viral transmission mainly occurs across VS and through “polysynapses,” a rosette-like structure formed between one infected cell and multiple adjacent recipients. Polysynapses are characterized by simultaneous HIV clustering and transfer at multiple membrane regions. HIV Gag proteins often adopt a ring-like supramolecular organization at sites of intercellular contacts and colocalize with CD63 tetraspanin and raft components GM1, Thy-1, and CD59. In donor cells engaged in polysynapses, there is no preferential accumulation of Gag proteins at contact sites facing the microtubule organizing center. The LFA-1 adhesion molecule, known to facilitate viral replication, enhances formation of polysynapses. Altogether, our results reveal an underestimated mode of viral transfer through polysynapses. In HIV-infected individuals, these structures, by promoting concomitant infection of multiple targets in the vicinity of infected cells, may facilitate exponential viral growth and escape from immune responses. PMID:19369333
Reversible Diffusion by Thermal Fluctuations
Donev, A.; Fai, T. G.; Vanden-Eijnden, and E.
2013-01-01
A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to satisfy a closed-form stochastic advection-diffusion equation that is used to investigate the collective diffusion of hydrodynamically-correlated tracers through a combination of Eulerian and Lagrangian numerical methods. This analysis indicates that transport ...
Fluctuating-friction molecular motors
Marrucci, Lorenzo; Paparo, Domenico; Kreuzer, Markus
2001-01-01
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of this motion requires the presence of two additional independent bodies interacting with the particle via friction and via the energy potential, respectively, which can move relative to each other. Such three-body system generalizes the classical Brownian r...
Evolution of waves subject to a randomly varying growth rate is considered and the statistical properties of the waves are calculated in terms of the mean, variance, and correlation time of the growth rate. This enables stochastic growth to be studied without needing full knowledge of the microphysics. However, where the microphysics is understood, this approach also allows it to be easily incorporated into studies of larger-scale phenomena involving stochastic growth. Stochastic differential equations and Fokker--Planck equations are obtained, which describe the wave evolution in the presence of a variety of linear and nonlinear processes and boundary conditions, and it is shown that these phenomena can be diagnosed observationally through their effects on the statistical distribution of the wave field strengths. The results are particularly useful for waves with small dispersion, where they explain the strong wave clumping often observed in nature and emphasize the role of marginal stability in setting the level about which fluctuations occur and in determining their magnitude. Application to type III solar radio bursts illustrates many of the main results and verifies and generalizes earlier conclusions reached using a less rigorous approach. In particular, a new condition for marginally stable propagation of type III solar electron beams is found. copyright 1995 American Institute of Physics
Chang, Mou-Hsiung
2015-01-01
The classical probability theory initiated by Kolmogorov and its quantum counterpart, pioneered by von Neumann, were created at about the same time in the 1930s, but development of the quantum theory has trailed far behind. Although highly appealing, the quantum theory has a steep learning curve, requiring tools from both probability and analysis and a facility for combining the two viewpoints. This book is a systematic, self-contained account of the core of quantum probability and quantum stochastic processes for graduate students and researchers. The only assumed background is knowledge of the basic theory of Hilbert spaces, bounded linear operators, and classical Markov processes. From there, the book introduces additional tools from analysis, and then builds the quantum probability framework needed to support applications to quantum control and quantum information and communication. These include quantum noise, quantum stochastic calculus, stochastic quantum differential equations, quantum Markov semigrou...
Gibson, Daniel; Chang, Frederick; Gnad, Florian; Gunawardena, Jeremy
2016-01-01
The molecular complexity within a cell may be seen as an evolutionary response to the external complexity of the cell’s environment. This suggests that the external environment may be harnessed to interrogate the cell’s internal molecular architecture. Cells, however, are not only nonlinear and non-stationary, but also exhibit heterogeneous responses within a clonal, isogenic population. In effect, each cell undertakes its own experiment. Here, we develop a method of cellular interrogation using programmable microfluidic devices which exploits the additional information present in cell-to-cell variation, without requiring model parameters to be fitted to data. We focussed on Ca2+ signalling in response to hormone stimulation, which exhibits oscillatory spiking in many cell types and chose eight models of Ca2+ signalling networks which exhibit similar behaviour in simulation. We developed a nonlinear frequency analysis for non-stationary responses, which could classify models into groups under parameter variation, but found that this question alone was unable to distinguish critical feedback loops. We further developed a nonlinear amplitude analysis and found that the combination of both questions ruled out six of the models as inconsistent with the experimentally-observed dynamics and heterogeneity. The two models that survived the double interrogation were mathematically different but schematically identical and yielded the same unexpected predictions that we confirmed experimentally. Further analysis showed that subtle mathematical details can markedly influence non-stationary responses under parameter variation, emphasising the difficulty of finding a “correct” model. By developing questions for the pathway being studied, and designing more versatile microfluidics, cellular interrogation holds promise as a systematic strategy that can complement direct intervention by genetics or pharmacology. PMID:27367445
Modelling the Impact of Cell-To-Cell Transmission in Hepatitis B Virus.
Goyal, Ashish; Murray, John M
2016-01-01
Cell-free virus is a well-recognized and efficient mechanism for the spread of hepatitis B virus (HBV) infection in the liver. Cell-to-cell transmission (CCT) can be a more efficient means of virus propagation. Despite experimental evidence implying CCT occurs in HBV, its relative impact is uncertain. We develop a 3-D agent-based model where each hepatocyte changes its viral state according to a dynamical process driven by cell-free virus infection, CCT and intracellular replication. We determine the relative importance of CCT in the development and resolution of acute HBV infection in the presence of cytolytic (CTL) and non-CTL mechanisms. T cell clearance number is defined as the minimum number of infected cells needed to be killed by each T cell at peak infection that results in infection clearance within 12 weeks with hepatocyte turnover (HT, number of equivalent livers) ≤3. We find that CCT has very little impact on the establishment of infection as the mean cccDNA copies/cell remains between 15 to 20 at the peak of the infection regardless of CCT strength. In contrast, CCT inhibit immune-mediated clearance of acute HBV infection as higher CCT strength requires higher T cell clearance number and increases the probability of T cell exhaustion. An effective non-CTL inhibition can counter these negative effects of higher strengths of CCT by supporting rapid, efficient viral clearance and with little liver destruction. This is evident as the T cell clearance number drops by approximately 50% when non-CTL inhibition is increased from 10% to 80%. Higher CCT strength also increases the probability of the incidence of fulminant hepatitis with this phenomenon being unlikely to arise for no CCT. In conclusion, we report the possibility of CCT impacting HBV clearance and its contribution to fulminant hepatitis. PMID:27560827
Fattouh, Ramzi; Kwon, Hyunwoo; Czuczman, Mark A; Copeland, John W; Pelletier, Laurence; Quinlan, Margot E; Muise, Aleixo M; Higgins, Darren E; Brumell, John H
2015-04-01
The Gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen whose virulence depends on its ability to spread from cell to cell within an infected host. Although the actin-related protein 2/3 (Arp2/3) complex is necessary and sufficient for Listeria actin tail assembly, previous studies suggest that other actin polymerization factors, such as formins, may participate in protrusion formation. Here, we show that Arp2/3 localized to only a minor portion of the protrusion. Moreover, treatment of L. monocytogenes-infected HeLa cells with a formin FH2-domain inhibitor significantly reduced protrusion length. In addition, the Diaphanous-related formins 1-3 (mDia1-3) localized to protrusions, and knockdown of mDia1, mDia2, and mDia3 substantially decreased cell-to-cell spread of L. monocytogenes. Rho GTPases are known to be involved in formin activation. Our studies also show that knockdown of several Rho family members significantly influenced bacterial cell-to-cell spread. Collectively, these findings identify a Rho GTPase-formin network that is critically involved in the cell-to-cell spread of L. monocytogenes. PMID:25281757
A stochastic approach to microphysics
The presently widespread idea of ''vacuum population'', together with the quantum concept of vacuum fluctuations leads to assume a random level below that of matter. This stochastic approach starts by a reminder of the author's previous work, first on the relation of diffusion laws with the foundations of microphysics, and then on hadron spectrum. Following the latter, a random quark model is advanced; it gives to quark pairs properties similar to those of a harmonic oscillator or an elastic string, imagined as an explanation to their asymptotic freedom and their confinement. The stochastic study of such interactions as electron-nucleon, jets in e+e- collisions, or pp → π0 + X, gives form factors closely consistent with experiment. The conclusion is an epistemological comment (complementarity between stochastic and quantum domains, E.P.R. paradox, etc...)
Crossing Statistics of Anisotropic Stochastic Surface
Nezhadhaghighi, M Ghasemi; Yasseri, T; Allaei, S M Vaez
2015-01-01
We use crossing statistics and its generalization to determine the anisotropic direction imposed on a stochastic fields in $(2+1)$Dimension. This approach enables us to examine not only the rotational invariance of morphology but also we can determine the Gaussianity of underlying stochastic field in various dimensions. Theoretical prediction of up-crossing statistics (crossing with positive slope at a given threshold $\\alpha$ of height fluctuation), $\
On the stochastic dynamics of molecular conformation
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.
