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Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons
Zhongwei Lin, Carl Tropper, Robert A. McDougal, Mohammand Nazrul Ishlam Patoary, William W. Lytton, Yiping Yao, Michael L. Hines
Article No.: 7
Cells exhibit stochastic behavior when the number of molecules is small. Hence a stochastic reaction-diffusion simulator capable of working at scale can provide a more accurate view of molecular dynamics within the cell. This article describes a...
Semantics and Efficient Simulation Algorithms of an Expressive Multilevel Modeling Language
Tobias Helms, Tom Warnke, Carsten Maus, Adelinde M. Uhrmacher
Article No.: 8
The domain-specific modeling and simulation language ML-Rules is aimed at facilitating the description of cell biological systems at different levels of organization. Model states are chemical solutions that consist of dynamically nested,...
‘Semantics and Efficient Simulation Algorithms on an Expressive Multi-Level Modeling Language,” by Helms et al. presents new work on the domain-specific modelling and simulation language ML-Rules [Maus et al. 2011]. For the first time,...
A Fine-Grain Time-Sharing Time Warp System
Alessandro Pellegrini, Francesco Quaglia
Article No.: 10
Several techniques have been proposed to improve the performance of Parallel Discrete Event Simulation platforms relying on the Time Warp (optimistic) synchronization protocol. Among them we can mention optimized approaches for state restore, as...
Transparently Mixing Undo Logs and Software Reversibility for State Recovery in Optimistic PDES
Davide Cingolani, Alessandro Pellegrini, Francesco Quaglia
Article No.: 11
The Time Warp synchronization protocol for Parallel Discrete Event Simulation (PDES) is universally considered a viable solution to exploit the intrinsic simulation model parallelism and to provide model execution speedup. Yet it leads the PDES...
Automatic Model Generation for Gate-Level Circuit PDES with Reverse Computation
Elsa Gonsiorowski, Justin M. Lapre, Christopher D. Carothers
Article No.: 12
Gate-level circuit simulation is an important step in the design and validation of complex circuits. This step of the process relies on existing libraries for gate specifications. We start with a generic gate model for Rensselaer’s...
Relaxing Synchronization in Parallel Agent-Based Road Traffic Simulation
Yadong Xu, Wentong Cai, Heiko Aydt, Michael Lees, Daniel Zehe
Article No.: 14
Large-scale agent-based traffic simulation is computationally intensive. Parallel computing can help to speed up agent-based traffic simulation. Parallelization of agent-based traffic simulations is generally achieved by decomposing the road...
Cloning Agent-Based Simulation
Xiaosong Li, Wentong Cai, Stephen J. Turner
Article No.: 15
Simulation cloning is an efficient way to analyze multiple configurations in a parameter exploration task. A simulation model usually contains a set of tunable parameters for exploring different configurations of a system. To evaluate different...