arXiv subjects

Quentin Thommen

Publications and source records attributed to Quentin Thommen.

16 recordsLinked to original sources

arXiv2026

Shared environmental risk selects asymmetric inheritance of a protective reserve

Environmental sharing changes the value of diversification even when the marginal statistics experienced by each lineage remain unchanged. A minimal model of cell division couples this effect to the inheritance of a conserved protective reserve. Each mother partitions its reserve between two daughters, and each fixed partition policy generates a random demographic operator whose top Lyapunov exponent determines long-term growth. Weak environmental sharing favors symmetric inheritance, whereas sufficiently shared innovation selects a separated asymmetric branch near {\alpha \simeq 0.2}. The transition therefore occurs by a finite branch crossing rather than by a continuous departure from equal partition. The asymmetric phase persists when the protection law or reserve turnover is changed, although its boundary depends on protection nonlinearity and reserve memory. Because shared and private environmental innovations have identical marginal statistics, the mean reproductive operator is independent of the shared-innovation fraction. A dominant-mode second-order approximation then separates the asymmetric advantage into a mean-operator growth cost of specialization and a reduction of sensitivity to collective fluctuations. This approximation predicts the finite asymmetric branch selected by the full random-operator dynamics, while the full operator product determines the numerical crossing. Environmental sharing can therefore drive symmetry breaking in the inheritance of a conserved protective resource when the loss of diversification between lineages increases the value of diversification generated at division.

q-bio.PE↗

arXiv2026

Low-frequency output fluctuations in an open exclusion process with particle pausing

Slow internal states reshape both the mean throughput and the temporal organization of a driven lattice gas. Exit-counting statistics reveal this effect in a finite open totally asymmetric simple exclusion process whose particles reversibly switch between active and paused states. Increasing pausing lowers the mean current smoothly, whereas the long-window Fano factor is strongly nonmonotonic. At the reference boundary rates, the maximum remains near a measured mean paused population \(N_p=L\rho_{\rm paused}\simeq1.5\)--\(2\) across lattice lengths L=50-500, while the corresponding pausing rate scales as \(k_p^{\rm max}\propto L^{-1}\). A minimal constant-birth, linear-death approximation translates an order-one collective crossover into this finite-size displacement and gives \(N_p^\star\simeq1.50\) in the independent-pause, strong-blocking limit. The simulations delimit this approximation: the pause number is overdispersed, and at fixed \(N_p\), slower unpausing increases both the correlation time and the noise amplitude. Residence-time and structural analyses further separate the relevant slow variables. The pause-free versus pause-containing residence-time scale tracks the fitted output-correlation time, whereas the noise amplitude follows fluctuations, rather than the mean size, of the largest particle cluster. Low-frequency output noise therefore identifies an intermittent finite-size regime shaped jointly by slow-defect kinetics and traffic-jam reorganization.

cond-mat.stat-mech↗

arXiv2022

Stochastic simulation algorithm for isotope-based dynamic flux analysis

Carbon isotope labeling method is a standard metabolic engineering tool for flux quantification in living cells. To cope with the high dimensionality of isotope labeling systems, diverse algorithms have been developed to reduce the number of variables or operations in metabolic flux analysis (MFA), but lacks generalizability to non-stationary metabolic conditions. In this study, we present a stochastic simulation algorithm (SSA) derived from the chemical master equation of the isotope labeling system. This algorithm allows to compute the time evolution of isotopomer concentrations in non-stationary conditions, with the valuable property that computational time does not scale with the number of isotopomers. The efficiency and limitations of the algorithm is benchmarked for the forward and inverse problems of 13C-DMFA in the pentose phosphate pathways. Overall, SSA constitute an alternative class to deterministic approaches for metabolic flux analysis that is well adapted to comprehensive dataset including parallel labeling experiments, and whose limitations associated to the sampling size can be overcome by using Monte Carlo sampling approaches.

q-bio.MN↗

arXiv2015

A minimal titration modelization of the mammalian dynamical heat shock response

Environmental stress, such as oxidative or heat stress, induces the activation of the Heat Shock Response (HSR) which leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular chaperones to maintain proteostasis. Even if the main heat shock response partners are well known, a detailed description of the dynamical properties of the HSR network is still missing. In this study, we derive a minimal mathematical model of cellular response to heat shock that reproduces available experimental data sets both on transcription factor activity and cell viability. This simplistic model highlights the key mechanistic processes that rule the HSR network and reveals (i) the titration of Heat Shock Factor 1 (HSF1) by chaperones as the guiding line of the network, (ii) that protein triage governs the fate of damaged proteins and (iii) three different temperature regimes describing normal, acute or chronic stress.

physics.bio-ph↗

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↗

arXiv2011

A quantum motor: directed wavepacket motion in an optical lattice

We propose a method for arbitrary manipulations of a quantum wavepacket in an optical lattice by a suitable modulation of the lattice amplitude. A theoretical model allows to determine the modulation corresponding to a given wavepacket motion, so that arbitrary atomic trajectories can be generated. The method is immediately usable in state of the art experiments.

quant-ph↗

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

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↗

arXiv2003

Atomic motion in tilted optical lattices

This paper presents a formalism describing the dynamics of a quantum particle in a one-dimensional, time-dependent, tilted lattice. The formalism uses the Wannier-Stark states, which are localized in each site of the lattice, and provides a simple framework allowing fully-analytical developments. Analytic solutions describing the particle motion are explicit derived, and the resulting dynamics is studied.

quant-ph↗

arXiv2003

Classical chaos with Bose-Einstein condensates in tilted optical lattices

A widely accepted definition of ``quantum chaos'' is ``the behavior of a quantum system whose \emph{classical} \emph{limit is chaotic}''. The dynamics of quantum-chaotic systems is nevertheless very different from that of their classical counterparts. A fundamental reason for that is the linearity of Schr{ö}dinger equation. In this paper, we study the quantum dynamics of an ultra-cold quantum degenerate gas in a tilted optical lattice and show that it displays features very close to \emph{classical} chaos. We show that its phase space is organized according to the Kolmogorov-Arnold-Moser theorem.

quant-ph↗

arXiv2002

Wavepacket reconstruction via local dynamics in a parabolic lattice

We study the dynamics of a wavepacket in a potential formed by the sum of a periodic lattice and of a parabolic potential. The dynamics of the wavepacket is essentially a superposition of ``local Bloch oscillations'', whose frequency is proportional to the local slope of the parabolic potential. We show that the amplitude and the phase of the Fourier transform of a signal characterizing this dynamics contains information about the amplitude and the phase of the wavepacket at a given lattice site. Hence, {\em complete} reconstruction of the the wavepacket in the real space can be performed from the study of the dynamics of the system.

quant-ph↗

arXiv2001

Theoretical analysis of quantum dynamics in 1D lattices: Wannier-Stark description

This papers presents a formalism describing the dynamics of a quantum particle in a one-dimensional tilted time-dependent lattice. The description uses the Wannier-Stark states, which are localized in each site of the lattice and provides a simple framework leading to fully-analytical developments. Particular attention is devoted to the case of a time-dependent potential, which results in a rich variety of quantum coherent dynamics is found.

quant-ph↗