Stochastic cooling is the damping of betatron oscillations and momentum spread of a particle beam by a feedback system. In its simplest form, a pickup electrode detects the transverse positions or momenta of particles in a storage ring, and the signal produced is amplified and applied downstream to a kicker. The time delay of the cable and electronics is designed to match the transit time of particles along the arc of the storage ring between the pickup and kicker so that an individual particle receives the amplified version of the signal it produced at the pick-up. If there were only a single particle in the ring, it is obvious that betatron oscillations and momentum offset could be damped. However, in addition to its own signal, a particle receives signals from other beam particles. In the limit of an infinite number of particles, no damping could be achieved; we have Liouville's theorem with constant density of the phase space fluid. For a finite, albeit large number of particles, there remains a residue of the single particle damping which is of practical use in accumulating low phase space density beams of particles such as antiprotons. It was the realization of this fact that led to the invention of stochastic cooling by S. van der Meer in 1968. Since its conception, stochastic cooling has been the subject of much theoretical and experimental work. The earliest experiments were performed at the ISR in 1974, with the subsequent ICE studies firmly establishing the stochastic cooling technique. This work directly led to the design and construction of the Antiproton Accumulator at CERN and the beginnings of p anti p colliding beam physics at the SPS. Experiments in stochastic cooling have been performed at Fermilab in collaboration with LBL, and a design is currently under development for a anti p accumulator for the Tevatron
Stochastic deformation of a thermodynamic symplectic structure
Kazinski, P. O.
2009-01-01
A stochastic deformation of a thermodynamic symplectic structure is studied. The stochastic deformation is analogous to the deformation of an algebra of observables such as deformation quantization, but for an imaginary deformation parameter (the Planck constant). Gauge symmetries of thermodynamics and corresponding stochastic mechanics, which describes fluctuations of a thermodynamic system, are revealed and gauge fields are introduced. A physical interpretation to the gauge transformations and gauge fields is given. An application of the formalism to a description of systems with distributed parameters in a local thermodynamic equilibrium is considered.
Fluctuation phenomena are the ''tip of the iceberg'' revealing the existence, behind even the most quiescent appearing macroscopic states, of an underlying world of agitated, ever-changing microscopic processes. While the presence of these fluctuations can be ignored in some cases, e.g. if one is satisfied with purely thermostatic description of systems in equilibrium, they are central to the understanding of other phenomena, e.g. the nucleation of a new phase following the quenching of a system into the co-existence region. This volume contains a collection of review articles, written by experts in the field, on the subject of fluctuation phenomena. Some of the articles are of a very general nature discussing the modern mathematical formulation of the problems involved, while other articles deal with specific topics such as kinetics of phase transitions and conductivity in solids. The juxtaposition of the variety of physical situations in which fluctuation phenomena play an important role is novel and should give the reader an insight into this subject
Exploration of the spontaneous fluctuating activity of single enzyme molecules
Schwabe, Anne; Maarleveld, Timo; Bruggeman, Frank
2013-01-01
Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activity, such as transcription, replication, translation, and histone modifications. Here we introduce the main theoretical concepts of stochastic single-enzyme activity starting from the Michaelis–Men...
Exploration of the spontaneous fluctuating activity of single enzyme molecules
Schwabe, A.; Maarleveld, T.R.; Bruggeman, F.J.
2013-01-01
Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activ
From cusps to cores: a stochastic model
El-Zant, Amr; Combes, Francoise
2016-01-01
The cold dark matter model of structure formation faces apparent problems on galactic scales. Several threads point to excessive halo concentration, including central densities that rise too steeply with decreasing radius. Yet, random fluctuations in the gaseous component can 'heat' the centres of haloes, decreasing their densities. We present a theoretical model deriving this effect from first principles: stochastic variations in the gas density are converted into potential fluctuations that act on the dark matter; the associated force correlation function is calculated and the corresponding stochastic equation solved. Assuming a power law spectrum of fluctuations with maximal and minimal cutoff scales, we derive the velocity dispersion imparted to the halo particles and the relevant relaxation time. We further perform numerical simulations, with fluctuations realised as a Gaussian random field, which confirm the formation of a core within a timescale comparable to that derived analytically. Non-radial colle...
Crisan, Dan
2011-01-01
"Stochastic Analysis" aims to provide mathematical tools to describe and model high dimensional random systems. Such tools arise in the study of Stochastic Differential Equations and Stochastic Partial Differential Equations, Infinite Dimensional Stochastic Geometry, Random Media and Interacting Particle Systems, Super-processes, Stochastic Filtering, Mathematical Finance, etc. Stochastic Analysis has emerged as a core area of late 20th century Mathematics and is currently undergoing a rapid scientific development. The special volume "Stochastic Analysis 2010" provides a sa
Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise
David Frigola; Laura Casanellas; Sancho, José M.; Marta Ibañes
2012-01-01
Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are i...
A Nonlinear Dynamic Characterization of The Universal Scrape-off Layer Plasma Fluctuations
Mekkaoui, A
2012-01-01
A stochastic differential equation of plasma density dynamic is derived, consistent with the experimentally measured pdf and the theoretical quadratic nonlinearity. The plasma density evolves on the turbulence correlation time scale and is driven by a stochastic white noise proportional to the turbulence fluctuations amplitude, while the linear growth is quadratically damped by the fluctuation level $n_e(t)/\\bar{n}_e$.
Shephard, Neil
2005-01-01
Stochastic volatility (SV) is the main concept used in the fields of financial economics and mathematical finance to deal with the endemic time-varying volatility and codependence found in financial markets. Such dependence has been known for a long time, early comments include Mandelbrot (1963) and Officer (1973). It was also clear to the founding fathers of modern continuous time finance that homogeneity was an unrealistic if convenient simplification, e.g. Black and Scholes (1972, p. 416) ...
Dynamics of a Stochastic Functional System for Wastewater Treatment
Xuehui Ji; Sanling Yuan
2013-01-01
The dynamics of a delayed stochastic model simulating wastewater treatment process are studied. We assume that there are stochastic fluctuations in the concentrations of the nutrient and microbes around a steady state, and introduce two distributed delays to the model describing, respectively, the times involved in nutrient recycling and the bacterial reproduction response to nutrient uptake. By constructing Lyapunov functionals, sufficient conditions for the stochastic stability of its posit...
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.
Human herpesvirus-8 (HHV-8) is known to interact with cell surface heparan sulfate (HS) for entry into a target cell. Here we investigated the role of HS during HHV-8 glycoproteins-induced cell fusion. Interestingly, the observed fusion demonstrated an unusual dependence on HS as evident from following lines of evidence: (1) a significant reduction in cell-to-cell fusion occurred when target cells were treated with heparinase; (2) in a competition assay, when the effector cells expressing HHV-8 glycoproteins were challenged with soluble HS, cell-to-cell fusion was reduced; and, (3) co-expression of HHV-8 glycoproteins gH-gL on target cells resulted in inhibition of cell surface HS expression. Taken together, our results indicate that cell surface HS can play an additional role during HHV-8 pathogenesis.
Stochastic Quantization and Casimir Forces
Rodriguez-Lopez, Pablo; Soto, Rodrigo
2011-01-01
In this paper we show how the stochastic quantization method developed by Parisi and Wu can be used to obtain Casimir forces. Both quantum and thermal fluctuations are taken into account by a Langevin equation for the field. The method allows the Casimir force to be obtained directly, derived from the stress tensor instead of the free energy. It only requires the spectral decomposition of the Laplacian operator in the given geometry. The formalism provides also an expression for the fluctuations of the force. As an application we compute the Casimir force on the plates of a finite piston of arbitrary cross section. Fluctuations of the force are also directly obtained, and it is shown that, in the piston case, the variance of the force is twice the force squared.
Balachandran, Suchandra; Xiang, Yu; Schobert, Christian; Thompson, Gary A.; Lucas, William J.
1997-01-01
In angiosperms, the functional enucleate sieve tube system of the phloem appears to be maintained by the surrounding companion cells. In this study, we tested the hypothesis that polypeptides present within the phloem sap traffic cell to cell from the companion cells, where they are synthesized, into the sieve tube via plasmodesmata. Coinjection of fluorescently labeled dextrans along with size-fractionated Cucurbita maxima phloem proteins, ranging in size from 10 to 200 kDa, as well as injec...
Cell-to-cell variability in cell death: can systems biology help us make sense of it all?
Xia, X; Owen, M. S.; Lee, R E C; Gaudet, S
2014-01-01
One of the most common observations in cell death assays is that not all cells die at the same time, or at the same treatment dose. Here, using the perspective of the systems biology of apoptosis and the context of cancer treatment, we discuss possible sources of this cell-to-cell variability as well as its implications for quantitative measurements and computational models of cell death. Many different factors, both within and outside of the apoptosis signaling networks, have been correlated...
A stochastic reorganizational bath model for electronic energy transfer
Fujita, Takatoshi; Aspuru-Guzik, Alan
2014-01-01
The fluctuations of optical gap induced by the environment play crucial roles in electronic energy transfer dynamics. One of the simplest approaches to incorporate such fluctuations in energy transfer dynamics is the well known Haken-Strobl-Reineker model, in which the energy-gap fluctuation is approximated as a white noise. Recently, several groups have employed molecular dynamics simulations and excited-state calculations in conjunction to take the thermal fluctuation of excitation energies into account. Here, we discuss a rigorous connection between the stochastic and the atomistic bath models. If the phonon bath is treated classically, time evolution of the exciton-phonon system can be described by Ehrenfest dynamics. To establish the relationship between the stochastic and atomistic bath models, we employ a projection operator technique to derive the generalized Langevin equations for the energy-gap fluctuations. The stochastic bath model can be obtained as an approximation of the atomistic Ehrenfest equ...
