Negative Interactions in Irreversible Self-Assembly

This paper explores the use of negative (i.e., repulsive) interaction the abstract Tile Assembly Model defined by Winfree. Winfree postulated negative interactions to be physically plausible in his Ph.D. thesis, and Reif, Sahu, and Yin explored their power in the context of reversible attachment operations. We explore the power of negative interactions with irreversible attachments, and we achieve two main results. Our first result is an impossibility theorem: after t steps of assembly, Omega(t) tiles will be forever bound to an assembly, unable to detach. Thus negative glue strengths do not afford unlimited power to reuse tiles. Our second result is a positive one: we construct a set of tiles that can simulate a Turing machine with space bound s and time bound t, while ensuring that no intermediate assembly grows larger than O(s), rather than O(s * t) as required by the standard Turing machine simulation with tiles

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required

Methods for Partitioning Data to Improve Parallel Execution Time for Sorting on Heterogeneous Clusters

International audienceThe aim of the paper is to introduce general techniques in order to optimize the parallel execution time of sorting on a distributed architectures with processors of various speeds. Such an application requires a partitioning step. For uniformly related processors (processors speeds are related by a constant factor), we develop a constant time technique for mastering processor load and execution time in an heterogeneous environment and also a technique to deal with unknown cost functions. For non uniformly related processors, we use a technique based on dynamic programming. Most of the time, the solutions are in O(p) (p is the number of processors), independent of the problem size n. Consequently, there is a small overhead regarding the problem we deal with but it is inherently limited by the knowing of time complexity of the portion of code following the partitioning

New results on pushdown module checking with imperfect information

Model checking of open pushdown systems (OPD) w.r.t. standard branching temporal logics (pushdown module checking or PMC) has been recently investigated in the literature, both in the context of environments with perfect and imperfect information about the system (in the last case, the environment has only a partial view of the system's control states and stack content). For standard CTL, PMC with imperfect information is known to be undecidable. If the stack content is assumed to be visible, then the problem is decidable and 2EXPTIME-complete (matching the complexity of PMC with perfect information against CTL). The decidability status of PMC with imperfect information against CTL restricted to the case where the depth of the stack content is visible is open. In this paper, we show that with this restriction, PMC with imperfect information against CTL remains undecidable. On the other hand, we individuate an interesting subclass of OPDS with visible stack content depth such that PMC with imperfect information against the existential fragment of CTL is decidable and in 2EXPTIME. Moreover, we show that the program complexity of PMC with imperfect information and visible stack content against CTL is 2EXPTIME-complete (hence, exponentially harder than the program complexity of PMC with perfect information, which is known to be EXPTIME-complete).Comment: In Proceedings GandALF 2011, arXiv:1106.081

Exact Cover with light

We suggest a new optical solution for solving the YES/NO version of the Exact Cover problem by using the massive parallelism of light. The idea is to build an optical device which can generate all possible solutions of the problem and then to pick the correct one. In our case the device has a graph-like representation and the light is traversing it by following the routes given by the connections between nodes. The nodes are connected by arcs in a special way which lets us to generate all possible covers (exact or not) of the given set. For selecting the correct solution we assign to each item, from the set to be covered, a special integer number. These numbers will actually represent delays induced to light when it passes through arcs. The solution is represented as a subray arriving at a certain moment in the destination node. This will tell us if an exact cover does exist or not.Comment: 20 pages, 4 figures, New Generation Computing, accepted, 200

The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square

In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles pre-formed by the joining of two square tiles. We show that the addition of duples allows for powerful behaviors of self-assembling systems at temperature 1, meaning systems which exclude the requirement of cooperative binding by tiles (i.e., the requirement that a tile must be able to bind to at least 2 tiles in an existing assembly if it is to attach). Cooperative binding is conjectured to be required in the standard aTAM for Turing universal computation and the efficient self-assembly of shapes, but we show that in the DaTAM these behaviors can in fact be exhibited at temperature 1. We then show that the DaTAM doesn't provide asymptotic improvements over the aTAM in its ability to efficiently build thin rectangles. Finally, we present a series of results which prove that the temperature-2 aTAM and temperature-1 DaTAM have mutually exclusive powers. That is, each is able to self-assemble shapes that the other can't, and each has systems which cannot be simulated by the other. Beyond being of purely theoretical interest, these results have practical motivation as duples have already proven to be useful in laboratory implementations of DNA-based tiles

Does Treewidth Help in Modal Satisfiability?

