Role Of Fluctuations Research Articles

Kinetic models for autopoietic chemical systems: the role of fluctuations in a homeostatic regime

Two kinetic models describing the emergence of autopoietic chemical units are presented and discussed: the single reagent autopoietic mechanism (SRAM) and a reduced version (rSRAM). The proposed schemes are inspired to the autopoietic vesicles studied by Zepik et al (2001 Angew. Chem., Int. Ed. Engl. 40 199–202). Deterministic and stochastic analyses are then performed in order to obtain conditions for growth, homeostasis and decay time behaviours of the overall amphiphiles concentration. Only the reduced SRAM is able to exhibit all the three regimes as experimentally observed and in order to obtain details on the time evolution of the aggregates' size distribution, stochastic simulations are carried out. What emerges from the rSRAM simulation outcomes is that random fluctuations can act as selection rules for the size of the autopoietic units in the homeostatic regime suggesting how, in a prebiotic scenario, stochastic fluctuations can select the more robust, in this case larger, as the fittest ‘organisms’.

Correction for Marmottant et al., The role of fluctuations and stress on the effective viscosity of cell aggregates

Correction for Marmottant et al., The role of fluctuations and stress on the effective viscosity of cell aggregates

The role of fluctuations and stress on the effective viscosity of cell aggregates

Cell aggregates are a tool for in vitro studies of morphogenesis, cancer invasion, and tissue engineering. They respond to mechanical forces as a complex rather than simple liquid. To change an aggregate's shape, cells have to overcome energy barriers. If cell shape fluctuations are active enough, the aggregate spontaneously relaxes stresses ("fluctuation-induced flow"). If not, changing the aggregate's shape requires a sufficiently large applied stress ("stress-induced flow"). To capture this distinction, we develop a mechanical model of aggregates based on their cellular structure. At stress lower than a characteristic stress tau*, the aggregate as a whole flows with an apparent viscosity eta*, and at higher stress it is a shear-thinning fluid. An increasing cell-cell tension results in a higher eta* (and thus a slower stress relaxation time t(c)). Our constitutive equation fits experiments of aggregate shape relaxation after compression or decompression in which irreversibility can be measured; we find t(c) of the order of 5 h for F9 cell lines. Predictions also match numerical simulations of cell geometry and fluctuations. We discuss the deviations from liquid behavior, the possible overestimation of surface tension in parallel-plate compression measurements, and the role of measurement duration.

Comparison of 2D models for the plasma edge with experimental measurements and assessment of deficiencies

Systematic discrepancies between 2D fluid edge codes predictions for scrape-off layer and divertor and existing tokamak experiments are described. Possible sources of the discrepancies, including incorrect implementation of the neutral model, the role of fluctuations in the plasma and non-local kinetic effect of parallel heat transport are analysed.

Développement de taillis d’aunes après l’abandon des prairies humides au cours des 70 dernières années

• The secondary succession of wet grasslands to communities of alder carr dominated by Alnus glutinosa was recorded in different parts of Europe during the 20th century. However, knowledge of such development of alder carr remains insufficient. • The development of alder carr was reconstructed at five sites in the Czech Republic, using historical aerial photographs and methods of dendrochronology. The aims were to investigate the succession from wet grasslands to alder carr at sites previously intensively managed for agriculture and to find out the role of fluctuations in the groundwater table, caused by artificial drainage channels, in the observed stand dynamics and tree growth. • The spread of forest (i.e., an increase in forest cover) predominated until the 1970s at all sites. This trend was disrupted by a large-scale dieback of forest stands in four of the five sites after the 1970s, followed by an increase in patch heterogeneity, as indicated by landscape metrics. The radial growth increment in Alnus glutinosa has been affected predominately by local environmental factors, probably including the changing degree of waterlogging. Forest dieback was presumably connected with a lesser extent of drainage channels. • Our results indicate that observed successional pathways at sites of alder carr were probably caused by local changes in the groundwater table.

Some unsolved problems relating to noise in biological systems

A faithful description of many biological processes requires us to take into account noiseand fluctuations. Simplified stochastic models may help to shed light on the role offluctuations in biological systems. Two kinds of theoretical problems for such simplifiedmodels are discussed in this paper. Firstly, I review approaches for calculating analyticallythe statistics of stochastic non-linear models of spontaneous neural activity. In particular, Idiscuss (i) interspike interval correlations in non-renewal neurons and (ii) the effect ofsynaptic short-term plasticity on neural signal transfer. Secondly, I discuss themore conceptual problem of how more detailed models are related to simplifiedmodels. I consider, as an example of an open problem of this kind, the relationbetween detailed models of coupled molecular motors and models of active Brownianmotion.