Stochastic Gravity: Theory and Applications
Hu Bei Lok
2004-01-01
Full Text Available Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel. The noise kernel is the vacuum expectation value of the (operator-valued stress-energy bi-tensor which describes the fluctuations of quantum matter fields in curved spacetimes. In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. The axiomatic approach is useful to see the structure of the theory from the framework of semiclassical gravity, showing the link from the mean value of the stress-energy tensor to their correlation functions. The functional approach uses the Feynman-Vernon influence functional and the Schwinger-Keldysh closed-time-path effective action methods which are convenient for computations. It also brings out the open systems concepts and the statistical and stochastic contents of the theory such as dissipation, fluctuations, noise, and decoherence. We then focus on the properties of the stress-energy bi-tensor. We obtain a general expression for the noise kernel of a quantum field defined at two distinct points in an arbitrary curved spacetime as products of covariant derivatives of the quantum field's Green function. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime. We offer an analytical solution of the Einstein-Langevin equation and compute the two-point correlation functions for the linearized Einstein tensor and for the metric perturbations. Second, we discuss structure formation from the stochastic gravity viewpoint, which can go beyond the standard treatment by incorporating the full quantum effect of the inflaton fluctuations. Third, we discuss the backreaction
Sasaki, Nobumitsu; Ogata, Takuya; Deguchi, Masakazu; Nagai, Shoko; Tamai, Atsushi; Meshi, Tetsuo; Kawakami, Shigeki; Watanabe, Yuichiro; Matsushita, Yasuhiko; Nyunoya, Hiroshi
2009-03-01
Tomato mosaic virus (ToMV) encodes a movement protein (MP) that is necessary for virus cell-to-cell movement. We have demonstrated previously that KELP, a putative transcriptional coactivator of Arabidopsis thaliana, and its orthologue from Brassica campestris can bind to ToMV MP in vitro. In this study, we examined the effects of the transient over-expression of KELP on ToMV infection and the intracellular localization of MP in Nicotiana benthamiana, an experimental host of the virus. In co-bombardment experiments, the over-expression of KELP inhibited virus cell-to-cell movement. The N-terminal half of KELP (KELPdC), which had been shown to bind to MP, was sufficient for inhibition. Furthermore, the over-expression of KELP and KELPdC, both of which were co-localized with ToMV MP, led to a reduction in the plasmodesmal association of MP. In the absence of MP expression, KELP was localized in the nucleus and the cytoplasm by the localization signal in its N-terminal half. It was also shown that ToMV amplified normally in protoplasts prepared from leaf tissue that expressed KELP transiently. These results indicate that over-expressed KELP interacts with MP in vivo and exerts an inhibitory effect on MP function for virus cell-to-cell movement, but not on virus amplification in individual cells. PMID:19236566
Stochastic Gravity: Theory and Applications
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
赵越; 覃大清; 刘文杰; 徐用良; 许建新
2012-01-01
本文采用试验和统计分析的方法,根据在某中水头模型水轮机的相同工况下采集的300组压力脉动数据,采用比较试验数据随机不确定度的方法,研究了特征峰峰值、均方根、标准偏差和最大分频幅值等表征压力脉动程度的特征参数的随机不确定度情况,并以此提出了采用均方根值来表征压力脉动程度的建议.%In this paper, according t0 300 groups of test data of pressure fluctuation at same operation condition on a middle head Francis turbine model, the statistical behaviors ofcharacteristicpeak-to-peak value, root-mean-square, standard deviation and main frequency amplitude are explored on stochastic uncertainty method. Root-mean-square is suggested to denote the extent of pressure fluctuation.
Fluctuations for galaxy formation from inflation models
Salopek, D.S.
1989-01-01
The theory of fluctuations for galaxy formation from chaotic inflation models is extended to include the effects of (1) multiple scalar fields, (2) curvature coupling of scalar fields to gravity, (3) nonlinear evolution of long wavelength metric and scalar fields, and (4) stochastic generation of initial conditions. Multiple scalar field models may generate more large scale power than the standard Cold Dark Matter (CDM) model if the Universe undergoes two inflation epochs giving a CDM+ plateau spectrum. If the scalar fields pass over a mogul in the potential, then CDM+ mountain fluctuations spectral may be generated. The chaotic inflation scenario may be housed within a grand unified theory (GUT) framework through a coupling of scalar Higgs field to curvature. Radiative corrections to the Higgs potential are small and the reheat temperature is typically high yielding successful baryogenesis. Using Hamilton-Jacobi theory, a general formalism is presented for following the nonlinear evolution of the metric (scalar, vector, and tensor modes) and scalar fields for fluctuations with wavelength greater than the Hubble radius. It is shown how nonlinear effects of the metric and scalar fields may be included in Starobinski's formulation of stochastic inflation. Stochastic noise terms in the long wavelength evolution equations model quantum fluctuations that are assumed to become classical at horizon crossing and which then contribute to the background. T = ln(Ha) proves to be a useful time variable because it enables one to solve for scalar field quantum fluctuations within the horizon in an inhomogeneous background.
Stochastic Resonance in Protein Folding Dynamics.
Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A
2016-05-01
Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics. PMID:26992148
A fluctuating energy-momentum may produce an unstable world
R. AloisioINFN/LNGS; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); Grillo, A. F.
2015-01-01
Quantum gravitational effects may induce stochastic fluctuations in the structure of space-time, to produce a characteristic foamy structure. It has been known for some time now that these fluctuations may have observable consequencies for the propagation of cosmic ray particles over cosmological distances. We note here that the same fluctuations, if they exist, imply that some decay reactions normally forbidden by elementary conservation laws, become kinematically allowed, inducing the decay...
Space Time Fluctuations and Ultra High Energy Cosmic Ray Interactions
R. AloisioINFN/LNGS; P. Blasi(INAF Arcetri); A. Galante(Univ. L'Aquila); P. L. Ghia(CNR and INFN Torino); Grillo, A. F.
2002-01-01
The intimate geometry of space-time is expected to suffer stochastic fluctuations as a result of quantum gravitational effects. These fluctuations may induce observable consequences on the propagation of high energy particles over large distances, so that the strength and the characteristics of these fluctuations may be constrained, mainly in the range of energies of interest for cosmic ray physics. While invoked as a possible explanation for the detection of the puzzling co...
Cucumber mosaic virus (CMV, a cucumovirus) and Brome mosaic virus (BMV, a bromovirus) require the coat protein (CP) in addition to the 3a movement protein (MP) for cell-to-cell movement, while Cowpea chlorotic mottle virus (CCMV, a bromovirus) does not. Using bombardment-mediated transcomplementation assays, we investigated whether the movement functions encoded by these viruses potentiate cell-to-cell movement of movement-defective Tomato mosaic virus (ToMV, a tobamovirus) and Potato virus X (PVX, a potexvirus) mutants in Nicotiana benthamiana. Coexpression of CMV 3a and CP, but neither protein alone, complemented the defective movement of ToMV and PVX. A C-terminal deletion in CMV 3a (3aΔC33) abolished the requirement of CP in transporting the ToMV genome. The action of 3aΔC33 was inhibited by coexpression of wild-type 3a. These findings were confirmed in tobacco with ToMV-CMV chimeric viruses. Either BMV 3a or CCMV 3a alone efficiently complemented the movement-defective phenotype of the ToMV mutant. Therefore, every 3a protein examined intrinsically possesses the activity required to act as MP. In transcomplementation of the PVX mutant, the activities of BMV 3a, CCMV 3a, and CMV 3aΔC33 were very low. The activities of the bromovirus 3a proteins were enhanced by coexpression of the cognate CP but the activity of CMV 3aΔC33 was not. Based on these results, possible roles of cucumo- and bromovirus CPs in cell-to-cell movement are discussed
Tamai, Atsushi; Kubota, Kenji; Nagano, Hideaki; Yoshii, Motoyasu; Ishikawa, Masayuki; Mise, Kazuyuki; Meshi, Tetsuo
2003-10-10
Cucumber mosaic virus (CMV, a cucumovirus) and Brome mosaic virus (BMV, a bromovirus) require the coat protein (CP) in addition to the 3a movement protein (MP) for cell-to-cell movement, while Cowpea chlorotic mottle virus (CCMV, a bromovirus) does not. Using bombardment-mediated transcomplementation assays, we investigated whether the movement functions encoded by these viruses potentiate cell-to-cell movement of movement-defective Tomato mosaic virus (ToMV, a tobamovirus) and Potato virus X (PVX, a potexvirus) mutants in Nicotiana benthamiana. Coexpression of CMV 3a and CP, but neither protein alone, complemented the defective movement of ToMV and PVX. A C-terminal deletion in CMV 3a (3a Delta C33) abolished the requirement of CP in transporting the ToMV genome. The action of 3a Delta C33 was inhibited by coexpression of wild-type 3a. These findings were confirmed in tobacco with ToMV-CMV chimeric viruses. Either BMV 3a or CCMV 3a alone efficiently complemented the movement-defective phenotype of the ToMV mutant. Therefore, every 3a protein examined intrinsically possesses the activity required to act as MP. In transcomplementation of the PVX mutant, the activities of BMV 3a, CCMV 3a, and CMV 3a Delta C33 were very low. The activities of the bromovirus 3a proteins were enhanced by coexpression of the cognate CP but the activity of CMV 3a Delta C33 was not. Based on these results, possible roles of cucumo- and bromovirus CPs in cell-to-cell movement are discussed. PMID:14592759
Communication: Embedded fragment stochastic density functional theory
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals
Assessing the quality of stochastic oscillations
Guillermo Abramson; Sebastián Risau-Gusman
2008-06-01
We analyze the relationship between the macroscopic and microscopic descriptions of two-state systems, in particular the regime in which the microscopic one shows sustained `stochastic oscillations' while the macroscopic tends to a fixed point. We propose a quantification of the oscillatory appearance of the fluctuating populations, and show that good stochastic oscillations are present if a parameter of the macroscopic model is small, and that no microscopic model will show oscillations if that parameter is large. The transition between these two regimes is smooth. In other words, given a macroscopic deterministic model, one can know whether any microscopic stochastic model that has it as a limit, will display good sustained stochastic oscillations.
