IST Lunch Bunch

Tuesday April 13, 2010 12:00 PM

A Simple Geometric Model for Elastic Deformations // A Verifying Compiler for DNA Chemical Reaction Networks

Location: Annenberg 105
(Two short talks will be given)<br><br>

A Simple Geometric Model for Elastic Deformations <br>(Isaac Chao) <br><br> A non rigid deformation is associated with some elastic potential, and we can measure this deviation from isometry by penalizing any scaling and shearing induced by the deformation. From this simple geometric picture we define a simple energy measuring the distance between the differential of a deformation map and the special orthogonal group, and arrive at an elasticity model. Dynamic simulations can be accommodated by incorporating (with minimal modification) the minimizer for static problems into a fully variational time integrator. <br><br> In addition to static and dynamic elastic simulations, we show that we can solve other geometry processing problems such as parameterization and shape space interpolation via minimizing our energy. The conclusion will discuss the shortcomings of this formulation and briefly go over proposed remedies. <br><br> This is a joint work with Patrick Sanan, Ulrich Pinkall, and Peter Schröder.<br><br><br>A Verifying Compiler for DNA Chemical Reaction Networks<br>(Seung Woo Shin)<br><br>

A goal of molecular programming and synthetic biology is to build chemical circuits to control chemical processes at the molecular level. Remarkably, carefully designed DNA molecules can be used to construct complex chemical circuits -- that operate without any enzymes or cellular components. However, designing DNA molecules at the sequence level can be difficult and error-prone. This calls for a higher-level programming language for DNA computation and as a result chemical reaction networks (CRNs) have recently been studied as a promising candidate. Several general-purpose schemes for implementing CRNs with DNA molecules have already been proposed, and many more are being actively investigated. To facilitate research in this domain, we propose a compiler that can automatically achieve the tedious procedure of applying such translation schemes to CRNs. In addition, our compiler will be able to verify each compilation instance and provide the user with more confidence in the correctness of the implementation.

Series IST Lunch Bunch

Contact: Sydney Garstang at x2813 sydney@caltech.edu
For more information visit: http://www.cs.caltech.edu/seminars/lunch_bunch.html