Search Results (9)

Reaction–diffusion equations can model complex systems where randomness plays a role, capturing the interaction between diffusion processes and random fluctuations. The Kolmogorov equations associated with these systems play an important role in understanding the long-term behavior, stability, and control of such complex systems. In this paper, we investigate the existence of a classical solution for the Kolmogorov equation associated with a stochastic reaction–diffusion equation driven by nonlinear multiplicative trace-class noise. We also establish the existence of an invariant measure $\nu$ for the corresponding transition semigroup $P_t$, where the infinitesimal generator in $L^2(H,\nu )$ is identified as the closure of the Kolmogorov operator $K_0$. Full article

Cell polarity refers to the asymmetric distribution of proteins and other molecules along a specified axis within a cell. Polarity establishment is the first step in many cellular processes. For example, directed growth or migration requires the formation of a cell front and back. In many cases, polarity occurs in the absence of spatial cues. That is, the cell undergoes symmetry breaking. Understanding the molecular mechanisms that allow cells to break symmetry and polarize requires computational models that span multiple spatial and temporal scales. Here, we apply a multiscale modeling approach to examine the polarity circuit of yeast. In addition to symmetry breaking, experiments revealed two key features of the yeast polarity circuit: bistability and rapid dismantling of the polarity site following a loss of signal. We used modeling based on ordinary differential equations (ODEs) to investigate mechanisms that generate these behaviors. Our analysis revealed that a model involving positive and negative feedback acting on different time scales captured both features. We then extend our ODE model into a coarse-grained reaction–diffusion equation (RDE) model to capture the spatial profiles of polarity factors. After establishing that the coarse-grained RDE model qualitatively captures key features of the polarity circuit, we expand it to more accurately capture the biochemical reactions involved in the system. We convert the expanded model to a particle-based model that resolves individual molecules and captures fluctuations that arise from the stochastic nature of biochemical reactions. Our models assume that negative regulation results from negative feedback. However, experimental observations do not rule out the possibility that negative regulation occurs through an incoherent feedforward loop. Therefore, we conclude by using our RDE model to suggest how negative feedback might be distinguished from incoherent feedforward regulation. Full article

This study deals with a stochastic reaction–diffusion biofilm model under quorum sensing. Quorum sensing is a process of communication between cells that permits bacterial communication about cell density and alterations in gene expression. This model produces two results: the bacterial concentration, which over time demonstrates the development and decomposition of the biofilm, and the biofilm bacteria collaboration, which demonstrates the potency of resistance and defense against environmental stimuli. In this study, we investigate numerical solutions and exact solitary wave solutions with the presence of randomness. The finite difference scheme is proposed for the sake of numerical solutions while the generalized Riccati equation mapping method is applied to construct exact solitary wave solutions. The numerical scheme is analyzed by checking consistency and stability. The consistency of the scheme is gained under the mean square sense while the stability condition is gained by the help of the Von Neumann criteria. Exact stochastic solitary wave solutions are constructed in the form of hyperbolic, trigonometric, and rational forms. Some solutions are plots in 3D and 2D form to show dark, bright and solitary wave solutions and the effects of noise as well. Mainly, the numerical results are compared with the exact solitary wave solutions with the help of unique physical problems. The comparison plots are dispatched in three dimensions and line representations as well as by selecting different values of parameters. Full article

In this paper, we concentrate on the propagation dynamics of stochastic reaction–diffusion equations, including the existence of travelling wave solution and asymptotic wave speed. Based on the stochastic Feynman–Kac formula and comparison principle, the boundedness of the solution of stochastic reaction–diffusion equations can be obtained so that we can construct a sup-solution and a sub-solution to estimate the upper bound and the lower bound of wave speed. Full article

For decades, understanding the dynamics of infectious diseases and halting their spread has been a major focus of mathematical modelling and epidemiology. The stochastic SIRS (susceptible–infectious–recovered–susceptible) reaction–diffusion model is a complicated but crucial computational scheme due to the combination of partial immunity and an incidence rate. Considering the randomness of individual interactions and the spread of illnesses via space, this model is a powerful instrument for studying the spread and evolution of infectious diseases in populations with different immunity levels. A stochastic explicit finite difference scheme is proposed for solving stochastic partial differential equations. The scheme is comprised of predictor–corrector stages. The stability and consistency in the mean square sense are also provided. The scheme is applied to diffusive epidemic models with incidence rates and partial immunity. The proposed scheme with space’s second-order central difference formula solves deterministic and stochastic models. The effect of transmission rate and coefficient of partial immunity on susceptible, infected, and recovered people are also deliberated. The deterministic model is also solved by the existing Euler and non-standard finite difference methods, and it is found that the proposed scheme forms better than the existing non-standard finite difference method. Providing insights into disease dynamics, control tactics, and the influence of immunity, the computational framework for the stochastic SIRS reaction–diffusion model with partial immunity and an incidence rate has broad applications in epidemiology. Public health and disease control ultimately benefit from its application to the study and management of infectious illnesses in various settings. Full article