Stochastic Effects; Application in Nuclear Physics
Stochastic effects in nuclear physics refer to the study of the dynamics of nuclear systems evolving under stochastic equations of motion. In this dissertation we restrict our attention to classical scattering models. We begin with introduction of the model of nuclear dynamics and deterministic equations of evolution. We apply a Langevin approach - an additional property of the model, which reflect the statistical nature of low energy nuclear behaviour. We than concentrate our attention on the problem of calculating tails of distribution functions, which actually is the problem of calculating probabilities of rare outcomes. Two general strategies are proposed. Result and discussion follow. Finally in the appendix we consider stochastic effects in nonequilibrium systems. A few exactly solvable models are presented. For one model we show explicitly that stochastic behaviour in a microscopic description can lead to ordered collective effects on the macroscopic scale. Two others are solved to confirm the predictions of the fluctuation theorem. (author)
Embedded fragment stochastic density functional theory
Neuhauser, Daniel; Rabani, Eran
2014-01-01
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals.
Fattouh, Ramzi; Kwon, Hyunwoo; Czuczman, Mark A.; Copeland, John W.; Pelletier, Laurence; Quinlan, Margot E.; Aleixo M Muise; Higgins, Darren E.; Brumell, John H.
2014-01-01
The Gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen whose virulence depends on its ability to spread from cell to cell within an infected host. Although the actin-related protein 2/3 (Arp2/3) complex is necessary and sufficient for Listeria actin tail assembly, previous studies suggest that other actin polymerization factors, such as formins, may participate in protrusion formation. Here, we show that Arp2/3 localized to only a minor portion of the protr...
Mitarai, Namiko; Semsey, Szabolcs; Sneppen, Kim
2015-08-01
Transcriptional repression may cause transcriptional noise by a competition between repressor and RNA polymerase binding. Although promoter activity is often governed by a single limiting step, we argue here that the size of the noise strongly depends on whether this step is the initial equilibrium binding or one of the subsequent unidirectional steps. Overall, we show that nonequilibrium steps of transcription initiation systematically increase the cell-to-cell heterogeneity in bacterial populations. In particular, this allows also weak promoters to give substantial transcriptional noise. PMID:26382435
Xu, Jinhu; Zhou, Yicang
2016-04-01
A within-host viral infection model with both virus-to-cell and cell-to-cell transmissions and time delay in immune response is investigated. Mathematical analysis shows that delay may destabilize the infected steady state and lead to Hopf bifurcation. Moreover, the direction of the Hopf bifurcation and the stability of the periodic solutions are investigated by normal form and center manifold theory. Numerical simulations are done to explore the rich dynamics, including stability switches, Hopf bifurcations, and chaotic oscillations. PMID:27105992
Stochastic inflation and nonlinear gravity
Salopek, D. S.; Bond, J. R.
1991-02-01
We show how nonlinear effects of the metric and scalar fields may be included in stochastic inflation. Our formalism can be applied to non-Gaussian fluctuation models for galaxy formation. Fluctuations with wavelengths larger than the horizon length are governed by a network of Langevin equations for the physical fields. Stochastic noise terms arise from quantum fluctuations that are assumed to become classical at horizon crossing and that then contribute to the background. Using Hamilton-Jacobi methods, we solve the Arnowitt-Deser-Misner constraint equations which allows us to separate the growing modes from the decaying ones in the drift phase following each stochastic impulse. We argue that the most reasonable choice of time hypersurfaces for the Langevin system during inflation is T=ln(Ha), where H and a are the local values of the Hubble parameter and the scale factor, since T is the natural time for evolving the short-wavelength scalar field fluctuations in an inhomogeneous background. We derive a Fokker-Planck equation which describes how the probability distribution of scalar field values at a given spatial point evolves in T. Analytic Green's-function solutions obtained for a single scalar field self-interacting through an exponential potential are used to demonstrate (1) if the initial condition of the Hubble parameter is chosen to be consistent with microwave-background limits, H(φ0)/mρUniverse, the distribution is non-Gaussian, with a tail extending to large energy densities; although there are no observable manifestations, it does show eternal inflation. Lattice simulations of our Langevin network for the exponential potential demonstrate how spatial correlations are incorporated. An initially homogeneous and isotropic lattice develops fluctuations as more and more quantum fluctuation modes leave the horizon, yielding Gaussian contour maps for a region corresponding to our observable patch and non-Gaussian contour maps for the ultra
Wei, Fengying; Chen, Fangxiang
2016-07-01
This article discusses a stochastic SIQS epidemic model with saturated incidence. We assume that random perturbations always fluctuate at the endemic equilibrium. The existence of a global positive solution is obtained by constructing a suitable Lyapunov function. Under some suitable conditions, we derive the stochastic boundedness and stochastic permanence of the solutions of a stochastic SIQS model. Some numerical simulations are carried out to check our results.
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.
无
2007-01-01
In this paper, the stochastic flow of mappings generated by a Feller convolution semigroup on a compact metric space is studied. This kind of flow is the generalization of superprocesses of stochastic flows and stochastic diffeomorphism induced by the strong solutions of stochastic differential equations.
Stochastic Averaging and Stochastic Extremum Seeking
Liu, Shu-Jun
2012-01-01
Stochastic Averaging and Stochastic Extremum Seeking develops methods of mathematical analysis inspired by the interest in reverse engineering and analysis of bacterial convergence by chemotaxis and to apply similar stochastic optimization techniques in other environments. The first half of the text presents significant advances in stochastic averaging theory, necessitated by the fact that existing theorems are restricted to systems with linear growth, globally exponentially stable average models, vanishing stochastic perturbations, and prevent analysis over infinite time horizon. The second half of the text introduces stochastic extremum seeking algorithms for model-free optimization of systems in real time using stochastic perturbations for estimation of their gradients. Both gradient- and Newton-based algorithms are presented, offering the user the choice between the simplicity of implementation (gradient) and the ability to achieve a known, arbitrary convergence rate (Newton). The design of algorithms...
Fluctuation preserving coarse graining for biochemical systems
Altaner, Bernhard
2011-01-01
Finite stochastic Markov models play a major role for modelling biochemical pathways. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a certain extend arbitrary since it depends on the resolution of accomodating measurements. Here, we present a way to simplify such stochastic descriptions, which preserves both the meso-micro and the meso-macro connection. The former is achieved by demanding locality, the latter by considering cycles on the network of states. Using single- and multicycle examples we demonstrate how our new method preserves fluctuations of observables much better than na\\"ive approaches.
Stochastic modeling of the auroral electrojet index
Anh, V. V.; Yong, J. M.; Yu, Z. G.
2008-10-01
Substorms are often identified by bursts of activities in the magnetosphere-ionosphere system characterized by the auroral electrojet (AE) index. The highly complex nature of substorm-related bursts suggests that a stochastic approach would be needed. Stochastic models including fractional Brownian motion, linear fractional stable motion, Fokker-Planck equation and Itô-type stochastic differential equation have been suggested to model the AE index. This paper provides a stochastic model for the AE in the form of fractional stochastic differential equation. The long memory of the AE time series is represented by a fractional derivative, while its bursty behavior is modeled by a Lévy noise with inverse Gaussian marginal distribution. The equation has the form of the classical Stokes-Boussinesq-Basset equation of motion for a spherical particle in a fluid with retarded viscosity. Parameter estimation and approximation schemes are detailed for the simulation of the equation. The fractional order of the equation conforms with the previous finding that the fluctuations of the magnetosphere-ionosphere system as seen in the AE reflect the fluctuations in the solar wind: they both possess the same extent of long-range dependence. The introduction of a fractional derivative term into the equation to capture the extent of long-range dependence together with an inverse Gaussian noise input describe the right amount of intermittency inherent in the AE data.
