Professor Samuel Isaacson

Associate Professor:
Department of Mathematics and Statistics
Boston University

Office: 
MCS 231

Mailing address:
Samuel Isaacson
Boston University
Department of Mathematics
111 Cummington St.
Boston, MA 02215


Email:


CV: pdf here


2014-2015 Courses

  • I will not be teaching during the 2014-2015 academic year as I am on sabbatical.

Publications

  • A Comparison of Bimolecular Reaction Models for Stochastic Reaction Diffusion Systems. (preprint pdf) (journal version)
    • With I. C. Agbanusi. Bulletin of Mathematical Biology, Vol 76., No. 4, pp 922-946 (2014).
  • A First-Passage Kinetic Monte Carlo Method for Reaction-Drift-Diffusion Processes. (preprint pdf) (journal version)
    • With A. J. Mauro, JK Sigurdsson, J. Shrake, and P. J. Atzberger. J. Computational Physics, Vol. 259, pp 536-567 (2014).
  • The Influence of Spatial Variation in Chromatin Density Determined by X-ray Tomograms on the Time to Find DNA Binding Sites. (preprint pdf), (journal version), (movieS1.mov)
    • With C. A. Larabell, M. A. Le Gros, D. M. McQueen, C. S. Peskin. Bulletin of Mathematical Biology, Vol. 75, No. 11, pp 2093-2117 (2013).
  • A Convergent Reaction-Diffusion Master Equation. (pdf)
    • J. Chem. Phys, Vol. 139, No. 5, 054101 (12 pp) (2013).
  • Uniform Asymptotic Approximation of Diffusion to a Small Target. (pdf
    • With J. Newby. Phys. Rev. E, 88, No. 1, 012820 (13 pp) (2013).
  • Numerical Solution of Linear Volterra Integral Equations of the Second Kind with Sharp Gradients. (preprint pdf) (journal version)
    • With R. M. Kirby, J. Comput. Appl. Math, Vol. 235, No. 14, pp 4283-4301, 2011.  (m-files will be posted)
  • The Influence of Volume Exclusion by Chromatin on the Time Required to Find Specific DNA Binding Sites by Diffusion. (pdf).
    • With D. M. McQueen and C. S. Peskin, PNAS, 2011. Available from PNAS online: here.  Supplementary material: here.
  • The Reaction-Diffusion Master Equation, Diffusion Limited Reactions, and Singular Potentials. (pdf)
    • With D. Isaacson, Phys. Rev. E, 80, No. 6, pg 066106, 2009
  • The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target. (pdf)
    • SIAM J. Appl. Math., 70, No. 1, 2009
  • A Microfluidic Pumping Mechanism Driven by Non-Equilibrium Osmotic Effects. (pdf)
    • With P. J. Atzberger and C. S. Peskin. Physica D, 238, 2009
  • Relationship Between the Reaction-Diffusion Master Equation and Particle Tracking Models. (pdf)
    • J. Phys. A: Math. Theor., 41 2008 
  • Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations. (pdf)
    • With C. S. Peskin. SIAM Journal on Scientific Computing, 28, No. 1, 2006 
  • Stochastic Reaction-Diffusion Methods for Modeling Gene Expression and Spatially Distributed Chemical Kinetics. (pdf)
    • Ph.D. thesis, September, 2005.

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

  • 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.

Matlab Libraries 

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

Media

  • The Influence of Volume Exclusion by Chromatin on the Time Required to Find Specific DNA Binding Sites by Diffusion. (pdf).
    • With D. M. McQueen and C. S. Peskin, PNAS, 2011. Available from PNAS online: here.  Supplementary material: here.
DNA image

Distribution of DNA in a mouse myoblast cell.
Random Walk Search Path of Protein for DNA Binding Site

Random walk search path of a protein (red sphere) for a fixed DNA binding site (purple sphere).
See quicktime movie: here. Note file is 17 megabytes. In the movie the protein is brown, the binding site yellow, and dense DNA regions white.


  • Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations. (pdf)
    • With C. S. Peskin. SIAM Journal on Scientific Computing, 28, no. 1, 2006

A 3D, stochastic reaction-diffusion model of transcription, mRNA export, translation, protein import, and gene regulation.
(See paper: "Incorporating Diffusion in Complex..." for details on a 2D version of this model).