Role of fluctuations in the response of coupled bistable units to weak time-periodic driving forces

We analyze the stochastic response of a finite set of globally coupled noisy bistable units driven by rather weak time-periodic forces. We focus on the stochastic resonance and phase frequency synchronization of the collective variable, defined as the arithmetic mean of the variable characterizing each element of the array. For single-unit systems, stochastic resonance can be understood with the powerful tools of linear response theory. Proper noise-induced phase frequency synchronization for a single-unit system in this linear response regime does not exist. For coupled arrays, our numerical simulations indicate an enhancement of the stochastic resonance effects leading to gains larger than unity as well as genuine phase frequency synchronization. The nonmonotonicity of the response with the strength of the coupling strength is investigated. Comparison with simplifying schemes proposed in the literature to describe the random response of the collective variable is carried out.

Free energy of twisted semiflexible polymers

We investigate the role of fluctuations in single-molecule measurements of torque-link (t-lk) curves. For semiflexible polymers of finite persistence length (i.e., polymers with contour length L comparable to the persistence length LP), the torque versus link curve in the constant-torque (isotorque) ensemble is distinct from the one in the constant-link (isolink) ensemble. Thus, one encounters the conceptually interesting issue of a "free energy of transition" in switching ensembles while making torque-link measurements. We predict the dependence on the semiflexibility parameter beta=L/LP of this extra contribution to the free energy, which shows up as an area in the torque-link plane. This can be tested against future torque-link experiments with single biopolymers. We bring out the inequivalence of torque-link curves for a stiff polymer and present explicit analytical expressions for the distinct torque-link relations in the two ensembles and the free-energy difference in switching ensembles in this context. The predictions of our work can be tested against single-molecule experiments on torsionally constrained biopolymers.

Dynamics of single-molecule force-ramp experiments: The role of fluctuations

In the force-ramp mode of the atomic force microscope, the force with which a macromolecule is stretched is increased linearly in time by properly controlling the motion of the cantilever through a feedback loop. Using a master equation approach for the coupled cantilever-macromolecule system, we mimic such a feedback loop, to study nonequilibrium effects in the measurements of force-extension curves and fluctuations. In particular, it is shown that the fluctuations are the same for force-ramp experiments and for the more commonly used constant velocity experiments. Thus the exact same statistics suffice for the explanation of either experiment. Specific results are presented for the stretching of Dextran.

Role of fluctuations in the primary energy estimation of cosmic rays

Energy spectrum and chemical composition of primary cosmic ray for energies higher than 1 PeV are obtained mainly from research on the intensity and properties of extensive air showers (EAS). Similar additional information is obtained from research on properties of gamma ray families. A common characteristic of these researches is the fact that we are working in the range of high fluctuation parameters serving us to obtain primary energy spectrum. In this research different probability distributions have been used as well as their convolutions with the power spectrum. The role of the influence of different parameters on measurements of the primary energy spectrum.

Two-step model of light propagation in biological tissues

This paper proposes a two-step model for calculating the transmission spectra of collimated light for a sample of biological tissue. The role of fluctuations of the orientation of the structural elements of biological tissue in determining the scattering cross section is considered, and it is shown that, for some types of biological tissues, the chief role in determining the scattering cross section is played by density fluctuation and, for others, by the fluctuation of the orientation of the structural elements of the biological tissue. There is shown to be good quantitative agreement between the spectra calculated from the proposed model and the experimental spectra of optical transmission by a tissue sample.

Role of fluctuations in nonlinear dynamics of a driven polariton system in semiconductor microcavities

The escape time from the lower energy state of the bistable nonlinear driven microcavity oscillator has been obtained analytically by means of the quasi-classical kinetic equation in the basis of quasi-energy states. The dependence of the escape time on the intensity of the external field is in rather good agreement with the results of numerical experiments. Moreover, the numerical dependencies of the escape time on the damping parameter reveal a smooth crossover from exponential to diffusive-like behavior.

The role of fluctuations in tRNA selection by the ribosome.

The detailed mechanism of how the ribosome decodes protein sequence information with an abnormally high accuracy, after 40 years of study, remains elusive. A critical element in selecting correct transfer RNA (tRNA) transferring correct amino acid is "induced fit" between the ribosome and tRNA. By using single-molecule methods, the induced fit mechanism is shown to position favorably the correct tRNA after initial codon recognition. We provide evidence that this difference in positioning and thermal fluctuations constitutes the primary mechanism for the initial selection of tRNA. This work demonstrates thermal fluctuations playing a critical role in the substrate selection by an enzyme.

Improving a radiative plus collisional energy loss model for application to RHIC and LHC

With the QGP opacity computed perturbatively and with the global entropy constraints imposed by the observed dNch/dy ≈ 1000, radiative energy loss alone cannot account for the observed suppression of single non-photonic electrons. Collisional energy loss is comparable in magnitude to radiative loss for both light and heavy jets. Two aspects that significantly affect the collisional energy loss are examined: the role of fluctuations and the effect of introducing a running QCD coupling as opposed to the fixed αs = 0.3 used previously.