Stochastic growth of localized plasma waves
Localized bursty plasma waves are detected by spacecraft in many space plasmas. The large spatiotemporal scales involved imply that beam and other instabilities relax to marginal stability and that mean wave energies are low. Stochastic wave growth occurs when ambient fluctuations perturb the system, causing fluctuations about marginal stability. This yields regions where growth is enhanced and others where damping is increased; bursts are associated with enhanced growth and can occur even when the mean growth rate is negative. In stochastic growth, energy loss from the source is suppressed relative to secular growth, preserving it far longer than otherwise possible. Linear stochastic growth can operate at wave levels below thresholds of nonlinear wave-clumping mechanisms such as strong-turbulence modulational instability and is not subject to their coherence and wavelength limits. These mechanisms can be distinguished by statistics of the fields, whose strengths are lognormally distributed if stochastically growing and power-law distributed in strong turbulence. Recent applications of stochastic growth theory (SGT) are described, involving bursty plasma waves and unstable particle distributions in type III solar radio sources, the Earth's foreshock, magnetosheath, and polar cap regions. It is shown that when combined with wave-wave processes, SGT also accounts for associated radio emissions
Stochastic effects in a seasonally forced epidemic model
Rozhnova, Ganna
2010-01-01
The interplay of seasonality, the system's nonlinearities and intrinsic stochasticity is studied for a seasonally forced susceptible-exposed-infective-recovered stochastic model. The model is explored in the parameter region that corresponds to childhood infectious diseases such as measles. The power spectrum of the stochastic fluctuations around the attractors of the deterministic system that describes the model in the thermodynamic limit is computed analytically and validated by stochastic simulations for large system sizes. Size effects are studied through additional simulations. Other effects such as switching between coexisting attractors induced by stochasticity often mentioned in the literature as playing an important role in the dynamics of childhood infectious diseases are also investigated. The main conclusion is that stochastic amplification, rather than these effects, is the key ingredient to understand the observed incidence patterns.
Pokharel, Deep; Wijesinghe, Philip; Oenarto, Vici; Lu, Jamie F; Sampson, David D; Kennedy, Brendan F; Wallace, Vincent P; Bebawy, Mary
2016-08-01
Deciphering the role of cell-to-cell communication in acquisition of cancer traits such as metastasis is one of the key challenges of integrative biology and clinical oncology. In this context, extracellular vesicles (EVs) are important vectors in cell-to-cell communication and serve as conduits in the transfer of cellular constituents required for cell function and for the establishment of cellular phenotypes. In the case of malignancy, they have been shown to support the acquisition of common traits defined as constituting the hallmarks of cancer. Cellular biophysics has contributed to our understanding of some of these central traits with changes in tissue biomechanics reflective of cell state. Indeed, much is known about stiffness of the tissue scaffold in the context of cell invasion and migration. This article advances this knowledge frontier by showing for the first time that EVs are mediators of tissue biomechanical properties and, importantly, demonstrates a link between the acquisition of cancer multidrug resistance and increased tissue stiffness of the malignant mass. The methodology used in the study employed optical coherence elastography and atomic force microscopy on breast cancer cell monolayers and tumor spheroids. Specifically, we show here that the acquired changes in tissue stiffness can be attributed to the intracellular transfer of a protein complex comprising ezrin, radixin, moesin, CD44, and P-glycoprotein. This has important implications in facilitating mechano-transduced signaling cascades that regulate the acquisition of cancer traits, such as invasion and metastasis. Finally, this study also introduces novel targets and strategies for diagnostic and therapeutic innovation in oncology, with a view to prevention of metastatic spread and personalized medicine in cancer treatment. PMID:27501296
Concentration fluctuations in gas releases by industrial accidents
Nielsen, M.; Chatwin, P.C.; Ejsing Jørgensen, Hans;
2002-01-01
The COFIN project studied existing remote-sensing Lidar data on concentration fluctuations in atmospheric dispersion from continuous sources at ground level. Fluctuations are described by stochastic models developed by a combination of statisticalanalyses and surface-layer scaling. The statistical...... and the probability distribution for the plume centreline. The distance-neighbour function generalizedfor higher-order statistics has a universal exponential shape. Simulation tools for concentration fluctuations have been developed for either multiple correlated time series or multi-dimensional fields. These tools...... risk assessment is illustrated by implementation of a typical heavy-gas dispersion model, enhanced for prediction and simulation of concentration fluctuations....
Constraints on Fluctuations in Sparsely Characterized Biological Systems
Hilfinger, Andreas; Norman, Thomas M.; Vinnicombe, Glenn; Paulsson, Johan
2016-02-01
Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.
Stochastic flux freezing and magnetic dynamo
Magnetic flux conservation in turbulent plasmas at high magnetic Reynolds numbers is argued neither to hold in the conventional sense nor to be entirely broken, but instead to be valid in a statistical sense associated to the ''spontaneous stochasticity'' of Lagrangian particle trajectories. The latter phenomenon is due to the explosive separation of particles undergoing turbulent Richardson diffusion, which leads to a breakdown of Laplacian determinism for classical dynamics. Empirical evidence is presented for spontaneous stochasticity, including numerical results. A Lagrangian path-integral approach is then exploited to establish stochastic flux freezing for resistive hydromagnetic equations and to argue, based on the properties of Richardson diffusion, that flux conservation must remain stochastic at infinite magnetic Reynolds number. An important application of these results is the kinematic, fluctuation dynamo in nonhelical, incompressible turbulence at magnetic Prandtl number (Prm) equal to unity. Numerical results on the Lagrangian dynamo mechanisms by a stochastic particle method demonstrate a strong similarity between the Prm=1 and 0 dynamos. Stochasticity of field-line motion is an essential ingredient of both. Finally, some consequences for nonlinear magnetohydrodynamic turbulence, dynamo, and reconnection are briefly considered.
Mechanical Autonomous Stochastic Heat Engine
Serra-Garcia, Marc; Foehr, André; Molerón, Miguel; Lydon, Joseph; Chong, Christopher; Daraio, Chiara
2016-07-01
Stochastic heat engines are devices that generate work from random thermal motion using a small number of highly fluctuating degrees of freedom. Proposals for such devices have existed for more than a century and include the Maxwell demon and the Feynman ratchet. Only recently have they been demonstrated experimentally, using, e.g., thermal cycles implemented in optical traps. However, recent experimental demonstrations of classical stochastic heat engines are nonautonomous, since they require an external control system that prescribes a heating and cooling cycle and consume more energy than they produce. We present a heat engine consisting of three coupled mechanical resonators (two ribbons and a cantilever) subject to a stochastic drive. The engine uses geometric nonlinearities in the resonating ribbons to autonomously convert a random excitation into a low-entropy, nonpassive oscillation of the cantilever. The engine presents the anomalous heat transport property of negative thermal conductivity, consisting in the ability to passively transfer energy from a cold reservoir to a hot reservoir.
Turbulence, Spontaneous Stochasticity and Climate
Eyink, Gregory
Turbulence is well-recognized as important in the physics of climate. Turbulent mixing plays a crucial role in the global ocean circulation. Turbulence also provides a natural source of variability, which bedevils our ability to predict climate. I shall review here a recently discovered turbulence phenomenon, called ``spontaneous stochasticity'', which makes classical dynamical systems as intrinsically random as quantum mechanics. Turbulent dissipation and mixing of scalars (passive or active) is now understood to require Lagrangian spontaneous stochasticity, which can be expressed by an exact ``fluctuation-dissipation relation'' for scalar turbulence (joint work with Theo Drivas). Path-integral methods such as developed for quantum mechanics become necessary to the description. There can also be Eulerian spontaneous stochasticity of the flow fields themselves, which is intimately related to the work of Kraichnan and Leith on unpredictability of turbulent flows. This leads to problems similar to those encountered in quantum field theory. To quantify uncertainty in forecasts (or hindcasts), we can borrow from quantum field-theory the concept of ``effective actions'', which characterize climate averages by a variational principle and variances by functional derivatives. I discuss some work with Tom Haine (JHU) and Santha Akella (NASA-Goddard) to make this a practical predictive tool. More ambitious application of the effective action is possible using Rayleigh-Ritz schemes.
Thermoemission of Ce+ ions and its fluctuations
Gladyszewski, Longin
1994-12-01
The surface ionization of cerium on tungsten and its fluctuatins (noises) have been studied using a single filament ion source in a 90° magnetic mass spectrometer. The statistical behaviour of the spectral density and autocorrelation functions for Ce+ ion thermoemission noise were investigated by means of a special stochastic analyser. These noises are generated as a result of adsorbate density fluctuations. The method used made it possible to determine the atom desorption and migration energy for cerium from tungsten.
Kallianpur, Gopinath; Hida, Takeyuki
1987-01-01
The use of probabilistic methods in the biological sciences has been so well established by now that mathematical biology is regarded by many as a distinct dis cipline with its own repertoire of techniques. The purpose of the Workshop on sto chastic methods in biology held at Nagoya University during the week of July 8-12, 1985, was to enable biologists and probabilists from Japan and the U. S. to discuss the latest developments in their respective fields and to exchange ideas on the ap plicability of the more recent developments in stochastic process theory to problems in biology. Eighteen papers were presented at the Workshop and have been grouped under the following headings: I. Population genetics (five papers) II. Measure valued diffusion processes related to population genetics (three papers) III. Neurophysiology (two papers) IV. Fluctuation in living cells (two papers) V. Mathematical methods related to other problems in biology, epidemiology, population dynamics, etc. (six papers) An important f...
Moawia Alghalith
2012-01-01
We present new stochastic differential equations, that are more general and simpler than the existing Ito-based stochastic differential equations. As an example, we apply our approach to the investment (portfolio) model.
Stochastic approximation: invited paper
Lai, Tze Leung
2003-01-01
Stochastic approximation, introduced by Robbins and Monro in 1951, has become an important and vibrant subject in optimization, control and signal processing. This paper reviews Robbins' contributions to stochastic approximation and gives an overview of several related developments.