Many tractable algorithms for solving the Constraint Satisfaction Problem (CSP) have been developed using the notion of the treewidth of some graph derived from the input CSP instance. In particular, the incidence graph of the CSP instance is one such graph. We introduce the notion of an incidence graph for modal logic formulae in a certain normal form. We investigate the parameterized complexity of modal satisfiability with the modal depth of the formula and the treewidth of the incidence graph as parameters. For various combinations of Euclidean, reflexive, symmetric and transitive models, we show either that modal satisfiability is FPT, or that it is W[1]-hard. In particular, modal satisfiability in general models is FPT, while it is W[1]-hard in transitive models. As might be expected, modal satisfiability in transitive and Euclidean models is FPT.Comment: Full version of the paper appearing in MFCS 2010. Change from v1: improved section 5 to avoid exponential blow-up in formula siz

Exponential Replication of Patterns in the Signal Tile Assembly Model

Chemical self-replicators are of considerable interest in the field of nanomanufacturing and as a model for evolution. We introduce the problem of self-replication of rectangular two-dimensional patterns in the practically motivated Signal Tile Assembly Model (STAM) [9]. The STAM is based on the Tile Assembly Model (TAM) which is a mathematical model of self-assembly in which DNA tile monomers may attach to other DNA tile monomers in a programmable way. More abstractly, four-sided tiles are assigned glue types to each edge, and self-assembly occurs when singleton tiles bind to a growing assembly, if the glue types match and the glue binding strength exceeds some threshold. The signal tile extension of the TAM allows signals to be propagated across assemblies to activate glues or break apart assemblies. Here, we construct a pattern replicator that replicates a two-dimensional input pattern over some fixed alphabet of size φ with O(φ) tile types, O(φ) unique glues, and a signal complexity of O(1). Furthermore, we show that this replication system displays exponential growth in n, the number of replicates of the initial patterned assembly

Blackbody Radiation and the Scaling Symmetry of Relativistic Classical Electron Theory with Classical Electromagnetic Zero-Point Radiation

It is pointed out that relativistic classical electron theory with classical electromagnetic zero-point radiation has a scaling symmetry which is suitable for understanding the equilibrium behavior of classical thermal radiation at a spectrum other than the Rayleigh-Jeans spectrum. In relativistic classical electron theory, the masses of the particles are the only scale-giving parameters associated with mechanics while the action-angle variables are scale invariant. The theory thus separates the interaction of the action variables of matter and radiation from the scale-giving parameters. Classical zero-point radiation is invariant under scattering by the charged particles of relativistic classical electron theory. The basic ideas of the matter -radiation interaction are illustrated in a simple relativistic classical electromagnetic example.Comment: 18 page

The accuracy of breast volume measurement methods: a systematic review

Breast volume is a key metric in breast surgery and there are a number of different methods which measure it. However, a lack of knowledge regarding a method’s accuracy and comparability has made it difficult to establish a clinical standard. We have performed a systematic review of the literature to examine the various techniques for measurement of breast volume and to assess their accuracy and usefulness in clinical practice. Each of the fifteen studies we identified had more than ten live participants and assessed volume measurement accuracy using a gold-standard based on the volume, or mass, of a mastectomy specimen. Many of the studies from this review report large (> 200 ml) uncertainty in breast volume and many fail to assess measurement accuracy using appropriate statistical tools. Of the methods assessed, MRI scanning consistently demonstrated the highest accuracy with three studies reporting errors lower than 10% for small (250 ml), medium (500 ml) and large (1,000 ml) breasts. However, as a high-cost, non-routine assessment other methods may be more appropriate