Relaxation and phase space singularities in time series of human magnetoencephalograms as indicator of photosensitive epilepsy

To analyze the crucial role of fluctuation and relaxation effects for the function of the human brain we studied some statistical quantifiers that support the information characteristics of neuromagnetic brain responses (magnetoencephalogram, MEG). The signals to a flickering stimulus of different color combinations have been obtained from a group of control subjects which is then contrasted with those of a patient suffering photosensitive epilepsy (PSE). We found that the existence of the specific stratification of the phase clouds and the concomitant relaxation singularities of the corresponding nonequilibrium dynamics of the chaotic behavior of the signals in separate areas in a patient provide likely indicators for the zones which are responsible for the appearance of PSE.

Silicon nanocrystal non-volatile memory for embedded memory scaling

In this paper, we present key features of silicon nanocrystal memory technology. This technology is an attractive candidate for scaling of embedded non-volatile memory (NVM). By replacing a continuous floating gate by electrically isolated silicon nanocrystals embedded in an oxide, this technology mitigates the vulnerability of charge loss through tunnel oxide defects and hence permits tunnel oxide and operating voltage scaling along with accompanied process simplifications. However, going to discrete nanocrystals brings new physical attributes that include the impact of Coulomb blockade or charge confinement, science of formation of nanocrystals of correct size and density and the role of fluctuations, all of which are addressed in this paper using single memory cell and memory array data.

Effect of Magnetic Configuration on Particle Transport and Density Fluctuation in LHD

The characteristics of particle transport in three different magnetic configurations are studied from density modulation experiments in the Large Helical Device (LHD). These three configurations are represented as different magnetic axis positions (Rax) of the vacuum field. Experiments were carried out in a range of different heating powers for each configuration with almost constant density. The experimental values of particle diffusion coefficients (D) and particle convection velocities (V) are compared with neoclassical estimates. The value of D is found to be anomalously large compared to neoclassical values in both the core and edge in all configurations. At low collisionality, this anomaly tends downward. The core convection velocities are comparable with neoclassical estimates. In more-outward-shifted configurations, particle transport is enhanced. The electron temperature and electron temperature gradient are the determinate parameters for D and V, respectively, in each configuration. The effective helical ripple is one of the important parameters for particle transport in the LHD; however, other hidden parameters exist. The role of fluctuations in particle transport is investigated from turbulence measurements using a two-dimensional phase contrast interferometer. Three kinds of fluctuation having different locations, propagation direction, and peak wave number are observed. One of these, which exists in the outermost edge region and propagates in the ion diamagnetic direction in the laboratory frame, plays a possible role in edge anomalous diffusion. The amplitudes of ion diamagnetic fluctuation components are compared with the linear growth rate of the ion temperature gradient mode.

Algorithm refinement for the stochastic Burgers’ equation

In this paper, we develop an algorithm refinement (AR) scheme for an excluded random walk model whose mean field behavior is given by the viscous Burgers’ equation. AR hybrids use the adaptive mesh refinement framework to model a system using a molecular algorithm where desired while allowing a computationally faster continuum representation to be used in the remainder of the domain. The focus in this paper is the role of fluctuations on the dynamics. In particular, we demonstrate that it is necessary to include a stochastic forcing term in Burgers’ equation to accurately capture the correct behavior of the system. The conclusion we draw from this study is that the fidelity of multiscale methods that couple disparate algorithms depends on the consistent modeling of fluctuations in each algorithm and on a coupling, such as algorithm refinement, that preserves this consistency.

Role of fluctuations in density wave and superconductivity of quasi-one-dimensional conductors

The response functions, χ , for the spin density wave (SDW) and the superconductivity in the quasi-one-dimensional electron systems at quarter-filling are calculated by the newly developed N-chain renormalization group method. It is shown that the interchain hopping, t ⊥ , enhances χ of SDW having the dependence on temperature with the power-law even below the crossover temperature T x ∼ t ⊥ . Further, χ of the d-wave singlet superconductivity (dSS) is enhanced rapidly below T x by t ⊥ , while there is no dominant behavior for dSS in the one-dimensional case ( t ⊥ = 0 ) . The results suggest that t ⊥ (or the pressure) rises the transition temperature of dSS even after the SDW is destroyed by the pressure.

Gelation of stochastic diffusion–coagulation systems

We investigate aerosol systems diffusing in space and study their gelation properties. In particular we work out the role of fluctuations which turn stable configurations into metastable ones, and the influence of randomly distributed sources and sinks.