Transitions in a genetic transcriptional regulatory system under Lévy motion

Tumor state transitions driven by Gaussian and non-Gaussian noises

Tumor state transitions between the excited (high-concentration) and nonexcited (low-concentration) basins under the Gaussian white noise and non-Gaussian colored noise are investigated via the most probable steady states (MPSS) and the first escape probability (FEP)-based stochastic basin of attraction (SBA), respectively. Reducing the non-Gaussian colored noise and then utilizing the unified colored noise approximation (UCNA), the Markov system is derived. The extremal controlling equation of stationary probability density function (SPDF) is derived to analyze the impacts of noise on transitions in terms of MPSS. The existence of the 'color' of the non-Gaussian colored noise induces the reappearance of the uncorrelated additive white noise parameter that had vanished from the extremal controlling equation, completely reversing the inability of the uncorrelated additive Gaussian white noise to operate on transitions. The FEP-dependent SBA characterizing the excited basin stability is performed to further analyze the role of noise on the likelihood of escaping to the nonexcited state. Results show that the cross-correlated noises play a dual role in regulating SBA. The increased SBA indicating more difficulty to escape to the nonexcited state reflects a worse therapeutic effect. Therefore, enhancing the negatively correlated noise intensities and augmenting the non-Gaussian noise correlation time is essential for destabilizing the excited basin and achieving optimal therapeutic efficacy.

Mean exit times as global measure of resilience of tropical forest systems under climatic disturbances-Analytical and numerical results

Both remotely sensed distribution of tree cover and models suggest three alternative stable vegetation states in the tropics: forest, savanna, and treeless states. Environmental fluctuation could cause critical transitions from the forest to the savanna state and quantifying the resilience of a given vegetation state is, therefore, crucial. While previous work has focused mostly on local stability concepts, we investigate here the mean exit time from a given basin of attraction, with partially absorbing and reflecting boundaries, as a global resilience measure. We provide detailed investigations using an established model for tropical tree cover with multistable precipitation regimes. We find that higher precipitation or weaker noise increases the mean exit time of the forest state and, thus, its resilience. Upon investigating the transition times from the forest state to other tree cover states, we find that in the bistable precipitation regime, the size of environmental fluctuations has a greater impact on the transition probabilities from the forest state compared to precipitation.

An Onsager-Machlup approach to the most probable transition pathway for a genetic regulatory network

We investigate a quantitative network of gene expression dynamics describing the competence development in Bacillus subtilis. First, we introduce an Onsager-Machlup approach to quantify the most probable transition pathway for both excitable and bistable dynamics. Then, we apply a machine learning method to calculate the most probable transition pathway via the Euler-Lagrangian equation. Finally, we analyze how the noise intensity affects the transition phenomena.

A data-driven method to learn a jump diffusion process from aggregate biological gene expression data

Dynamic models of gene expression are urgently required. In this paper, we describe the time evolution of gene expression by learning a jump diffusion process to model the biological process directly. Our algorithm needs aggregate gene expression data as input and outputs the parameters of the jump diffusion process. The learned jump diffusion process can predict population distributions of gene expression at any developmental stage, obtain long-time trajectories for individual cells, and offer a novel approach to computing RNA velocity. Moreover, it studies biological systems from a stochastic dynamic perspective. Gene expression data at a time point, which is a snapshot of a cellular process, is treated as an empirical marginal distribution of a stochastic process. The Wasserstein distance between the empirical distribution and predicted distribution by the jump diffusion process is minimized to learn the dynamics. For the learned jump diffusion process, its trajectories correspond to the development process of cells, the stochasticity determines the heterogeneity of cells, its instantaneous rate of state change can be taken as "RNA velocity", and the changes in scales and orientations of clusters can be noticed too. We demonstrate that our method can recover the underlying nonlinear dynamics better compared to previous parametric models and the diffusion processes driven by Brownian motion for both synthetic and real world datasets. Our method is also robust to perturbations of data because the computation involves only population expectations.

