arXiv subjects

Marc Lefranc

Publications and source records attributed to Marc Lefranc.

14 recordsLinked to original sources

arXiv2014

Minimal model of transcriptional elongation processes with pauses

Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally asymmetric exclusion principle (TASEP). This model describes particles hopping between sites of a one-dimensional lattice, with the particle current determining the transcription or translation rate. An open problem is how to analyze a TASEP where particles can pause randomly, as has been observed during transcription. In this work, we report that surprisingly, a simple mean-field model predicts well the particle current for all values of the average pause duration, using a simple description of blocking behind paused particles.

q-bio.QM↗

arXiv2013

Stochastic oscillations induced by intrinsic fluctuations in a self-repressing gene: a deterministic approach

Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical systems, depending on which point of view is favored. Here, we investigate the dynamics of a self-repressing gene using an intermediate approach based on a moment closure approximation of the master equation, which allows us to take into account the binary character of gene activity. We thereby obtain deterministic equations that describe how nonlinearity feeds back fluctuations into the mean-field equations, providing insight into the interplay of determinism and stochasticity. This allows us to identify regions of parameter space where fluctuations induce relatively regular oscillations.

q-bio.MN↗

arXiv2011

Robust and flexible response of Ostreococcus tauri circadian clock to light/dark cycles of varying photoperiod

The green microscopic alga Ostreococcus tauri has recently emerged as a promising model for understanding how circadian clocks, which drive the daily biological rythms of many organisms, synchronize to the day/night cycle in changing weather and seasons. Here, we analyze translational reporter time series data of its central clock genes CCA1 and TOC1 for a wide range of daylight durations (photoperiods). The variation of temporal profiles with day duration is complex, with the two actors tracking different moments of the day. Nevertheless, all profiles are accurately reproduced by a simple two-gene transcriptional loop model whose parameters are affected by light only through the photoperiod value. We show that this non-intuitive behavior allows the circadian clock to combine flexibility and robustness to daylight fluctuations.

q-bio.QM↗

arXiv2010

A robust two-gene oscillator at the core of Ostreococcus tauri circadian clock

The microscopic green alga Ostreococcus tauri is rapidly emerging as a promising model organism in the green lineage. In particular, recent results by Corellou et al. [Plant Cell, 21, 3436 (2009)] and Thommen et al. [PLoS Comput. Biol. 6, e1000990 (2010)] strongly suggest that its circadian clock is a simplified version of Arabidopsis thaliana clock, and that it is architectured so as to be robust to natural daylight fluctuations. In this work, we analyze time series data from luminescent reporters for the two central clock genes TOC1 and CCA1 and correlate them with microarray data previously analyzed. Our mathematical analysis strongly supports both the existence of a simple two-gene oscillator at the core of Ostreococcus tauri clock and the fact that its dynamics is not affected by light in normal entrainment conditions, a signature of its robustness.

q-bio.QM↗

arXiv2010

Robust entrainment of circadian oscillators requires specific phase response curves

The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental cues are unreliable due to the variability of habitats, weather conditions or cue-sensing mechanisms among individuals. A tempting hypothesis is that circadian clocks have evolved so as to be robust to fluctuations in daylight or other cues when entrained by the day/night cycle. To test this hypothesis, we analyze the synchronization behavior of weakly and periodically forced oscillators in terms of their phase response curve (PRC), which measures phase changes induced by a perturbation applied at different phases. We establish a general relationship between, on the one side, the robustness of key entrainment properties such as stability and phase shift and, on the other side, the shape of the PRC as characterized by a specific curvature or the existence of a dead zone. This result can be applied to computational models of circadian clocks where it accounts for the disparate robustness properties of various forcing schemes. Finally, the analysis of PRCs measured experimentally in several organisms strongly suggests a case of convergent evolution toward an optimal strategy for maintaining a clock that is accurate and robust to environmental fluctuations.

q-bio.QM↗

arXiv2010

Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri

The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are under control of external signals and thus quantitative agreement between experimental data and a mathematical model is difficult. Circadian biology has been one notable exception: quantitative models of the internal clock that orchestrates biological processes over the 24-hour diurnal cycle have been constructed for a few organisms, from cyanobacteria to plants and mammals. In most cases, a complex architecture with interlocked feedback loops has been evidenced. Here we present first modeling results for the circadian clock of the green unicellular alga Ostreococcus tauri. Two plant-like clock genes have been shown to play a central role in Ostreococcus clock. We find that their expression time profiles can be accurately reproduced by a minimal model of a two-gene transcriptional feedback loop. Remarkably, best adjustment of data recorded under light/dark alternation is obtained when assuming that the oscillator is not coupled to the diurnal cycle. This suggests that coupling to light is confined to specific time intervals and has no dynamical effect when the oscillator is entrained by the diurnal cycle. This intringuing property may reflect a strategy to minimize the impact of fluctuations in daylight intensity on the core circadian oscillator, a type of perturbation that has been rarely considered when assessing the robustness of circadian clocks.

q-bio.MN↗

arXiv2009

Cooperative oscillation of non-degenerate transverse modes in an optical system: multimode operation in parametric oscillators