Stochasticity or the fatal `imperfection' of cloning
Reiner A Veitia
2005-02-01
The concept of clone is analysed with the aim of exploring the limits to which a phenotype can be said to be determined geneticaly. First of all, mutations that result from the replication, topological manipulation or lesion of DNA introduce a source of heritable variation in an otherwise identical genetic background. But more important, stochastic effects in many biological processes may superimpose a phenotypic variation which is not encoded in the genome. The source of stochasticity ranges from the random selection of alleles or whole chromosomes to be expressed in small cell populations, to fluctuations in processes such as gene expression, due to limiting amounts of the players involved. The picture emerging is that the term clone is a statistical over-simplification representing a series of individuals having essentially the same genome but capable of exhibiting wide phenotypic variation. Finally, to what extent fluctuations in biological processes, usually thought of as noise, are in fact signal is also discussed.
Stochastic tools in turbulence
Lumey, John L
2012-01-01
Stochastic Tools in Turbulence discusses the available mathematical tools to describe stochastic vector fields to solve problems related to these fields. The book deals with the needs of turbulence in relation to stochastic vector fields, particularly, on three-dimensional aspects, linear problems, and stochastic model building. The text describes probability distributions and densities, including Lebesgue integration, conditional probabilities, conditional expectations, statistical independence, lack of correlation. The book also explains the significance of the moments, the properties of the
Stochastic component mode synthesis
Bah, Mamadou T.; Nair, Prasanth B.; Bhaskar, Atul; Keane, Andy J.
2003-01-01
In this paper, a stochastic component mode synthesis method is developed for the dynamic analysis of large-scale structures with parameter uncertainties. The main idea is to represent each component displacement using a subspace spanned by a set of stochastic basis vectors in the same fashion as in stochastic reduced basis methods [1, 2]. These vectors represent however stochastic modes in contrast to the deterministic modes used in conventional substructuring methods [3]. The Craig-Bampton r...
Modeling stochasticity in biochemical reaction networks
Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.
2016-03-01
Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.
Validity conditions for moment closure approximations in stochastic chemical kinetics
Schnoerr, David; Sanguinetti, Guido; Grima, Ramon
2014-01-01
Approximations based on moment-closure (MA) are commonly used to obtain estimates of the mean molecule numbers and of the variance of fluctuations in the number of molecules of chemical systems. The advantage of this approach is that it can be far less computationally expensive than exact stochastic simulations of the chemical master equation. Here, we numerically study the conditions under which the MA equations yield results reflecting the true stochastic dynamics of the system. We show tha...
Dynamic correlations in stochastic rotation dynamics
Tuzel, Erkan; Ihle, Thomas; Kroll, Daniel M.
2006-01-01
The dynamic structure factor, vorticity and entropy density dynamic correlation functions are measured for Stochastic Rotation Dynamics (SRD), a particle based algorithm for fluctuating fluids. This allows us to obtain unbiased values for the longitudinal transport coefficients such as thermal diffusivity and bulk viscosity. The results are in good agreement with earlier numerical and theoretical results, and it is shown for the first time that the bulk viscosity is indeed zero for this algor...
Quasiparticle spectra via Kolmogorov stochasticity parameter
In this study on three-quasiparticle states, we present results of statistical analysis of the one-quasiparticle (1qp) and three-quasiparticle (3qp) excitations by calculating a stochasticity parameter introduced by Kolmogorov. The objective for this statistical study is to test whether there is any change in the fluctuation properties (i.e. any transition from chaotic to integrable domain or vice versa) while going from the 1qp excitations to the 3qp excitations
The stochastic dynamics of biochemical systems
Challenger, Joseph Daniel
2013-01-01
The topic of this thesis is the stochastic dynamics of biochemical reaction systems. The importance of the intrinsic fluctuations in these systems has become more widely appreciated in recent years, and should be accounted for when modelling such systems mathematically. These models are described as continuous time Markov processes and their dynamics defined by a master equation. Analytical progress is made possible by the use of the van Kampen system-size expansion, which splits the dynamics...
Stochastic strategies in the Minority Game
Hart, M.; Jefferies, P.; Johnson, N. F.; Hui, P. M.
2000-01-01
We show analytically how the fluctuations (i.e. standard deviation) in the Minority Game (MG) can decrease below the random coin-toss limit if the agents use more general, stochastic strategies. This suppression of the standard deviation results from a cancellation between the actions of a crowd, in which agents act collectively and make the same decision, and an anticrowd in which agents act collectively by making the opposite decision to the crowd.
Mellin Transform Method for European Option Pricing with Hull-White Stochastic Interest Rate
Ji-Hun Yoon
2014-01-01
Full Text Available Even though interest rates fluctuate randomly in the marketplace, many option-pricing models do not fully consider their stochastic nature owing to their generally limited impact on option prices. However, stochastic dynamics in stochastic interest rates may have a significant impact on option prices as we take account of issues of maturity, hedging, or stochastic volatility. In this paper, we derive a closed form solution for European options in Black-Scholes model with stochastic interest rate using Mellin transform techniques.
Stochastic transport processes in discrete biological systems
Frehland, Eckart
1982-01-01
These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio logical 'transport systems can be complex. For example, the tr...
Modified diffusion with memory for cyclone track fluctuations
Bernido, Christopher C., E-mail: cbernido@mozcom.com [Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol 6308 (Philippines); Carpio-Bernido, M. Victoria [Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol 6308 (Philippines); Escobido, Matthew G.O. [W. Sycip Graduate School of Business, Asian Institute of Management, 123 Paseo de Roxas Ave., Makati City 1260 (Philippines)
2014-06-13
Fluctuations in a time series for tropical cyclone tracks are investigated based on an exponentially modified Brownian motion. The mean square displacement (MSD) is evaluated and compared to a recent work on cyclone tracks based on fractional Brownian motion (fBm). Unlike the work based on fBm, the present approach is found to capture the behavior of MSD versus time graphs for cyclones even for large values of time. - Highlights: • Cyclone track fluctuations are modeled as stochastic processes with memory. • Stochastic memory functions beyond fractional Brownian motion are introduced. • The model captures the behavior of cyclone track fluctuations for longer periods of time. • The approach can model time series for other fluctuating phenomena.
Modified diffusion with memory for cyclone track fluctuations
Fluctuations in a time series for tropical cyclone tracks are investigated based on an exponentially modified Brownian motion. The mean square displacement (MSD) is evaluated and compared to a recent work on cyclone tracks based on fractional Brownian motion (fBm). Unlike the work based on fBm, the present approach is found to capture the behavior of MSD versus time graphs for cyclones even for large values of time. - Highlights: • Cyclone track fluctuations are modeled as stochastic processes with memory. • Stochastic memory functions beyond fractional Brownian motion are introduced. • The model captures the behavior of cyclone track fluctuations for longer periods of time. • The approach can model time series for other fluctuating phenomena
Going with the flow: enhancing stochastic switching rates in multi-gyre systems
Heckman, Christoffer R; Schwartz, Ira B
2014-01-01
A control strategy is employed that modifies the stochastic escape times from one basin of attraction to another in a model of a double-gyre flow. The system studied captures the behavior of a large class of fluid flows that circulate and have multiple almost invariant sets. In the presence of noise, a particle in one gyre may randomly switch to an adjacent gyre due to a rare large fluctuation. We show that large fluctuation theory may be applied for controlling autonomous agents in a stochastic environment, in fact leveraging the stochastic- ity to the advantage of switching between regions of interest and concluding that patterns may be broken or held over time as the result of noise. We demonstrate that a controller can effectively manipulate the probability of a large fluctuation, thereby modifying escape times exponentially; this demonstrates the potential of optimal control strategies that work in combination with the endemic stochastic environment. To demonstrate this, stochastic simulations and numeri...
Fluctuation geometry: A counterpart approach of inference geometry
Velazquez, L.
2011-01-01
Starting from an axiomatic perspective, \\emph{fluctuation geometry} is developed as a counterpart approach of inference geometry. This approach is inspired on the existence of a notable analogy between the general theorems of \\emph{inference theory} and the the \\emph{general fluctuation theorems} associated with a parametric family of distribution functions $dp(I|\\theta)=\\rho(I|\\theta)dI$, which describes the behavior of a set of \\emph{continuous stochastic variables} driven by a set of contr...
Semiclassical Aspects of Quantum Mechanics by Classical Fluctuations
De Martino, S; Illuminati, F; Martino, Salvatore De; Siena, Silvio De
1998-01-01
Building on a model recently proposed by F. Calogero, we postulate the existence of a coherent, long--range universal tremor affecting any stable and confined classical dynamical system. Deriving the characteristic fluctuative unit of action for each classical interaction, we obtain in all cases its numerical coincidence with the Planck action constant. We therefore suggest that quantum corrections to classical dynamics can be simulated by suitable classical stochastic fluctuations.
Gabriella Schiera
2015-01-01
Full Text Available Extracellular vesicles are involved in a great variety of physiological events occurring in the nervous system, such as cross talk among neurons and glial cells in synapse development and function, integrated neuronal plasticity, neuronal-glial metabolic exchanges, and synthesis and dynamic renewal of myelin. Many of these EV-mediated processes depend on the exchange of proteins, mRNAs, and noncoding RNAs, including miRNAs, which occurs among glial and neuronal cells. In addition, production and exchange of EVs can be modified under pathological conditions, such as brain cancer and neurodegeneration. Like other cancer cells, brain tumours can use EVs to secrete factors, which allow escaping from immune surveillance, and to transfer molecules into the surrounding cells, thus transforming their phenotype. Moreover, EVs can function as a way to discard material dangerous to cancer cells, such as differentiation-inducing proteins, and even drugs. Intriguingly, EVs seem to be also involved in spreading through the brain of aggregated proteins, such as prions and aggregated tau protein. Finally, EVs can carry useful biomarkers for the early diagnosis of diseases. Herein we summarize possible roles of EVs in brain physiological functions and discuss their involvement in the horizontal spreading, from cell to cell, of both cancer and neurodegenerative pathologies.
