EE546 Winter 2008

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Contents 1 Stochastic Processes in Nanoscale Systems 2 Assignments 3 Lecture Materials 4 Literature

Stochastic Processes in Nanoscale Systems

• Winter 2008
• MW, 9:30a-10:50a
• Room: EE 026
• Syllabus

Note: The time for the course has changed to the above and should stay that way.

In this course I will introduce the mathematical theory of stochastic processes and apply the theory to models of nanoscale systems such self-assembly, low-copy-number chemical reactions and single-cell gene regulatory networks. Topics will include a measure theoretic approach to stochastic processes, the master equation, intrinsic versus extrinsic noise, the Fokker-Plank equation, the Langevin equation, moment dynamics and truncation, stochastic simulation, and the approximation of stochastic processes by nearby processes. Special attention will be given to the control of the above-mentioned stochastic processes using feedback. The course assumes a basic familiarity with probability and differential equations. EE505 and/or EE508 may be helpful background, but are not required. The course is open to all engineering and science graduate students.

Text: Stochastic Processes in Physics and Chemistry by N. G. Van Kampen.

Note: We will probably use Mathematica quite heavily in this course. See UWare and COE's Computing Services for details on how to obtain or find this software.

Assignments

• Homework 1 Assigned 1/7, Due 1/16 in class.
• Homework 2 Assigned 1/16, Due 1/23 in class.
• Homework 3 Assigned 1/23, Due 1/30 in class.
• Homework 4 Assigned 1/30, Due 2/6 in class.
• Homework 5 Assigned 2/6, Due 2/13 in class.
• Homework 6 Assigned 2/13, Due 2/20 in class.
• Homework 7 Assigned 2/20, Due 2/27 in class.
• Homework 8 Assigned 2/27, Due 3/5 in class.
• Homework 9 Assigned 3/4, Due 3/12 in class.

Lecture Materials

• Mathematica file of introductory examples
• Mathematica Ffle for the robotic chemistry simulation
• Mathematica file for chapter 1 (subject to change)
• Master Equation Mathematica file
• Class Notes, Pages 1-70
• Notes from David Thorsely's Class

Literature

• van Oudenaarden's presentation about phenotype switching and a few other really cool stochastic phenomena in cells.

• Winfree's papers on self-assembling DNA tiles can be found here.

• Mesquita, Hespanha and Astrom on optimotaxis (a general treatment of chemotaxis-like behavior).