DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

Billiards in Nearly Isosceles Triangles

We prove that any sufficiently small perturbation of an isosceles triangle has a periodic billiard path. Our proof involves the analysis of certain infinite families of Fourier series that arise in connection with triangular billiards, and reveals some self-similarity phenomena in irrational triangular billiards. Our analysis illustrates the surprising fact that billiards on a triangle near a Veech triangle is extremely complicated even though Billiards on a Veech triangle is very well understood.Comment: Errors have been corrected in Section 9 from the prior and published versions of this paper. In particular, the formulas associated to homology classes of curves corresponding to stable periodic billiard paths in obtuse Veech triangles were corrected. See Remark 9.1 of the paper for more information. The main results and the results from other sections are unaffected. 82 pages, 43 figure

Grid diagram for singular links

In this paper, we define the set of singular grid diagrams $\mathcal{SG}$ which provides a unified description for singular links, singular Legendrian links, singular transverse links, and singular braids. We also classify the complete set of all equivalence relations on $\mathcal{SG}$ which induce the bijection onto each singular object. This is an extension of the known result of Ng-Thurston for non-singular links and braids.Comment: 33 pages, 34 figure

Proofreading tile sets: Error correction for algorithmic self-assembly

For robust molecular implementation of tile-based algorithmic self-assembly, methods for reducing errors must be developed. Previous studies suggested that by control of physical conditions, such as temperature and the concentration of tiles, errors (ε) can be reduced to an arbitrarily low rate - but at the cost of reduced speed (r) for the self-assembly process. For tile sets directly implementing blocked cellular automata, it was shown that r ≈ βε^2 was optimal. Here, we show that an improved construction, which we refer to as proofreading tile sets, can in principle exploit the cooperativity of tile assembly reactions to dramatically improve the scaling behavior to r ≈ βε and better. This suggests that existing DNA-based molecular tile approaches may be improved to produce macroscopic algorithmic crystals with few errors. Generalizations and limitations of the proofreading tile set construction are discussed