Tubule-guided cell-to-cell movement of a plant virus requires class XI myosin motors.
Khalid Amari
2011-10-01
Full Text Available Cell-to-cell movement of plant viruses occurs via plasmodesmata (PD, organelles that evolved to facilitate intercellular communications. Viral movement proteins (MP modify PD to allow passage of the virus particles or nucleoproteins. This passage occurs via several distinct mechanisms one of which is MP-dependent formation of the tubules that traverse PD and provide a conduit for virion translocation. The MP of tubule-forming viruses including Grapevine fanleaf virus (GFLV recruit the plant PD receptors called Plasmodesmata Located Proteins (PDLP to mediate tubule assembly and virus movement. Here we show that PDLP1 is transported to PD through a specific route within the secretory pathway in a myosin-dependent manner. This transport relies primarily on the class XI myosins XI-K and XI-2. Inactivation of these myosins using dominant negative inhibition results in mislocalization of PDLP and MP and suppression of GFLV movement. We also found that the proper targeting of specific markers of the Golgi apparatus, the plasma membrane, PD, lipid raft subdomains within the plasma membrane, and the tonoplast was not affected by myosin XI-K inhibition. However, the normal tonoplast dynamics required myosin XI-K activity. These results reveal a new pathway of the myosin-dependent protein trafficking to PD that is hijacked by GFLV to promote tubule-guided transport of this virus between plant cells.
Spinner, Neil S.; Field, Christopher R.; Hammond, Mark H.; Williams, Bradley A.; Myers, Kristina M.; Lubrano, Adam L.; Rose-Pehrsson, Susan L.; Tuttle, Steven G.
2015-04-01
A 5-cubic meter decompression chamber was re-purposed as a fire test chamber to conduct failure and abuse experiments on lithium-ion batteries. Various modifications were performed to enable remote control and monitoring of chamber functions, along with collection of data from instrumentation during tests including high speed and infrared cameras, a Fourier transform infrared spectrometer, real-time gas analyzers, and compact reconfigurable input and output devices. Single- and multi-cell packages of LiCoO2 chemistry 18650 lithium-ion batteries were constructed and data was obtained and analyzed for abuse and failure tests. Surrogate 18650 cells were designed and fabricated for multi-cell packages that mimicked the thermal behavior of real cells without using any active components, enabling internal temperature monitoring of cells adjacent to the active cell undergoing failure. Heat propagation and video recordings before, during, and after energetic failure events revealed a high degree of heterogeneity; some batteries exhibited short burst of sparks while others experienced a longer, sustained flame during failure. Carbon monoxide, carbon dioxide, methane, dimethyl carbonate, and ethylene carbonate were detected via gas analysis, and the presence of these species was consistent throughout all failure events. These results highlight the inherent danger in large format lithium-ion battery packs with regards to cell-to-cell failure, and illustrate the need for effective safety features.
In Vivo HIV-1 Cell-to-Cell Transmission Promotes Multicopy Micro-compartmentalized Infection
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.
Cell-to-cell communication is an important factor for understanding the mechanisms of radiation-induced responses such as bystander effects. In this study, a new mathematical model of intercellular signalling between individual cells in a cellular population is proposed. The authors considered two types of transmission of signals: via culture medium and via gap junction. They focus on the effects that radiation and intercellular signalling have on cell-cycle modification. The cell cycle is represented as a virtual clock that includes several checkpoint pathways within a cyclic process. They also develop a grid model and set up diffusion equations to model the propagation of signals to and from spatially located cells. The authors have also considered the role that DNA damage plays in the cycle of cells which can progress through the cell cycle or stop at the G1, S, G2 or M-phase checkpoints. Results of testing show that the proposed model can simulate intercellular signalling and cell-cycle progression in individual cells during and after irradiation. (authors)
Ding, Chuanlin; Cai, Yihua; Marroquin, Jose; Ildstad, Suzanne T; Yan, Jun
2009-12-01
Plasmacytoid dendritic cells (pDCs) are specialized type I IFN producers, which play an important role in pathogenesis of autoimmune disorders. Dysregulated autoreactive B cell activation is a hallmark in most autoimmune diseases. This study was undertaken to investigate interactions between pDCs and autoreactive B cells. After coculture of autoreactive B cells that recognize self-Ag small nuclear ribonucleoprotein particles with activated pDCs, we found that pDCs significantly enhance autoreactive B cell proliferation, autoantibody production, and survival in response to TLR and BCR stimulation. Neutralization of IFN-alpha/beta and IL-6 abrogated partially pDC-mediated enhancement of autoreactive B cell activation. Transwell studies demonstrated that pDCs could provide activation signals to autoreactive B cells via a cell-to-cell contact manner. The involvement of the ICAM-1-LFA-1 pathway was revealed as contributing to this effect. This in vitro enhancement effect was further demonstrated by an in vivo B cell adoptive transfer experiment, which showed that autoreactive B cell proliferation and activation were significantly decreased in MyD88-deficient mice compared with wild-type mice. These data suggest the dynamic interplay between pDCs and B cells is required for full activation of autoreactive B cells upon TLR or BCR stimulation. PMID:19890051
Competitive learning behavior in a stochastic neural network
Cho, Myoung Won
2015-11-01
Stochastic behavior is a natural and inevitable property of biological neurons. The effect of stochastic behavior or thermal fluctuation in neural firings on the learning process in a neural system is investigated. A learning model, which is derived from the stochastic differential equation of the firing-rate model, is presented as an estimate of the gradient flow of free energy. The model reveals that the learning process becomes competitive owing to the effect of entropy even through the synapse modifications only follow the simple Hebbian rule.
Stochastic samples versus vacuum expectation values in cosmology
Tsamis, N.C.; Tzetzias, Aggelos [Department of Physics, University of Crete, GR-710 03 Heraklion (Greece); Woodard, R.P., E-mail: tsamis@physics.uoc.gr, E-mail: tzetzias@physics.uoc.gr, E-mail: woodard@phys.ufl.edu [Department of Physics, University of Florida, Gainesville, FL 32611 (United States)
2010-09-01
Particle theorists typically use expectation values to study the quantum back-reaction on inflation, whereas many cosmologists stress the stochastic nature of the process. While expectation values certainly give misleading results for some things, such as the stress tensor, we argue that operators exist for which there is no essential problem. We quantify this by examining the stochastic properties of a noninteracting, massless, minimally coupled scalar on a locally de Sitter background. The square of the stochastic realization of this field seems to provide an example of great relevance for which expectation values are not misleading. We also examine the frequently expressed concern that significant back-reaction from expectation values necessarily implies large stochastic fluctuations between nearby spatial points. Rather than viewing the stochastic formalism in opposition to expectation values, we argue that it provides a marvelously simple way of capturing the leading infrared logarithm corrections to the latter, as advocated by Starobinsky.
Stochastic Samples versus Vacuum Expectation Values in Cosmology
Tsamis, N C; Woodard, R P
2010-01-01
Particle theorists typically use expectation values to study the quantum back-reaction on inflation, whereas many cosmologists stress the stochastic nature of the process. While expectation values certainly give misleading results for some things, such as the stress tensor, we argue that operators exist for which there is no essential problem. We quantify this by examining the stochastic properties of a noninteracting, massless, minimally coupled scalar on a locally de Sitter background. The square of the stochastic realization of this field seems to provide an example of great relevance for which expectation values are not misleading. We also examine the frequently expressed concern that significant back-reaction from expectation values necessarily implies large stochastic fluctuations between nearby spatial points. Rather than viewing the stochastic formalism in opposition to expectation values, we argue that it provides a marvelously simple way of capturing the leading infrared logarithm corrections to the...
A NOTE ON THE STOCHASTIC ROOTS OF STOCHASTIC MATRICES
Qi-Ming HE; Eldon GUNN
2003-01-01
In this paper, we study the stochastic root matrices of stochastic matrices. All stochastic roots of 2×2 stochastic matrices are found explicitly. A method based on characteristic polynomial of matrix is developed to find all real root matrices that are functions of the original 3×3 matrix, including all possible (function) stochastic root matrices. In addition, we comment on some numerical methods for computing stochastic root matrices of stochastic matrices.
Stochastic Lie group integrators
Malham, Simon J A
2007-01-01
We present Lie group integrators for nonlinear stochastic differential equations with non-commutative vector fields whose solution evolves on a smooth finite dimensional manifold. Given a Lie group action that generates transport along the manifold, we pull back the stochastic flow on the manifold to the Lie group via the action, and subsequently pull back the flow to the corresponding Lie algebra via the exponential map. We construct an approximation to the stochastic flow in the Lie algebra via closed operations and then push back to the Lie group and then to the manifold, thus ensuring our approximation lies in the manifold. We call such schemes stochastic Munthe-Kaas methods after their deterministic counterparts. We also present stochastic Lie group integration schemes based on Castell--Gaines methods. These involve using an underlying ordinary differential integrator to approximate the flow generated by a truncated stochastic exponential Lie series. They become stochastic Lie group integrator schemes if...
