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By Andrew Phillips, Peng Yin

This publication constitutes the refereed court cases of the twenty first overseas convention on DNA Computing and Molecular Programming, DNA 21, held in Boston and Cambridge, MA, united states, in August 2015.

The thirteen complete papers provided have been rigorously chosen from sixty three submissions. The papers deal with all present matters regarding biomolecular computing, reminiscent of: algorithms and types for computation on biomolecular structures; computational approaches in vitro and in vivo; molecular switches, gates, units, and circuits; molecular folding and self-assembly of nanostructures; research and theoretical versions of laboratory strategies; molecular cars and molecular robotics; experiences of fault-tolerance and mistake correction; software program instruments for research, simulation, and layout; artificial biology and in vitro evolution; purposes in engineering, physics, chemistry, biology, and medicine.

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Additional info for DNA Computing and Molecular Programming: 21st International Conference, DNA 21, Boston and Cambridge, MA, USA, August 17-21, 2015. Proceedings

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Smaller examples took only a few seconds. We can approximate the total run-time for parameter tuning as a function of the number of iterations of the MCMC algorithm and the number of input combinations assessed. For example, doing 200 iterations over 10 input Synthesizing and Tuning Chemical Reaction Networks a b Number of solutions Number of solutions 10 4 10 3 AM3,3 10 2 AM4,3 AM3,4 10 1 10 0 10 0 AM4,4 10 1 10 2 10 3 10 4 10 3 10 2 10 1 10 0 10 4 27 2 3 4 5 6 K Time (seconds) Fig. 3. Computation times for the SMT-based synthesis of majority decision-making CRNs.

However, currently this method is limited to relatively small CRNs with few reactions, species, and which have short computation paths. Secondly, the CTMC methods we apply require an explicit representation of the state space, which must be finite (which is always the case for biomolecular CRNs initialised with a finite number of molecules) and contain few reachable states — this makes the method suitable for systems involving relatively few species and numbers of molecules. To circumvent the need for an explicit representation of the state space, stochastic dynamical behaviour could be approximated by averaging multiple trajectories from Gillespie’s stochastic simulation algorithm [27], using fluid or central limit approximations [28], or using ordinary differential equations.

If A(x, y) = ε, then the site is said to be unoccupied, since there is no tile there. To be a valid assembly at temperature τ , A must satisfy these properties: – The origin must be occupied by a tile A(0, 0) = ε, which we call the seed of the assembly. – The occupied sites of the assembly must be connected. – The total binding strength of each tile in the assembly is at least τ . g. A , or shown in a different color from tiles. The definitions given in Definitions 1 and 2 are identical to those in previous models of tile-based self-assembly derived from the abstract tile assembly model [2,16,22,29].

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