Welcome to the web site of the MASA group engaged in the Modeling and Analysis of Self Assembly
(begun May 30, 2007 and under construction)











Double crossover molecule used in self assembly

Members:  Yuliy Baryshnikov, Bell Labs Ed Coffman, Columbia University Petar Momcilovic, University of Michigan Ned Seeman, New York University Peter Winkler, Dartmouth University Teddy Yimwadsana, Columbia University

Self Assembly and Molecular  Computing Advances in chemical synthesis have laid the groundwork for computation at nanoscale, where self assembly becomes the core process, either as a computation itself, or as a mechanism for fabricating nanodevices. By such processes, elementary particles, such as DNA molecules, perform computations by assembling  autonomously into large complexes following built-in bonding rules.  The MASA group studies self assembly viewed as a random growth process, addressing such as questions as:``How long does the structure corresponding to a given computation take to self-assemble?'' ``How does one optimize the yield of a self-assembly process?''  ``What are the trade-offs between the reliability (error tolerance) and speed of self assembly?''  Answers to these questions  bring out unexpected connections with classical areas of mathematics . The outline of a tutorial to be given at Performance 2007 can be found in File:  tutorial.pdf

            








Group Publications:                                                

1. Baryshnikov, Y., Coffman, E.G., Jr., Momcilovic, P., Phase Transitions and Control in Self Assembly , Proceedings, Foundations of Nanoscience: Self-Assembled Architectures and Devices, Snowbird, 2004.
   File:  pdf

2. Baryshnikov, Y., Coffman, E.G., Jr., Momcilovic, P., Incremental Self Assembly in the Fluid Limit , Proceedings, 38th Ann. Conf. Inf. Sys. Sci., Princeton, 2004.
   File:  pdf

3. Baryshnikov, Y., Coffman, E.G., Jr., Momcilovic, P., DNA-Based Computation Times, , Proc. of the 10th International Meeting on DNA Computing, Milan, Italy, June 2004..
   File:  pdf

4. Baryshnikov, Y., Coffman, E.G., Jr., Seeman, N., Yimwadsana, B., Self Correcting Self Assembly: Growth Models and the Hammersley Process, Proc. of the 11th International Meeting on DNA Computing, London, Ontario, 2005.
   File:  pdf

5. Baryshnikov, Y., Coffman, E.G., Jr., Yimwadsana, B., Stochastic Yield Analysis of Self-Assembling, Single-Enzyme Reaction Networks, Proceedings, Foundations of Nanoscience: Self-Assembled Architectures and Devices, Snowbird, 2005.
   File:  ps

6. Baryshnikov, Y., Coffman, E.G., Jr., Yimwadsana, B., On Creating Shapes in 2D Tile Self-Assembly, Proceedings, Foundations of Nanoscience: Self-Assembled Architectures and Devices, Snowbird, 2006.
   File:  ps

7. Baryshnikov, Y., Coffman, E.G., Jr., Yimwadsana, B., Times to Compute Shapes in 2D Self Assembly, Proc. of the 12th International Meeting on DNA Computing, 2006.
   File:  pdf

8. Baryshnikov, Y., Coffman, E.G., Jr., Yimwadsana, B., Experiments in Stochastic Self-Assembly, Proceedings, Foundations of Nanoscience: Self-Assembled Architectures and Devices, Snowbird, 2007.
   File:  pdf