Fluctuation relation for a L\'evy particle

We study the work fluctuations of a particle subjected to a deterministic drag force plus a random forcing whose statistics is of the L\'evy type. In the stationary regime, the probability density of the work is found to have ``fat'' power-law tails which assign a relatively high probability to large fluctuations compared with the case where the random forcing is Gaussian. These tails lead to a strong violation of existing fluctuation theorems, as the ratio of the probabilities of positive and negative work fluctuations of equal magnitude behaves in a non-monotonic way. Possible experiments that could probe these features are proposed.Comment: 5 pages, 2 figures, RevTeX4; v2: minor corrections and references added; v3: typos corrected, new conclusion, close to published versio

Activity driven fluctuations in living cells

We propose a model for the dynamics of a probe embedded in a living cell, where both thermal fluctuations and nonequilibrium activity coexist. The model is based on a confining harmonic potential describing the elastic cytoskeletal matrix, which undergoes random active hops as a result of the nonequilibrium rearrangements within the cell. We describe the probe's statistics and we bring forth quantities affected by the nonequilibrium activity. We find an excellent agreement between the predictions of our model and experimental results for tracers inside living cells. Finally, we exploit our model to arrive at quantitative predictions for the parameters characterizing nonequilibrium activity, such as the typical time scale of the activity and the amplitude of the active fluctuations.Comment: 6 pages, 4 figure

Exact solution of a model DNA-inversion genetic switch with orientational control

DNA inversion is an important mechanism by which bacteria and bacteriophage switch reversibly between phenotypic states. In such switches, the orientation of a short DNA element is flipped by a site-specific recombinase enzyme. We propose a simple model for a DNA inversion switch in which recombinase production is dependent on the switch state (orientational control). Our model is inspired by the fim switch in Escherichia coli. We present an exact analytical solution of the chemical master equation for the model switch, as well as stochastic simulations. Orientational control causes the switch to deviate from Poissonian behaviour: the distribution of times in the on state shows a peak and successive flip times are correlated.Comment: Revised version, accepted for publicatio

Spatial fluctuations at vertices of epithelial layers: quantification of regulation by Rho pathway

In living matter, shape fluctuations induced by acto-myosin are usually studied in vitro via reconstituted gels, whose properties are controlled by changing the concentrations of actin, myosin and cross-linkers. Such an approach deliberately avoids to consider the complexity of biochemical signaling inherent to living systems. Acto-myosin activity inside living cells is mainly regulated by the Rho signaling pathway which is composed of multiple layers of coupled activators and inhibitors. We investigate how such a pathway controls the dynamics of confluent epithelial tissues by tracking the displacements of the junction points between cells. Using a phenomenological model to analyze the vertex fluctuations, we rationalize the effects of different Rho signaling targets on the emergent tissue activity by quantifying the effective diffusion coefficient, the persistence time and persistence length of the fluctuations. Our results reveal an unanticipated correlation between layers of activation/inhibition and spatial fluctuations within tissues. Overall, this work connects the regulation via biochemical signaling with mesoscopic spatial fluctuations, with potential application to the study of structural rearrangements in epithelial tissues.Comment: 8 pages, 3 figure

Probing active forces via a fluctuation-dissipation relation: Application to living cells

We derive a new fluctuation-dissipation relation for non-equilibrium systems with long-term memory. We show how this relation allows one to access new experimental information regarding active forces in living cells that cannot otherwise be accessed. For a silica bead attached to the wall of a living cell, we identify a crossover time between thermally controlled fluctuations and those produced by the active forces. We show that the probe position is eventually slaved to the underlying random drive produced by the so-called active forces.Comment: 5 page

Granular Brownian motion

We study the stochastic motion of an intruder in a dilute driven granular gas. All particles are coupled to a thermostat, representing the external energy source, which is the sum of random forces and a viscous drag. The dynamics of the intruder, in the large mass limit, is well described by a linear Langevin equation, combining the effects of the external bath and of the "granular bath". The drag and diffusion coefficients are calculated under few assumptions, whose validity is well verified in numerical simulations. We also discuss the non-equilibrium properties of the intruder dynamics, as well as the corrections due to finite packing fraction or finite intruder mass.Comment: 19 pages, 4 figures, in press on Journal of Statistical Mechanics: Theory and Experiment