We show experimentally that parametric interaction can induce a cooperative oscillation of non simultaneously resonant transverse modes in an optical parametric oscillator. More generally, this effect is expected to occur in any spatially extended system subjected to boundary conditions where nonlinear wave mixing of two nonresonant spatial modes can generate a resonant oscillation.

physics.optics↗

arXiv2009

Oscillations in the expression of a self-repressed gene induced by a slow transcriptional dynamics

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of sustained oscillations and find that they require degradation mechanisms much less nonlinear than for infinitely fast regulation. Deterministic predictions are also compared with stochastic simulations of this minimal genetic oscillator.

q-bio.QM↗

arXiv2007

Embeddings of low-dimensional strange attractors: Topological invariants and degrees of freedom

When a low dimensional chaotic attractor is embedded in a three dimensional space its topological properties are embedding-dependent. We show that there are just three topological properties that depend on the embedding: parity, global torsion, and knot type. We discuss how they can change with the embedding. Finally, we show that the mechanism that is responsible for creating chaotic behavior is an invariant of all embeddings. These results apply only to chaotic attractors of genus one, which covers the majority of cases in which experimental data have been subjected to topological analysis. This means that the conclusions drawn from previous analyses, for example that the mechanism generating chaotic behavior is a Smale horseshoe mechanism, a reverse horseshoe, a gateau roule, an S-template branched manifold, ..., are not artifacts of the embedding chosen for the analysis.

nlin.CD↗

arXiv2006

Alternative determinism principle for topological analysis of chaos

The topological analysis of chaos based on a knot-theoretic characterization of unstable periodic orbits has proved a powerful method, however knot theory can only be applied to three-dimensional systems. Still, the core principles upon which this approach is built, determinism and continuity, apply in any dimension. We propose an alternative framework in which these principles are enforced on triangulated surfaces rather than curves and show that in dimension three our approach numerically predicts the correct topological entropies for periodic orbits of the horseshoe map.

nlin.CD↗

arXiv2006

Mode hopping strongly affects observability of dynamical instability in optical parametric oscillators

Theoretical investigations of dynamical behavior in optical parametric oscillators (OPO) have generally assumed that the cavity detunings of the interacting fields are controllable parameters. However, OPOs are known to experience mode hops, where the system jumps to the mode of lowest cavity detuning. We note that this phenomenon significantly limits the range of accessible detunings and thus may prevent instabilities predicted to occur above a minimum detuning from being evidenced experimentally. As a simple example among a number of instability mechanisms possibly affected by this limitation, we discuss the Hopf bifurcation leading to periodic behavior in the monomode mean-field model of a triply resonant OPO and show that it probably can be observed only in very specific setups.

physics.optics↗

arXiv2004

Topological signature of deterministic chaos in short nonstationary signals from an optical parametric oscillator

Although deterministic chaos has been predicted to occur in the triply resonant optical parametric oscillator (TROPO) fifteen years ago, experimental evidence of chaotic behavior in this system has been lacking so far, in marked contrast with most nonlinear systems, where chaos has been actively tracked and found. This situation is probably linked to the high sensitivity of the TROPO to perturbations, which adversely affects stationary operation at high power. We report the experimental observation in this system of a burst of irregular behavior of duration 80 microseconds. Although the system is highly nonstationary over this time interval, a topological analysis allows us to extract a clearcut signature of deterministic chaos from a time series segment of only 9 base cycles (3 microseconds). This result suggests that nonstationarity is not necessarily an obstacle to the characterization of chaos.

nlin.CD↗

arXiv1999

From template analysis to generating partitions I: Periodic orbits, knots and symbolic encodings

We present a detailed algorithm to construct symbolic encodings for chaotic attractors of three-dimensional flows. It is based on a topological analysis of unstable periodic orbits embedded in the attractor and follows the approach proposed by Lefranc et al. [Phys. Rev. Lett. 73, 1364 (1994)]. For each orbit, the symbolic names that are consistent with its knot-theoretic invariants and with the topological structure of the attractor are first obtained using template analysis. This information, and the locations of the periodic orbits in the section plane, are then used to construct a generating partition by means of triangulations. We provide numerical evidence of the validity of this method by applying it successfully to sets of more than 1500 periodic orbits extracted from numerical simulations, and obtain partitions whose border is localized with a precision of 0.01%. A distinctive advantage of this approach is that the solution is progressively refined using higher-period orbits, which makes it robust to noise, and suitable for analyzing experimental time series. Furthermore, the resulting encodings are by construction consistent in the corresponding limits with those rigorously known for both one-dimensional and hyperbolic maps.

chao-dyn↗

arXiv1999

From template analysis to generating partitions II: Characterization of the symbolic encodings

We give numerical evidence of the validity of a previously described algorithm for constructing symbolic encodings of chaotic attractors from a template analysis. We verify that the different solutions that can be found are dynamically equivalent, and that our approach yields results that are consistent with those obtained from methods based on homoclinic tangencies. This is further confirmed by verifying directly that the computed partitions are generating to a high degree of accuracy, and that they can be used to estimate precisely the metric entropy. It is also shown that the correct number of symbols needed to describe the dynamics is naturally provided, and that a compact parameterization of a partition can easily be determined, which makes our algorithm suitable for applications such as real-time encoding.

chao-dyn↗