Consider the challenge of trying to design molecular machines from scratch.
Toward this goal, we are developing a general computational framework
for encoding mechanical function in DNA and RNA strands. A useful design algorithm
must identify molecular sequences for experimental study that adopt desired
conformations with both high affinity and high specificity. In addition to these
thermodynamic considerations, the kinetic behavior of the strands may also be crucial
to the intended function. This talk will describe algorithms for evaluating the thermodynamic and
kinetic properties of designed molecules and provide some experimental
results on novel devices.
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