Ecopharmacology: Deliberated or casual dispersion of pharmaceutical principles, phytosanitary, personal health care and veterinary products in environment needs a multivariate analysis or expert systems for the control, the measure and the remediation

.The increasing human and animal use and abuse of drugs as well as of personalhealthcare and gross domestic products, involve disposal and waste problems and, as a consequence, affect the environmental condition. Actually most of the active principles are complex synthesised organic molecules that react, inside human or animal body, by specific biochemical reactions that in no case can reach a 100% yield and produce residues that could be more noxious of the starting compounds. Just reading the indication sheet accompanying any drugs, it is easy to state that no drug can be considered healthy, so, their use constitutes a serious pollution source. The full awareness of this relatively new environmental problem let many researchers to face it from different point of view. Current studies are considering the sources of these substances in the environment, the effects on human health as well as on the flora and fauna species, the recalcitrance and possible degradation methods, analytical techniques able to determine them and their metabolites even at low concentrations and in complex matrices. Literature on the subject continuously increases and a comparison of all data became more and more difficult both for a single drug and for different ones based on the same or different active principles. This is a typical case in which chemometrics can extract a full information in the easier way, so the design of a European database coupled to suitable expertsystem software should be strongly suggested

Is it possible to experimentally verify the fluctuation relation? A review of theoretical motivations and numerical evidence

The theoretical motivations to perform experimental tests of the stationary state fluctuation relation are reviewed. The difficulties involved in such tests, evidenced by numerical simulations, are also discussed.Comment: 36 pages, 4 figures. Extended version of a presentation to the discussion "Is it possible to experimentally verify the fluctuation theorem?", IHP, Paris, December 1, 2006. Comments are very welcom

Assessment of Carbon Stock and Greenhouse Gas Emissions of Selected Coffee-Based Agroforestry Farms in Timor Leste

Agroforestry is an important carbon sequestration strategy because of carbon storage potential in its multiple plant species and soil as well as its applicability in agricultural lands and in reforestation.  The study was conducted in selected coffee-based agroforestry farms in Gleno, Ermera District, Timor Leste to determine the amount of carbon stocks and greenhouse gas emissions in the management of coffee-based agroforestry farms. Results reveal that agroforestry coffee cropping pattern had a carbon stock composed of 6.425 Mg ha-1 biomass, 2.01 Mg ha-1 necromass, and 157.17 Mg ha-1 soil organic carbon. For the carbon stock stored in the monoculture coffee cropping pattern, a biomass of 5.321 Mg ha-1, necromass of 1.32 Mg ha-1, and soil organic carbon of 128.74. Mg ha-1 were recorded while for the pruned coffee cropping pattern, biomass of 2.771 Mg ha-1, necromass of 1.82 Mg ha-1, and soil organic carbon of 69.29 Mg ha-1 were found.  Moreover, the greenhouse gas emission CO2 absorbed by coffee plants across cropping patterns were the following: agroforestry coffee, 24.156 t/ha-1, monoculture coffee, 19.520 t/ha-1 and pruned coffee, 10.177 t/ha-1.  Abovementioned results reveal that coffee-based agroforestry system a coffee-based agroforestry is considered as an effective solution in combatting heightened atmospheric GHGs concentration and climate change while at the same time addressing concerns on socio-economic stability

Entropy production and fluctuation theorems under feedback control: the molecular refrigerator model revisited

We revisit the model of a Brownian particle in a heat bath submitted to an actively controlled force proportional to the velocity that leads to thermal noise reduction (cold damping). We investigate the influence of the continuous feedback on the fluctuations of the total entropy production and show that the explicit expression of the detailed fluctuation theorem involves different dynamics and observables in the forward and backward processes. As an illustration, we study the analytically solvable case of a harmonic oscillator and calculate the characteristic function of the entropy production in a nonequilibrium steady state. We then determine the corresponding large deviation function which results from an unusual interplay between 'boundary' and 'bulk' contributions.Comment: 16 pages, 5 figures. References 9,10,13,14,15 added. A few changes in the text. Accepted for publication in J. Stat. Mec