Article
Physics, Fluids & Plasmas
Ernesto Berrios-Caro, Tobias Galla
Summary: The proposed tau-leaping simulation algorithm captures environmental noise beyond the adiabatic limit, achieving good performance in the regime of fast environmental dynamics. It retains environmental stochasticity to subleading order and requires significantly less computing time compared to full simulations of the combined system and environment.
Article
Computer Science, Interdisciplinary Applications
Jie Du, Yang Yang
Summary: This paper presents high-order bound-preserving discontinuous Galerkin (DG) methods for multicomponent chemically reacting flows. The proposed methods address the challenges of positivity preservation, ensuring the mass fractions sum up to 1, and handling stiff sources. The numerical experiments demonstrate the effectiveness of the proposed schemes.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Riccardo Malpica Galassi
Summary: PyCSP is a Python package for analyzing and simplifying chemically reacting systems, based on CSP theory. It provides tools for identifying rate-controlling chemical reactions, chemical timescales, etc., and can be used for analyzing numerical simulations and reducing chemical kinetics models.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Physics, Fluids & Plasmas
Jian Teng, Jianchun Wang, Shiyi Chen
Summary: The flow topology and enstrophy production in chemically reacting compressible isotropic turbulence are studied through numerical simulations. The study finds that heat release from chemical reaction increases internal energy and turbulent length scales, and reduces compressibility and density gradient magnitude. The statistical properties of different flow topologies are investigated, showing that chemical reaction significantly reduces the effect of compressibility on flow topologies and enstrophy production.
PHYSICAL REVIEW FLUIDS
(2022)
Article
Operations Research & Management Science
Tahir Ekin, Stephen Walker, Paul Damien
Summary: This article proposes an augmented simulation approach to solve discrete stochastic optimization problems by converting them into a simulation problem in the joint space of random and decision variables. The optimal decision is obtained using a new multivariate extension of the Barker's algorithm, and illustrations on different versions of the news-vendor problem are provided.
ANNALS OF OPERATIONS RESEARCH
(2023)
Article
Biochemical Research Methods
Mohammad Ahmadi, Payton J. Thomas, Lukas Buecherl, Chris Winstead, Chris J. Myers, Hao Zheng
Summary: Rare events are of great importance in synthetic biology, as they can have catastrophic effects on biological systems. Weighted stochastic simulation methods have been developed to estimate the probability of rare events efficiently. However, these methods require computationally expensive calibration procedures and further development is needed before they can be widely used in biological simulations.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Physics, Mathematical
Jialin Hong, Jialin Ruan, Liying Sun, Lijin Wang
Summary: This study introduces a numerical integration methodology for stochastic Poisson systems (SPSs) with multiple noises and different Hamiltonians in diffusion coefficients. By transforming SPSs into their canonical form and using a generating function approach, the proposed method is able to preserve the Poisson structure and Casimir functions of the systems while efficiently integrating them numerically.
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Takashi Goda, Wataru Kitade
Summary: This paper studies stochastic gradient descent for solving conditional stochastic optimization problems. It demonstrates the unbiasedness and finite properties of a multilevel Monte Carlo gradient estimator, and discusses the construction of another unbiased gradient estimator in a special case.
MATHEMATICS AND COMPUTERS IN SIMULATION
(2023)
Article
Engineering, Civil
Li Zhu, Yang Li, F. Richard Yu, Bin Ning, Tao Tang, Xiaoxuan Wang
Summary: Communication-based Train Control (CBTC) systems are the future direction for train control systems, but they are more vulnerable to cyber-attacks. This paper proposes a cross-layer defense scheme including a model prediction control algorithm, a multi-stage stochastic game model, and a dynamic train travel speed profile generation algorithm to mitigate the impact of jamming attacks on CBTC systems. The simulation results show that the proposed defense scheme effectively mitigates the impact of jamming attacks.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2021)
Article
Mathematics, Applied
Cristina Anton
Summary: This article gives conditions for stochastic Runge-Kutta methods to nearly preserve quadratic invariants and discusses the corresponding simplified order conditions. For stochastic Hamiltonian systems, a systematic approach is proposed to construct explicit stochastic Runge-Kutta pseudo-symplectic schemes based on colored trees and B-series. Pseudo-symplectic stochastic Runge-Kutta methods with strong convergence order are constructed, and the long-term performance of the proposed schemes is numerically illustrated.
APPLIED NUMERICAL MATHEMATICS
(2023)
Article
Multidisciplinary Sciences
Timothy C. Stutz, Alfonso Landeros, Jason Xu, Janet S. Sinsheimer, Mary Sehl, Kenneth Lange
Summary: Interacting Particle Systems (IPSs) are simplified to well-mixed Chemical Reaction Networks (CRNs) using an algorithmic framework, allowing for a wide range of techniques to be applied. The approach is implemented in Julia and applied to complex spatial stochastic phenomena, aiding in standardizing mathematical models and generating hypotheses based on observed spatial phenomena.
Article
Mathematics, Applied
Jie Du, Yong Liu, Yang Yang
Summary: This paper presents an oscillation-free discontinuous Galerkin (OFDG) method for solving multi-component chemically reacting flows. The method successfully controls spurious oscillations without sacrificing accuracy and preserves conservative property. The proposed OFDG method is compatible with the bound-preserving limiter and numerical experiments validate its desired properties.
JOURNAL OF SCIENTIFIC COMPUTING
(2023)
Article
Mathematics, Applied
Tong Tang, Jianzhu Sun
Summary: This work proves the local well-posedness of strong solutions to the compressible flow of a chemically reacting gaseous mixture with initial data containing vacuum, without assuming any compatibility condition on the initial data.
ZEITSCHRIFT FUR ANGEWANDTE MATHEMATIK UND PHYSIK
(2021)
Article
Mathematics, Applied
Roland Pulch, Adrian Sandu
Summary: This work studies efficient implicit methods for the time integration of stiff stochastic Galerkin systems consisting of ordinary differential equations. Linearly-implicit Rosenbrock-Wanner schemes are considered, and a block-diagonal approximation of the Jacobian is employed to improve computational efficiency.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2024)
Article
Computer Science, Software Engineering
Americo Cunha, Luis Fernando Figueira da Silva
Summary: This paper presents CRFlowLib, a computational package for simulating chemically reacting flows using the ISAT algorithm. The simulation of reactive flows is a challenging task that requires considering the complex aspects of fluid dynamics and chemical kinetics.