Transition pathways for a class of high dimensional stochastic dynamical systems with Lévy noise

This work is devoted to deriving the Onsager-Machlup action functional for a class of stochastic differential equations with (non-Gaussian) Lévy process as well as Brownian motion in high dimensions. This is achieved by applying the Girsanov transformation for probability measures and then by a path representation. The Poincaré lemma is essential to handle such a path representation problem in high dimensions. We provide a sufficient condition on the vector field such that this path representation holds in high dimensions. Moreover, this Onsager-Machlup action functional may be considered as the integral of a Lagrangian. Finally, by a variational principle, we investigate the most probable transition pathways analytically and numerically.

The maximum likelihood climate change for global warming under the influence of greenhouse effect and Lévy noise

An abrupt climatic transition could be triggered by a single extreme event, and an α-stable non-Gaussian Lévy noise is regarded as a type of noise to generate such extreme events. In contrast with the classic Gaussian noise, a comprehensive approach of the most probable transition path for systems under α-stable Lévy noise is still lacking. We develop here a probabilistic framework, based on the nonlocal Fokker-Planck equation, to investigate the maximum likelihood climate change for an energy balance system under the influence of greenhouse effect and Lévy fluctuations. We find that a period of the cold climate state can be interrupted by a sharp shift to the warmer one due to larger noise jumps with low frequency. Additionally, the climate change for warming 1.5^°C under an enhanced greenhouse effect generates a steplike growth process. These results provide important insights into the underlying mechanisms of abrupt climate transitions triggered by a Lévy process.

Predicting noise-induced critical transitions in bistable systems

Critical transitions from one dynamical state to another contrasting state are observed in many complex systems. To understand the effects of stochastic events on critical transitions and to predict their occurrence as a control parameter varies are of utmost importance in various applications. In this paper, we carry out a prediction of noise-induced critical transitions using a bistable model as a prototype class of real systems. We find that the largest Lyapunov exponent and the Shannon entropy can act as general early warning indicators to predict noise-induced critical transitions, even for an earlier transition due to strong fluctuations. Furthermore, the concept of the parameter dependent basin of the unsafe regime is introduced via incorporating a suitable probabilistic notion. We find that this is an efficient tool to approximately quantify the range of the control parameter where noise-induced critical transitions may occur. Our method may serve as a paradigm to understand and predict noise-induced critical transitions in multistable systems or complex networks and even may be extended to a broad range of disciplines to address the issues of resilience.

Thermodynamics of Superdiffusion Generated by Lévy-Wiener Fluctuating Forces

Scale free Lévy motion is a generalized analogue of the Wiener process. Its time derivative extends the notion of “white noise” to non-Gaussian noise sources, and as such, it has been widely used to model natural signal variations described by an overdamped Langevin stochastic differential equation. Here, we consider the dynamics of an archetypal model: a Brownian-like particle is driven by external forces, and noise is represented by uncorrelated Lévy fluctuations. An unperturbed system of that form eventually attains a steady state which is uniquely determined by the set of parameter values. We show that the analyzed Markov process with the stability index α<2 violates the detailed balance, i.e., its stationary state is quantified by a stationary probability density and nonvanishing current. We discuss consequences of the non-Gibbsian character of the stationary state of the system and its impact on the general form of the fluctuation–dissipation theorem derived for weak external forcing.

Lévy noise induced transition and enhanced stability in a gene regulatory network

We investigate a quantitative bistable two-dimensional model (MeKS network) of gene expression dynamics describing the competence development in the Bacillus subtilis under the influence of Lévy as well as Brownian motions. To analyze the transitions between the vegetative and the competence regions therein, two dimensionless deterministic quantities, the mean first exit time (MFET) and the first escape probability, are determined from a microscopic perspective, as well as their averaged versions from a macroscopic perspective. The relative contribution factor λ, the ratio of non-Gaussian and Gaussian noise strengths, is adopted to identify an optimum choice in these transitions. Additionally, we use a recent geometric concept, the stochastic basin of attraction (SBA), to exhibit a pictorial comprehension about the influence of the Lévy motion on the basin stability of the competence state. Our main results indicate that (i) the transitions between the vegetative and the competence regions can be induced by the noise intensities, the relative contribution factor λ and the Lévy motion index α; (ii) a higher noise intensity and a larger α with smaller jump magnitude make the MFET shorter, and the MFET as a function of λ exhibits one maximum value, which is a signature of the noise-enhanced stability phenomenon for the vegetative state; (iii) a larger α makes the transition from the vegetative to the adjacent competence region to occur at the highest probability. The Lévy motion index α₀≈0.5 (a larger jump magnitude with a lower frequency) is an ideal choice to implement the transition to the non-adjacent competence region; (iv) there is an expansion in SBA when α decreases.

