Samuel Isaacson

Associate Professor
Department of Mathematics and Statistics
Boston University
Office: MCS 231

Mailing address:
Samuel Isaacson
Boston University
Department of Mathematics and Statistics
111 Cummington Mall
Boston, MA 02215

Email:

CV: [pdf]

Fall 2016 Courses

  • MA579, Numerical Methods in the Biological Sciences: [here].
  • MA861 A1, Numerical Solution of Partial Differential Equations: [here].

Publications

  • J. Goyette, C. S. Salas, N. C. Gordon, M. Bridge, S. A. Isaacson, J. Allard and O. Dushek, Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1, Submitted (2016). [bioRχiv preprint]
  • S. A. Isaacson, A. J. Mauro and J. Newby, Uniform Asymptotic Approximation of Diffusion to a Small Target: Generalized Reaction Models, Phys. Rev. E, Vol 94, No. 4, 042414 (17 pp) (2016). [journal version] [arXiv version]
  • S. J. Chapman, R. Erban and S. A. Isaacson, Reactive Boundary Conditions as Limits of Interaction Potentials for Brownian and Langevin Dynamics, SIAM Journal on Applied Mathematics, Vol. 76, No. 1, pp 368-390 (2016). [journal version]
  • M. Do, S. A. Isaacson, G. McDermott, M. A. Le Gros, and C. A. Larabell, Imaging and Characterizing Cells using Tomography, Arch. Biochem. and Biophys., Vol. 581, pp 111-121 (2015). [journal version]
  • I. C. Agbanusi and S. A. Isaacson, A Comparison of Bimolecular Reaction Models for Stochastic Reaction Diffusion Systems, Bulletin of Mathematical Biology, Vol 76, No. 4, pp 922-946 (2014). [preprint pdf] [journal version]
  • A. J. Mauro, JK Sigurdsson, J. Shrake, P. J. Atzberger and S. A. Isaacson, A First-Passage Kinetic Monte Carlo Method for Reaction-Drift-Diffusion Processes, J. Computational Physics, Vol. 259, pp 536-567 (2014). [preprint pdf] [journal version]
  • S. A. Isaacson, C. A. Larabell, M. A. Le Gros, D. M. McQueen and C. S. Peskin, The Influence of Spatial Variation in Chromatin Density Determined by X-ray Tomograms on the Time to Find DNA Binding Sites, Bulletin of Mathematical Biology, Vol. 75, No. 11, pp 2093-2117 (2013). [preprint pdf] [journal version] [movieS1.mov]
  • S. A. Isaacson, A Convergent Reaction-Diffusion Master Equation, J. Chem. Phys, Vol. 139, No. 5, 054101 (12 pp) (2013). [pdf]
  • S. A. Isaacson and J. Newby, Uniform Asymptotic Approximation of Diffusion to a Small Target, J. Newby. Phys. Rev. E, Vol. 88, No. 1, 012820 (13 pp) (2013). [pdf]
  • S. A. Isaacson and R. M. Kirby, Numerical Solution of Linear Volterra Integral Equations of the Second Kind with Sharp Gradients, J. Comput. Appl. Math, Vol. 235, No. 14, pp 4283-4301 (2011). [preprint pdf] [journal version]
  • S. A. Isaacson, D. M. McQueen and C. S. Peskin, The Influence of Volume Exclusion by Chromatin on the Time Required to Find Specific DNA Binding Sites by Diffusion, Proceedings of the National Academy of Sciences, Vol. 108, No. 9, pp 3815-3820 (2011). [pdf] [journal link] [supplementary material - journal link]
  • S. A. Isaacson and D. Isaacson, The Reaction-Diffusion Master Equation, Diffusion Limited Reactions, and Singular Potentials, Phys. Rev. E, Vol. 80, No. 6, pg 066106 (9pp) (2009). [pdf]
  • S. A. Isaacson, The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target, SIAM J. Appl. Math., Vol. 70, No. 1, pp 77-111 (2009). [pdf]
  • P. J. Atzberger, S. A. Isaacson and C. S. Peskin, A Microfluidic Pumping Mechanism Driven by Non-Equilibrium Osmotic Effects, Physica D, Vol. 238, No. 14, pp 1168-1179 (2009). [pdf]
  • S. A. Isaacson, Relationship Between the Reaction-Diffusion Master Equation and Particle Tracking Models, J. Phys. A: Math. Theor., Vol. 41, No. 6, 065003 (15 pp) (2008). [pdf]
  • S. A. Isaacson and C. S. Peskin, Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations, SIAM Journal on Scientific Computing, Vol. 28, No. 1, pp 47-74 (2006). [pdf]
  • S. A. Isaacson, Stochastic Reaction-Diffusion Methods for Modeling Gene Expression and Spatially Distributed Chemical Kinetics, Ph. D. thesis (September 2005). [pdf]

Posters

  • A Stochastic Reaction-Diffusion Active Transport Method for Studying the Control of Gene Expression in Eukaryotic Cells, [pdf]
    • With C. S. Peskin. Presented at "Workshop on Applications of Methods of Stochastic Systems and Statistical Physics in Biology", Notre Dame, 2005.
  • A Stochastic Reaction-Diffusion Method for Studying the Control of Gene Expression in Eukaryotic Cells, [pdf]
    • With C. S. Peskin. Presented at "Symposium on Computational Cell Biology", Lenox, MA 2005.

Online Talks

  • BIRS Workshop on Particle-Based Stochastic Reaction-Diffusion Models in Biology 2014
    • Lattice Approximation of Spatially-Continuous Particle-Based Stochastic Reaction-Diffusion Models, [here].
  • SIAM Conference on the Life Sciences 2012
    • Minitutorial on Stochastic Simulation of Spatially-Distributed Models Arising in the Life Sciences,
    • Keynote (with movies): [here], pdf (no movies): [here].
  • Workshop on Stochastic Modeling of Stochastic Reaction-Diffusion Processes in Biology 2012
    • Talk on Influence of Nuclear Substructure on Gene Regulation and Expression,
    • Keynote (with movies): [here]. Pdf (no movies): [here].
  • National Centers for Systems Biology Annual Meeting 2009: [here].
    • The talk is about 24 minutes into the video stream for day 2.

Numerical Codes (all on Gitlab: [here])

  • ibmethod2D, A 2D Periodic, Cartesian Grid Immersed Boundary Navier-Stokes Solver: [here].
  • Volterra Integral Equation Solvers (to be posted).