Fluctuation-Enhanced Sensing of Bacterium Odors
Chang, Hung-Chih; King, Maria D; Kwan, Chiman
2009-01-01
The goal of this paper is to explore the possibility to detect and identify bacteria by sensing their odor via fluctuation-enhanced sensing with commercial Taguchi sensors. The fluctuations of the electrical resistance during exposure to different bacterial odors, Escherichia coli and anthrax-surrogate Bacillus subtilis, have been measured and analyzed. In the present study, the simplest method, the measurement and analysis of power density spectra was used. The sensors were run in the normal heated and the sampling-and-hold working modes, respectively. The results indicate that Taguchi sensors used in these fluctuation-enhanced modes are effective tools of bacterium detection and identification even when they are utilizing only the power density spectrum of the stochastic sensor signal.
X. Frank Xu
2010-03-30
Multiscale modeling of stochastic systems, or uncertainty quantization of multiscale modeling is becoming an emerging research frontier, with rapidly growing engineering applications in nanotechnology, biotechnology, advanced materials, and geo-systems, etc. While tremendous efforts have been devoted to either stochastic methods or multiscale methods, little combined work had been done on integration of multiscale and stochastic methods, and there was no method formally available to tackle multiscale problems involving uncertainties. By developing an innovative Multiscale Stochastic Finite Element Method (MSFEM), this research has made a ground-breaking contribution to the emerging field of Multiscale Stochastic Modeling (MSM) (Fig 1). The theory of MSFEM basically decomposes a boundary value problem of random microstructure into a slow scale deterministic problem and a fast scale stochastic one. The slow scale problem corresponds to common engineering modeling practices where fine-scale microstructure is approximated by certain effective constitutive constants, which can be solved by using standard numerical solvers. The fast scale problem evaluates fluctuations of local quantities due to random microstructure, which is important for scale-coupling systems and particularly those involving failure mechanisms. The Green-function-based fast-scale solver developed in this research overcomes the curse-of-dimensionality commonly met in conventional approaches, by proposing a random field-based orthogonal expansion approach. The MSFEM formulated in this project paves the way to deliver the first computational tool/software on uncertainty quantification of multiscale systems. The applications of MSFEM on engineering problems will directly enhance our modeling capability on materials science (composite materials, nanostructures), geophysics (porous media, earthquake), biological systems (biological tissues, bones, protein folding). Continuous development of MSFEM will
Density dependence and stochastic variation in a newly established population of a small songbird
Sæther, Bernt-Erik; Engen, Steinar; Lande, Russell; Both, Christiaan; Visser, Marcel E.
2002-01-01
Models describing fluctuations in population size should include both density dependence and stochastic effects. We examine the relative contribution of variation in parameters of the expected dynamics as well as demographic and environmental stochasticity to fluctuations in a population of a small passerine bird, the pied flycatcher, that was newly established in a Dutch study area. Using the theta-logistic model of density regulation, we demonstrate that the estimated quasi-stationary distr...
Ramsey Stochastic Model via Multistage Stochastic Programming
Kaňková, Vlasta
Vol. Part II. České Budějovice: University of South Bohemia in České Budějovice, Faculty of Economy , 2010 - (Houda, M.; Friebelová, J.), s. 328-333 ISBN 978-80-7394-218-2. [28th International Conference on Mathematical Methods in Economics 2010. České Budějovice (CZ), 08.09.2010-10.09.2010] R&D Projects: GA ČR GAP402/10/0956; GA ČR(CZ) GA402/08/0107; GA ČR GAP402/10/1610 Institutional research plan: CEZ:AV0Z10750506 Keywords : Ramsey stochastic model * Multistage stochastic programming * Confidence intervals * Autoregressive sequences * Stability * Empirical estimates Subject RIV: AH - Economics http://library.utia.cas.cz/separaty/2010/E/kankova-ramsey stochastic model via multistage stochastic programming.pdf
Anisotropies in the Gravitational-Wave Stochastic Background
Olmez, S; Siemens, X
2011-01-01
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a function of angle and frequency.
Anisotropies in the Gravitational-Wave Stochastic Background
Olmez, S.; Mandic, V.; Siemens, X.
2011-01-01
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a ...
Anisotropies in the gravitational-wave stochastic background
We consider anisotropies in the stochastic background of gravitational-waves (SBGW) arising from random fluctuations in the number of gravitational-wave sources. We first develop the general formalism which can be applied to different cosmological or astrophysical scenarios. We then apply this formalism to calculate the anisotropies of SBGW associated with the fluctuations in the number of cosmic string loops, considering both cosmic string cusps and kinks. We calculate the anisotropies as a function of angle and frequency
Extension of Nelson's Stochastic Quantization to Finite Temperature Using Thermo Field Dynamics
Kobayashi, Keita; Yamanaka, Yoshiya
2010-01-01
We present an extension of Nelson's stochastic quantum mechanics to finite temperature. Utilizing the formulation of Thermo Field Dynamics (TFD), we can show that Ito's stochastic equations for tilde and non-tilde particle positions reproduce the TFD-type Schr\\"odinger equation which is equivalent to the Liouville-von Neumann equation. In our formalism, the drift terms in the Ito's stochastic equation have the temperature dependence and the thermal fluctuation is induced through the correlati...
Lee, Soo Young; Gertler, Frank B; Goldberg, Marcia B
2015-11-01
Shigella spp. are intracellular bacterial pathogens that cause diarrhoeal disease in humans. Shigella utilize the host actin cytoskeleton to enter cells, move through the cytoplasm of cells and pass into adjacent cells. Ena/VASP family proteins are highly conserved proteins that participate in actin-dependent dynamic cellular processes. We tested whether Ena/VASP family members VASP (vasodilator-stimulated phosphoprotein), Mena (mammalian-enabled) or EVL (Ena-VASP-like) contribute to Shigella flexneri spread through cell monolayers. VASP and EVL restricted cell-to-cell spread without significantly altering actin-based motility, whereas Mena had no effect on these processes. Phosphorylation of VASP on Ser153, Ser235 and Thr274 regulated its subcellular distribution and function. VASP derivatives that lack the Ena/VASP homology 1 (EVH1) domain or contain a phosphoablative mutation of Ser153 were defective in restricting S. flexneri spread, indicating that the EVH1 domain and phosphorylation on Ser153 are required for this process. The EVH1 domain and Ser153 of VASP were required for VASP localization to focal adhesions, and localization of VASP to focal adhesions and/or the leading edge was required for restriction of spread. The contribution of the EVH1 domain was from both the donor and the recipient cell, whereas the contribution of Ser153 phosphorylation was only from the donor cell. Thus, unlike host proteins characterized in Shigella pathogenesis that promote bacterial spread, VASP and EVL function to limit it. The ability of VASP and EVL to limit spread highlights the critical role of focal adhesion complexes and/or the leading edge in bacterial passage between cells. PMID:26358985
Takegahara, Yuki; Yamanouchi, Keitaro, E-mail: akeita@mail.ecc.u-tokyo.ac.jp; Nakamura, Katsuyuki; Nakano, Shin-ichi; Nishihara, Masugi
2014-05-15
Intramuscular adipose tissue (IMAT) formation is observed in some pathological conditions such as Duchenne muscular dystrophy (DMD) and sarcopenia. Several studies have suggested that IMAT formation is not only negatively correlated with skeletal muscle mass but also causes decreased muscle contraction in sarcopenia. In the present study, we examined w hether adipocytes affect myogenesis. For this purpose, skeletal muscle progenitor cells were transfected with siRNA of PPARγ (siPPARγ) in an attempt to inhibit adipogenesis. Myosin heavy chain (MHC)-positive myotube formation was promoted in cells transfected with siPPARγ compared to that of cells transfected with control siRNA. To determine whether direct cell-to-cell contact between adipocytes and myoblasts is a prerequisite for adipocytes to affect myogenesis, skeletal muscle progenitor cells were cocultured with pre- or mature adipocytes in a Transwell coculture system. MHC-positive myotube formation was inhibited when skeletal muscle progenitor cells were cocultured with mature adipocytes, but was promoted when they were cocultured with preadipocytes. Similar effects were observed when pre- or mature adipocyte-conditioned medium was used. These results indicate that preadipocytes play an important role in maintaining skeletal muscle mass by promoting myogenesis; once differentiated, the resulting mature adipocytes negatively affect myogenesis, leading to the muscle deterioration observed in skeletal muscle pathologies. - Highlights: • We examined the effects of pre- and mature adipocytes on myogenesis in vitro. • Preadipocytes and mature adipocytes affect myoblast fusion. • Preadipocytes play an important role in maintaining skeletal muscle mass. • Mature adipocytes lead to muscle deterioration observed in skeletal muscle pathologies.
Growth and decay of large fluctuations far from equilibrium
Shrabani Sen; Syed Shahed Riaz; Deb Shankar Ray
2009-09-01
We have explored the weak noise limit of stochastic processes in nonlinear dissipative systems which admit of stable dynamical attractors in absence of noise. An interesting `detailed balance’ like condition in the steady state which is manifested in the time reversal symmetry between growth and decay of fluctuation far from equilibrium, similar to what is observed in thermally equilibrated systems, is demonstrated.
Entanglement and quantum fluctuations
Klyachko, Alexander A.; Shumovsky, Alexander S.
2003-01-01
We discuss maximum entangled states of quantum systems in terms of quantum fluctuations of all essential measurements responsible for manifestation of entanglement. Namely, we consider maximum entanglement as a property of states, for which quantum fluctuations come to their extreme.
The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed