Hairpin formation by single-stranded DNA molecules was exploited in a DNA-based computation in order to explore the feasibility of autonomous molecular computing. An instance of the satisfiability problem, a famous hard combinatorial problem, was solved by using molecular biology techniques. The satisfiability of a given Boolean formula was examined autonomously, on the basis of hairpin formation by the molecules that represent the formula. This computation algorithm can test several clauses in the given formula simultaneously, which could reduce the number of laboratory steps required for computation.

No abstract

We present methods for computation of flow-driven string dynamics in a pump and related residence time. The string dynamics computations help us understand how the strings carried by a fluid interact with the pump surfaces, including the blades, and get stuck on or around those surfaces. The residence time computations help us to have a simplified but quick understanding of the string behavior. The core computational method is the Space–Time Variational Multiscale (ST-VMS) method, and the other key methods are the ST Isogeometric Analysis (ST-IGA), ST Slip Interface (ST-SI) method, ST/NURBS Mesh Update Method (STNMUM), a general-purpose NURBS mesh generation method for complex geometries, and a one-way-dependence model for the string dynamics. The ST-IGA with NURBS basis functions in space is used in both fluid mechanics and string structural dynamics. The ST framework provides higher-order accuracy. The VMS feature of the ST-VMS addresses the computational challenges associated with the turbulent nature of the unsteady flow, and the moving-mesh feature of the ST framework enables high-resolution computation near the rotor surface. The ST-SI enables moving-mesh computation of the spinning rotor. The mesh covering the rotor spins with it, and the SI between the spinning mesh and the rest of the mesh accurately connects the two sides of the solution. The ST-IGA enables more accurate representation of the pump geometry and increased accuracy in the flow solution. The IGA discretization also enables increased accuracy in the structural dynamics solution, as well as smoothness in the string shape and fluid dynamics forces computed on the string. The STNMUM enables exact representation of the mesh rotation. The general-purpose NURBS mesh generation method makes it easier to deal with the complex geometry we have here. With the one-way-dependence model, we compute the influence of the flow on the string dynamics, while avoiding the formidable task of computing the influence of the string on the flow, which we expect to be small.

No abstract

In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3%-end sequence encodes the current state of the machine. Successive state transitions are performed in such a way that the current state is annealed onto an appropriate portion of DNA encoding the transition table of the state machine and the next state is copied to the 3%-end by extension with polymerase. In this paper, we first show that combined with parallel overlap assembly, a single series of successive transitions can solve NP-complete problems. This means that the number of necessary laboratory steps is independent from the problem size. We then report the results of two experiments concerning the implementation of our method. One is on isothermal reactions which greatly increase the efficiency of state transitions compared with reactions controlled by thermal cycles. The other is on the use of unnatural bases for avoiding out-of-frame annealing. The latter result can also be applied to many DNA-based computing paradigms.