Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations. - Samuel A. Isaacson; Charles S. Peskin (SIAM J. Sci. Comput., 2006)

The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target. - Samuel A. Isaacson (SIAM J. Appl. Math., 2009)

Numerical solution of linear Volterra integral equations of the second kind with sharp gradients. - Samuel A. Isaacson; Robert M. Kirby (J. Comput. Appl. Math., 2011)

A First-Passage Kinetic Monte Carlo method for reaction-drift-diffusion processes. - Ava J. Mauro; Jon Karl Sigurdsson; Justin Shrake; Paul J. Atzberger; Samuel A. Isaacson (J. Comput. Phys., 2014)

Reactive Boundary Conditions as Limits of Interaction Potentials for Brownian and Langevin Dynamics. - S. Jonathan Chapman; Radek Erban; Samuel A. Isaacson (SIAM J. Appl. Math., 2016)

An unstructured mesh convergent reaction-diffusion master equation for reversible reactions. - Samuel A. Isaacson; Ying Zhang 018 (J. Comput. Phys., 2018)

Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. - Jingwei Ma; Myan Do; Mark A. Le Gros; Charles S. Peskin; Carolyn A. Larabell; Yoichiro Mori; Samuel A. Isaacson (PLoS Comput. Biol., 2020)

How Reaction-Diffusion PDEs Approximate the Large-Population Limit of Stochastic Particle Models. - Samuel A. Isaacson; Jingwei Ma; Konstantinos Spiliopoulos (SIAM J. Appl. Math., 2021)

Mean Field Limits of Particle-Based Stochastic Reaction-Diffusion Models. - Samuel A. Isaacson; Jingwei Ma; Konstantinos Spiliopoulos (SIAM J. Math. Anal., 2022)

Extending JumpProcess.jl for fast point process simulation with time-varying intensities. - Guilherme Augusto Zagatti; Samuel A. Isaacson; Christopher Rackauckas; Vasily Ilin; See-Kiong Ng; Stéphane Bressan (CoRR, 2023)

Catalyst: Fast and flexible modeling of reaction networks. - Torkel E. Loman; Yingbo Ma; Vasily Ilin; Shashi Gowda; Niklas Korsbo; Nikhil Yewale; Chris Rackauckas; Samuel A. Isaacson (PLoS Comput. Biol., 2023)

An Unstructured Mesh Reaction-Drift-Diffusion Master Equation with Reversible Reactions. - Samuel A. Isaacson; Ying Zhang 018 (CoRR, 2024)