Likelihood for transcriptions in a genetic regulatory system under asymmetric stable Lévy noise

This work is devoted to investigating the evolution of concentration in a genetic regulation system, when the synthesis reaction rate is under additive and multiplicative asymmetric stable Lévy fluctuations. By focusing on the impact of skewness (i.e., non-symmetry) in the probability distributions of noise, we find that via examining the mean first exit time (MFET) and the first escape probability (FEP), the asymmetric fluctuations, interacting with nonlinearity in the system, lead to peculiar likelihood for transcription. This includes, in the additive noise case, realizing higher likelihood of transcription for larger positive skewness (i.e., asymmetry) index β, causing a stochastic bifurcation at the non-Gaussianity index value α = 1 (i.e., it is a separating point or line for the likelihood for transcription), and achieving a turning point at the threshold value β≈-0.5 (i.e., beyond which the likelihood for transcription suddenly reversed for α values). The stochastic bifurcation and turning point phenomena do not occur in the symmetric noise case (β = 0). While in the multiplicative noise case, non-Gaussianity index value α = 1 is a separating point or line for both the MFET and the FEP. We also investigate the noise enhanced stability phenomenon. Additionally, we are able to specify the regions in the whole parameter space for the asymmetric noise, in which we attain desired likelihood for transcription. We have conducted a series of numerical experiments in "regulating" the likelihood of gene transcription by tuning asymmetric stable Lévy noise indexes. This work offers insights for possible ways of achieving gene regulation in experimental research.

Switches in a genetic regulatory system under multiplicative non-Gaussian noise

The non-Gaussian noise is multiplicatively introduced to model the universal fluctuation in the gene regulation of the bacteriophage λ. To investigate the key effect of non-Gaussian noise on the genetic on/off switch dynamics from the viewpoint of quantitative analysis, we employ the high-order perturbation expansion to deduce the stationary probability density of repressor concentration and the mean first passage time from low concentration to high concentration and vice versa. The occupation probability of different concentration states can be estimated from the height and shape of the peaks of the stationary probability density, which could be used to determine the overall expression level. A further concern is the mean first passage time, also referred to as the mean switching time, which can be adopted as an important measure to characterize the adaptability of gene expression to the environmental variation. Through our investigation, it is observed that the non-Gaussian heavy-tailed noise can better induce the switches between distinct genetic expression states and additionally, it accelerates the switching process more evidently compared to the Gaussian noise and the bounded noise.

Metastability for discontinuous dynamical systems under Lévy noise: Case study on Amazonian Vegetation

For the tipping elements in the Earth’s climate system, the most important issue to address is how stable is the desirable state against random perturbations. Extreme biotic and climatic events pose severe hazards to tropical rainforests. Their local effects are extremely stochastic and difficult to measure. Moreover, the direction and intensity of the response of forest trees to such perturbations are unknown, especially given the lack of efficient dynamical vegetation models to evaluate forest tree cover changes over time. In this study, we consider randomness in the mathematical modelling of forest trees by incorporating uncertainty through a stochastic differential equation. According to field-based evidence, the interactions between fires and droughts are a more direct mechanism that may describe sudden forest degradation in the south-eastern Amazon. In modeling the Amazonian vegetation system, we include symmetric α-stable Lévy perturbations. We report results of stability analysis of the metastable fertile forest state. We conclude that even a very slight threat to the forest state stability represents L´evy noise with large jumps of low intensity, that can be interpreted as a fire occurring in a non-drought year. During years of severe drought, high-intensity fires significantly accelerate the transition between a forest and savanna state.