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- Samuel A. Isaacson, Charles S. Peskin
- SIAM J. Scientific Computing
- 2006

A method is developed for incorporating diffusion of chemicals in complex geometries into stochastic chemical kinetics simulations. Systems are modeled using the reaction-diffusion master equation,â€¦ (More)

- Samuel A. Isaacson
- The Journal of chemical physics
- 2013

The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME is often interpreted asâ€¦ (More)

The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target

- Samuel A. Isaacson
- SIAM Journal of Applied Mathematics
- 2009

The reaction-diffusion master equation (RDME) has recently been used as a model for biological systems in which both noise in the chemical reaction process and diffusion in space of the reactingâ€¦ (More)

- Samuel A. Isaacson, David McQueen, Charles S. Peskin
- Proceedings of the National Academy of Sciencesâ€¦
- 2011

Within the nuclei of eukaryotic cells, the density of chromatin is nonuniform. We study the influence of this nonuniform density, which we derive from microscopic images [Schermelleh L, et al. (2008)â€¦ (More)

- Samuel A. Isaacson, Jay M. Newby
- Physical review. E, Statistical, nonlinear, andâ€¦
- 2013

The problem of the time required for a diffusing molecule, within a large bounded domain, to first locate a small target is prevalent in biological modeling. Here we study this problem for a smallâ€¦ (More)

The reactionâ€“diffusion master equation (RDME) is a model for chemical systems in which both noise in the chemical reaction process and the diffusion of molecules are important. It extends theâ€¦ (More)

A mechanism is presented which drives a fluid flow using two chemically reacting molecular species and osmotic effects. For concreteness the mechanism is discussed in the context of a tube which atâ€¦ (More)

- Jesse Goyette, Citlali Solis Salas, +4 authors Omer Dushek
- Science Advances
- 2017

Tethered enzymatic reactions are ubiquitous in signaling networks but are poorly understood. A previously unreported mathematical analysis is established for tethered signaling reactions in surfaceâ€¦ (More)

- Ikemefuna Agbanusi, Samuel A. Isaacson
- Bulletin of mathematical biology
- 2014

Stochastic reaction-diffusion models have become an important tool in studying how both noise in the chemical reaction process and the spatial movement of molecules influences the behavior ofâ€¦ (More)

- Ava J. Mauro, Jon Karl Sigurdsson, Justin Shrake, Paul J. Atzberger, Samuel A. Isaacson
- J. Comput. Physics
- 2014

Stochastic reaction-diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play importantâ€¦ (More)