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Stochastic differential equations (SDEs) are a powerful tool to model fluctuations and uncertainty in complex systems. Although numerical methods have been designed to simulate SDEs effectively, it is still problematic when numerical solutions may be negative, but application problems require positive simulations. To address this issue, we propose balanced implicit Patankar–Euler methods to ensure positive simulations of SDEs. Instead of considering the addition of balanced terms to explicit methods in existing balanced methods, we attempt the deletion of possible negative terms from the explicit methods to maintain positivity of numerical simulations. The designed balanced terms include negative-valued drift terms and potential negative diffusion terms. The proposed method successfully addresses the issue of divisions with very small denominators in our recently designed stochastic Patankar method. Stability analysis shows that the balanced implicit Patankar–Euler method has much better stability properties than our recently designed composite Patankar–Euler method. Four SDE systems are used to examine the effectiveness, accuracy, and convergence properties of balanced implicit Patankar–Euler methods. Numerical results suggest that the proposed balanced implicit Patankar–Euler method is an effective and efficient approach to ensure positive simulations when any appropriate stepsize is used in simulating SDEs of biological regulatory systems. [ABSTRACT FROM AUTHOR]

Stochastic differential equations (SDE) are a powerful tool to model biological regulatory processes with intrinsic and extrinsic noise. However, numerical simulations of SDE models may be problematic if the values of noise terms are negative and large, which is not realistic for biological systems since the molecular copy numbers or protein concentrations should be non-negative. To address this issue, we propose the composite Patankar-Euler methods to obtain positive simulations of SDE models. A SDE model is separated into three parts, namely, the positive-valued drift terms, negative-valued drift terms, and diffusion terms. We first propose the deterministic Patankar-Euler method to avoid negative solutions generated from the negative-valued drift terms. The stochastic Patankar-Euler method is designed to avoid negative solutions generated from both the negative-valued drift terms and diffusion terms. These Patankar-Euler methods have the strong convergence order of a half. The composite Patankar-Euler methods are the combinations of the explicit Euler method, deterministic Patankar-Euler method, and stochastic Patankar-Euler method. Three SDE system models are used to examine the effectiveness, accuracy, and convergence properties of the composite Patankar-Euler methods. Numerical results suggest that the composite Patankar-Euler methods are effective methods to ensure positive simulations when any appropriate stepsize is used. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a new method based on a library of chemical reactions for constructing a system of ordinary differential equations from stochastic simulations arising from an agent-based model. The advantage of this approach is that this library respects any coupling between systems components, whereas the SINDy algorithm (introduced by Brunton et al.) treats the individual components as decoupled from one another. Another advantage of our approach is that we can use a non-negative least squares algorithm to find the non-negative rate constants in a very robust, stable and simple manner. We illustrate our ideas on an agent-based model of tumour growth on a 2D lattice. [ABSTRACT FROM AUTHOR]