Stochastic parameter estimation and inversion have become increasingly popular in recent years. Nowadays, it is computationally reasonable and regular to solve complex inverse problems within the Bayesian framework. Applications of Bayesian inferences for inverse problems require investigation of the posterior distribution, which usually has a complex landscape and is highly dimensional. In these cases, Markov chain Monte Carlo methods (MCMC) are often used. This paper discusses a Bayesian approach for identifying adsorption and desorption rates in combination with a pore-scale reactive flow. Markov chain Monte Carlo sampling is used to estimate adsorption and desorption rates. The reactive transport in porous media is governed by incompressible Stokes equations, coupled with convection–diffusion equation for species’ transport. Adsorption and desorption are accounted via Robin boundary conditions. The Henry isotherm is considered for describing the reaction terms. The measured concentration at the outlet boundary is provided as additional information for the identification procedure. Metropolis–Hastings and Adaptive Metropolis algorithms are implemented. Credible intervals have been plotted from sampled posterior distributions for both algorithms. The impact of the noise in the measurements and influence of several measurements for Bayesian identification procedure is studied. Sample analysis using the autocorrelation function and acceptance rate is performed to estimate mixing of the Markov chain. As result, we conclude that MCMC sampling algorithm within the Bayesian framework is good enough to determine an admissible set of parameters via credible intervals. Full article

We consider the estimation of parameter-dependent statistics of functional outputs of steady-state convection–diffusion–reaction equations with parametrized random and deterministic inputs in the framework of linear elliptic partial differential equations. For a given value of the deterministic parameter, a stochastic Galerkin finite element (SGFE) method can estimate the statistical moments of interest of a linear output at the cost of solving a single, large, block-structured linear system of equations. We propose a stochastic Galerkin reduced basis (SGRB) method as a means to lower the computational burden when statistical outputs are required for a large number of deterministic parameter queries. Our working assumption is that we have access to the computational resources necessary to set up such a reduced-order model for a spatial-stochastic weak formulation of the parameter-dependent model equations. In this scenario, the complexity of evaluating the SGRB model for a new value of the deterministic parameter only depends on the reduced dimension. To derive an SGRB model, we project the spatial-stochastic weak solution of a parameter-dependent SGFE model onto a reduced basis generated by a proper orthogonal decomposition (POD) of snapshots of SGFE solutions at representative values of the parameter. We propose residual-corrected estimates of the parameter-dependent expectation and variance of linear functional outputs and provide respective computable error bounds. We test the SGRB method numerically for a convection–diffusion–reaction problem, choosing the convective velocity as a deterministic parameter and the parametrized reactivity or diffusivity field as a random input. Compared to a standard reduced basis model embedded in a Monte Carlo sampling procedure, the SGRB model requires a similar number of reduced basis functions to meet a given tolerance requirement. However, only a single run of the SGRB model suffices to estimate a statistical output for a new deterministic parameter value, while the standard reduced basis model must be solved for each Monte Carlo sample. Full article

The recent success of biological engineering is due to a tremendous amount of research effort and the increasing number of market opportunities. Indeed, this has been partially possible due to the contribution of advanced mathematical tools and the application of engineering principles in genetic-circuit development. In this work, we use a rationally designed genetic circuit to show how models can support research and motivate students to apply mathematics in their future careers. A genetic four-state machine is analyzed using three frameworks: deterministic and stochastic modeling through differential and master equations, and a spatial approach via a cellular automaton. Each theoretical framework sheds light on the problem in a complementary way. It helps in understanding basic concepts of modeling and engineering, such as noise, robustness, and reaction–diffusion systems. The designed automaton could be part of a more complex system of modules conforming future bio-computers and it is a paradigmatic example of how models can assist teachers in multidisciplinary education. Full article

A conditional Gaussian framework for understanding and predicting complex multiscale nonlinear stochastic systems is developed. Despite the conditional Gaussianity, such systems are nevertheless highly nonlinear and are able to capture the non-Gaussian features of nature. The special structure of the system allows closed analytical formulae for solving the conditional statistics and is thus computationally efficient. A rich gallery of examples of conditional Gaussian systems are illustrated here, which includes data-driven physics-constrained nonlinear stochastic models, stochastically coupled reaction–diffusion models in neuroscience and ecology, and large-scale dynamical models in turbulence, fluids and geophysical flows. Making use of the conditional Gaussian structure, efficient statistically accurate algorithms involving a novel hybrid strategy for different subspaces, a judicious block decomposition and statistical symmetry are developed for solving the Fokker–Planck equation in large dimensions. The conditional Gaussian framework is also applied to develop extremely cheap multiscale data assimilation schemes, such as the stochastic superparameterization, which use particle filters to capture the non-Gaussian statistics on the large-scale part whose dimension is small whereas the statistics of the small-scale part are conditional Gaussian given the large-scale part. Other topics of the conditional Gaussian systems studied here include designing new parameter estimation schemes and understanding model errors. Full article